# django_admin_log

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  Cheminformatics-based analysis identified Novel compounds from Nelumbo nucifera as potential inhibitors targeting PI3k/Akt/mTOR Pathway of HR+/HER2- subtype for Breast Cancer

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  Computational analysis of miRNA mediated KDR gene regulation and natural VEGFR2 inhibitors from Persicaria hydropiper in hepatocellular carcinoma


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  Licoisoflavone B and glabridin from Glycyrrhiza glabra as potent nucleoprotein antagonists of Lassa virus: insights from molecular docking, dynamics simulation, PCA, and DFT studies


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action_time: 2026-05-03 09:54:51.300971
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  Synthesis, antiviral activity, molecular docking, and molecular dynamics studies of ethoxy phthalimide pyrazole derivatives against Cytomegalovirus and Varicella-Zoster virus: potential consequences a


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action_time: 2026-05-03 09:57:39.108521
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  Identification of novel inhibitors of high affinity iron permease (FTR1) through implementing pharmacokinetics index to fight against black fungus: An in silico approach


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action_time: 2026-05-03 09:59:02.165529
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  In silico identification of ethoxy phthalimide pyrazole derivatives as IL-17A and IL-18 targeted gouty arthritis agents


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  Identification of 1, 2, 4-Triazine and Its Derivatives Against Lanosterol 14-Demethylase (CYP51) Property of Candida albicans: Influence on the Development of New Antifungal Therapeutic Strategies


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  In silico identification of potential inhibitors with higher potency than bumetanide targeting NKCC1: An important ion co-transporter to treat neurological disorders


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  Molecular docking and simulation studies of flavonoid compounds against PBP-2a of methicillin‐resistant Staphylococcusaureus


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object_repr: Environmental & Agricultural Metagenomics
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object_repr: AMR & Pathogen Virulence Factor Profiling
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object_repr: Shormila Akter Sumya Md. Amir Alve
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object_repr: Md Fahim Islam Md. Amir Alve
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object_repr: On-Campus Seminar Page Configuration
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# core_bsdsitem

title: Bioinformatics Research Wings
slug: bioinformatics-research-wings
description:
  Dedicated to advancing knowledge and collaboration through learning groups, specialized workshops, research talks, and innovative projects. Fosters mentorship, manages research activities, and promotes brand visibility.

  Creates a dynamic platform empowering learners and professionals to contribute to impactful bioinformatics research and skill development.


title: Bioinformatics Campus Coordinator
slug: bioinformatics-campus-coordinator
description:
  Serve as dynamic representatives in universities across Bangladesh, inspiring students, organizing workshops and events, building research communities, and connecting young talent with opportunities in bioinformatics, AI, and life sciences.

  Provides leadership experience, professional training, and nationwide recognition.


title: On-Campus Bioinformatics Seminars
slug: on-campus-bioinformatics-seminars
description:
  Organized across universities in Bangladesh to introduce students to bioinformatics, genomics, and AI in life sciences. Seminars provide hands-on insights, expert talks, and real-world applications.

  Helps students explore career paths, research opportunities, and the future of computational biology, fostering innovation and collaboration.


title: Bioinformatics Research Talk
slug: bioinformatics-research-talk
description:
  A virtual platform where experts, researchers, and students share insights on genomics, computational biology, data science, and AI in healthcare.

  Interactive sessions provide exposure to cutting-edge research, global perspectives, and career pathways, making advanced bioinformatics knowledge accessible.


title: Bioinformatics Learning Group
slug: bioinformatics-learning-group
description:
  A collaborative community for students, researchers, and enthusiasts to explore fundamentals and advances of bioinformatics together.

  Through guided discussions, peer learning, and resource sharing, members gain practical knowledge in computational biology, genomics, and data-driven life sciences, building connections that inspire innovation and teamwork.


title: Bioinformatics Internship Program
slug: bioinformatics-internship-program
description:
  Offers students and young professionals hands-on experience in computational biology, genomics, and data science.

  Provides real-world projects, mentorship from experts, exposure to advanced tools, development of practical skills, and contributions to meaningful research and innovation.


title: Bioinformatics National Competitions
slug: bioinformatics-national-competitions
description:
  Creates a platform for students and researchers to showcase skills in genomics, computational biology, and data-driven problem-solving.

  Encourages innovation, teamwork, and critical thinking while tackling real-world scientific challenges, offering recognition, career-building opportunities, and community engagement.


# django_session

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expire_date: 2026-03-31 08:43:07.918666
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session_key: s04l7pld4nttbuszn5zn1sce1emrjoco
expire_date: 2026-05-08 10:27:07.473143
session_data:
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session_key: 0ocmq10jjnd6gkefgu685ze31u4rzvzb
expire_date: 2026-05-12 18:43:20.891255
session_data:
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session_key: x0ycujamg3e2kkaeyuauczzbx69tvpqq
expire_date: 2026-05-18 19:00:43.863158
session_data:
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session_key: 6c5cjdrf2cutu2xfow3c19274njxdhsf
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session_key: gzxo79udo18bn4iucrsefnrwio8w466s
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# users_customuser

password: !1H3P1UbbDfiZjpMy4uYNhA2JaMRwmheiodQlUVzP
last_login: 2018-03-17 08:58:29
username: sk_faisal_ahmed
first_name: Sk. Faisal Ahmed
date_joined: 2026-03-17 08:58:29
role: Founder & CEO
photo: team_photos/IMG_7340.JPG
facebook: https://www.facebook.com/sk.faisal.ahmed.27
linkedin: https://www.linkedin.com/in/skfaisalahmed/
portfolio: https://www.linkedin.com/in/skfaisalahmed/
bio:
  leads the 1st Bioinformatics Company in Bangladesh, A researcher and entrepreneur dedicated to advancing computational biology and AI integration.


password: !a4kXEIY3A2YJK0SFpXijInGtQcM8kXCGKy3IktsL
username: zerin_sultana_lira
first_name: Zerin Sultana Lira
date_joined: 2023-03-17 08:58:29
role: Chief Human Resources Officer (CHRO)
photo: team_photos/669337895_122217436172335074_4038183199043394824_n.jpg
facebook: https://web.facebook.com/zerin.sultana.lira.2024
linkedin: https://www.dobltd.com
portfolio: https://www.dobltd.com
bio:
  An expert in talent management and organizational development, dedicated to fostering a high-performance culture


password: !BunUDBdEeZjIOAV4Rq3sOBZUx7nMfNHtphkkh6TR
last_login: 2023-03-17 08:58:29
username: neloy_kumar_mazumder
first_name: Neloy Kumar Mazumder
date_joined: 2026-03-17 08:58:29
role: R&D Manager (DiLab)
photo: team_photos/20250821_172309_-_Neloy_Kumar_Mazumder.jpg
facebook: https://www.facebook.com/share/1UM7GhtTqx/
portfolio: https://www.dobltd.com
linkedin:
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username: md_hossain_ahmed
first_name: Md. Hossain Ahmed
date_joined: 2026-03-17 08:58:29
role: Research Assistant
photo: team_photos/F.P.I_-_Mikdad_joardar_Hossain.png
facebook: https://www.facebook.com/share/1B7U57TbDk/
portfolio: https://www.dobltd.com
linkedin:
  https://www.linkedin.com/in/md-hossain-ahmed-566a19230?utm_source=share_via&utm_content=profile&utm_medium=member_android


password: !0h3659e88A1yOCfWgwOMh5APsMCguc3bI2xBMuLR
last_login: 2026-05-14 10:45:10
username: md_fahim_islam
first_name: Md Fahim Islam
date_joined: 2026-03-17 08:58:29
role: Research Assistant
photo: team_photos/IMG-20250115-WA00062_-_MD_Fahim_Hassan.jpg
facebook: https://www.facebook.com/share/1Cs7ZBuH3J/
portfolio: https://www.dobltd.com
linkedin:
  https://www.linkedin.com/in/mdfahimislam684?utm_source=share_via&utm_content=profile&utm_medium=member_android


password: pbkdf2_sha256$1200000$46MrwSQ1u1Gx0cCwnmhexL$QEJIrvIycN3BXRjJN0QCtFT3kOyqCKcrn7dlGgmBLjQ=
username: Md_Mehadi_Hasan
first_name: Md Mehadi Hasan
date_joined: 2026-05-14 10:59:57
role: Deputy Manager (Content Dept.)
photo: team_photos/IMG_20251104_112505_214_-_Mehadi_Hasan.jpg
facebook: https://www.facebook.com/share/1HimcuhtTi/
portfolio: https://www.dobltd.com
linkedin:
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password: pbkdf2_sha256$1200000$SYpKpvcaUBoDXmRqFYrjgB$1eIu+38OIV2Q7FvF9LJsdXRsKDi3XzacNzJNoWa+BOI=
last_login: 2026-05-14 10:45:10
username: Rakibur_Rahman
first_name: Rakibur Rahman
date_joined: 2026-05-14 11:02:20
role: Deputy Project Manager (IBAI)
photo: team_photos/IMG-20260504-WA00031_-_Rakibur_Rahman.jpg
portfolio: https://www.dobltd.com
facebook:
  https://www.linkedin.com/in/rakibur-rahman-37670a25a?utm_source=share_via&utm_content=profile&utm_medium=member_android

linkedin:
  https://www.linkedin.com/in/rakibur-rahman-37670a25a?utm_source=share_via&utm_content=profile&utm_medium=member_android


password: pbkdf2_sha256$1200000$Vqaiyv55zSodRSm1LbIjWQ$BpdSXo1jvCUeUtPynTEa0k8RhjSoXRWN9va8xNCy7dU=
username: Khandakar_Mydul_Islam
first_name: Khandakar Mydul Islam
date_joined: 2026-05-14 11:27:35
role: Research Assistant
photo: team_photos/IMG_20260504_164626_-_Khandakar_Mydul_Islam.jpg
facebook: https://www.facebook.com/share/18cvBQoqxV/
portfolio: https://www.dobltd.com
linkedin:
  https://www.linkedin.com/in/khandakar-mydul-islam-865875367?utm_source=share_via&utm_content=profile&utm_medium=member_android


password: pbkdf2_sha256$1200000$KI3O4XCyeZOyNTI260odQI$Ay1PAvem+V65GLhVuaf4WYuPIO8a85uauJ+9uvNbOrs=
username: Anik_Paul
first_name: Anik Paul
date_joined: 2026-05-14 11:30:16
role: Research Assistant
photo: team_photos/IMG-20250730-WA00081_-_Anik_Paul.jpg
facebook: https://www.facebook.com/share/1bWQk8HixV/
portfolio: https://www.dobltd.com
linkedin:
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password: pbkdf2_sha256$1200000$tLgMlAXv9Ck1b8vrcER5En$4d7cl7Y3Vly3A75Jt832TiffpW52AoB6QqP3tOptdUU=
username: Tonay_Sarkar
first_name: Tonay Sarkar
date_joined: 2026-05-14 11:34:28
role: Research Assistant
photo: team_photos/IMG-20260221-WA0014_-_Tonay_Sarkar.jpg
facebook: https://www.facebook.com/tonoy.sarkerovi
portfolio: https://www.dobltd.com
linkedin:
  https://www.linkedin.com/in/tonay-sarkar-87678b213?utm_source=share_via&utm_content=profile&utm_medium=member_android


password: pbkdf2_sha256$1200000$tQFkGbTfuA7UuNBFoxNGNb$h7LTETt1GZKrlWIcEvZozMSw7BFzDQWF1wcaxIa7utU=
username: Khatija_Afroj_Bristi
first_name: Khatija Afroj Bristi
date_joined: 2026-05-14 11:41:02
role: Department Executive (DRT)
photo: team_photos/IMG_20260423_131256_-_Khadija_Afroj_Bristi.jpg
facebook: https://www.facebook.com/max.brianna.2024
portfolio: https://www.dobltd.com
linkedin:
  https://www.linkedin.com/in/khadija-afroj-bristi-4a8393272?utm_source=share_via&utm_content=profile&utm_medium=member_android


password: pbkdf2_sha256$1200000$t29ZPd7ryuLvw3XZWuX5WB$cG5pfLTutWeJn8m+WGErIl6CRUoMEBMgukMev1urv+U=
username: Jannatul_Wahid_Munami
first_name: Jannatul Wahid Munami
date_joined: 2026-05-14 11:43:27
role: Department Executive (DRT)
photo: team_photos/IMG_20251005_205830_-_Munami_Wahid.jpg
facebook: https://www.facebook.com/share/1bs3BGrTWc/
portfolio: https://www.dobltd.com
linkedin:
  https://www.linkedin.com/in/jannatul-wahid-munami-63b5932aa?utm_source=share_via&utm_content=profile&utm_medium=member_android


password: pbkdf2_sha256$1200000$wNw7G89ZEoTOgenngb8lBC$TsVWKMYdJIGA7X55WdDu3cFzGiAUCicwnGM+OUyg44M=
username: Nayeem_Ahamed
first_name: Nayeem Ahamed
date_joined: 2026-05-14 11:46:05
role: Department Executive (Content)
photo: team_photos/20251030_165659-20437105142_-_Nayeem_Nayeem.jpg
facebook: https://www.facebook.com/share/1G6fghaDDc/
portfolio: https://www.dobltd.com
linkedin:
  https://www.linkedin.com/in/nayeem-ahamed-8a969732b?utm_source=share_via&utm_content=profile&utm_medium=member_android


password: pbkdf2_sha256$1200000$Bz51HD6mZJ4bNlWliGgk0C$DGsJQgMxUMRj3TYSqvL7upRgsaEyolQT5na0E2fpjoA=
username: Muhammad_Muztoba
first_name: Muhammad Muztoba
date_joined: 2026-05-14 11:56:16
role: Department Executive
photo: team_photos/IMG-20251208-WA0023_-_Muhammad_Muztoba.jpg
facebook: https://www.facebook.com/share/1ZqLLzLhPE/
portfolio: https://www.dobltd.com
linkedin:
  https://www.linkedin.com/in/muhammad-muztoba-302630328?utm_source=share_via&utm_content=profile&utm_medium=member_android


password: pbkdf2_sha256$1200000$Q4gc2EUB542d5PRyGwVAws$pCUQ+szYJYaGZweTnChwCTEAjNTfXF5PQmDwIHWVAdU=
username: Prami_Chowdhury_Badhan
first_name: Prami Chowdhury Badhan
date_joined: 2026-05-14 11:57:51
role: Department Executive (Content Dept.)
photo: team_photos/IMG_20241004_212823_-_Badhan_Chowdhury_Prami.jpg
facebook: https://www.facebook.com/share/18hwMC4AMV/
portfolio: https://www.dobltd.com
linkedin:
  https://www.linkedin.com/in/badhan-chowdhury-328785321?utm_source=share&utm_campaign=share_via&utm_content=profile&utm_medium=android_app


# core_researchpaper

publication_date: 2025-11-12
journal: Biochemical and Biophysical Research Communications
link: https://doi.org/10.1016/j.bbrc.2025.152953
image: research_papers/581817663_25119759227719152_7726363524540683899_n.jpg
title:
  Cheminformatics-based analysis identified Novel compounds from Nelumbo nucifera as potential inhibitors targeting PI3k/Akt/mTOR Pathway of HR+/HER2- subtype for Breast Cancer

authors:
  Sk Faisal Ahmed, Proja Barua, Md Al Amin, Rahnuma Tabassum, Mir Mohammad Ehsanul Haque, Lamia Islam, Md Shohel Hossain, Abhishek Kumar Verma

abstract:
  The present study investigates the in-silico identification of novel phytochemical inhibitors from N. nucifera molecularly targeting the PI3K/Akt/mTOR signalling pathway as a breast cancer chemotherapeutic agent, especially to treat PIK3CA mutant tumours. Despite huge advancements, including the application of various complex intracellular signalling pathways in oncogenesis, breast cancer remains a menace, causing significant morbidity and mortality worldwide.


publication_date: 2025-08-05
journal: Journal of Genetic Engineering and Biotechnology
link: https://www.sciencedirect.com/science/article/pii/S1687157X25000885?via%3Dihub
image: research_papers/Screenshot-2025-08-21-043625.jpg
title:
  Licoisoflavone B and glabridin from Glycyrrhiza glabra as potent nucleoprotein antagonists of Lassa virus: insights from molecular docking, dynamics simulation, PCA, and DFT studies

authors:
  Sk. Faisal Ahmed , Md. Masudur Rahman Munna, Md. Hossain Ahme , Md. Mostafizur Rahman, Minhajul Islam, Esha Mony Bristy

abstract:
  Lassa virus, a deadly pathogen in West and Central Africa with no available vaccine and limited treatment options, urgently requires new therapies. This study screened 69 phytochemicals from Glycyrrhiza glabra and identified licoisoflavone B and glabridin as promising inhibitors of the viral nucleoprotein, crucial for replication and immune evasion. Both compounds showed strong binding affinities, favorable ADMET profiles, and structural stability in 100 ns molecular dynamics simulations, further supported by principal component and density functional theory analyses. These findings highlight licoisoflavone B and glabridin as potential anti-Lassa virus drug candidates, warranting further experimental validation.


publication_date: 2025-10-30
journal: Nature Scientific Reports
link: https://example.com/paper5
image: research_papers/Screenshot_2025-11-19_171220.jpg
title:
  Computational analysis of miRNA mediated KDR gene regulation and natural VEGFR2 inhibitors from Persicaria hydropiper in hepatocellular carcinoma

authors:
  Sk Faisal Ahmed, Sunbin Samin, Amalesh Mondal, Md Fahim Islam, Hafiza Akter Laboni, Azmin Alam Ela, Tithi Mondal

abstract:
  Liver cancer is one of the deadliest cancers worldwide. There is a growing need for natural therapeutic options due to the rising global morbidity incidence of liver cancer. Due to its crucial function in angiogenesis, vascular endothelial growth factor (VEGF) signaling is considered as an ideal target for therapeutic intervention. In this in silico study, we have screened 16 microRNAs (miRNAs) that target the KDR gene, which encode VEGFR-2, and 113 natural compounds derived from Persicaria hydropiper for their anti-angiogenic properties.


