Overview:
The Bioinformatics Lab at BILSAB, led by Dr Khan, has a wide array of interests in solving biological problems. Specifically, the lab is interested in the area of biological data warehousing and applications of data science to the study of immune responses, vaccines, viruses, venom toxins, drug design, and disease biomarkers.
Publications (selected):
Işık EB, Brazas MD, Schwartz R, Gaeta B, Palagi PM, van Gelder CWG, Suravajhala P, Singh H, Morgan SL, Zahroh H, Ling M, Satagopam VP, McGrath A, Nakai K, Tan TW, Gao G, Mulder N, Schönbach C, Zheng Y, De Las Rivas J, Khan AM. Grand challenges in bioinformatics education and training. Nat Biotechnol. 2023 Aug;41(8):1171-1174. doi: 10.1038/s41587-023-01891-9. [Public link: https://rdcu.be/djhh8]. [*Corresponding author].
Raman HS, Tan S, August JT, Khan AM*. Dynamics of Influenza A virus (H5N1) protein sequence diversity. PeerJ. 2020, e7954 [*Corresponding author].
Suwinski P, Poh YM, Ling MHT, Ong CK, Khan AM* and Ong HS*. Advancing personalized medicine through the application of whole exome sequencing and big data analytics. Frontiers in Genetics. 2019, 10, 49. [*Co-Corresponding author].
Khan AM*, Hu Y, Miotto O, Thevasagayam NM, Sukumaran R, Raman HSA, Brusic V, Tan TW and August, JT. Analysis of Viral Diversity for Vaccine Target Discovery. BMC Med. Genomics. 2017. 10(4), 78. [*Corresponding author] [Award = Best Paper, Gold @ International Conference on Bioinformatics (InCoB) 2017]
Lim WC and Khan AM*. Mapping HLA-A2, -A3, and -B7 supertype-restricted T-cell epitopes in ebolavirus proteome. BMC Genomics. 2018, 19 (1), 42. [*Corresponding author; Award = Best Paper, Gold @ International Conference on Bioinformatics (InCoB) 2017]
Outlink (GScholar, AVESIS, or ORCID ID): http://bit.ly/khanam
Grants (Completed):
2020-2023
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Title: Advanced Studies Institutes (ASI); International Research Experiences for Students (IRES)
Sponsor: National Science Foundation (NSF), USA
Total direct cost: USD 300,000
Role: Collaborator
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2022-2023
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Title: Cross-Disciplinary Training for Future Computational Biologists in Asia
Sponsor: Asi@Connect (http://www.tein.asia)
Total direct cost: Approx. Euro 150,000
Role: Collaborator
Partners: USA, UK, Malaysia, Turkey, Thailand, Indonesia, Bangladesh, India, and Singapore.
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2022-2023
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Title: Building a high bandwidth distributed High Performance Computing
Sponsor: Asi@Connect (http://www.tein.asia)
Total direct cost: Approx. Euro 150,000
Role: Collaborator
Partners: Australia, Korea, Pakistan, Malaysia and Turkey
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2021 |
Title: Educational workflow on computer aided drug design:
investigating possible inhibitors against Factor H as a case study
Sponsor: National Supercomputing Centre (NSCC), Singapore
Total direct cost: 1M corehours and 0.1TB of storage (in-kind)
Role: Co-PI
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2019-2020
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Title: Cheminformatics-based, high-throughput virtual screening for candidate inhibitory peptides against the spike protein of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
Sponsor: Bezmialem Vakif University
Total direct cost: TLR 20,000
Principal Investigator: Assist. Prof. Dr Serdar Uysal
Role: Collaborator (lead, bioinformatics component of the project)
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2019-2020
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Title: Bilgisayar yardımlı geliştirilen Fakt.r H inhibit.rlerinin glioblastoma hayvan modellerinin tedavisinde kullanımının değerlendirilmesi
Sponsor: Bezmialem Vakif University
Total direct cost: TLR 22,550.19
Principal Investigator: Prof. Dr. Rümeyza Kazancıoğlu
Role: Collaborator (lead, bioinformatics component of the project)
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Projects:
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The development of a Viral Variome Analyzer (ViVA) with application to surveillance, diagnostics, drug design and vaccine target discovery.
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Novel Coronavirus (nCoV): Acute Respiratory Infection Clinical Characterisation Data Tool Design.
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Investigating possible inhibitors against Factor H in relation to glioblastoma.
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Large-scale analysis of B-cell epitopes on Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein – implications for cross-reactivity of neutralizing antibodies.
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Mapping and characterising sequences shared between coronaviruses and human proteomes: structural, functional and immunological implications.
Tools Developed:
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Tool |
Description |
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ViVA |
Viral Variome Analyser (ViVA) is a systematic bioinformatics approach as an ecosystem to understand viral diversity and map targets that can facilitate diagnostic, surveillance, drug, and vaccine design by processing the large amounts of viral sequence data and metadata produced by genomics, proteomics, and host-pathogen interaction studies, available in public databases, which are continuing to grow rapidly.
Status: In Progress
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SEVANT |
Sequence Diversity Dynamics Visualisers and Interpreter (SEVANT) is an all-in-one visualizer-interpreter that uses an embedded Diversity Motif Analyser (DiMA) Python package to quantify and dissect viral protein sequence diversity dynamics. The resulting output is then visualized as plot/tables, delineating inherent patterns in the organization of sequence changes that function in the viral fitness selection.
