Bishnu Sarker, PhD

Assistant Professor of Computer Science and Data Science

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

School of Applied Computational Sciences.

Meharry Medical College, Nashville, TN, 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 in Data Science / Biomedical Data Science) for Fall 2024. Apply here if you are a Permanent Resident/Citizen of the USA.

Send me an email if you are interested.

Welcome ; Bienvenue; সু-স্বাগতম;

I am currently a Tenure-Track Assistant Professor of Computer Science and Data Science at Meharry Medical College within the School of Applied Computational Sciences(SACS). My research expertise lies in the intersection of computer science and biology, particularly, in applying artificial intelligence to answer biological questions. I am interested in developing graph based machine learning tools for biomedical knowledge discovery such as Prot-A-GAN: GAN-based link prediction from biomedical knowledge graph , GrAPFI-understanding protein's function from protein network, and Using Language Model for Protein Function Annotation.

I recieved PhD in computer science from Inria-University of Lorraine, France; Masters in Data Mining and Knowledge Management from Sorbonne University, France; Bachelor in Computer Science and Engineering from Khulna University of Engineering and Technology, Bangladesh.

Prior to joining Meharry, I worked as Research Engineer at CNRS, France; Visiting researcher at Mila-University of Montreal, Canada for brief period of time; Assistant Professor of Computer Science and Engineering at Khulna University of Engineering and Technology.

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 )

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