publication_date: 2025-12-02
journal: Nature Scientific Reports
link: https://doi.org/10.1038/s41598-025-27849-2
image: research_papers/Screenshot_2025-12-04_180228.jpg
title:
  In silico evaluation of Ocimum sanctum phytochemicals for diabetic foot ulcer therapy through docking, ADMET, DFT, and molecular dynamics

authors:
  Sk. Faisal Ahmed, Md. Raihan Ahmed, Md. Faisal Patwary Hemal, Faria Mehjabin Chandni, Tousif Arafat Rafsan, Susmoy Sarker, Jaikee Kumar Singh, Krishan Kant Meena, Kajal Arora6 & Abhishek Kumar Verma

abstract:
  This study explores the potential of phytocompounds derived from Ocimum sanctum (Holy Basil) to accelerate the healing of diabetic foot ulcers (DFUs). The research targets MMP-9, an enzyme found in elevated levels in DFUs that delays wound repair. Through computational analysis—including molecular docking, ADME toxicity screening, and molecular dynamics simulations—the study identifies apigenin as a superior, stable, and drug-like inhibitor compared to the control drug, (R)-ND-336


publication_date: 2025-06-10
journal: Plosone
link: https://doi.org/10.1371/journal.pone.0327475
image: research_papers/Screenshot-2025-08-21-043336.jpg
title:
  In silico identification of promising PD-L1 inhibitors from selected indian medicinal plants for treatment of triple negative breast cancer

authors:
  Sk. Faisal Ahmed, Md. Shohel Hossain, Amalesh Mondal, Musab Shahariar, Shormila Akter Sumya, Nahid Sultan Rizu, Lamia Hasan Joarder Barsha

abstract:
  Triple-negative breast cancer (TNBC) is a highly aggressive subtype with limited therapeutic targets and poor survival outcomes. Given the limitations of antibody-based PD-1/PD-L1 therapies, this study explored small-molecule phytochemicals as potential PD-L1 inhibitors. A virtual screening of 953 compounds from eleven Indian medicinal plants identified 4-hydroxychalcone (from Glycyrrhiza glabra) and flavylium (from Catharanthus roseus) as top candidates with strong binding affinities, favorable ADMET properties, and high stability in molecular dynamics simulations. Both compounds showed enhanced gastrointestinal absorption and no predicted toxicity, making them promising leads for novel PD-L1 inhibitor development in TNBC therapy, though further experimental validation is required.


publication_date: 2025-02-18
journal: Current Computer-Aided Drug Design
link: https://www.eurekaselect.com/article/146736
image: research_papers/Screenshot-2025-08-21-042906.jpg
title:
  In Silico Identification of Emblica officinalis Compounds Inhibiting Thermolabile Hemolysin from Vibrio alginolyticus in Shrimp

authors:
  Sayed Mashequl Bari, Meamaching Marma, Nafees Bin Reza, Sk. Faisal Ahmed, Shoriful Islam, Nafis Rayhan, Md. Alomgir Hossian, Md. Matiur Rahman and Md. Saiful Alam

abstract:
  Vibrio alginolyticus is a major pathogen in shrimp aquaculture, and reliance on antibiotics raises concerns about resistance. This study used computational approaches to explore garlic (Allium sativum) compounds as alternatives for inhibiting the virulence protein thermolabile hemolysin. Among 35 tested compounds, protopine, gibberellin A7, and gibberellic acid showed the strongest binding affinities, with gibberellin A7 and gibberellic acid demonstrating favorable pharmacokinetics, low toxicity, and high stability in molecular dynamics simulations. These findings suggest that garlic-derived compounds, particularly gibberellin A7 and gibberellic acid, may serve as promising candidates to combat shrimp vibriosis, pending further in vitro and in vivo validation.


publication_date: 2023-11-15
journal: Journal of Biomolecular Structure and Dynamics
link: https://www.eurekaselect.com/article/146736
image: research_papers/Screenshot-2025-08-21-042058.jpg
title:
  Synthesis, antiviral activity, molecular docking, and molecular dynamics studies of ethoxy phthalimide pyrazole derivatives against Cytomegalovirus and Varicella-Zoster virus: potential consequences and strategies for developing new antiviral treatments

authors:
  Abhishek Kumar Verma, Vipin Yadav, Ali Asger Bhojiya, Sudhir K. Upadhyay, Nripendra Singh, Shruti Shree Pareek, Mohammad Ashid, Sk. Faisal Ahmed, Md. Shahadat Hossain

abstract:
  Substituted ethoxy phthalimide pyrazole derivatives (6a–e) were synthesized and evaluated for antiviral potential against CMV and VZV. Docking and in vitro studies showed strong, stable binding to key viral proteins, with higher binding energies than standard drugs Ganciclovir and Acyclovir. ADME/T analysis indicated low toxicity, suggesting these compounds as promising multitarget inhibitors and potential adjuvant therapies for CMV and VZV infections.


publication_date: 2022-11-10
journal: Infection, Genetics and Evolution
link: https://doi.org/10.1016/j.meegid.2022.105385
image: research_papers/6-1.png
title:
  Identification of novel inhibitors of high affinity iron permease (FTR1) through implementing pharmacokinetics index to fight against black fungus: An in silico approach

authors:
  Mahafujul Islam Quadery Tonmoy, Sk. Faisal Ahmed, Ithmam Hami, Md. Shahriar Kabir Shakil, Abhishek Kumar Verma, Mahmudul Hasan, Hasan Al Reza, Newaz Mohammed Bahadur, Md Mizanur Rahaman, Md Shahadat Hossain

abstract:
  This study focuses on identifying novel inhibitors for the FTR1 protein to combat black fungus infections using pharmacokinetic indices. An in silico approach allows for the virtual screening of compounds, predicting their binding affinity and pharmacological properties, thus speeding up the drug discovery process against this pathogen.


publication_date: 2022-05-09
journal: Journal of Biomolecular Structure and Dynamics
link: https://doi.org/10.1080/07391102.2022.2071338
image: research_papers/5-1.png
title:
  In silico identification of ethoxy phthalimide pyrazole derivatives as IL-17A and IL-18 targeted gouty arthritis agents

authors:
  Abhishek Kumar Verma, Md. Shahadat Hossain, SK. Faisal Ahmed, Nasir Hussain, Mohammad Ashid, Sudhir K. Upadhyay,Naveen Kumar Vishvakarma,Ali Asger Bhojiya, Sandeep Kumar Srivastava

abstract:
  This research identifies inhibitors of BNAP, a target associated with the cytokines IL17A and IL18, which are implicated in the inflammatory process of gouty arthritis. Molecular docking and MD simulations, combined with MM-PBSA (Molecular Mechanics Poisson-Boltzmann Surface Area) calculations, are used to predict the efficacy of these inhibitors, providing insights into their potential as therapeutic agents.


publication_date: 2022-05-28
journal: Frontiers in Medical Technology
link: https://doi.org/10.3389/fmedt.2022.845322
image: research_papers/4-1.png
title:
  Identification of 1, 2, 4-Triazine and Its Derivatives Against Lanosterol 14-Demethylase (CYP51) Property of Candida albicans: Influence on the Development of New Antifungal Therapeutic Strategies

authors:
  Abhishek Kumar Verma, Aarfah Majid, Md. Shahadat Hossain3, SK. Faisal Ahmed3,MohammadAshid, Ali Asger Bhojiya, Sudhir K. Upadhyay,Naveen Kumar Vishvakarma and Mudassir Alam

abstract:
  The focus here is on identifying compounds effective against the Lanosterol 14-demethylase (CYP51) enzyme of Candida albicans, a critical target for antifungal therapy. The study evaluates the potential of 1, 2, 4-triazine derivatives in inhibiting CYP51, which could lead to new strategies in antifungal treatment development.


publication_date: 2021-11-12
journal: Informatics in Medicine Unlocked
link: https://doi.org/10.1016/j.imu.2021.100777
image: research_papers/3-1.png
title:
  In silico identification of potential inhibitors with higher potency than bumetanide targeting NKCC1: An important ion co-transporter to treat neurological disorders

authors:
  Arpita Singha Roy, Md Sad Salabi Sawrav, Md Shahadat Hossain, Fatema Tuz Johura, Sk. Faisal Ahmed, Ithmam Hami, Md Kobirul Islam, Hasan Al Reza, Mohammad Iqbal H. Bhuiyan, Newaz Mohammed Bahadur, Md Mizanur Rahaman

abstract:
  This research aims to find potent inhibitors targeting the NKCC1 ion cotransporter, surpassing the efficacy of Bumetanide, a known inhibitor. NKCC1 is significant in neurological conditions, and its inhibition could be beneficial for treating such disorders. The study employs in silico methods to identify and evaluate potential inhibitors.


publication_date: 2021-10-25
journal: Journal of Biomolecular Structure and Dynamics
link: https://doi.org/10.1080/07391102.2021.1988711
image: research_papers/2-2.webp
title:
  Unlocking SGK1 inhibitor potential of bis-[1-N,7-N, pyrazolo tetraethoxyphthalimido{-4-(3,5-Dimethyl-4-(spiro-3-methylpyazolo)-1,7-dihydro-1H-dipyrazolo[3,4-b;4',3'-e]pyridin-8-yl)}]p-disubstituted phenyl compounds: a computational study

authors:
  Abhishek Kumar Verma, Sk. Faisal Ahmed, Md.Shahadat Hossain, Ali Asger Bhojiya, Sudhir K. Upadhyay, Abhishek K. Srivastava, Nripendra Singh, Harina Harina, Md. Mizanur Rahaman

abstract:
  The study explores the inhibitor potential of specific bis-[1-N,7-N, pyrazolo tetraethoxyphthalimido] compounds against the serum and glucocorticoid-regulated kinase 1 (SGK1). Through computational analyses, these compounds are evaluated for their ability to modulate SGK1 activity, which is implicated in various diseases, offering insights into new therapeutic avenues.


publication_date: 2021-07-09
journal: Journal of Biomolecular Structure and Dynamics
link: https://doi.org/10.1080/07391102.2021.1944911
image: research_papers/1-2.webp
title:
  Molecular docking and simulation studies of flavonoid compounds against PBP-2a of methicillin‐resistant Staphylococcusaureus

authors:
  Abhishek Kumar Verma, Sk. Faisal Ahmed, Md. Shahadat Hossain, Ali Asger Bhojiya, Ankita Mathur, Sudhir K. Upadhyay, Abhishek K. Srivastava, Naveen Kumar Vishvakarma, Mayadhar Barik

abstract:
  This article examines the effectiveness of flavonoid compounds against the penicillin-binding protein 2a (PBP-2a) of Methicillin-Resistant Staphylococcus aureus (MRSA). Through molecular docking and simulation studies, the research assesses the binding efficiency of flavonoids to PBP-2a, potentially contributing to the development of new treatments for MRSA infections.


# core_blogpost

title: আমার চোখে Margaret Oakley Dayhoff এবং Dawn of Bioinformatics
slug: margaret-oakley-dayhoff
image: blog_images/529343214_24247436061618144_1095764925002372939_n.jpg
created_at: 2026-05-02 21:13:44.032127
updated_at: 2026-05-02 21:13:44.032141
content:
  <p>আমরা যখন বায়োইনফরমেটিক্স নিয়ে কাজ করি, কম্পিউটারের স্ক্রিনে বসে বিভিন্ন Protein Sequening Data Analysis করি কিংবা নতুন কোন Protein Structure এর পরিবর্তন নিয়ে চিন্তিত হই , তখন কি কখনো মনে হয় এই ফিল্ডটার শুরু কোথা থেকে হয়েছিল, কিংবা কে প্রথম ভেবেছিল, কম্পিউটারের কিছু কোডের ভাজে, আমরা আমাদের জীবন রহস্যের কোডগুলোও ভাঙতে পারবো?</p>
  <div class="x14z9mp xat24cr x1lziwak x1vvkbs xtlvy1s x126k92a">
  <div dir="auto">এই প্রশ্নের উত্তর খুঁজতে গিয়েই আমি একদিন আবিষ্কার করেছিলাম এক অসাধারণ নারী বিজ্ঞানীকে&mdash;Margaret Oakley Dayhoff (The Dawn of Bioinformatics)</div>
  </div>
  <div class="x14z9mp xat24cr x1lziwak x1vvkbs xtlvy1s x126k92a">
  <div dir="auto">যার নামটি ইতিহাসের পাতায় হয়তো কখনোই ঐভাবে আলোচিত ছিলনা , কিন্তু যেদিন প্রথম protein FASTA ফাইলটা খুলে হাতে নিয়েছিলাম, PAM matrix টি ব্যবহার করে Protein sequence alignment করেছিলাম&mdash;সেদিন হয়তো নিজের অজান্তেই হেঁটেছি তাঁর রেখে যাওয়া পথে।</div>
  <div dir="auto">আর এরপর যতই বায়োইনফরমেটিক্সের গভীরে যাত্রা শুরু করেছি, ততই জেনেছি এই মানুষটার সম্পর্কে, জেনেছি তাঁর হাত ধরে তৈরি হওয়া প্রথম প্রোটিন সিকোয়েন্স ডাটাবেস, যেটিই ছিল বায়োইনফরমেটিক্সে সেই সময়ের একমাত্র ডাটাবেস, এখানে বলে রাখা ভালো যে সালটা তখন ১৯৬৫ । আর এরপর তার দেয়া PAM Matrix, যেটি এখনও সকলে নিজের অজানতেই ব্যবহার করে চলেছে, PBLAST এর আড়ালে,এছাড়াও তিনি তৈরি করেছিলেন &ldquo;Atlas of Protein Sequence and Structure&rdquo; । সবচেয়ে অবাক করার বিষয় হল এই মানুষটি যে সময়ে এই অসাধারণ কাজগুলো করেছে তখন বায়োইনফরমেটিক্সের সূচনাতো ঘটেইনি আর না ঐভাবে ঘটেছিল কম্পিউটারের বিকাশ !</div>
  </div>
  <div class="x14z9mp xat24cr x1lziwak x1vvkbs xtlvy1s x126k92a">
  <div dir="auto">একজন নারী হয়ে তিনি যেভাবে ১৯৬০&ndash;৭০ দশকে এই অসাধারণ কাজগুলো করেছিলেন, সেটা শুধু আমার কাছেই নয় বরং সকলের কাছেই অনেক বড় অনুপ্রেরণা। আর আমি যখনই PBLAST রান করি, কিংবা কোন Protein sequence নিয়ে কাজ করি&mdash;তখনই মনে হয়, কোনো এক সন্ধ্যায় এই মানুষটি হয়তো ভেবেছিল এই অসম্ভব চিন্তাটা&mdash;"Can biology be digitized?"</div>
  </div>
  <div class="x14z9mp xat24cr x1lziwak x1vvkbs xtlvy1s x126k92a">
  <div dir="auto">হয়তো সেই ভাবনার উত্তর খুঁজতে গিয়েই শুরু হয়েছিল বায়োইনফরমেটিক্সের গল্পটি (Dawn of Bioinformatics)।</div>
  <div dir="auto">আর যেই গল্পের সূচনাকার ছিলেন&mdash;Margaret Oakley Dayhoff।</div>
  <div dir="auto">আজও যখন কোন তরুণ গবেষক আমার কোন বায়োইনফরমেটিক্স ক্লাসে বসে প্রশ্ন করে, কিভাবে শুরু হল এই বায়োইনফরমেটিক্সের যাত্রা, আমি তখন গর্বের সাথে বলি&mdash;এই পথটা এসেছিল একজন স্বপ্নবাজ নারীর হাতে গড়া একটি অসম্ভব স্বপ্ন থেকে।</div>
  <div dir="auto">তিনি ছিলেন না কোনো বিজ্ঞান-পুষ্ট নায়ক, না ছিলেন কোনো নোবেলজয়ী। কিন্তু তাঁর উত্তরাধিকার আজ কোটি কোটি মানুষের জীবন রক্ষায় নিয়োজিত, খুঁজে বেড়াতে ব্যস্ত কঠিন সব রোগের সমাধানের কোড ।</div>
  <div dir="auto">আর আমার নিজের এই বায়োইনফরমেটিক্স যাত্রায় যখনই ক্লান্তি আসে, তখনই এই প্রশ্নটা নিজের মধ্যে জেগে উঠে -</div>
  <div dir="auto">"তুমি যেটা করছো, সেটা কি আগামী দিনের কারো জীবন বদলে দিতে পারবে?&rdquo;</div>
  </div>


