Dr. Madhusudan Choudhary: Bioinformatics Lab
McMaster University, PhD
Duke University, Post-doctoral
Research Focus
Multipartite Genome, Contig Mapping, Genome Alignment, Microgravity, Microbiomes, and Microbial Phylogenetics
My research interests are in bacterial cell-cycle regulation, role of gene duplication in metabolic innovations, and evolution of genomic complexity in prokaryotes. Rhodobacter sphaeroides, a member of α-3 Proteobacteria, is a model organism for these investigations in my laboratory. R. sphaeroides possesses a complex genome structure, including multiple chromosomes and abundance of duplicated genes, and it also exhibits a great repertoire of metabolic capabilities.
Bacterial cell cycle involves DNA replication, chromosome segregation, and septum formation (cytokinesis). These molecular and cellular processes are coordinated and controlled by regulatory networks. Since prokaryotic cells lack mitosis-like apparatus, multiple chromosomes in bacteria pose a considerable problem for the coordinated replication and the accurate segregation of the chromosomes. To understand the behavior of two chromosomes throughout cell cycle in R. sphaeroides, cloned origins of replication from two chromosomes is being investigated for their replication and cellular localization. Different genetic, biochemical, and bioinformatic methods are employed for this investigation.
The genome of R. sphaeroides contains ~29% of gene duplications, and its roles have been implicated in evolutionary novelties for genome and organismic evolution. We are interested how do different structural and functional constraints of duplicate copies of each gene-pair affect their mRNA expression. This study utilizes both bioinformatic and molecular approaches, such as Ka/Ks estimates, phylogenetic tree construction, and microarray expression analysis.
We are also interested in origin and evolution of genome complexity in bacteria. We performed genome analyses on bacterial species, which possess multiple chromosomes, and have conclusively demonstrated the ancient origin of second chromosome. Since the second chromosome rapidly evolved, we want to investigate further whether second chromosome has specialized role or has evolved to a level where it has become important for the organism in all growth conditions.
Recent Publications
- Guiterrez, E., Choudhary, M., Ho, A., & Karki, A. B. (2026). Differential Gene Expression of Acidovorax SP. 1608163 Under Simulated Microgravity. Microgravity Science and Technology. 38:25 (DOI: 10.1007/s12217-026-10245-4)
- Weerakkody Ranasinghe, Docie Gillette, Alexis Ho, Hyuk Cho, and Madhusudan Choudhary (2024) Taxonomic Distribution, Phylogenetic Relationship, and Domain Conservation of CRISPR-Associated CAS Proteins. Bioinformatics and Biology Insights Vol. 18:1-9.
- Weerakkody Ranasinghe, Eduardo Gutierrez, Zelaya Alyson, Sabrina Vazquez Ashleigh Ogg, Rajesh Prabhu Balaraman, Hyuk Cho, and Madhusudan Choudhary (2023) Analysis of Growth Characteristics and Differentially Expressed Homologous Genes in Rhodobacter sphaeroides Under Normal and Simulated Microgravity Conditions. Advances in Microbiology, Vol 13 (11): 539-558
- Almalki, Fatemah, Madhusudan Choudhary, and Rajeev K. Azad (2022) Analysis of multipartite bacterial genomes using alignment-free and alignment-based pipelines. Archives in Microbiology, 205: 25 (DOI: 10.1007/s00203-022-03354-2)
- Jha, T., Mendel, J., Cho, H., & Choudhary, M. (2022). Prediction of Bacterial sRNAs Using Sequence-Derived Features and Machine Learning. Bioinformatics and Biology Insights, 16 (DOI: 10.1177/11779322221118335)
Recent Presentations
- Chito Ofodum and Madhusudan Choudhary (2025) Microbiome Composition and Community Structure in Soil Sediments of Lake Raven and Lake Conroe. Presented at the Texas Branch ASM Fall Meeting, Oct 30-Nov 1, University of Texas at Tyler, Tyler, Texas, USA (platform presentation) O. B. Williams Award, 2nd Place in oral presentation for graduate students in General Microbiology
- Jaqueline Basurto, Madison M. Schultz, Anand B. Karki, and Madhusudan Choudhary (2025) Comparative Analysis of Plasmid Genomes in Cereibacter Species. Presented at the Texas Branch ASM Fall Meeting, Oct 30-Nov 1, University of Texas at Tyler, Tyler, Texas, USA (poster presentation)
- Weerakkody Ranasinghe and M. Choudhary (2024) Microbial Diversity of the Ganges River. Presented at the Texas Branch ASM Spring Meeting, March 21-23. 2024, Cedar Hill, Texas, USA (platform presentation) Charlie Gaunt Award, 1st Place in oral presentation for graduate students.
Awards & Honors
- Faculty Award of Excellence in Service, Sam Houston State University (August 2022).
- Faculty Award of Excellence in Service, College of Science and Engineering Technology (August 2021).
- Faculty Excellence Award in Scholarly and Creative Accomplishment, San Houston State University (August 2016).
- Eugene and Millicent Goldschmidt Mentoring Award, Texas Branch-American Society of Microbiology (November 2015).
- Faculty Award of Excellence in Research, College of Science and Engineering Technology (August 2014).