Bishnu Sarker, PhD

Assistant Professor of Health Informatics

PI: L'OMAR - Laboratory of Omics Mining and Algorithmic Reasoning

College of Information, University of North Texas, Denton, TX, USA.

bsarker[AT]mmc[DOT]edu | LinkedIn | Twitter | Github | Google Scholar | CV

Openings for MS students with RAs.

I am looking for full time graduate students (MS/PhD Information Science, Data Science, Computer Science) for Fall 2026. Send me your CV to bishnu.sarker@unt.edu

Welcome ; Bienvenue; সু-স্বাগতম;

I am an Assistant Professor of Health Informatics in the Department of Information Science under College of Information at University of North Texas, Denton, TX. Prior to that, I was an Assistant Professor of Computer Science and Data Science in the School of Applied Computational Science at Meharry Medical College, Nashville, TN. He also worked as Research Engineer at CNRS, France; a visiting researcher at Mila-University of Montreal, Canada; Assistant Professor of Computer Science and Engineering at Khulna University of Engineering and Technology, Bangladesh.

My research expertise lies in the intersection of computer science and biomedical science, particularly in applying artificial intelligence to answer biomedical questions. I am interested in developing graph-based machine learning tools for biomedical knowledge discovery. Categorically, my research interests include 1) Health Informatics: Clinical Risk Prediction, Clinical Notes Analytics, EHR Data Modeling, Clinical Language Models, 2) Computational Biology: Automatic Enzyme Classification, Metal Binding Site Prediction, Generative Protein Design, Drug Discovery, Drug Repurposing, Cell Type Annotation; 3) Omics Data Mining: Bioinformatics, Next Generation Sequencing (NGS) Data Analysis, Variant Calling, SNP/SNVs. B-Cell Repertoire Analysis, Sequence Visualization, Clustering. Integrative multi-omics data analysis. Muti-modal genomics data science; 4) Network Science: Graph Data Mining, Geometric Deep Learning, Knowledge Graph Embedding, Link Prediction, Graph Neural Network, 5) Artificial Intelligence: AI/ML, Deep Learning, Generative Adversarial Network, Explainable Reasoning.

I have received a Bachelor of Science in Computer Science and Engineering from Khulna University of Engineering & Technology (KUET), Bangladesh in May 2011. I have completed a Master’s in Science, Technology and Health specializing in Computer Science with a focus to Data Mining and Knowledge Management from University of Paris 6 (Formerly know as Pierre and Marie Curie University) and Telecom Paris Tech, Paris, France, in July 2016. I graduated with a Ph.D. in Computer Science from the University of Lorraine while working at the French National Institute for Computer Science and Automation (Inria), France, in April 2021.

REsearch Interests

Computational Biology: Automatic Enzyme classification, Metal Binding Site Prediction, Generative Protein Design, Drug Discovery, Drug Repurposing, Cell Type Annotation.
Omics data mining: Bioinformatics, Next Generation Sequencing(NGS) data analysis, Variant Calling, SNP/SNVs. B-Cell Repertoire Analysis, Sequence Visualization, Clustering.Integrative multi-omics data analysis. Muti-modal genomics data science.
Network Data Science: Graph Data Mining, Geometric Deep Learning, Knowledge Graph Embedding, Link Prediction, Graph Neural Network.
Artificial Intelligence: Machine Learning, Deep Learning, Generative Adversarial Network, Explainable Reasoning.

News & Updates

HRSA Awarded $2.2M to research on Maternal Health. Happy to be Co-Investigator to lead clincal note analysis.
I will be speaking at Nashville Analytics Summit on Oct 3, 2023.
Tutorial proposal accepted at ADSA Annual Meeting 2023, San Antonio, TX.
I have been awarded HBCU Excellence in Research Grant to support my research project for 3 years. Award-Link
Joined the Advisory Board of the Department of Physical Therapy, Tennessee State University, Nashville, TN.
Presented a tutorial on "Protein Sequence Analysis using Transformers-based Large Language Model" at ISMB/ECCB 2023. Link to tutorial
Joined International Society for Computational Biology as a member (06/2023-06/2024)
Joined as Program Committee Member of ICML-Computational Biology Workshop, 2023.
In the Age of Machine Learning Cryo-EM Research is Still Necessary: A path toward precision medicine is accepted for publication in Advanced Biology, May 2023.
MetaLLM: Residue-wise Metal ion Prediction Using Deep Transformer Model is accepted for Oral presentation in IWBBIO 2023, Spain.
Tutorial Proposal accepted in ISMB/ECCB 2023, Lyon, France. Link to Tutorial and Register here
Improving Automatic GO Annotation With Semantic Similarity is published in BMC Bioinformatics. Link to paper
A Semi-supervised Graph Deep Neural Network for Automatic Protein Function Annotation accepted at IWBBIO 2022 and Published by Springer LNCS Bioinformatics and Biomedical Engineering. Link to Paper
July 22-23 - Serving as the Program Committee member of Workshop on Computational Biology (WCB)of 2022-International Conference of Machine Learning (ICML), Baltimore, Maryland, USA.
May 18, 2022 - Served as the Opponent (External Reviewer) of PhD Licentiate (2-years Defense) of Saleha Javed from Machine Learning Research group of Lulea University of Technology, Sweden. Thesis Title: Towards Digitization and Machine Learning Automation of Cyber Physical System of Systems.
March 12, 2022 - I did a invited talk on Machine Learning for Graph: Introduction and Application to Biomedical Knowledge Discovery at Jessore Science and Technology University, Jessore, Bangladesh.
March 6, 2022 - I did a invited talk on Machine Learning for Graph: Introduction and Application to Biomedical Knowledge Discovery at Khulna University, Khulna, Bangladesh.

Here is a non-exhaustive list of my wonderful mentors:

Dr. David W. Ritchie (https://members.loria.fr/DRitchie/ )
Dr. Marie-Dominque Devignes (https://members.loria.fr/MDDevignes/ )
Dr. Sabeur Aridhi (https://members.loria.fr/SAridhi/ )
Dr. Guy Wolf ( https://mila.quebec/en/person/guy-wolf/ )
Dr. Juliana Bernerdes (http://www.lcqb.upmc.fr/julianab/advising.html )
Dr. Jean-Gabriel Ganascia (http://www-poleia.lip6.fr/~ganascia )
Dr. Nataliya Sokolovska (https://sites.google.com/view/nsokolovska/home )
Dr. Traian Rebedea (https://scholar.google.com/citations?hl=en&user=7NxaE1MAAAAJ&view_op=list_works&sortby=pubdate )
Dr. Costin-Gabriel Chiru (https://scholar.google.com/citations?hl=en&user=NlijAdgAAAAJ&view_op=list_works&sortby=pubdate )