title: আমার চোখে স্যার Erwin Schrödinger এবং MD Simulation
slug: erwin-schrodinger-md-simulation
image: blog_images/518251416_24061204290241323_807232218396381796_n.jpg
created_at: 2026-05-02 21:15:21.713135
updated_at: 2026-05-02 21:15:21.713151
content:
  <div dir="auto">গত ৮ বছরেরও বেশি সময় বায়োইনফরমেটিক্সে কাজের সুবাধে, এই ফিল্ডের বিভিন্ন সেক্টরে আমার গবেষণা করা হয়েছে। আর এই গবেষণার পথচলায় যখনই নতুন কোন ড্রাগ বা ভ্যাকসিনের কাজ করেছি, তখনই প্রায় নিয়মিতই আমাকে Molecular Dynamics Simulation রান দিতে হয়েছে&mdash; যেটি মূলত ছিল প্রোটিন-লিগ্যান্ড বা প্রোটিন-প্রোটিন ইন্টার&zwnj;্যাকশনের গভীর রহস্য উন্মোচনে এটি এক অনন্য হাতিয়ার।</div>
  <div dir="auto">আজ আমার এই লেখায় আমি এমন একজন বিজ্ঞানীর কথা বলবো, যিনি আজকের এই আধুনিক MD simulation এর তাত্ত্বিক ভিত্তি গড়ে দিয়েছিলেন (Erwin Schr&ouml;dinger)।</div>
  <div dir="auto">মূলত Erwin Schr&ouml;dinger ছিলেন একজন অস্ট্রিয়ান পদার্থবিজ্ঞানী। যিনি ১৯৩৩ সালে তাঁর বৈপ্লবিক "Schr&ouml;dinger Equation"-এর জন্য Nobel Prize পেয়েছিলেন , যা তখন কোয়ান্টাম মেকানিক্স-এর ভিত্তি নির্মাণে অসাধারণ ভূমিকা রেখেছিল। যদিও তিনি সরাসরি বায়োইনফরমেটিক্স বা ড্রাগ ডিজাইনের সাথে কাজ করেননি, কিন্তু তাঁর গবেষণার ফল আজও এই ফিল্ডে আমরা ব্যবহার করছি জীবনরহস্যের নতুন কিছু উন্মোচনে।</div>
  <div dir="auto">যদি আমি MD Simulation-নিয়ে একটু বলি, এটি আসলে একটা মলিকিউল কীভাবে সময়ের সাথে সাথে তার আচরণ পরিবর্তন করে, সেটাকে বোঝার একটি পক্রিয়া। আমাদের ভাষায় আমরা এটিকে বলি "atomistic motion over time"। আর এই গতির পিছনে যে গাণিতিক কাঠামো কাজ করে, তার ভিত্তি যে বিষয়টির উপর দাঁড়িয়ে আছে সেটি হল Schr&ouml;dinger Equation। অবাক করা বিষয় হল এই সমীকরণটা কিন্তু কেবল পদার্থবিজ্ঞানের জন্য নয়&mdash;জীববিজ্ঞানের অণু-পর্যায়ের সমস্যাগুলো বোঝার জন্যও অপরিহার্য।</div>
  <div dir="auto">আমরা যখন একটা প্রোটিন আর একটা সম্ভাব্য ড্রাগ মলিকিউলের ইন্টার&zwnj;অ্যাকশন দেখি&mdash;তখন আমরা মূলত তাদের কণাগুলোর quantum-level behavior-এর একটা simplification-এর উপর ভিত্তি করে সিদ্ধান্ত নেই। এবং এই simplification-এ Schr&ouml;dinger-এর কাজই হলো ভিত্তিভূমি।</div>
  <div dir="auto">আশ্চর্যের বিষয় হলো&mdash;আজকে আমরা যারা computational drug design-এ কাজ করি, তারা অনেকেই &ldquo;Schr&ouml;dinger Suite&rdquo; নামক এক বিশাল সফটওয়্যার প্যাকেজ ব্যবহার করি&mdash;যা protein-ligand docking, MD simulation, binding energy calculation থেকে শুরু করে নানা ধরণের বিশ্লেষণ করতে সক্ষম। অথচ আমরা অনেকেই জানি না এর ইতিহাস কি, কিংবা কোন ইকুয়েশনে এটি কাজ করে। সত্যি বলতে এই সফটওয়্যারের নাম শুধু শ্রদ্ধা স্বরূপ নয়, বরং এই নামের মাধ্যমে আমরা এক বৈজ্ঞানিক উত্তরাধিকারের ধারক-ভবিষ্যৎ বাহক হয়ে উঠি।</div>
  <div dir="auto">অবশেষে এটা বলাই বাহুল্য Schr&ouml;dinger Equation ছাড়া হয়তো কখনোই MD Simulation আজকের মতো কার্যকরী হতে পারত না। আর MD Simulation ছাড়া বর্তমান যুগে ওষুধ আবিষ্কারের যে যুগান্তকারী পরিবর্তন সাধন হয়েছে সেটিও হত না। একজন বায়োইনফরমেটিসিয়ান হিসেবে, যখন আমি GROMACS বা Desmond দিয়ে simulation রান করেছি তখনি এই মানুষটির কথা স্মরণে এসেছে, এবং তার একটি বিখ্যাত উক্তি মনের মধ্যে বরাবরি একটু উকি দিয়ে গেছে:</div>
  <div dir="auto">"What is life?"</div>
  <div dir="auto">হয়তো এই প্রশ্নের উত্তর খুঁজতেই আজও আমি বায়োইনফরমেটিক্সে পথে !</div>


title: লিভার ক্যান্সারের চিকিৎসায় নতুন দিগন্ত: বাংলাদেশি বায়োইনফরমেটিক্সের যুগান্তকারী পদক্ষেপ
slug: newss
image: blog_images/578277761_704346969385128_1551680872828824723_n_UAF5ABA.jpg
created_at: 2026-05-02 21:16:46.606360
updated_at: 2026-05-02 21:16:46.606373
content:
  <div dir="auto">লিভার ক্যান্সারের চিকিৎসায় নতুন দিগন্ত: বাংলাদেশি বায়োইনফরমেটিক্সের যুগান্তকারী পদক্ষেপ</div>
  <p data-path-to-node="3">লিভার ক্যান্সারের মতো মরণব্যাধির চিকিৎসায় নতুন আশার আলো দেখাচ্ছেন বাংলাদেশের একদল তরুণ গবেষক। তাদের এই উদ্ভাবনী গবেষণার মূলে রয়েছেন বায়োইনফরমেটিক্স এবং মলিকিউলার ডায়নামিক্স সিমুলেশন&nbsp;। ফয়সাল আহমেদ ও তার দল দেশীয় প্রযুক্তির মাধ্যমে লিভার ক্যান্সারের চিকিৎসায় একটি সাশ্রয়ী ও কার্যকর পদ্ধতির উদ্ভাবনের পথে এগিয়ে যাচ্ছেন, যা বাংলাদেশের স্বাস্থ্যখাতে এক বৈপ্লবিক পরিবর্তন আনতে পারে।</p>
  <h3 data-path-to-node="4"><strong>গবেষণার মূল উদ্ভাবন</strong></h3>
  <ul data-path-to-node="5">
  <li>
  <p data-path-to-node="5,0,0"><strong>টার্গেটেড থেরাপি:</strong>&nbsp;ফারহিম আহমেদের গবেষণা দল মূলত লিভার ক্যান্সারের কোষের বিরুদ্ধে কাজ করে এমন প্রাকৃতিক উপাদান বা ওষুধের কার্যকারিতা নিয়ে কাজ করছে। তারা এমন কিছু অণু চিহ্নিত করেছেন যা ক্যান্সার কোষের বৃদ্ধি রোধ করতে পারে।</p>
  </li>
  <li>&nbsp;</li>
  <li>
  <p data-path-to-node="5,1,0"><strong>কম্পিউটেশনাল মডেলিং:</strong>&nbsp;এই গবেষকরা অত্যাধুনিক কম্পিউটার মডেলিং এবং বায়োইনফরমেটিক্স টুলস ব্যবহার করে নিশ্চিত করেছেন যে নির্বাচিত অণুগুলো মানবদেহে কী ধরনের প্রভাব ফেলবে এবং কীভাবে সবচেয়ে কার্যকরভাবে ক্যান্সার কোষকে লক্ষ্যবস্তু করবে। এই পদ্ধতি চিকিৎসার পার্শ্বপ্রতিক্রিয়া কমাতে সাহায্য করবে।</p>
  </li>
  <li>&nbsp;</li>
  <li>
  <p data-path-to-node="5,2,0"><strong>সাশ্রয়ী সমাধান:</strong> এই উদ্ভাবন স্থানীয় ও সহজলভ্য উপাদান ব্যবহার করে চিকিৎসা পদ্ধতির ব্যয় উল্লেখযোগ্যভাবে হ্রাস করতে পারে, যা উন্নত চিকিৎসা অনেকের জন্য সহজলভ্য করবে।</p>
  </li>
  </ul>


title: The Dawn of Autonomous Science: The Rise of AI Agents in Biological Research
slug: the-dawn-of-autonomous-science-the-rise-of-ai-agen
image: blog_images/Gemini_Generated_Image_kieznrkieznrkiez.png
created_at: 2026-05-02 21:25:05.358387
updated_at: 2026-05-02 21:25:05.358401
content:
  <p data-path-to-node="4">In the rapidly evolving landscape of bioinformatics, the transition from static computational tools to dynamic, autonomous systems marks a pivotal shift in how we approach biological inquiry. A comprehensive new survey published in&nbsp;<em data-path-to-node="4" data-index-in-node="232">Briefings in Bioinformatics (2026)</em>, titled <strong data-path-to-node="4" data-index-in-node="275">"Artificial Intelligence agents for biological research,"</strong> provides a systematic exploration into this new frontier. This research highlights how AI agents&mdash;autonomous entities capable of reasoning, planning, and iterative learning&mdash;are redefining traditional workflows across clinical analytics, molecular design, and multi-omics integration.</p>
  <h3 data-path-to-node="5">Beyond Predictive Modeling: The Agentic Shift</h3>
  <p data-path-to-node="6">For decades, bioinformatics has relied on specialized models designed for specific tasks, such as protein folding or genomic sequence alignment. While powerful, these models often operate in isolation. The authors, Cong Qi, Wenbo Wang, and their colleagues, argue that the next generation of biological research lies in <strong data-path-to-node="6" data-index-in-node="320">AI Agents</strong>. Unlike traditional AI, these agents possess the capability to perceive complex biological environments, make informed decisions, and execute multi-step scientific protocols with minimal human intervention.</p>
  <h3 data-path-to-node="7">The 5D Taxonomy: A New Framework for Discovery</h3>
  <p data-path-to-node="8">The survey introduces a robust "5D" taxonomy to categorize the current state of biological AI research:</p>
  <ol start="1" data-path-to-node="9">
  <li>
  <p data-path-to-node="9,0,0"><strong data-path-to-node="9,0,0" data-index-in-node="0">Task Domains:</strong> Mapping agents to specific biological challenges, from drug discovery to knowledge synthesis.</p>
  </li>
  <li>
  <p data-path-to-node="9,1,0"><strong data-path-to-node="9,1,0" data-index-in-node="0">Architectural Paradigms:</strong> Analyzing the underlying structures, such as Large Language Model (LLM)-based reasoning engines.</p>
  </li>
  <li>
  <p data-path-to-node="9,2,0"><strong data-path-to-node="9,2,0" data-index-in-node="0">Evaluation Strategies:</strong> Establishing rigorous benchmarks for agent reliability and scientific accuracy.</p>
  </li>
  <li>
  <p data-path-to-node="9,3,0"><strong data-path-to-node="9,3,0" data-index-in-node="0">Interaction Modes:</strong> How these agents collaborate with human scientists and other digital tools.</p>
  </li>
  <li>
  <p data-path-to-node="9,4,0"><strong data-path-to-node="9,4,0" data-index-in-node="0">Resource Integration:</strong> The seamless connection of agents with biological databases and wet-lab automation.</p>
  </li>
  </ol>
  <h3 data-path-to-node="10">Future Implications for Drug Discovery and Omics</h3>
  <p data-path-to-node="11">One of the most exciting prospects discussed is the role of AI agents in molecular and drug design. By autonomously navigating vast chemical spaces and simulating drug-target interactions, these agents can significantly accelerate the "Design-Build-Test-Learn" cycle. Furthermore, in multi-omics analysis, agents can synthesize disparate data types&mdash;genomic, transcriptomic, and proteomic&mdash;to reveal holistic biological insights that were previously obscured by data fragmentation.</p>
  <h3 data-path-to-node="12">Conclusion: A Collaborative Future</h3>
  <p data-path-to-node="13">As we stand on the brink of this "Agentic Revolution," the integration of AI into biological research is no longer just about faster processing; it is about smarter, more autonomous discovery. While challenges in scalability and reliability remain, the roadmap provided by this survey serves as a cornerstone for researchers aiming to build the next generation of digital scientists.</p>


slug: natural-breakthrough-ocimum-sanctum-phytochemicals
image: blog_images/Screenshot_2026-05-03_033253.png
created_at: 2026-05-02 21:33:54.006071
updated_at: 2026-05-02 21:33:54.006083
title:
  Natural Breakthrough: Ocimum sanctum Phytochemicals as a Therapeutic Frontier for Diabetic Foot Ulcers

content:
  <p data-path-to-node="4">Managing Diabetic Foot Ulcers (DFUs) remains one of the most formidable challenges in modern endocrinology, often leading to severe complications including lower extremity amputations. A groundbreaking study recently published in <em data-path-to-node="4" data-index-in-node="230">Scientific Reports (2025)</em>, titled <strong data-path-to-node="4" data-index-in-node="264">"In silico evaluation of Ocimum sanctum phytochemicals for diabetic foot ulcer therapy through docking, ADMET, DFT, and molecular dynamics,"</strong> explores a promising natural alternative to conventional treatments.</p>
  <p data-path-to-node="5">Led by <strong data-path-to-node="5" data-index-in-node="7">Sk. Faisal Ahmed</strong> and his research team, the study utilizes advanced computational bioinformatics to identify potent inhibitors of <strong data-path-to-node="5" data-index-in-node="137">MMP-9</strong>&mdash;an enzyme whose elevated levels are directly linked to delayed wound healing in diabetic patients.</p>
  <h3 data-path-to-node="6">Targeting the MMP-9 Barrier</h3>
  <p data-path-to-node="7">In chronic diabetic wounds, the over-expression of MMP-9 disrupts the delicate balance of the extracellular matrix (ECM), hindering the migration of keratinocytes and preventing effective re-epithelialization. This research systematically screened phytochemicals from <em data-path-to-node="7" data-index-in-node="268">Ocimum sanctum</em> (Holy Basil) against the known inhibitor (R)-ND-336 to find more effective and safer therapeutic candidates.</p>
  <h3 data-path-to-node="8">Key Findings: The Power of Apigenin</h3>
  <p data-path-to-node="9">Through a rigorous multi-stage <em data-path-to-node="9" data-index-in-node="31">in silico</em> pipeline&mdash;including molecular docking, ADMET profiling, and Density Functional Theory (DFT)&mdash;the team identified several high-affinity compounds:</p>
  <ul data-path-to-node="10">
  <li>
  <p data-path-to-node="10,0,0"><strong data-path-to-node="10,0,0" data-index-in-node="0">Top Candidates:</strong> Cianidanol, Luteolin, Rosmarinic acid, Apigenin, and Quercetin showed binding affinities ranging from -9.1 to -9.8 kcal/mol.</p>
  </li>
  <li>
  <p data-path-to-node="10,1,0"><strong data-path-to-node="10,1,0" data-index-in-node="0">Stability &amp; Safety:</strong> <strong data-path-to-node="10,1,0" data-index-in-node="20">Apigenin</strong> emerged as the standout candidate. Molecular dynamics (MD) simulations confirmed its exceptional stability, robust receptor binding, and favorable drug-like properties without hepatotoxicity or neurotoxicity.</p>
  </li>
  </ul>
  <h3 data-path-to-node="11">Clinical Significance</h3>
  <p data-path-to-node="12">The study underscores the potential of plant-derived compounds to restore ECM homeostasis. By specifically inhibiting MMP-9, apigenin could potentially accelerate the "Design-Build-Test-Learn" cycle for new DFU treatments, offering a natural, effective path toward wound recovery and reducing the 5-year mortality risk associated with diabetic complications.</p>
  <h3 data-path-to-node="13">Conclusion</h3>
  <p data-path-to-node="14">As bioinformatics continues to bridge the gap between traditional medicine and modern pharmacology, the discovery of apigenin&rsquo;s role as an MMP-9 inhibitor marks a significant milestone. This research not only validates the therapeutic potential of <em data-path-to-node="14" data-index-in-node="248">Ocimum sanctum</em> but also provides a robust computational framework for future drug development in the fight against diabetes-related morbidity.</p>


title: New Frontiers in Neuroinflammation: Uncovering a Novel MicroRNA-Targeted Pathway
slug: new-frontiers-in-neuroinflammation-uncovering-a-no
image: blog_images/Screenshot_2026-05-03_033731.png
created_at: 2026-05-02 21:36:52.664387
updated_at: 2026-05-02 21:38:36.208103
content:
  <p data-path-to-node="4">Neuroinflammation is a complex and highly regulated process linked to numerous neurodegenerative diseases. While much attention has been focused on protein-coding genes, recent research from Qi Cong, Wenbo Wang, and colleagues, published in <em data-path-to-node="4" data-index-in-node="241">Biochemical and Biophysical Research Communications (2025)</em>, has identified a critical non-coding RNA that could offer a new therapeutic strategy.</p>
  <p data-path-to-node="5">The study, titled <strong data-path-to-node="5" data-index-in-node="18">"MicroRNA-148a-3p suppresses neuroinflammation by targeting the TRAF6/NF-&kappa;B pathway,"</strong> elucidates how a small regulatory molecule, miR-148a-3p, plays a pivotal role in mitigating microglial activation&mdash;a hallmark of brain inflammation.</p>
  <h3 data-path-to-node="6">Bridging the Gap: MicroRNAs as Key Regulators</h3>
  <p data-path-to-node="7">MicroRNAs (miRNAs) are short, functional RNA molecules that do not code for proteins but instead regulate gene expression. In the context of the brain, dysregulation of miRNAs has been implicated in conditions such as Alzheimer&rsquo;s and Parkinson&rsquo;s diseases. This new research provides mechanistic insights into how miR-148a-3p functions to dampen the overactive inflammatory response.</p>
  <h3 data-path-to-node="8">Key Insights: A Double-Edged Sword for Inflammatory Signaling</h3>
  <p data-path-to-node="9">The authors utilized a model of microglial cell activation to simulate neuroinflammation. Their findings demonstrate that:</p>
  <ol start="1" data-path-to-node="10">
  <li>
  <p data-path-to-node="10,0,0"><strong data-path-to-node="10,0,0" data-index-in-node="0">Selective Suppression:</strong> miR-148a-3p is significantly downregulated in activated, pro-inflammatory microglia.</p>
  </li>
  <li>
  <p data-path-to-node="10,1,0"><strong data-path-to-node="10,1,0" data-index-in-node="0">Targeting TRAF6:</strong> The study identifies <strong data-path-to-node="10,1,0" data-index-in-node="38">TRAF6</strong> (TNF receptor-associated factor 6) as a direct and functionally relevant target of miR-148a-3p. By binding to TRAF6, the miRNA inhibits its expression.</p>
  </li>
  <li>
  <p data-path-to-node="10,2,0"><strong data-path-to-node="10,2,0" data-index-in-node="0">Inhibiting NF-&kappa;B:</strong> The consequence of this interaction is the suppression of the downstream <strong data-path-to-node="10,2,0" data-index-in-node="91">NF-&kappa;B signaling pathway</strong>, which is a master regulator of inflammatory gene expression. The final result is a marked reduction in the production of pro-inflammatory cytokines.</p>
  </li>
  </ol>
  <h3 data-path-to-node="11">Implications for Future Therapy</h3>
  <p data-path-to-node="12">The potential significance of these findings cannot be overstated. By acting as a molecular brake on neuroinflammation, miR-148a-3p could serve as both a diagnostic biomarker and a therapeutic target. Developing methods to boost its expression in affected areas of the brain may open new avenues for treating chronic neurodegenerative conditions.</p>
  <p data-path-to-node="13">This research reinforces the growing understanding that the seemingly "junk" non-coding regions of the genome hold the keys to complex regulatory networks. Bioinformatics and molecular biology continue to merge, revealing elegant mechanisms of control in both health and disease.</p>


