I'm an Assistant Professor at Rutgers University in the Department of Genetics.
Born and raised in India, as per cultural norm, I became an engineer/technologist. I received my undergraduate degree in Biotechnology from Anna University (pronounced un-nah).
I then received Ph.D. in Ecology and Evolutionary Biology from University of Tennessee, Knoxville, advised by Mike Gilchrist. During this time, I built models to understand the evolution of codon usage patterns.
I then did a postdoc with Josh Plotkin at University of Pennsylvania, where I worked on whole-cell models of protein translation, the role of epistasis in protein evolution, built codon substitution models, and methods for identifying rate variation in phylogenetic trees.
riboviz: analysis and visualization of ribosome profiling datasets.
Carja et al. BMC Bioinfo 2017
Epistasis and the dynamics of reversion in molecular evolution.
McCandlish et al. Genetics 2016
Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation.
Weinberg & Shah et al. Cell Rep 2016
A codon model of nucleotide substitution with selection on synonymous codon usage.
Kubatko et al. Mol Phylo Evol 2016
Contingency and entrenchment in protein evolution under purifying selection.
Shah & McCandlish et al. PNAS 2015
Estimating gene expression and codon specific translational efficiencies, mutation biases, and selection coefficients from genomic data alone.
Gilchrist et al. Genome Biol Evol 2015
iteRates: An R package for implementing a parametric rate comparison on phylogenetic trees.
Fordyce et al. Evol Bioinfo 2014
Rate-limiting steps in yeast protein translation.
Shah et al. Cell 2013
The role of epistasis in protein evolution.
McCandlish et al. Nature 2013
Non-optimal codon usage is a mechanism to achieve circadian clock conditionality.
Xu et al. Nature 2013
Evidence for repeated loss of selective constraint in rhodopsin of amblyopsid cavefishes (Teleostei: Amblyopsidae).
Niemiller et al. Evolution 2013
A parametric method for assessing diversification-rate variation in phylogenetic trees.
Shah et al. Evolution 2013
Weak 5′-mRNA Secondary Structures in Short Eukaryotic Genes.
Ding et al. Genome Biol Evol 2012
Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift.
Shah & Gilchrist PNAS 2011
Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias.
Shah & Gilchrist PLOS Genet 2010
Is thermosensing property of RNA thermometers unique?
Shah & Gilchrist PLOS ONE 2010
Measuring and detecting molecular adaptation in codon usage against nonsense errors during protein translation.
Gilchrist et al. Genetics 2009
Postdoc positions available
Our new lab website