Vivek Ramanan

Vivek Ramanan

Computational Biology Researcher. PhD Candidate. Focusing on microbes.

Publications

Augmenting bacterial similarity measures using a graph-based genome representation

Published in ASM Journals: mSystems, 2024

Genome relationships amongst bacteria are commonly performed using 16S rRNA comparisons or whole genome comparisons. A motivation of interest in this common protocol was how to consider orthologous sections of the genomes that may have moved around in dynamic circular bacterial genomes.This method is an exploration of taking functional regions of genomes and using them to calculate a distance metric, using a linear genome representation and a geometric distance measure instead of a nucleotide based measure.

Recommended citation: Ramanan V, Sarkar IN. 2024. Augmenting bacterial similarity measures using a graph-based genome representation. mSystems 9:e00497-24. https://doi.org/10.1128/msystems.00497-24 https://journals.asm.org/doi/full/10.1128/msystems.00497-24

Genbank as a source to monitor and analyze Host-Microbiome Data

Published in Bioinformatics, 2022

This paper uses data mining, natural language processing, and phylogenetics techniques to explore the current status of Genbank microbiome data. As an important source of reference genomes, Genbank is a valuable resource to demonstrate our current understanding and data collection on the microbiome thus far.

Recommended citation: Ramanan,V.;Mechery,S.;Sarkar,I.N. (2022). "Genbank as a source to monitor and analyze Host-Microbiome Data." Bioinformatics. DOI: 10.1093/bioinformatics/btac487 https://academic.oup.com/bioinformatics/article/38/17/4172/6633928?login=true

Clustered 8-Oxo-Guanine Mutations and Oncogenic Gene Fusions in Microsatellite-Unstable Colorectal Cancer

Published in JCO Precision Oncology, 2022

MSI-H colorectal cancer cases are often characterized by oncogenic fusions in driver genes. Junction sequences of these fusions (50 base pair combinations surrounding the breakpoint) revealed a particular type of mutation, known as 8-oxo-guanine mutations, that are linked to environmental causes and potentially to the microbial metabolite, butyrate, which can modulate oxidative damage.

Recommended citation: Madison,R.;Hu,X.;Ramanan,V.;et al. (2022). "Clustered 8-Oxo-Guanine Mutations and Oncogenic Gene Fusions in Microsatellite-Unstable Colorectal Cancer." JCO Precision Ongoloy. DOI: 10.1200/PO.21.00477. http://vivekramanan.github.io/files/VR-ASCO-Paper.pdf

Interactions between species introduce spurious associations in microbiome studies

Published in PLoS Computational Biology, 2017

Interactions between populations of microbes in microbiomes influence one anothers population distributions, thus standard statistical analysis between two microbiome datasets may find more statistically significant, but non-interpretable, taxa of difference. This method, termed Direct Association Analysis, uses maximum entropy principles to correct for microbial interaction noise and identify potential causative taxa by removing taxa that are influencing one another, rather than driving the differential.

Recommended citation: Menon,R.;Ramanan,V.;Korolev,K. (2017) "Interactions between species introduce spurious associations in microbiome studies." PLoS Computational Biology. DOI:10.1371/journal.pcbi.1005939. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005939#sec007