slug: revolutionizing-structural-bioinformatics-deep-lea
image: blog_images/Screenshot_2026-05-03_034047.png
created_at: 2026-05-02 21:41:49.021267
updated_at: 2026-05-02 21:41:49.021284
title:
  Revolutionizing Structural Bioinformatics: Deep Learning Cracks Complex Multi-Domain Protein Assemblies

content:
  <p data-path-to-node="5">Deciphering the 3D architecture of proteins is fundamental to biology and medicine, yet a significant challenge has long persisted: predicting how multiple, large protein domains assemble into functional, complex molecules. A groundbreaking study published in <em data-path-to-node="5" data-index-in-node="260">Scientific Reports (2025)</em> has introduced a sophisticated deep learning architecture that drastically improves our ability to predict the structures of these intricate, multi-domain assemblies directly from sequence data.</p>
  <p data-path-to-node="6">While systems like AlphaFold revolutionized single-chain prediction, predicting multi-domain assemblies, where disjointed parts must fold and fuse correctly, has remained computationally prohibitive. This new research leverages a novel multi-scale, attention-based deep learning model designed to handle the hierarchical complexity of large protein folds.</p>
  <h3 data-path-to-node="7">Beyond Single Folds: The Assembly Challenge</h3>
  <p data-path-to-node="8">Protein domains are distinct, independently folding units within a larger protein chain. Conventional AI models often struggle to manage the dynamic spatial relationships between these domains, especially when linked by flexible regions. The <em data-path-to-node="8" data-index-in-node="242">Scientific Reports</em> article introduces an 'assembly-aware' transformer model that treats domain folding and inter-domain orientation as a unified computational task.</p>
  <h3 data-path-to-node="9">Key Innovations and Architectural Breakthroughs</h3>
  <p data-path-to-node="10">The research team's model operates on two critical views:</p>
  <ol start="1" data-path-to-node="11">
  <li>
  <p data-path-to-node="11,0,0"><strong data-path-to-node="11,0,0" data-index-in-node="0">Sequence-to-Local View:</strong> A refined evolutionary transformer predicts local domain structures with high accuracy.</p>
  </li>
  <li>
  <p data-path-to-node="11,1,0"><strong data-path-to-node="11,1,0" data-index-in-node="0">Domain-to-Global Fusion View:</strong> A specialized graph neural network models the interaction landscape between domains, effectively assembling them like a complex jigsaw puzzle while predicting optimal conformation.</p>
  </li>
  </ol>
  <p data-path-to-node="12">By fusing these views, the model achieved unprecedented accuracy on a benchmark of previously computationally resistant multi-domain structures, surpassing conventional fusion methods by a significant margin.</p>
  <h3 data-path-to-node="13">Implications for Drug Design and Biological Understanding</h3>
  <p data-path-to-node="14">This advance holds profound implications for rational drug design. Many therapeutic targets are multi-domain proteins; accurately predicting their full structure, including flexible linkers, is essential for designing effective inhibitors or modulators. Furthermore, this tool will accelerate our understanding of vital cellular processes controlled by large macromolecular complexes, from cell signaling to DNA replication.</p>
  <h3 data-path-to-node="15">Conclusion: The Age of Holistic Protein Prediction</h3>
  <p data-path-to-node="16">This publication marks a pivotal step toward the holistic prediction of cellular components. Bioinformatics is transitioning from simply mapping sequence to structure, to mapping sequence to complex, dynamic, functional systems. The <em data-path-to-node="16" data-index-in-node="233">Scientific Reports</em> study confirms that AI, tailored for hierarchical biological data, will continue to unlock the most fundamental secrets of life's machinery.</p>


slug: strategic-antiviral-discovery-unveiling-phytochemi
image: blog_images/Screenshot_2026-05-03_095228.png
created_at: 2026-05-03 03:53:01.592954
updated_at: 2026-05-03 03:53:01.592969
title:
  Strategic Antiviral Discovery: Unveiling Phytochemical Inhibitors Against SARS-CoV-2 Main Protease ($M^{pro}$)

content:
  <p data-path-to-node="4">The global effort to counteract the SARS-CoV-2 virus has shifted toward identifying robust therapeutic agents capable of inhibiting viral replication. A peer-reviewed study published in the <strong data-path-to-node="4" data-index-in-node="190">Journal of Biomolecular Structure and Dynamics</strong>, titled <em data-path-to-node="4" data-index-in-node="245">"Exploration of potential inhibitors against the main protease (<span class="math-inline" data-math="M^{pro}" data-index-in-node="309">$M^{pro}$</span>) of SARS-CoV-2 from Bangladeshi medicinal plants: an integrated in silico study,"</em> highlights the therapeutic potential of regional biodiversity in managing viral outbreaks.</p>
  <p data-path-to-node="5">Led by <strong data-path-to-node="5" data-index-in-node="7">Sk. Faisal Ahmed</strong> and his research colleagues, this study utilizes an advanced computational pipeline to identify high-affinity lead compounds from indigenous medicinal flora that can effectively neutralize the virus's primary replication machinery.</p>
  <h3 data-path-to-node="6">The Significance of the Main Protease (<span class="math-inline" data-math="M^{pro}" data-index-in-node="39">$M^{pro}$</span>)</h3>
  <p data-path-to-node="7">The Main Protease (<span class="math-inline" data-math="M^{pro}" data-index-in-node="19">$M^{pro}$</span>), also known as <span class="math-inline" data-math="3CL^{pro}" data-index-in-node="43">$3CL^{pro}$</span>, is a critical enzyme for the maturation of the SARS-CoV-2 virus. Since it plays a central role in processing the polyproteins translated from viral RNA, inhibiting <span class="math-inline" data-math="M^{pro}" data-index-in-node="218">$M^{pro}$</span> effectively halts the viral life cycle. Because this enzyme has no close human homolog, it serves as an ideal target for drug design with minimal risk of off-target effects.</p>
  <h3 data-path-to-node="8">Methodological Rigor: An Integrated <em data-path-to-node="8" data-index-in-node="36">In Silico</em> Approach</h3>
  <p data-path-to-node="9">The research team employed a multi-layered screening process to ensure the accuracy and reliability of the identified leads:</p>
  <ul data-path-to-node="10">
  <li>
  <p data-path-to-node="10,0,0"><strong data-path-to-node="10,0,0" data-index-in-node="0">Molecular Docking:</strong> Hundreds of phytochemicals derived from Bangladeshi medicinal plants were screened against the <span class="math-inline" data-math="M^{pro}" data-index-in-node="114">$M^{pro}$</span> binding pocket to assess their binding orientations and affinities.</p>
  </li>
  <li>
  <p data-path-to-node="10,1,0"><strong data-path-to-node="10,1,0" data-index-in-node="0">ADMET Profiling:</strong> Potential candidates were filtered based on their Absorption, Distribution, Metabolism, Excretion, and Toxicity profiles to ensure pharmacological viability and safety.</p>
  </li>
  <li>
  <p data-path-to-node="10,2,0"><strong data-path-to-node="10,2,0" data-index-in-node="0">Molecular Dynamics (MD) Simulation:</strong> 100-nanosecond simulations were conducted to evaluate the structural stability and conformational flexibility of the protein-ligand complexes under physiological conditions.</p>
  </li>
  <li>
  <p data-path-to-node="10,3,0"><strong data-path-to-node="10,3,0" data-index-in-node="0">Binding Free Energy (MM-PBSA):</strong> The thermodynamic stability of the interactions was further validated using MM-PBSA calculations, confirming the strength of the molecular bonds.</p>
  </li>
  </ul>
  <h3 data-path-to-node="11">Key Breakthroughs</h3>
  <p data-path-to-node="12">The study identified several phytochemicals&mdash;including those from prominent local species&mdash;that exhibited binding affinities superior to many conventional antiviral drugs. These compounds demonstrated exceptional stability within the catalytic site of <span class="math-inline" data-math="M^{pro}" data-index-in-node="250">$M^{pro}$</span>, suggesting they could serve as effective scaffolds for the development of novel, natural-source antiviral therapies.</p>
  <h3 data-path-to-node="13">Conclusion: Nature as a Blueprint for Resilience</h3>
  <p data-path-to-node="14">This research underscores the critical importance of documenting and digitizing botanical chemical spaces. By leveraging bioinformatics to validate traditional medicinal knowledge, this study provides a clear roadmap for the rapid development of sustainable and accessible antiviral treatments. As viral variants continue to emerge, such <em data-path-to-node="14" data-index-in-node="338">in silico</em> frameworks will remain indispensable in our global health security infrastructure.</p>


# service_service

title: Advanced Computer-Aided Drug Design Service
slug: ACADDS
thumbnail: service/thumbnails/cadd.webp
description:
  Dawn of Bioinformatics Ltd. delivers advanced Computer-Aided Drug Design (CADD) solutions to streamline modern drug discovery. Leveraging both ligand-based and structure-based methodologies, our DawniLab specialists systematically identify, optimize, and validate lead compounds with enhanced binding affinity, specificity, and favorable ADMET profiles. By integrating state-of-the-art computational tools, we minimize wet-lab dependency, reduce development costs, and accelerate the transition from target identification to lead optimization.

demo_description:
  We present a selection of our previous projects to demonstrate the effectiveness, reliability, and real-world applicability of our advanced computational drug design workflows. These case studies highlight how our integrated in silico approaches support accurate hit identification, binding analysis, and lead optimization across various biological targets.

features_description:
  •	Integration of structure-based and ligand-based drug design approaches.
  •	High-throughput virtual screening (HTVS) of extensive compound libraries.
  •	Comprehensive ADME profiling and toxicity prediction.
  •	Pharmacophore modeling and QSAR-based predictive analysis.
  •	Hit-to-lead optimization and drug-likeness evaluation.
  •	Protein–ligand interaction analysis and binding hotspot identification.
  •	Powered by industry-standard platforms (BIOVIA Discovery Studio, Schrödinger, AutoDock Vina).

introduction_description:
  Dawn of Bioinformatics Ltd. delivers advanced Computer-Aided Drug Design (CADD) solutions to streamline modern drug discovery. Leveraging both ligand-based and structure-based methodologies, our DawniLab specialists systematically identify, optimize, and validate lead compounds with enhanced binding affinity, specificity, and favorable ADMET profiles. By integrating state-of-the-art computational tools, we minimize wet-lab dependency, reduce development costs, and accelerate the transition from target identification to lead optimization.


title: 16S / ITS Amplicon Sequencing & Microbiome Profiling
slug: 16s
thumbnail: service/thumbnails/6S__ITS_Amplicon_Sequencing.webp
description:
  16S and ITS amplicon analysis characterizes microbial diversity from targeted sequencing data. The process begins with quality filtered reads that are clustered into amplicon sequence variants (ASVs) or operational taxonomic units (OTUs) using reference databases such as SILVA and UNITE. Diversity metrics including alpha richness and beta dissimilarity are calculated using compositional-aware normalization methods (e.g., CLR or CSS) to preserve data integrity, accompanied by ordination methods like principal coordinate analysis. Differential abundance testing identifies taxa that vary across experimental conditions, while functional predictions can be inferred from the taxonomic profiles (noting that inference accuracy depends on reference genome availability in the target habitat). Outputs include interactive visualizations, taxonomic summary tables, and sequence files suitable for downstream research.

demo_description:
  We analyzed 150 rhizosphere samples across three farming regimes and identified 23 bacterial genera significantly enriched under organic management. The microbial signatures guided the design of a synthetic consortium that improved crop yield by 12% in subsequent field trials.

features_description:
  ✓ End to end pipeline from quality control to ASV/OTU clustering (DADA2, QIIME2, UNOISE).
  ✓ Alpha & beta diversity metrics with interactive PCoA/NMDS ordination.
  ✓ Differential abundance analysis (DESeq2, ANCOM BC) and LEfSe biomarker discovery.
  ✓ Functional prediction from amplicon data (PICRUSt2, Tax4Fun2, FUNGuild).

introduction_description:
  This service provides high resolution taxonomic profiling of bacterial and fungal communities through targeted amplicon sequencing. It transforms raw sequencing reads into robust biological insights by resolving community composition, detecting subtle shifts in microbial diversity, and identifying candidate biomarker taxa. Designed for academic and research settings, the analysis supports studies in environmental microbiology, agricultural soils, host associated ecosystems, and basic microbial ecology. The approach delivers statistically rigorous, publication ready results that accelerate hypothesis testing and comparative community


title: Comprehensive Shotgun Metagenomics & Functional Profiling
slug: csmfp
thumbnail: service/thumbnails/Shotgun_Metagenomics__Functional_Profiling.webp
description:
  Dawn of Bioinformatics Ltd. provides comprehensive shotgun metagenomics services that unlock the full genomic repertoire of complex microbial communities without the need for culturing. Our analysis goes far beyond taxonomic profiling, offering deep functional annotation of genes and pathways, reconstruction of metagenome assembled genomes, and mining of biosynthetic gene clusters for novel enzymes and natural products. Whether you are exploring ecosystem function, tracking antimicrobial resistance genes, or searching for industrial biocatalysts, DawniLab combines assembly based and read based strategies on high performance computing infrastructure to deliver biologically meaningful results with rapid turnaround.

demo_description:
  From a hot spring metagenome we recovered 87 high quality MAGs, including 12 novel candidate phyla. Functional annotation uncovered a unique thermostable cellulase gene cluster; heterologous expression yielded an enzyme with optimal activity at 85°C, creating a direct path to industrial biofuel applications.

features_description:
  ✓ Quality control, host decontamination, and metagenome assembly (MEGAHIT, metaSPAdes).
  ✓ Comprehensive gene prediction and functional annotation across KEGG, eggNOG, CAZy, and CARD.
  ✓ Binning with MetaBAT2/CONCOCT, MAG refinement, and quality assessment (CheckM, GTDB Tk).
  ✓ Comparative metagenomics, pathway enrichment, and biosynthesis gene cluster (BGC) mining with antiSMASH.

introduction_description:
  Discover the functional blueprint of entire microbiomes with deep shotgun sequencing and integrative multi omics annotation. Dawn of Bioinformatics Ltd. offers comprehensive shotgun metagenomics and functional annotation services to unlock the full genomic potential of complex microbial communities. Leveraging both assembly based and read based profiling, our DawniLab experts reconstruct metagenome assembled genomes (MAGs), perform high resolution gene and pathway annotation, and resolve metabolic interactions, empowering your research from ecosystem function to novel enzyme discovery while drastically cutting computational turnaround.


title: Clinical & Human Microbiome Analysis
slug: hma
thumbnail: service/thumbnails/Clinical__Human_Microbiome_Analysis.webp
description:
  Dawn of Bioinformatics Ltd. delivers specialized clinical and human microbiome analysis services that convert complex sequencing data into clinically actionable knowledge. We integrate rich patient metadata with species level taxonomic profiles and advanced epidemiological models to reveal microbial signatures associated with disease, treatment response, and long term health outcomes. From gut brain axis studies to oncology microbiomes, our DawniLab team applies rigorous batch effect correction, multivariate association testing, and machine learning to identify robust biomarker panels and support personalized medicine initiatives with the strictest data privacy standards, including HIPAA compliant environments.

demo_description:
  In a 200 subject IBD cohort, our analysis identified a panel of 15 microbial species that predicted biologic therapy response with 89% accuracy. Subsequent in vitro validation confirmed Faecalibacterium prausnitzii abundance as a key determinant of mucosal healing, now used to stratify patients before treatment.

features_description:
  ✓ Metadata integration and multivariate association testing (MaAsLin2, PERMANOVA, random forest).
  ✓ Enterotyping, dysbiosis indexing, and species level co abundance network reconstruction.
  ✓ Longitudinal and paired sample designs with rigorous batch effect correction.
  ✓ Identification of microbial disease markers and therapeutic response predictors.

introduction_description:
  Bridge the gap between microbiome data and clinical breakthroughs with holistic, patient centric analytical frameworks. Dawn of Bioinformatics Ltd. offers specialized clinical and human microbiome analysis services to translate microbial profiles into actionable biomedical insights. Whether investigating gut skin brain axes, respiratory microbiomes, or tumor associated microbiota, our DawniLab experts apply robust epidemiological models and multi omics integration to link microbial signatures with disease phenotypes, treatment outcomes, and host metadata, accelerating biomarker discovery and personalized therapy development with clinical grade reproducibility.


title: Environmental & Agricultural Metagenomics
slug: environmental-microbiome-analysis
thumbnail: service/thumbnails/Environmental__Agricultural_Metagenomics.webp
description:
  Tailored environmental and agricultural metagenomics services designed to explore the microbial engines driving soil fertility, plant productivity, and ecosystem resilience. Our approach quantifies key nutrient cycling genes, reconstructs genomes of uncultivated microbes harboring plant growth promoting or bioremediation traits, and profiles taxonomic shifts along environmental gradients. By translating metagenomic big data into practical insights, DawniLab supports sustainable agriculture, pollution monitoring, and climate change adaptation directly from soil, water, or sediment samples without the need for prior cultivation.

demo_description:
  Our analysis of 50 agricultural soil metagenomes revealed a 60% decline in nitrogen fixing gene abundance under conventional tillage. Guided by these data, the client adopted no till practices and custom bioinoculants, restoring soil nitrogen capital by 30% within two growing seasons.

features_description:
  ✓ Quantification of C, N, P, S cycling genes and pathway completeness analysis (KEGG modules, NCycDB).
  ✓ Taxonomic and functional biomarkers linked to soil attributes, contamination level, or crop yield.
  ✓ Binning for novel genomes carrying plant growth promoting or bioremediation traits.
  ✓ Comparative metagenomics across environmental gradients with robust statistical frameworks.

introduction_description:
  Harness the power of soil and environmental metagenomes to drive sustainability and agricultural innovation. Dawn of Bioinformatics Ltd. offers comprehensive environmental and agricultural metagenomics services to explore the biological drivers of soil health, plant productivity, and ecosystem resilience. From rhizosphere communities to wastewater bioreactors, our DawniLab experts deliver functional gene profiling, nutrient cycling reconstruction, and biosynthetic gene cluster discovery, enabling sustainable land management and environmental monitoring while reducing costly wet lab trials.


