L’OMAR – Laboratory of Omics Mining and Algorithmic Reasoning

Bishnu Sarker

Bishnu Sarker, Ph.D.
Assistant Professor of Computer Science and Data Science
Dr. Sarker’s personal website

Research Dimensions: Computational Biology, Artificial Intelligence/Deep Learning, Natural Language Processing, Data Science, and Computational Drug Discovery.

The primary focus of L’OMAR is mining omics (aka multi-omics) data such as genomics (DNA), transcriptomics (RNA), proteomics (proteins), metabolomics (metabolites), metagenomics (microbiomes) etc. to understand human biology computationally. L’OMAR develops algorithmic reasoning techniques leveraging artificial intelligence (AI), machine learning, deep learning and natural language processing (NLP) emphasizing on explanations (XAI) to the predictions and decisions an AI-agent may bring in 1) understanding the biology of diseases, 2) identifying promising drug-targets and drug molecules, and 3) repurposing existing drugs for drawing faster response against future pandemic.

One particular niche area L’OMAR exploring is how to build models that are capable of integrating multi-omics data by using knowledge graphs, and building explainable AI-driven reasoning approaches to elucidate the hidden links and connections among biological entities that may help discover new biomedical knowledge and insights. 

Linguistically, OMAR in L’OMAR is a Bengali word meaning Immortal. While achieving immortality is definitely not the purpose, L’OMAR aims to bring health care innovations to help people live equal, longer and healthier.

Keywords:

Multi-omics data analysis, Knowledge Graph, Computational Biology, bioinformatics, Artificial Intelligence/Deep Learning, Natural Language Processing, Algorithmic Reasoning, Recommender System, Drug Repurposing, Drug Discovery.

Publications

All publications are available here.

Lab Members and Affiliates:

Internal:

  • Bradford Patton, M.S. Data Science student (NIH R25)
  • Aleesa Mann, M.S. Data Science student
  • Shara Taylor, M.S. Data Science graduate

External:

  • Nyla Weatherington
    U. of Alabama, Montgomery (SURP, Jointly with Dr. Davis)
  • Evan M Powell
    University of Kansas, US (MS, Jointly with Dr. Shomaji)
  • Fairuz Shadmani Shishir
    University of Kansas (PhD, Jointly with Dr. Shomaji)

Grant Support

  • RCMI Subaward
  • Meharry CANCER SUMMER UNDERGRADUATE RESEARCH PROGRAM (SURP)NIH R25 Scholars Award
  • NSF HBCU Excellence in Research 

Collaborators

Internal

Dr. Aize Cao
Associate Professor, Biomedical Data Science
School of Applied Computational Sciences, Meharry Medical College, USA

Dr. Jamaine Davis
Assistant Professor, Biochemistry and Cancer Biology
School of Medicine, Meharry Medical College, USA

Dr. Bindong Liu
Professor of Microbiology and Immunology
Meharry Medical College, USA

Dr. Edilberto Raynes
Professor of Professional and Medical Education
Meharry Medical College, USA

External

Dr. Sabeur Aridhi
Associate Professor of Computer Science
University of Lorraine, France. 

Dr. Marie-Dominique Devignes
Research Director
CNRS, France

Dr. Farzan Rahman
Lecturer, Data Science
Kingston University, UK

Dr. Sumaya Shomaji
Assistant Professor, Electrical Engineering and Computer Science
University of Kansas, USA.

Dr. Guy Wolf
Associate Professor of Mathematics and Statistics
University of Montreal, Canada.