Status:
Click Here
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DiMA |
Diversity Motif Analyser (DiMA) is a tool designed to facilitate the dissection of protein sequence diversity dynamics for viruses. DiMA provides a quantitative measure of sequence diversity by use of Shannon's entropy, applied via a user-defined k-mer sliding window.
Status:
Click Here
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MoSwA |
Motif Switch Analyser (MoSwA) is a tool that not only identifies all alignment k-mer positions that exhibit motif switching but also provides a multi-faceted and extensive characterization of the switches.
Status:
Click Here
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CROSTA |
Cross-Species Transmissibility Analyser (CROSTA) compares the viral protein sequence of two host populations (donor and recipient) that are co-aligned and are analyzed for zoonotic transmission. It provides users with the incidences and motifs of diversity for aligned k-mer positions of each host with a simple interface, including a graphical representation of the results.
Status: In Progres
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IDTA |
Inhibitory Drug Target Analyser (IDTA) is a tool to identify conserved sites that can be used as pockets for drug design.
Status: In Progres
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ViTA |
Vaccine Target Analyser (VITA) is part of the ViVA ecosystem that aims to give the users the viral sequences that could be used as effective vaccine targets.
Status: In Progres
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DiTA |
Diagnostics Target Analyser (DiTA). This tool is to detect the sequences in question and provide the main information that can lead the user to the correct diagnosis.
Status: In Progress
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ViM |
Viva Integration Module (VIM) is the web-based graphical user interface (GUI) for all the analytical modules of VIVA. It allows users to select and perform analysis with SEVANT, IDTA, ViTA, DiTA, and CROSTA applications from the interface at the same time.
Status: In Progress
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UNIQmın |
UNIQmin, a tool that utilises an alignment independent method to generate the minimal set of pathogen sequences, as a way to study their diversity, across any rank of taxonomic lineage. The minimal set refers to the smallest possible number of sequences required to capture the entire repertoire of pathogen peptidome diversity present in a sequence dataset.
Availability:
Click Here
Publication:
Click Here
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Kmerslıcer |
Mapping shared sequences (Share-ome) #Python code for generating k-mers of any defined length from an input biological sequence kmerslicer is a source code, for constructing/generating generate k-mer (either peptides or nucleotide) sequences of any desired length, based on the sliding window method across given FASTA sequences from an input file.
Publication:
Click Here
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g-FLUA2H |
g-FLUA2H is a web-based application focused on the analysis of the dynamics of influenza virus animal-to-human (A2H) mutation transmissions. The application only requires the viral protein sequences from both the animal and human host populations as input datasets.
Publication:
Click Here
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Teaching:
Graduate Courses
Module code & title: DDD6028, Introductory Bioinformatics.
Programme: Doctorate in Philosophy (PhD)
Location: Bezmialem Vakif University, Turkey
Module code & title: DDD6031, Introductory to Machine Learning
Programme: Doctorate in Philosophy (PhD)
Location: Bezmialem Vakif University, Turkey
Graduate Student Supervision
1. MSc, Rashid Mukaila, Istanbul University. 2021 – 2023. Comparative Diversity Dynamics of Influenza A Virus Subtypes
2. MSc, Faruk Üstünel, Bezialem Vakif University. 2020 – 2022. Dissecting the diversity dynamics of human respiratory syncytial virus (HRSV).
3. PhD, Omer Aysar, Faculty of Pharmacy, Bezmialem Vakif University, 2020 – 2022.
Lab Research Team
1. Mohammad Asif Khan, PhD: Principal Investigator
2. Esra Büşra Işık: Research Assistant, TUBITAK Researcher, Project Lead, Lab Manager
3. Ebru Sarsılmaz: Technician, Administrator
Lab Alumni / Former members
1. Adnaane Bawa: Consultant
2. Ayesha Fatima: Post-Doctoral Fellow, TUBITAK Researcher, Project Lead
3. Emre Herdan: Intern, Project Lead
4. Esin Özkan: Intern, Project Lead
5. Eyyub Selim Ünlü: Intern, TUBITAK Scholar, Project Lead
6. Faruk Üstünel: Research Assistant, Graduate Student (MSc), TUBITAK Researcher, Project Lead
7. Gizem Yılmaz: Intern, Project Lead
8.Gökçen Şahin: Technician, TUBITAK Scholar, Project Lead
9. Hasiba Karimi: Intern, Project Lead
10. Hilal Hekimoğlu: TUBITAK Scholar, Project Lead
11. Levent Faruk Soysal: Intern
12. Li Chuin Chong: International Visiting Researcher, Project Lead
13. Melike Karakaya: TUBITAK Scholar, Project Lead
14. Melda Mermer: Intern, Project Lead
15. Moosa Farhan: Intern
16. Muhammad Farhan Sjaugi: International Visiting Researcher, Project Lead
17. Shan Tharanga: Intern (international; remote), Project Lead
18. Muhammed Miran Öncel: Intern, TUBITAK Scholar, Project Lead
19. Muhammet Çelik: Lab Manager, Project Lead, TUBITAK Scholar, Consultant
20. Omer Avşar: Intern
21. Pendy Tok: Intern (international; remote), Project Lead
22. Rashid Mukaila: TUBITAK Scholar, Graduate Student (MSc), Project Lead, Consultant
23. Rumeysa Meriç: Technician, Administrator
24. Shazia Naqshbandi: Intern
25. Zarife Aslan: Intern, Project Lead
Contact Info:
E-mail: bilsab.bioinfo@gmail.com