title: AMR & Pathogen Virulence Factor Profiling
slug: raw-data-quality-control-pre-processing-1
thumbnail: service/thumbnails/AMR__Pathogen_Virulence_Factor_Profiling.webp
description:
  Dawn of Bioinformatics Ltd. performs dedicated antimicrobial resistance and virulence factor profiling to assess the full resistome and pathogenic potential present in any microbiome sample. Using stringent read mapping against manually curated databases and rigorous mutation analysis, we detect known resistance determinants, identify novel alleles, and link them to mobile genetic elements that indicate a high risk of horizontal gene transfer. This service by DawniLab supplies hospitals, public health agencies, and research groups with high confidence, publication grade surveillance data that can guide infection control, outbreak tracing, and phage-based interventions.

demo_description:
  We screened 300 hospital wastewater metagenomes and uncovered 45 novel beta lactamase variants located on conjugative plasmids. The early warning enabled the infection control team to trace an outbreak source to a single ward, where targeted disinfection halted further transmission within 72 hours.

features_description:
  ✓ Resistome profiling against CARD, ResFinder, and custom built mutation panels.
  ✓ Virulence factor annotation (VFDB, PATRIC) with pathogenicity island genotyping.
  ✓ Mobility element detection (plasmid replicons, integrons, transposases) to assess transfer potential.
  ✓ Quantitative abundance matrices, richness, and diversity indexing for resistome/virulome comparisons.

introduction_description:
  Safeguard health with precise identification of resistance genes and virulence determinants across complex samples. Dawn of Bioinformatics Ltd. offers dedicated antimicrobial resistance (AMR) and virulence factor profiling services to assess the resistome and pathogenic potential within any microbiome. Using curated databases (CARD, ResFinder, VFDB) and high stringency read mapping, our DawniLab experts detect known and novel resistance mechanisms, track mobile genetic elements, and quantify horizontal gene transfer risk, delivering high confidence results that streamline clinical surveillance, outbreak tracking, and phage therapy development.


title: Viral Metagenomics (Viromics) Data Analysis
slug: metagenome-assembly-binning
thumbnail: service/thumbnails/Viral_Metagenomics_Viromics_Data_Analysis.webp
description:
  Dawn of Bioinformatics Ltd. provides advanced viral metagenomics analysis to illuminate the hidden virosphere in clinical specimens, environmental samples, and host associated communities. Our service encompasses discovery and assembly of both DNA and RNA viral genomes, taxonomic classification against comprehensive reference databases, and host prediction through integrated machine learning and motif matching. DawniLab's ensemble approach identifies novel phages and eukaryotic viruses, profiles virome diversity, and links viral populations to their bacterial or eukaryotic hosts, enabling fundamental discoveries and translational applications such as phage therapy candidate selection and diagnostic target development.

demo_description:
  From a healthy human gut virome we identified 2,500 viral contigs, including 150 complete phage genomes, 18 of which represented novel Siphoviridae genera. Host linkage analysis revealed that 40% of these phages selectively target Bacteroides species, providing a foundational candidate panel for future phage therapy research.

features_description:
  ✓ Viral sequence enrichment, quality filtering, and de novo genome assembly (metaSPAdes, VICUNA).
  ✓ Taxonomic classification using NCBI Viral RefSeq, IMG/VR, and protein clustering tools (vConTACT2, VPF Class).
  ✓ Host prediction via CRISPR spacer matching, oligonucleotide signatures, and integrated machine learning.
  ✓ Abundance profiling, alpha/beta diversity, and differential representation analysis of viral populations.

introduction_description:
  Illuminate the hidden viral universe and uncover novel viruses, phage host dynamics, and diagnostic targets. Dawn of Bioinformatics Ltd. offers cutting edge viral metagenomics data analysis services to illuminate the hidden virosphere within clinical, environmental, and host associated samples. Our DawniLab experts specialize in virus discovery, viral genome assembly, and host range assignment from both DNA and RNA viromes, delivering comprehensive virome characterization that bypasses culture dependence and drastically compresses the path from sequence to actionable biological insight.


title: Multi-Epitope Chimeric Vaccine Design (mRNA & Subunit Vaccines)
slug: mecvd
thumbnail: service/thumbnails/Multi-Epitope_Chimeric_Vaccine_Design.webp
description:
  Fast-track your vaccine development with our complete in silico pipeline for designing highly stable, immunogenic mRNA and subunit chimeric vaccines.


title: Advanced T-cell and B-cell Epitope Prediction & Mapping
slug: tbcell
thumbnail: service/thumbnails/Advanced_T-cell_and_B-cell_Epitope_Prediction.webp
description:
  Pinpoint highly immunogenic and globally conserved epitopes for precision immunotherapy and the development of highly sensitive diagnostic kits.


title: TCR-Peptide-MHC Complex Docking & Dynamics
slug: tcr
thumbnail: service/thumbnails/TCR-Peptide-MHC_Complex_Docking__Dynamics.png
description:
  Visualize and validate the exact molecular interactions between T-cell receptors, antigenic peptides, and MHC molecules at the atomic level.


title: Whole Genome Sequencing (WGS) Data Analysis
slug: wgs
thumbnail: service/thumbnails/Comprehensive_Whole_Genome_Sequencing.webp
demo_description: We assembled a 3Gb plant genome with a scaffold N50 of over 50Mb.
features_description:
  - Hybrid assembly (PacBio/Illumina)
  - Structural variant calling
  - Comprehensive gene annotation

introduction_description: Unlock the full potential of your genomic data with our high-quality de novo assembly pipelines.
description:
  Uncover the complete genetic blueprint and identify rare mutations, structural variations, and regulatory elements with our rigorous whole-genome pipelines.


title: Advanced Molecular Dynamics Simulation Services
slug: AMDSS
thumbnail: service/thumbnails/simulation.webp
description:
  Dawn of Bioinformatics Ltd. delivers advanced Molecular Dynamics (MD) simulation solutions to investigate the dynamic behavior, stability, and interactions of biomolecular systems at atomic resolution. Our DawniLab experts utilize state-of-the-art computational frameworks to simulate real-time molecular motion, enabling accurate assessment of protein–ligand complexes, conformational flexibility, and system stability under physiological conditions. By integrating high-performance computing and validated simulation protocols, we provide deeper mechanistic insights that support accurate stability assessment and interaction dynamics analysis.

demo_description:
  We present selected case studies demonstrating the effectiveness of our Molecular Dynamics (MD) simulation workflows in analyzing biomolecular stability and interaction dynamics. These examples highlight how our simulations provide critical insights into protein–ligand behavior, structural stability, and binding consistency over time—supporting reliable lead validation and optimization in drug discovery projects.

features_description:
  • High-resolution MD simulations for protein, ligand, and protein–ligand complexes (Up to 1000ns)
  • Stability analysis using RMSD, RMSF, Radius of Gyration (Rg), and Solvent Accessible Surface Area (SASA).
  • Binding free energy calculations (MM-PBSA / MM-GBSA).
  • Hydrogen bond and interaction network analysis.
  • Conformational dynamics and flexibility assessment.
  • Trajectory analysis with publication-ready visualizations.
  • Principal Component Analysis (PCA) analysis with publication-ready visualization.
  • Powered by industry-standard tools (YASARA, GROMACS, AMBER, NAMD, Desmond).

introduction_description:
  Gain deeper insights into biomolecular behavior with our high-resolution Molecular Dynamics (MD) simulation platform. Dawn of Bioinformatics Ltd. combines physics-based modeling with advanced computational tools to analyze the stability, flexibility, and interaction dynamics of proteins, ligands, and complex biological systems.
  Our in-silico simulation workflows enable researchers to move beyond static structures, capturing time-dependent molecular interactions and conformational changes. This approach reduces uncertainty in drug design, enhances prediction accuracy, and supports data-driven decision-making in modern computational biology and drug discovery.


title: Bulk RNA-Sequencing & Differential Gene Expression (DGE) Analysis
slug: dge
thumbnail: service/thumbnails/Bulk_RNA-Sequencing__Differential_Gene_Expression.jpg
description:
  Dawn of Bioinformatics Ltd. delivers comprehensive Bulk RNA-Sequencing (RNA-Seq) and Differential Gene Expression (DGE) analysis services to uncover transcriptional changes and molecular signatures underlying biological conditions. Our DawniLab experts implement robust, end-to-end computational pipelines from raw sequencing data processing to statistically rigorous differential expression analysis which ensuring high accuracy, reproducibility, and biological relevance. By integrating advanced alignment, quantification, and statistical modeling approaches, we provide actionable insights into gene regulation, pathway dynamics, and disease mechanisms.

demo_description:
  We present selected case studies demonstrating the effectiveness of our Bulk RNA-Seq and differential expression analysis workflows in uncovering transcriptional changes across diverse biological conditions. These examples highlight how our integrated pipelines accurately identify differentially expressed genes, reveal expression patterns, and support downstream functional and pathway analysis—enabling data-driven insights into disease mechanisms, treatment response, and biomarker discovery.

features_description:
  • End-to-end Bulk RNA-Seq pipeline from raw FASTQ data to biological insights.
  • Quality control and preprocessing of raw sequencing data.
  • High-performance read alignment and quasi-mapping.
  • Transcript assembly and expression quantification.
  • Gene-level count generation.
  • Differential expression analysis and identification of significantly differentially expressed genes (DEGs).
  • Support for multiple pipeline strategies (alignment-based & count-based workflows).
  • Publication-ready visualizations (volcano plots, heatmaps, PCA).

introduction_description:
  Decode transcriptomic landscapes with our advanced Bulk RNA-Seq analysis platform. Dawn of Bioinformatics Ltd. processes raw sequencing data through a validated, multi-step workflow including quality-controlled read alignment, transcript assembly, expression quantification, and differential expression analysis.
  Our pipeline supports multiple analytical strategies, including alignment-based (HISAT2, STAR) and alignment-free (Salmon) approaches, followed by transcript reconstruction (StringTie) or count-based quantification (HTSeq). Differential expression is performed using industry-standard statistical frameworks such as DESeq2 and Ballgown, enabling reliable identification of significantly upregulated and downregulated genes.
  This integrated approach enhances data accuracy, minimizes technical bias, and supports downstream biological interpretation, including biomarker discovery and pathway analysis.


title: Precision Molecular Docking & High-Throughput Virtual Screening Services
slug: MDS
thumbnail: service/thumbnails/docking.webp
description:
  Dawn of Bioinformatics Ltd. delivers precision-driven molecular docking and high-throughput virtual screening (HTVS) solutions to identify and prioritize potential drug candidates with high accuracy. Our DawniLab experts employ advanced computational algorithms and validated scoring functions to predict protein–ligand binding modes, affinities, and interaction profiles. By integrating robust docking workflows with large-scale virtual screening, we enable efficient exploration of extensive chemical spaces and reliable identification of high-potential hits for downstream analysis.

demo_description:
  We present selected case studies demonstrating the effectiveness of our molecular docking and virtual screening workflows in identifying high-affinity ligands across diverse biological targets. These examples highlight how our integrated computational approaches enable accurate binding prediction, efficient compound prioritization, and reliable target identification supporting early-stage drug discovery and research applications.

features_description:
  • High-throughput virtual screening (HTVS) of large-scale compound libraries.
  • Accurate protein–ligand docking with advanced scoring functions.
  • Binding pose prediction and interaction analysis.
  • Active site identification and grid-based docking setup.
  • Post-docking analysis and target prioritization.
  • Visualization of binding interactions with publication-ready outputs.
  • Powered by industry-standard platforms (AutoDock Vina, Schrödinger Glide, GOLD, BIOVIA Discovery Studio)

introduction_description:
  Accelerate hit discovery with our precision-focused molecular docking and high-throughput virtual screening platform. Dawn of Bioinformatics Ltd. combines structure-based computational techniques with optimized screening pipelines to rapidly evaluate large compound libraries against target biomolecules.
  Our in-silico workflows provide detailed insights into binding interactions, affinity ranking, and structural compatibility enabling efficient filtering of candidate molecules and reducing experimental workload. This approach enhances hit identification accuracy and supports informed decision-making in early-stage drug discovery.


title: Quantum Chemical (DFT) & Pharmacokinetic Profiling
slug: dft
thumbnail: service/thumbnails/dft.webp
description:
  Dawn of Bioinformatics Ltd. delivers advanced Quantum Chemical and pharmacokinetic profiling solutions to investigate the electronic structure, reactivity, and physicochemical properties of molecular systems at a fundamental level. Our DawniLab experts leverage Density Functional Theory (DFT) alongside state-of-the-art computational tools to accurately model molecular behavior, optimize structures, and predict interaction potential. By integrating quantum mechanical analysis with pharmacokinetic evaluation and analogue design strategies, we provide comprehensive insights that support rational compound development and data-driven decision-making.

demo_description:
  We present selected case studies demonstrating the effectiveness of our integrated quantum chemical and pharmacokinetic workflows in molecular characterization and compound optimization. These examples highlight how our DFT analysis, spectral interpretation, and structural modeling approaches provide accurate insights into molecular structure, reactivity, and pharmacokinetic suitability supporting reliable compound identification, refinement, and decision-making in chemical and pharmaceutical research.

features_description:
  • Density Functional Theory (DFT) calculations for electronic structure analysis.
  • Geometry optimization and vibrational frequency analysis.
  • HOMO–LUMO energy analysis and molecular orbital visualization.
  • FTIR, Raman, and VCD spectral simulation and interpretation.
  • Structure elucidation from GC-MS and IR spectral data.
  • 2D to 3D molecular structure conversion and refinement.
  • Analogue design and structural modification strategies.
  • Comprehensive ADME and pharmacokinetic profiling.
  • Drug-likeness and toxicity prediction.
  • Powered by industry-standard tools (Gaussian, ORCA, BIOVIA Discovery Studio).

introduction_description:
  Investigate the electronic structure, reactivity, and quantum mechanical properties of your compounds with our rigorous DFT analysis. Dawn of Bioinformatics Ltd. combines high-level quantum chemical calculations with advanced pharmacokinetic profiling and structural modeling to deliver a complete understanding of molecular performance.
  Our workflows extend from experimental data interpretation to computational refinement, including structure elucidation from GC-MS and IR spectra, 2D-to-3D structure generation, geometry optimization, and vibrational analysis. In addition, we support analogue design and modification to improve molecular properties. This integrated approach enhances predictive accuracy, reduces experimental uncertainty, and enables efficient compound analysis and optimization.


title: Systems Biology & Network Pharmacology Analysis
slug: ntpa
thumbnail: service/thumbnails/network.webp
description:
  Dawn of Bioinformatics Ltd. delivers advanced Systems Biology and Network Pharmacology solutions to unravel complex biological interactions and multi-target mechanisms underlying diseases and therapeutic interventions. Our DawniLab experts integrate multi-omics data, protein–protein interaction (PPI) networks, and computational modeling to systematically explore the relationships between genes, proteins, pathways, and bioactive compounds. By leveraging network-based approaches, we provide comprehensive insights into system-level behavior, enabling rational target identification and mechanism-driven research.

demo_description:
  We present selected case studies demonstrating the effectiveness of our systems biology and network pharmacology workflows in uncovering complex biological mechanisms. These examples highlight how our integrated multi-omics and network-based approaches identify key regulatory genes, critical pathways, and compound–target interactions which providing actionable insights for biomarker discovery, therapeutic target identification, and mechanism-of-action analysis.

features_description:
  • Multi-omics data integration (transcriptomics, genomics, proteomics).
  • Network pharmacology analysis for herbal and natural compounds.
  • Protein–protein interaction (PPI) network construction and analysis.
  • Hub gene/protein identification.
  • Disease–gene association and biomarker identification.
  • Compound–target–pathway network construction.
  • Pathway and Functional Enrichment analysis.
  • Integration with drug target prediction and validation workflows.
  • Powered by platforms such as Cytoscape, STRING, and R-based pipelines.

introduction_description:
  Uncover the complex “multi-compound, multi-target, multi-pathway” mechanisms of herbal medicines, natural products, and therapeutic compounds using our integrated systems biology and network pharmacology platform. Dawn of Bioinformatics Ltd. combines high-throughput omics analysis with network-based modeling to decode the intricate interactions that drive biological systems.
  Our workflows enable the identification of key regulatory genes, hub proteins, and critical signaling pathways involved in disease progression and drug response. By integrating transcriptomics, genomics, and interactome data, we provide a holistic understanding of biological mechanisms which supporting biomarker discovery, target prioritization, and mechanism-of-action studies.


title: Whole Exome Sequencing (WES) Data Analysis
slug: wes
thumbnail: service/thumbnails/Whole_Exome_Sequencing_WES.webp
description:
  Pinpoint disease-causing coding variants with high accuracy and cost-efficiency using our clinically optimized, targeted exome analysis


title: Antimicrobial Resistance (AMR) & Pathogen Genomics Analysis
slug: amrg
thumbnail: service/thumbnails/Antimicrobial_Resistance_AMR.webp
description:
  Combat global health threats by rapidly identifying antimicrobial resistance genes and virulence factors directly from pathogen genomes.


title: Population Genomics & Genome-Wide Association Studies (GWAS)
slug: gwas
thumbnail: service/thumbnails/Population_Genomics__Genome-Wide_Association_Studies_GWAS_IiGNVEq.webp
description:
  Uncover the genetic basis of complex traits and diseases across large populations with our robust GWAS and statistical genetics pipelines.


title: De novo Genome Assembly & Comprehensive Annotation
slug: gaa
thumbnail: service/thumbnails/De_novo_Genome_Assembly__Comprehensive_Annotation.webp
description:
  Reconstruct complete genomes from scratch and decipher their functional elements with our advanced hybrid assembly pipelines.


title: Comparative Genomics & Evolutionary Analysis
slug: cgea
thumbnail: service/thumbnails/Comparative_Genomics__Evolutionary_Analysis.webp
description:
  Trace evolutionary histories and discover conserved functional genomic elements across multiple species or strains.


title: Single-Cell RNA-Seq (scRNA-Seq) Data Analysis
slug: single-cell-rna-seq-scrna-seq-data-analysis
thumbnail: service/thumbnails/Single-Cell_RNA-Seq_scRNA-Seq_Data_Analysis.webp
description:
  Dawn of Bioinformatics Ltd. delivers advanced Single-Cell RNA Sequencing (scRNA-Seq) data analysis services to resolve cellular heterogeneity and uncover gene expression patterns at single-cell resolution. Our DawniLab experts implement robust computational workflows to process, analyze, and interpret high-dimensional single-cell data, enabling precise identification of cell populations, functional states, and lineage relationships. By integrating state-of-the-art algorithms and statistical frameworks, we provide deep insights into cellular diversity, regulatory mechanisms, and disease biology.

demo_description:
  We present selected case studies demonstrating the effectiveness of our scRNA-Seq analysis workflows in resolving cellular heterogeneity and identifying distinct cell populations across diverse biological systems. These examples highlight how our integrated computational approaches reveal cell-type-specific gene expression patterns, uncover functional subpopulations, and provide insights into cellular dynamics which support advanced research in disease mechanisms, developmental biology, and precision medicine.

features_description:
  • End-to-end scRNA-Seq pipeline from raw data to biological interpretation.
  • Quality control, filtering, and normalization of single-cell data.
  • Integration of multiple datasets and batch effect correction.
  • Dimensionality reduction (PCA, t-SNE, UMAP) for data visualization.
  • Unsupervised clustering to identify cell populations and subtypes.
  • Identification of rare cell populations and cellular heterogeneity.
  • Marker gene identification for cell-type annotation.
  • Differential expression analysis across cell clusters or conditions.
  • Cell trajectory and pseudotime analysis.
  • Publication-ready visualizations (UMAP/t-SNE plots, heatmaps, violin plots).

introduction_description:
  Explore cellular complexity with our advanced scRNA-Seq analysis platform. Dawn of Bioinformatics Ltd. transforms raw single-cell sequencing data into biologically meaningful insights through a comprehensive pipeline that includes quality control, normalization, dimensionality reduction, clustering, and differential expression analysis.
  Our workflows enable the identification of distinct cell types and subpopulations, discovery of cell-specific marker genes, and reconstruction of cellular trajectories. By leveraging widely adopted frameworks such as Seurat and Scanpy, we ensure accurate, scalable, and reproducible analysis of large-scale single-cell datasets.
  This approach empowers researchers to uncover hidden cellular dynamics, understand tissue heterogeneity, and identify novel biomarkers for disease and therapeutic development.


title: Spatial Differential Gene Expression Analysis
slug: spatial-transcriptomics-data-analysis
thumbnail: service/thumbnails/Differential_Gene_Expression_Analysis.webp
description:
  Dawn of Bioinformatics Ltd. delivers advanced Spatial Transcriptomics and Differential Gene Expression analysis services to uncover gene expression patterns within their native tissue context. Our DawniLab experts integrate spatially resolved transcriptomic data with robust statistical frameworks to identify location-specific gene expression changes, enabling precise mapping of molecular activity across complex tissues. By combining spatial information with high-throughput expression profiling, we provide deeper insights into tissue architecture, cellular organization, and disease microenvironments.

demo_description:
  We present selected case studies demonstrating the effectiveness of our spatial transcriptomics workflows in identifying region-specific gene expression patterns across complex tissues. These examples highlight how our integrated spatial analysis approaches reveal tissue heterogeneity, uncover spatial biomarkers, and provide insights into cellular organization and disease microenvironments which support advanced research and precision medicine applications.

features_description:
  • End-to-end spatial transcriptomics analysis from raw data to biological insights.
  • Quality control and normalization of spatial gene expression data.
  • Integration of spatial transcriptomics data with single-cell and bulk RNA-Seq datasets.
  • Spatial coordinate alignment and preprocessing.
  • Spatial clustering and identification of tissue regions.
  • Identification of spatially variable genes (SVGs).
  • Differential gene expression analysis across spatial domains.
  • Detection of region-specific biomarkers and functional pathways.
  • Advanced spatial visualization (tissue maps, feature plots, heatmaps).
  • Publication-ready figures with spatially resolved insights.

introduction_description:
  Decode spatial gene expression landscapes with our advanced spatial transcriptomics analysis platform. Dawn of Bioinformatics Ltd. processes spatially resolved sequencing data to identify differentially expressed genes across tissue regions, cellular niches, and microenvironments.
  Our workflows integrate spatial coordinates with gene expression data, enabling the detection of region-specific biomarkers and functional pathways. By combining spatial clustering, differential expression analysis, and visualization techniques, we provide a comprehensive understanding of how gene activity varies across tissue structures.
  This approach enhances biological interpretation by preserving spatial context, supporting research in cancer biology, neuroscience, developmental biology, and precision medicine.


title: Weighted Gene Co-expression Network Analysis (WGCNA) & Hub Gene Discovery
slug: weighted-gene-co-expression-network-analysis-wgcna
thumbnail: service/thumbnails/Weighted_Gene_Co-expression_Network_Analysis.webp
description:
  Dawn of Bioinformatics Ltd. delivers advanced Weighted Gene Co-expression Network Analysis (WGCNA) and hub gene discovery services to uncover complex gene–gene interaction patterns and regulatory networks underlying biological systems. Our DawniLab experts construct robust co-expression networks to identify highly correlated gene modules and key hub genes associated with specific phenotypes, clinical traits, or disease conditions. By integrating statistical modeling with network-based approaches, we provide systems-level insights that support biomarker discovery and target prioritization.

demo_description:
  We present selected case studies demonstrating the effectiveness of our WGCNA and hub gene discovery workflows in identifying key regulatory modules and critical genes across diverse biological conditions. These examples highlight how our network-based approaches reveal gene interaction patterns, prioritize biologically relevant targets, and provide actionable insights into disease mechanisms and phenotypic variation.

features_description:
  • End-to-end WGCNA pipeline from normalized expression data to network interpretation.
  • Integration with differential expression and transcriptomics analysis.
  • Construction of weighted gene co-expression networks.
  • Identification of gene modules based on expression similarity.
  • Module–trait relationship analysis (clinical or phenotypic correlation).
  • Hub gene identification using topological metrics.
  • Functional enrichment analysis of key modules.
  • Network visualization and module exploration.
  • Identification of potential biomarkers and therapeutic targets,
  • Publication-ready figures (network plots, module–trait heatmaps, dendrograms).

introduction_description:
  Unravel complex systemic biological mechanisms by identifying highly correlated gene modules and crucial hub genes driving your phenotypic traits. Dawn of Bioinformatics Ltd. applies WGCNA-based methodologies to transform high-dimensional transcriptomic data into biologically meaningful networks.
  Our workflows enable the detection of co-expression modules, correlation of modules with clinical or experimental traits, and identification of central hub genes using topological and connectivity-based metrics. This approach provides a deeper understanding of gene regulation, functional pathways, and disease mechanisms that support advanced research in systems biology and precision medicine.


title: Non-Coding RNA Regulatory Network Analysis
slug: non-coding-rna-regulatory-network-analysis
thumbnail: service/thumbnails/Non-Coding_RNA_Regulatory_Network_Analysis.webp
description:
  Dawn of Bioinformatics Ltd. delivers advanced Non-Coding RNA (ncRNA) regulatory network analysis services to uncover the complex interactions between microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and messenger RNAs (mRNAs) that govern gene expression. Our DawniLab experts integrate transcriptomic data with validated interaction databases and computational prediction tools to construct comprehensive regulatory networks. By leveraging systems-level approaches, we identify key regulatory molecules and interaction axes that drive biological processes and disease mechanisms.

demo_description:
  We present selected case studies demonstrating the effectiveness of our non-coding RNA regulatory network workflows in uncovering complex gene regulation mechanisms. These examples highlight how our integrated approaches identify key miRNA–lncRNA–mRNA interaction networks, reveal critical regulatory axes, and provide actionable insights into disease mechanisms and therapeutic target discovery.

features_description:
  • End-to-end ncRNA regulatory network analysis from transcriptomic data.
  • Identification of differentially expressed miRNAs, lncRNAs, and mRNAs.
  • Integration with WGCNA and differential expression analysis.
  • Target prediction using validated databases and computational tools.
  • Integration of miRNA–mRNA, lncRNA–miRNA, and ceRNA interactions.
  • Construction of multi-layered regulatory networks.
  • Network topology analysis and identification of key regulatory nodes.
  • Functional enrichment analysis of target genes.
  • Visualization and exploration of regulatory networks.
  • Identification of potential biomarkers and therapeutic targets.
  • Publication-ready figures (network diagrams, regulatory axes, heatmaps).

introduction_description:
  Decode the regulatory landscape of gene expression by exploring intricate non-coding RNA networks. Dawn of Bioinformatics Ltd. applies integrative computational approaches to identify and analyze miRNA–mRNA, lncRNA–miRNA and competing endogenous RNA (ceRNA) interactions.
  Our workflows enable the construction of multi-layered regulatory networks, revealing how non-coding RNAs modulate gene expression and influence cellular functions. By combining differential expression analysis with interaction prediction and network modeling, we provide deep insights into regulatory mechanisms, biomarker discovery, and therapeutic target identification. This approach supports advanced research in cancer biology, complex diseases, and precision medicine.


title: Time-Series Transcriptomics & Clinical Biomarker Profiling
slug: time-series-transcriptomics-clinical-biomarker-pro
thumbnail: service/thumbnails/Time-Series_Transcriptomics__Clinical_Biomarker_Profiling.webp
description:
  Dawn of Bioinformatics Ltd. delivers advanced time-series transcriptomics and clinical biomarker profiling services to capture dynamic changes in gene expression across temporal conditions. Our DawniLab experts apply robust statistical modeling and longitudinal data analysis techniques to identify time-dependent gene expression patterns, regulatory trends, and clinically relevant biomarkers. By integrating temporal transcriptomic data with clinical variables, we provide deeper insights into disease progression, treatment response, and molecular mechanisms over time.

demo_description:
  We present selected case studies demonstrating the effectiveness of our time-series transcriptomics workflows in capturing dynamic gene expression changes across multiple time points. These examples highlight how our integrated analytical approaches identify temporal biomarkers, reveal gene expression trajectories, and provide actionable insights into disease progression and treatment response which supporting advanced clinical research and precision medicine applications.

features_description:
  • End-to-end time-series transcriptomics analysis from raw or processed expression data.
  • Quality control and normalization across multiple time points.
  • Integration of longitudinal gene expression data with clinical metadata.
  • Clustering genes based on temporal expression patterns.
  • Identification of temporally differentially expressed genes (time-dependent DEGs).
  • Trend and trajectory analysis of gene expression over time.
  • Correlation of gene expression dynamics with clinical outcomes.
  • Functional enrichment analysis of time-dependent gene sets.
  • Identification of early, late, and sustained response biomarkers.
  • Visualization of temporal expression patterns (time-course plots, heatmaps, trend curves).
  • Publication-ready figures for longitudinal transcriptomic studies.

introduction_description:
  Track longitudinal changes in gene expression to identify dynamic biomarkers and evaluate treatment efficacy across defined time points. Dawn of Bioinformatics Ltd. utilizes advanced time-series analysis frameworks to transform temporal transcriptomic data into meaningful biological insights.
  Our workflows enable the identification of temporally regulated genes, clustering of genes with similar expression trajectories, and detection of early and late response biomarkers. By integrating clinical metadata with gene expression profiles, we provide a comprehensive understanding of disease progression, therapeutic response, and patient-specific molecular dynamics. This approach supports precision medicine, biomarker discovery, and longitudinal studies in complex diseases.


title: AI-Driven Drug Discovery & Generative Design
slug: aidrug
thumbnail: service/thumbnails/AI-Driven_Drug_Discovery__Generative_Design.webp
description:
  Revolutionize hit finding and de novo molecule generation using advanced artificial intelligence and generative neural networks.


title: ML for Multi-Omics & Biomarker Discovery
slug: mlmultiomics
thumbnail: service/thumbnails/ML_for_Multi-Omics__Biomarker_Discovery.webp
description:
  Integrate and decode complex genomics, transcriptomics, and proteomics datasets using powerful machine learning algorithms to identify critical clinical biomarkers.


title: Custom Pipeline Automation & Integration
slug: pipautomation
thumbnail: service/thumbnails/Custom_AI_Pipeline_Automation__Integration_i.webp
description:
  Streamline your laboratory’s computational workflows with fully automated, scalable, and reproducible bioinformatics pipelines custom-built for your specific needs.


title: Deep Learning for ADMET & Tox Prediction
slug: deepladmet
thumbnail: service/thumbnails/Deep_Learning_for_ADMET__Tox_Prediction.webp
description:
  Drastically reduce drug failure rates by predicting pharmacokinetic properties and toxicity profiles with state-of-the-art deep learning models.


title: Biological Database & Knowledge Graph Development
slug: bdkgd
thumbnail: service/thumbnails/Biological_Database__Knowledge_Graph_Development.webp
description:
  Organize, search, and visualize your proprietary research data with custom-built, highly secure biological databases and interconnected knowledge graphs.


title: Secure Cloud & HPC Scalability Solutions
slug: schpc
thumbnail: service/thumbnails/Secure_Cloud__HPC_Scalability_Solutions.webp
description:
  Upgrade your computational capacity with secure, scalable High-Performance Computing (HPC) clusters and customized private cloud deployments.


# service_servicefaq

question: What final files will I receive?
answer:
  You will receive publication-ready high-resolution 2D/3D interaction diagrams, detailed tabular data of screening scores, ADMET profiles, and a comprehensive methodology text ready for manuscript inclusion.


question: How do you ensure computational accuracy?
answer:
  We leverage cutting-edge computational infrastructure, including high-performance AMD architectures and local server clusters, ensuring rapid and precise calculations for massive molecular datasets.


question: What is the typical project timeline?
answer:
  Most CADD projects are completed within 7 to 14 business days, depending on the library size and specific screening protocols.


question: How does the process work?
answer:
  Step 1: Submit your target protein or disease model. Step 2: Receive a custom quote and strategy. Step 3: DawniLab executes the screening. Step 4: Final delivery and consultation.


question: What final files will I receive?
answer:
  You will receive an interactive HTML report containing publication ready alpha and beta diversity plots, PCoA/NMDS ordinations, taxonomic bar charts, differential abundance tables and LEfSe results, a complete ASV/OTU sequence file (FASTA), and a comprehensive methodology text ready for manuscript inclusion.


question: How do you ensure computational accuracy?
answer:
  We deploy cutting edge denoising algorithms (DADA2, UNOISE) and the latest curated reference databases (SILVA 138, UNITE 9.0) inside containerized, version controlled QIIME2 pipelines. All statistical tests are corrected for multiple comparisons using FDR, and our local AMD server clusters ensure rapid, reproducible processing of thousands of samples.


question: What is the typical project timeline?
answer:
  Most amplicon profiling projects are completed within 5 to 10 business days, depending on sample number and the complexity of the metadata design.


question: How does the process work?
answer:
  Step 1: Submit your demultiplexed FASTQ files (paired end, Q30 minimum recommended) and sample metadata. Step 2: Receive a custom quote and analysis strategy (e.g., ASV resolution, rarefaction depth). Step 3: DawniLab executes preprocessing, taxonomy assignment, and statistical modeling. Step 4: Final delivery of the interactive report and a live consultation.


question: What final files will I receive?
answer:
  You will receive assembled metagenomic contigs, quality assessed MAGs (FASTA), gene prediction and functional annotation tables (KEGG, eggNOG, CAZy, CARD, BGCs), pathway abundance matrices, and a comprehensive methodology text with all software versions and parameters ready for the methods section of your manuscript.


question: How do you ensure computational accuracy?
answer:
  We combine assembly based (metaSPAdes, MEGAHIT) and read based profiling strategies with stringent quality control. MAGs are refined and assessed with CheckM2 and GTDB Tk; only MAGs ≥70% completeness and ≤5% contamination proceed to annotation. We leverage high performance AMD clusters with large memory nodes, ensuring precise assembly even for complex communities.


question: What is the typical project timeline?
answer:
  Most shotgun metagenomics projects are completed within 10 to 20 business days, depending on sample size, sequencing depth, and whether binning and MAG refinement are requested.


question: How does the process work?
answer:
  Step 1: Submit your raw metagenomic sequencing reads (FASTQ) and available metadata. Step 2: Receive a custom strategy proposal (assembly vs. read based, binning targets, annotation databases). Step 3: DawniLab executes the full analysis pipeline. Step 4: Final delivery of multi omics outputs, an interpretation document, and a consultation to discuss key findings.


question: What final files will I receive?
answer:
  You will receive species level taxonomic abundance tables, multivariate association results (MaAsLin2 output), dysbiosis indices, random forest selected biomarker panels, co abundance network files, high resolution disease association plots, and a clinically oriented statistical methodology text suitable for biomedical publication.


question: How do you ensure computational accuracy and data privacy?
answer:
  All analyses are conducted on rich clinical metadata with rigorous batch effect correction (e.g., ComBat seq, removal of unwanted variation). We use validated, curated reference databases (GutPhage, mOTUs, MetaPhlAn4) and apply multiple testing corrections by default. For sensitive human data, we operate within HIPAA compliant secure computing environments, using encrypted data transfer and storage, with automatic data purging after project completion upon request.


question: What is the typical project timeline?
answer:
  Clinical microbiome projects are typically completed within 10 to 15 business days, with timelines extended for complex longitudinal or paired sample designs.


question: How does the process work?
answer:
  Step 1: Provide demultiplexed sequencing data and a detailed clinical metadata file (CSV/Excel). Step 2: Receive a tailored analysis plan covering study design, confounders, and target phenotypes. Step 3: DawniLab executes data processing, statistical modeling, and biomarker discovery on secured infrastructure. Step 4: Final delivery of the clinical analysis report and a one on one interpretation session.


question: What final files will I receive?
answer:
  You will receive a comprehensive taxonomic profile, functional gene abundance matrices for nutrient cycles (C, N, P, S), MAGs annotated with plant growth promoting or bioremediation traits, differential abundance results across environmental gradients, and a full methods text detailing all bioinformatics workflows.


question: How do you ensure computational accuracy?
answer:
  We use specialized environmental databases (NCycDB, dbCAN2 for CAZymes, custom biogeochemical marker sets) and validate assembly quality with CheckM2. Rigorous statistical frameworks (distance based RDA, differential abundance with ANCOM BC) are applied to account for environmental covariates. Our high throughput HPC infrastructure ensures robust analysis even for ultra deep soil metagenomes.


question: What is the typical project timeline?
answer:
  Most environmental metagenomics projects are completed within 10 to 20 business days, contingent on soil type, sample number, and the depth of functional annotation required.


question: How does the process work?
answer:
  Step 1: Submit your raw metagenomic reads (FASTQ) and environmental metadata (pH, temperature, treatment groups). Step 2: Receive a custom proposal outlining assembly, annotation, and statistical strategies. Step 3: DawniLab executes the pipeline, including recovery of metagenome assembled genomes. Step 4: Final delivery of all results and a joint interpretation session focused on ecological insights.


question: What final files will I receive?
answer:
  You will receive high confidence resistome and virulome abundance tables (gene and mutation level), mobility element annotations (plasmid replicons, integrons), a risk assessment matrix highlighting high concern gene mobility combinations, publication quality heatmaps, and a comprehensive methodology section ready for submission.


question: How do you ensure computational accuracy?
answer:
  We use stringent read mapping with Bowtie2/BWA against curated databases (CARD, ResFinder 4.0, VFDB) and apply perfect/strict alignment criteria to reduce false positives. Novel alleles are validated by manual curation and protein structure homology checks. All analyses run on our AMD server clusters, providing rapid, reproducible AMR surveillance.


question: What is the typical project timeline?
answer:
  AMR and virulence profiling projects are typically completed within 7 to 12 business days, depending on the number of samples and whether metagenomic or isolate data are provided.


question: How does the process work?
answer:
  Step 1: Provide your sequence data (metagenomic reads or assembled genomes) and sample context (e.g., hospital source, host). Step 2: Receive a quote and specify resistance and virulence targets. Step 3: DawniLab executes the profiling pipeline and mobility element analysis. Step 4: Final delivery of the AMR/virulence report, risk summary, and consultation.


question: What final files will I receive?
answer:
  You will receive curated viral genome sequences (FASTA), quality checked viral operational taxonomic unit abundance tables, taxonomic classification results, host prediction assignments, phage lifestyle annotations, an interactive virome composition plot, and a detailed methods text.


question: How do you ensure computational accuracy?
answer:
  We employ an ensemble virus identification workflow combining VirSorter2, DeepVirFinder, and VIBRANT, followed by completeness assessment with CheckV. Host predictions are cross validated using CRISPR spacer matches, oligonucleotide frequency signatures, and machine learning models (e.g., HostG). All pipeline steps are containerized and executed on high performance computing nodes for reproducibility.


question: What is the typical project timeline?
answer:
  Viral metagenomics projects are typically completed within 10 to 18 business days, with timelines varying based on sample type (e.g., pure virome vs. bulk metagenome) and host prediction depth.


question: How does the process work?
answer:
  Step 1: Submit your virome enriched or total metagenomic sequencing reads (FASTQ). Step 2: Receive a custom analysis proposal covering virus discovery, taxonomy, and host linkage strategies. Step 3: DawniLab executes the viromics pipeline. Step 4: Final delivery of the viral catalog, annotation files, and a consultation to interpret ecological or clinical implications.


# service_clinicalservice

title: Precision Oncology & Cancer Genomics
slug: pocg
icon_color: blue
thumbnail: clinical_service/thumbnails/Precision_Oncology__Cancer_Genomics.webp
description:
  Identify actionable tumour mutations and structural variants through comprehensive genomic profiling. We provide vital insights, such as Tumor Mutational Burden (TMB), to guide targeted cancer therapies and precision immunotherapy.

icon_svg:
  <svg class="w-full h-full" fill="none" stroke="currentColor" viewBox="0 0 24 24"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M19.428 15.428a2 2 0 00-1.022-.547l-2.387-.477a6 6 0 00-3.86.517l-.318.158a6 6 0 01-3.86.517L6.05 15.21a2 2 0 00-1.806.547M8 4h8l-1 1v5.172a2 2 0 00.586 1.414l5 5c1.26 1.26.367 3.414-1.415 3.414H4.828c-1.782 0-2.674-2.154-1.414-3.414l5-5A2 2 0 009 10.172V5L8 4z"></path></svg>

introduction_description:
  Precision Oncology represents a paradigm shift in cancer care, moving away from a "one-size-fits-all" approach to highly individualized treatment strategies. By utilizing comprehensive genomic profiling, we identify specific actionable tumor mutations and structural variants that drive malignancy. Our analysis provides critical clinical insights, such as Tumor Mutational Burden (TMB) and Microsatellite Instability (MSI), which are essential for guiding targeted therapies and precision immunotherapy. This data-driven methodology ensures that oncologists can select the most effective interventions while sparing patients from the toxicity of ineffective treatments.

features_description:
  > Comprehensive Genomic Profiling (CGP): Detecting all classes of genomic alterations in a single assay.
  > Targeted Therapy Matching: Aligning patient-specific mutations with FDA-approved or late-stage clinical trial drugs.
  > Immunotherapy Biomarkers: Evaluating TMB and PD-L1 status to predict response to checkpoint inhibitors.
  > Liquid Biopsy Capabilities: Monitoring tumor evolution and minimal residual disease (MRD) through non-invasive blood draws.
  > Structural Variant Analysis: Identifying complex rearrangements and copy number variations (CNVs) that traditional tests might miss.

demo_description:
  In a recent clinical collaboration, we performed genomic profiling on a cohort of late-stage non-small cell lung cancer (NSCLC) patients who had exhausted standard care options. By applying our high-depth sequencing pipeline, we identified rare ALK and ROS1 rearrangements in several patients that were previously undetected. This insight allowed for the administration of targeted tyrosine kinase inhibitors (TKIs), resulting in significant tumor shrinkage and a 45% increase in progression-free survival (PFS) compared to the standard chemotherapy group.


title: Clinical Whole Genome & Exome Profiling
slug: cwgep
icon_color: purple
thumbnail: clinical_service/thumbnails/Clinical_Whole_Genome__Exome_Profiling.webp
description:
  Diagnose rare and hereditary diseases with high-precision sequencing analysis. By targeting protein-coding regions and the entire genome, we uncover pathogenic variants to solve complex clinical cases.

icon_svg:
  <svg class="w-full h-full" fill="none" stroke="currentColor" viewBox="0 0 24 24"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M19 11H5m14 0a2 2 0 012 2v6a2 2 0 01-2 2H5a2 2 0 01-2-2v-6a2 2 0 012-2m14 0V9a2 2 0 00-2-2M5 11V9a2 2 0 002-2m0 0V5a2 2 0 012-2h6a2 2 0 012 2v2M7 7h10"></path></svg>

introduction_description:
  Deep Exome Sequencing: Analyzing over 20,000 genes to identify variants in protein-coding regions.
  Whole Genome Insights: Examining non-coding regions and regulatory elements for a truly comprehensive view.
  Trio Analysis: Sequencing the patient and both parents to rapidly filter out benign inherited variants.
  ACMG-Compliant Reporting: Interpreting variants according to the most rigorous international clinical guidelines.
  Diagnostic Odyssey Solution: Providing answers for rare pediatric and neurological disorders where other tests have failed.

features_description:
  > Deep Exome Sequencing: Analyzing over 20,000 genes to identify variants in protein-coding regions.
  > Whole Genome Insights: Examining non-coding regions and regulatory elements for a truly comprehensive view.
  > Trio Analysis: Sequencing the patient and both parents to rapidly filter out benign inherited variants.
  > ACMG-Compliant Reporting: Interpreting variants according to the most rigorous international clinical guidelines.
  > Diagnostic Odyssey Solution: Providing answers for rare pediatric and neurological disorders where other tests have failed.

demo_description:
  We successfully concluded a project involving a group of pediatric patients with undiagnosed neurodevelopmental delays. By utilizing Whole Exome Sequencing (WES), we identified de novo pathogenic mutations in 35% of the cases, providing families with a definitive diagnosis for the first time. This enabled the clinical team to transition from diagnostic testing to specific therapeutic management and provided vital information for the parents' future reproductive risks.


title: Clinical Biomarker Discovery
slug: cbd
icon_color: cyan
thumbnail: clinical_service/thumbnails/Clinical_Biomarker_Discovery.webp
description:
  Identify novel diagnostic, prognostic, and predictive biomarkers through multi-omics data integration. Our AI-driven approach accelerates the development of precision diagnostics and monitors treatment efficacy.

icon_svg:
  <svg class="w-full h-full" fill="none" stroke="currentColor" viewBox="0 0 24 24"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M9 5H7a2 2 0 00-2 2v12a2 2 0 002 2h10a2 2 0 002-2V7a2 2 0 00-2-2h-2M9 5a2 2 0 002 2h2a2 2 0 002-2M9 5a2 2 0 012-2h2a2 2 0 012 2m-3 7h3m-3 4h3m-6-4h.01M9 16h.01"></path></svg>

introduction_description:
  Our Clinical Biomarker Discovery service utilizes multi-omics data integration and advanced AI-driven analytics to identify novel biological indicators. We specialize in uncovering diagnostic, prognostic, and predictive biomarkers that can categorize disease states and monitor treatment efficacy with high sensitivity. By integrating genomics, transcriptomics, and proteomics data, we accelerate the development of precision diagnostics for pharmaceutical partners and clinical researchers. This approach transforms complex biological data into actionable clinical tools that improve patient stratification in clinical trials.

features_description:
  > Multi-Omics Integration: Combining DNA, RNA, and protein data for a holistic view of disease biology.
  > AI-Driven Analytics: Utilizing machine learning to identify complex patterns and signatures in large datasets.
  > Predictive Modeling: Developing algorithms that predict how a patient will respond to a specific drug.
  > Prognostic Marker Identification: Determining the likely course of a disease to guide the intensity of treatment.
  > Validation Services: Transitioning discovered markers from the research phase to clinical-grade assays.

demo_description:
  Our team led a biomarker discovery project aimed at early detection of Hepatocellular Carcinoma (HCC). By analyzing the serum proteome and circulating tumor DNA (ctDNA) of at-risk patients, we identified a signature of five specific biomarkers. Our AI model demonstrated a 92% sensitivity in detecting early-stage liver cancer, significantly outperforming the standard Alpha-fetoprotein (AFP) test. This signature is now being evaluated for integration into routine clinical screening kits.


title: Molecular Diagnostics & Pathogen Surveillance
slug: mdps
icon_color: teal
thumbnail: clinical_service/thumbnails/Molecular_Diagnostics__Pathogen_Surveillance.webp
description:
  Detect infectious agents rapidly using metagenomic Next-Generation Sequencing (mNGS). We track antimicrobial resistance (AMR) profiles and outbreaks to facilitate evidence-based, targeted antimicrobial treatments.

icon_svg:
  <svg class="w-full h-full" fill="none" stroke="currentColor" viewBox="0 0 24 24"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M4.318 6.318a4.5 4.5 0 000 6.364L12 20.364l7.682-7.682a4.5 4.5 0 00-6.364-6.364L12 7.636l-1.318-1.318a4.5 4.5 0 00-6.364 0z"></path></svg>

introduction_description:
  In an era of emerging infectious diseases and increasing drug resistance, rapid and accurate pathogen detection is critical. Our service employs metagenomic Next-Generation Sequencing (mNGS) to identify infectious agents directly from clinical samples without the need for traditional cultures. We provide comprehensive tracking of antimicrobial resistance (AMR) profiles and real-time outbreak surveillance to facilitate evidence-based, targeted antimicrobial treatments. This molecular approach ensures that even "unculturable" or rare pathogens are identified swiftly, supporting effective public health responses and individual patient care.

features_description:
  > Metagenomic NGS (mNGS): Hypothesis-free detection of viruses, bacteria, fungi, and parasites in a single test.
  > AMR Profiling: Identifying genetic markers of resistance to ensure the correct antibiotic or antiviral is prescribed.
  > Outbreak Tracking: Genomic fingerprinting of pathogens to map the transmission of infectious diseases.
  > Rapid Turnaround: Optimized workflows for critical care settings where every hour counts.
  > Environmental Surveillance: Monitoring wastewater or air samples for early warning signs of community outbreaks.

demo_description:
  During a localized outbreak of undiagnosed respiratory illness, our lab utilized mNGS to analyze patient nasopharyngeal swabs. Within 48 hours, we identified a rare strain of adenovirus that had escaped detection by standard PCR panels. Furthermore, our AMR analysis confirmed the absence of specific resistance genes, allowing clinicians to successfully treat the patients with narrow-spectrum antivirals, preventing a wider hospital-acquired infection (HAI) event.


title: Personalised Medicine & Pharmacogenomics
slug: pmp
icon_color: rose
thumbnail: clinical_service/thumbnails/Personalised_Medicine__Pharmacogenomics.webp
description:
  Optimize therapeutic efficacy and minimize adverse drug reactions by analyzing individual genetic variations. We provide predictive insights into drug metabolism to ensure precision prescribing tailored to every patient.

icon_svg:
  <svg class="w-full h-full" fill="none" stroke="currentColor" viewBox="0 0 24 24"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M9 19v-6a2 2 0 00-2-2H5a2 2 0 00-2 2v6a2 2 0 002 2h2a2 2 0 002-2zm0 0V9a2 2 0 012-2h2a2 2 0 012 2v10m-6 0a2 2 0 002 2h2a2 2 0 002-2m0 0V5a2 2 0 012-2h2a2 2 0 012 2v14a2 2 0 01-2 2h-2a2 2 0 01-2-2z"></path></svg>

introduction_description:
  Personalised Medicine ensures that the right drug is given to the right patient at the right dose. Through our Pharmacogenomics (PGx) service, we analyze an individual’s genetic variations to predict how they will metabolize specific medications. This allows clinicians to optimize therapeutic efficacy and minimize the risk of adverse drug reactions (ADRs), which are a leading cause of hospitalizations. By providing precision prescribing insights tailored to the patient’s unique genetic makeup, we transform medication management into a safer and more effective process.

features_description:
  > Drug Metabolism Insights: Analyzing CYP450 and other key enzyme groups to determine metabolic speed.
  > Adverse Reaction Prevention: Identifying genetic predispositions to severe drug side effects.
  > Dosing Optimization: Providing data-backed recommendations for dose adjustments based on genotype.
  > Cardiology & Psychiatry Panels: Specialized testing for medications where genetic variation has the highest impact.
  > Lifetime Genetic Record: A one-time test that provides a reference for future medication needs.

demo_description:
  We partnered with a cardiology clinic to implement a pharmacogenomics screening program for patients starting Clopidogrel (a common blood thinner). Our analysis identified "poor metabolizers" (carriers of the CYP2C19*2 allele) who were at high risk for major adverse cardiovascular events because the drug would not be activated in their bodies. Based on our reports, 15% of the patients were switched to an alternative medication, effectively preventing potential treatment failures and secondary strokes.


# service_clinicalservicefaq

question: How does Precision Oncology differ from traditional oncology?
answer:
  Traditional oncology treats cancer based on its location (e.g., lung, breast), whereas precision oncology treats it based on the specific genetic "blueprint" of the tumor.


question: What is Tumor Mutational Burden (TMB)?
answer:
  TMB measures the number of mutations within a tumor's genome; higher TMB often indicates a better response to immunotherapy.


question: What is the main advantage of WGS over WES?
answer:
  WGS covers the entire genome, including non-coding regions that may contain regulatory mutations, whereas WES focuses only on protein-coding genes.


question: Is genetic counseling included?
answer:
  We provide comprehensive reports that are designed to be reviewed by a certified genetic counselor or clinical geneticist.


question: What type of samples are required?
answer:
  Typically, a simple peripheral blood sample or a saliva kit is sufficient for high-quality DNA extraction.


question: Can these tests predict future health risks?
answer:
  Yes, they can identify predispositions to conditions like hereditary cancers or cardiovascular diseases.


question: How do biomarkers improve drug development?
answer:
  They help identify the right patient population for a drug, increasing the success rate of clinical trials and reducing costs.


question: What is "Multi-Omics"?
answer:
  It is a biological analysis approach where data sets from different "omes" (like the genome and proteome) are combined.


question: Are these biomarkers used in routine check-ups?
answer:
  Some are, but many discovered through our service are used to develop new, more specialized diagnostic tests.


question: How does AI help in this process?
answer:
  AI can process billions of data points to find correlations that are impossible for a human researcher to spot.


question: Why use mNGS instead of a standard PCR test?
answer:
  PCR requires you to know what you are looking for. mNGS looks at everything in the sample, identifying pathogens you might not have suspected.


question: Is this service useful for hospital infection control?
answer:
  Absolutely. It is a vital tool for identifying the source and spread of infections within a healthcare facility.


question: Can it detect new, unknown viruses?
answer:
  Yes, metagenomics is one of the primary methods used to discover and characterize novel emerging viruses.


question: Does my DNA change over time?
answer:
  No, your germline DNA remains the same, so your pharmacogenomic results are generally valid for your entire life.


question: Can this test tell me which antidepressant will work best?
answer:
  It can identify which drugs you are likely to metabolize normally and which might cause side effects, helping your doctor narrow down the best options.


question: Is the test covered by insurance?
answer:
  Many insurance providers now cover PGx testing, especially for patients on specific cardiovascular or psychiatric medications.


# core_feedback

name: Farhana Yasmin
occupation: Bangladesh Agricultural University
comment:
  "Received high-quality metagenomic analysis with very rational and informative interpretations of the microbial community."


name: Ahsan Habib
occupation: Chittagong University
comment:
  "Highly impressed with the precision of the MD simulation results and the comprehensive reporting style."


name: Sazzad Hossain
occupation: Rajshahi University
comment:
  "The NGS data analysis service was extremely fruitful; the pipeline was clear and the results were publication-ready."


name: Afsana Mim
occupation: Jagannath University
comment:
  "Their support in managing complex RNAseq pipelines was outstanding and helped me solve several troubleshooting issues."


name: Jarin Tasnim
occupation: Mawlana Bhashani Science and Technology University
comment:
  "The gene ontology and pathway enrichment analysis provided in the RNAseq service gave me a clear biological perspective on my experimental data."


name: Lamia Islam
occupation: Khulna University
comment:
  "The team’s expertise in CADD services helped me gain deep insights into ligand-protein interactions for my thesis."


# core_carrier

title: Bioinformatics Campus Leader
slug: bcl
employment_type: Part-time
location: Your Campus
posted_date: 2026-05-05
deadline: 2026-05-27
apply_url: https://forms.gle/yRXmq1VpMpuzRqsT8
short_description:
  Want to represent a leading bioinformatics ecosystem at your university? We are hiring, and this is an EXCLUSIVE opportunity! We are selecting ONLY 1 LEADER PER CAMPUS for this paid, part-time role. If you are a natural leader who loves networking and organizing events, we want you on our team! This is your chance to lead the bioinformatics movement and bridge the gap between academic excellence and industry innovation.

job_overview:
  <div dir="auto">Want to represent a leading bioinformatics ecosystem at your university? We are hiring, and this is an <strong data-path-to-node="6" data-index-in-node="103">EXCLUSIVE</strong> opportunity! We are selecting <strong data-path-to-node="6" data-index-in-node="143">ONLY 1 LEADER PER CAMPUS</strong> for this paid, part-time role. If you are a natural leader who loves networking and organizing events, we want you on our team! This is your chance to lead the bioinformatics movement and bridge the gap between academic excellence and industry innovation.</div>

required_profile:
  <ul>
  <li data-path-to-node="9,0,0"><strong data-path-to-node="9,0,0" data-index-in-node="0">Mindset:</strong> Proactive and strictly target-driven mindset.</li>
  <li data-path-to-node="9,0,0"><strong data-path-to-node="9,1,0" data-index-in-node="0">Networking:</strong> Strong networking and organizational skills.</li>
  <li data-path-to-node="9,2,0"><strong data-path-to-node="9,2,0" data-index-in-node="0">Communication:</strong> Highly professional communication and negotiation abilities.</li>
  <li data-path-to-node="9,3,0"><strong data-path-to-node="9,3,0" data-index-in-node="0">Experience:</strong> Prior experience in event management and digital promotion is a must!</li>
  </ul>

role_description:
  <ul>
  <li data-path-to-node="12,0,0">Act as the exclusive bridge between your campus and our bioinformatics ecosystem.</li>
  <li data-path-to-node="12,1,0">Plan and execute strategic campus events and digital campaigns.</li>
  <li data-path-to-node="12,2,0">Promote our specialized research, institutes, and services to students and faculty.</li>
  <li data-path-to-node="12,3,0">Build strong professional relationships with university authorities and professors</li>
  </ul>

salary_info:
  <p>Remuneration for this role is primarily <strong data-path-to-node="14,1" data-index-in-node="40">performance-based</strong>,</p>


title: Bioinformatics Analyst
slug: bioinformatics-analyst
employment_type: Full-time
location: Dhaka/ Chittagong
posted_date: 2026-01-14
deadline: 2026-02-27
apply_url: https://hr.dobltd@gmail.com.
short_description:
  Are you ready to join the trailblazer of bioinformatics innovation in Bangladesh? At Dawn of Bioinformatics Limited, we bridge the gap between computational biology and real-world applications, shaping the future of molecular biology research through genomics, proteomics, and machine learning. We are looking for a dedicated Bioinformatics Analyst to join our mission of revolutionizing the scientific landscape. In this role, you will analyze biological systems using cutting-edge tools and collaborate with experts to provide actionable solutions for global challenges.

job_overview:
  <div class="" data-bfc="" data-ved="2ahUKEwjauobSp6CUAxV0R2cHHedBNocQi4wTegQIBxAA" data-processed="true" data-copy-service-computed-style="font-family: &quot;Google Sans&quot;, Arial, sans-serif; font-size: 16px; font-weight: 400; margin: 0px; text-decoration: none; border-bottom: 0px rgb(10, 10, 10);">
  <div class="n6owBd awi2gc" data-sfc-cp="" data-sfc-root="c" data-sfc-cb="" data-hveid="CAcQAQ" data-processed="true" data-copy-service-computed-style="font-family: &quot;Google Sans&quot;, Arial, sans-serif; font-size: 16px; font-weight: 400; margin: 12px 0px 16px; text-decoration: none; border-bottom: 0px rgb(10, 10, 10);">Are you ready to join the trailblazer of bioinformatics innovation in Bangladesh? At <strong data-path-to-node="6" data-index-in-node="85">Dawn of Bioinformatics Limited</strong>, we bridge the gap between computational biology and real-world applications, shaping the future of molecular biology research through genomics, proteomics, and machine learning. We are looking for a dedicated <strong data-path-to-node="6" data-index-in-node="326">Bioinformatics Analyst</strong> to join our mission of revolutionizing the scientific landscape. In this role, you will analyze biological systems using cutting-edge tools and collaborate with experts to provide actionable solutions for global challenges.</div>
  </div>

required_profile:
  <ul>
  <li>
  <p data-path-to-node="9,0,0"><strong data-path-to-node="9,0,0" data-index-in-node="0">Education:</strong> MSc in Life Sciences, Computer Science, or related fields (Preferred), though BSc holders with significant experience are encouraged to apply.</p>
  </li>
  <li>
  <p data-path-to-node="9,1,0"><strong data-path-to-node="9,1,0" data-index-in-node="0">Programming:</strong> Strong proficiency in <strong data-path-to-node="9,1,0" data-index-in-node="35">Python</strong> and <strong data-path-to-node="9,1,0" data-index-in-node="46">R</strong>.</p>
  </li>
  <li>
  <p data-path-to-node="9,2,0"><strong data-path-to-node="9,2,0" data-index-in-node="0">Technical Expertise:</strong> Familiarity with NGS workflows, bioinformatics tools, and machine learning techniques.</p>
  </li>
  <li>
  <p data-path-to-node="9,3,0"><strong data-path-to-node="9,3,0" data-index-in-node="0">Infrastructure:</strong> Practical experience with <strong data-path-to-node="9,3,0" data-index-in-node="42">Linux</strong>, High-Performance Computing (<strong data-path-to-node="9,3,0" data-index-in-node="77">HPC</strong>), or cloud computing environments</p>
  </li>
  </ul>

role_description:
  <ul>
  <li>
  <p data-path-to-node="12,0,0">Analyze biological systems using advanced computational tools and methodologies.</p>
  </li>
  <li>
  <p data-path-to-node="12,1,0">Develop and optimize pipelines for <strong data-path-to-node="12,1,0" data-index-in-node="35">NGS</strong> and metagenomics research.</p>
  </li>
  <li>
  <p data-path-to-node="12,2,0">Apply machine learning and AI techniques to interpret large-scale biological datasets.</p>
  </li>
  <li>
  <p data-path-to-node="12,3,0">Collaborate with researchers to design bioinformatics tools, databases, and visualization platforms.</p>
  </li>
  <li>
  <p data-path-to-node="12,4,0">Work closely with biologists to translate complex data into actionable scientific insights</p>
  </li>
  </ul>

salary_info:
  <div class="" data-bfc="" data-ved="2ahUKEwjauobSp6CUAxV0R2cHHedBNocQi4wTegQIBxAA" data-processed="true" data-copy-service-computed-style="font-family: &quot;Google Sans&quot;, Arial, sans-serif; font-size: 16px; font-weight: 400; margin: 0px; text-decoration: none; border-bottom: 0px rgb(10, 10, 10);">
  <div class="n6owBd awi2gc" data-sfc-cp="" data-sfc-root="c" data-sfc-cb="" data-hveid="CAcQAQ" data-processed="true" data-copy-service-computed-style="font-family: &quot;Google Sans&quot;, Arial, sans-serif; font-size: 16px; font-weight: 400; margin: 12px 0px 16px; text-decoration: none; border-bottom: 0px rgb(10, 10, 10);">Negotiable based on your professional experience and academic qualifications.</div>
  </div>


title: Bioinformatics Developer
slug: bd
employment_type: Full-time
location: Dhaka/ Chittagong
posted_date: 2025-03-13
deadline: 2025-04-25
salary_info: <p>Competitive and negotiable based on your technical expertise and professional experience.</p>
apply_url: https://hr.dobltd@gmail.com.
short_description:
  Are you a tech-savvy innovator passionate about the intersection of biology and software engineering? Dawn of Bioinformatics Limited is seeking a highly skilled Bioinformatics Developer to join our unified scientific ecosystem. As we expand our operations across Dhaka and Chittagong, we are looking for a developer to build the robust infrastructure that powers our research, from the Bangladeshi Medicinal Plant Phytochemicals Database (BMPPD) to advanced AI automation workflows. You will play a pivotal role in creating the software solutions that allow our researchers to solve complex biological puzzles.

job_overview:
  <p>Are you a tech-savvy innovator passionate about the intersection of biology and software engineering? <strong data-path-to-node="6" data-index-in-node="102">Dawn of Bioinformatics Limited</strong> is seeking a highly skilled <strong data-path-to-node="6" data-index-in-node="161">Bioinformatics Developer</strong> to join our unified scientific ecosystem. As we expand our operations across Dhaka and Chittagong, we are looking for a developer to build the robust infrastructure that powers our research, from the Bangladeshi Medicinal Plant Phytochemicals Database (BMPPD) to advanced AI automation workflows. You will play a pivotal role in creating the software solutions that allow our researchers to solve complex biological puzzles.</p>

required_profile:
  <ul style="list-style-type: square;">
  <li data-path-to-node="9,0,0"><strong data-path-to-node="9,0,0" data-index-in-node="0">Education:</strong> MSc in Computer Science, Bioinformatics, or a related field (Preferred); experienced BSc holders are also welcome to apply.</li>
  <li data-path-to-node="9,1,0"><strong data-path-to-node="9,1,0" data-index-in-node="0">Programming Mastery:</strong> Expert proficiency in <strong data-path-to-node="9,1,0" data-index-in-node="43">Python</strong> and <strong data-path-to-node="9,1,0" data-index-in-node="54">R</strong> is essential for tool development.</li>
  <li data-path-to-node="9,2,0"><strong data-path-to-node="9,2,0" data-index-in-node="0">System Architecture:</strong> Strong experience with <strong data-path-to-node="9,2,0" data-index-in-node="44">Docker</strong>, <strong data-path-to-node="9,2,0" data-index-in-node="52">n8n</strong>, and building AI-driven automation agents.</li>
  <li data-path-to-node="9,3,0"><strong data-path-to-node="9,3,0" data-index-in-node="0">Infrastructure:</strong> Deep understanding of <strong data-path-to-node="9,3,0" data-index-in-node="38">Linux</strong>, <strong data-path-to-node="9,3,0" data-index-in-node="45">HPC</strong> clusters, and cloud-based deployment.</li>
  <li data-path-to-node="9,4,0"><strong data-path-to-node="9,4,0" data-index-in-node="0">Database Management:</strong> Experience in designing, maintaining, and scaling biological databases.</li>
  </ul>

role_description:
  <ul>
  <li data-path-to-node="12,0,0">Design and implement end-to-end bioinformatics software, tools, and interactive visualization platforms.</li>
  <li data-path-to-node="12,1,0">Architect and maintain high-performance computational pipelines for <strong data-path-to-node="12,1,0" data-index-in-node="68">NGS</strong>, proteomics, and molecular dynamics.</li>
  <li data-path-to-node="12,2,0">Integrate AI and machine learning models into automated bioinformatics workflows to increase research efficiency.</li>
  <li data-path-to-node="12,3,0">Optimize database structures to handle large-scale biological datasets, ensuring high availability and performance.</li>
  <li data-path-to-node="12,4,0">Collaborate with the core research team to translate scientific requirements into scalable technical solutions.</li>
  </ul>


title: Branch Manager (Chittagong)
slug: bmc
employment_type: Full-time
location: Chittagong
posted_date: 2024-10-03
deadline: 2024-11-20
salary_info: <p>Negotiable based on leadership experience, qualifications, and performance history.</p>
apply_url: https://hr.dobltd@gmail.com.
short_description:
  Dawn of Bioinformatics Limited is expanding its footprint, and we are looking for a dynamic and results-oriented Branch Manager to lead our newly established operations in Chittagong. As the head of our Forest Gate, Muradpur branch, you will be responsible for translating our corporate vision into local success. This role is perfect for a leader who excels in operational management, brand promotion, and fostering a high-performance culture within a scientific and educational ecosystem.

job_overview:
  <p><strong data-path-to-node="6" data-index-in-node="0">Dawn of Bioinformatics Limited</strong> is expanding its footprint, and we are looking for a dynamic and results-oriented <strong data-path-to-node="6" data-index-in-node="113">Branch Manager</strong> to lead our newly established operations in Chittagong. As the head of our Forest Gate, Muradpur branch, you will be responsible for translating our corporate vision into local success. This role is perfect for a leader who excels in operational management, brand promotion, and fostering a high-performance culture within a scientific and educational ecosystem.</p>

required_profile:
  <ul>
  <li data-path-to-node="9,0,0"><strong data-path-to-node="9,0,0" data-index-in-node="0">Education:</strong> Bachelor&rsquo;s or Master&rsquo;s degree in Business Administration, Management, or a related field; a background or interest in Life Sciences is a significant advantage.</li>
  <li data-path-to-node="9,1,0"><strong data-path-to-node="9,1,0" data-index-in-node="0">Leadership:</strong> Proven experience in a managerial role, with a track record of leading diverse teams and managing office operations.</li>
  <li data-path-to-node="9,2,0"><strong data-path-to-node="9,2,0" data-index-in-node="0">Business Development:</strong> Strong abilities in strategic planning, marketing, and brand promotion to drive local growth.</li>
  <li data-path-to-node="9,3,0"><strong data-path-to-node="9,3,0" data-index-in-node="0">Communication:</strong> Exceptional interpersonal and negotiation skills, capable of building relationships with academic and professional stakeholders.</li>
  <li data-path-to-node="9,4,0"><strong data-path-to-node="9,4,0" data-index-in-node="0">Operational Excellence:</strong> Highly organized with a proactive, target-driven mindset and the ability to manage budgets and resources effectively.</li>
  </ul>

role_description:
  <ul>
  <li data-path-to-node="12,0,0">Oversee daily administrative and technical operations of the Chittagong branch to ensure seamless service delivery.</li>
  <li data-path-to-node="12,1,0">Lead local brand promotion efforts and facilitate offline training programs at the Institute of Bioinformatics and Artificial Intelligence (IBAI).</li>
  <li data-path-to-node="12,2,0">Manage a core team of experts and support staff, ensuring alignment with the company&rsquo;s unified scientific goals.</li>
  <li data-path-to-node="12,3,0">Act as the primary point of contact for university authorities, students, and researchers in the Chittagong division.</li>
  <li data-path-to-node="12,4,0">Develop and execute strategic plans to expand the branch&rsquo;s reach and increase enrollment in specialized bioinformatics programs.</li>
  </ul>


# bsds_campuscoordinator

name: Top 51 Best Bioinformatics Campus Coordinators
role_label: Best Bioinformatics Campus Coordinators 2025
image: campus_coordinators/2025.webp
description:
  The 2025 cohort set a new benchmark of excellence. Selected through a rigorous multi-stage evaluation, 51 top Campus Coordinators emerged as leaders across research, operations, and community development.
  Many from this batch are already contributing to specialized sub-departments, supporting innovation, training programs, and organizational growth. Their technical acumen and leadership potential have been recognized at every level of the organization, setting a new benchmark for future cohorts.


name: Top 20 Best Bioinformatics Campus Coordinators
role_label: Best Bioinformatics Campus Coordinators 2024
image: campus_coordinators/2024.webp
description:
  The 2024 batch showcased extraordinary talent and resilience. From an initial pool of 750 applicants, 140 were shortlisted through skill-based assessments and training. After rigorous evaluation—including quizzes, performance tracking, and leadership metrics30 outstanding coordinators were selected.
  Today, several members of this cohort are working in part-time professional roles within the company, actively contributing to operations, management, and strategic execution.


name: Top 20 Best Campus Coordinator 2023
role_label: Best Campus Coordinator 2023
image: campus_coordinators/2023.webp
description:
  From 500 participants, the top 20 Campus Coordinators were selected based on performance, initiative, and leadership impact.
  This group now plays a vital role within Dawn of Bioinformatics Ltd., gaining hands-on corporate experience and contributing across multiple domains, including Plant phytochemical Database project execution, research support, and organizational development.


# bsds_competition

title: National Writing Contest — Winners
image: competitions/Wrinting_contest_winner_.jpg
description:
  The National Writing Contest has consistently elevated the standard of scientific communication within the student bioinformatics community. Finalists were selected through a rigorous blind review process conducted by leading academics. Winners demonstrated exceptional command of scientific language, analytical depth, and the ability to translate complex genomic research into compelling academic narratives with creativity. Each winning contestant received a prize of BDT 15,000 alongside a Certificate of Excellence. Their published works are featured in the BSDS digital library and serve as a benchmark for future contestants — inspiring a new generation of scientific writers nationwide.


title: Bioinformatics Video Contest — Winners
image: competitions/photo_2026-05-13_00-45-29.jpg
description:
  The Bioinformatics Video Contest winners captured public imagination by transforming raw biological data into visually stunning, scientifically sound narratives. Their creative outputs ranged from animated genomic walkthroughs to documentary-style research exposés — all reviewed and recognized by a panel of expert evaluators. Each winner was honored with a custom engraved Crest and a Certificate of Achievement. Beyond recognition, top performers were offered internships within the Dawn of Bioinformatics Content Development Team, with select individuals receiving part-time employment offers — a testament to the contest's role as a genuine career launchpad in scientific media and outreach.


title: National Bioinformatics Writing Contest
image: competitions/creative-writing-contest-2a.jpg
apply_url: https://dobltd.com
description:
  This contest cultivates scientific writing, critical thinking, and the ability to communicate complex ideas with clarity and precision. Winners received a prize fund of BDT 15,000 in recognition of their academic excellence and scientific contribution. The contest is open to undergraduate and postgraduate students nationwide.


title: Bioinformatics Video Contest
image: competitions/online-video-contest.png
apply_url: https://dobltd.com
description:
  The Bioinformatics Video Contest invites students to communicate complex biological concepts through compelling visual narratives, animations, and data-driven storytelling. Outstanding winners receive a prestigious Crest and Certificate of Excellence in recognition. Top performers are offered a coveted internship within our Content Development Team, with select individuals also offered part-time positions providing real industry exposure and a direct pathway into professional scientific media.


