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.
Papers
Evolution of tRNA pool shapes variation in selection on codon usage across the Saccharomycotina subphylum.
Cope et al. bioRxiv 2024
Translational profiling of stress-induced small proteins uncovers an unexpected connection among distinct signaling systems.
Vellappan et al. bioRxiv 2024
Evolutionary principles underpinning codon usage bias:1patterns, functions, and mechanisms.
Cope et al. ecoevoRxiv 2024
Intestinal transit-amplifying cells require METTL3 for growth factor signaling and cell survival.
Danan et al. JCI Insight 2023
Celf4 controls mRNA translation underlying synaptic development in the prenatal mammalian neocortex.
Salamon et al. Nature Comm. 2023
Evaluating single-cell variability in proteasomal decay.
Das et al. bioRxiv 2023
NADcapPro and circNC: methods for accurate profiling of NAD and non-canonical RNA caps in eukaryotes.
Sharma et al. Commun Biol 2023
Linking genotypic and phenotypic changes in the LTEE using metabolomics.
Favate et al. eLife 2023
IMP1/IGF2BP1 in human colorectal cancer extracellular vesicles.
Kuhn et al. Am. J. Physiol. 2022
The landscape of transcriptional and translational changes over 22 years of bacterial adaptation.
Favate et al. eLife 2022
The hypoxia response pathway promotes PEP carboxykinase and gluconeogenesis in C. elegans.
Vora et al. Nature Comm. 2022
Intragenomic variation in mutation biases causes underestimation of selection on synonymous codon usage.
Cope & Shah PLoS Genetics 2022
Isolation, profiling, and tracking of extracellular vesicle cargo in Caenorhabditis elegans.
Nikonorova et al. Curr. Biol. 2022
riboviz 2: A flexible and robust ribosome profiling data analysis and visualization workflow.
Cope et al. Bioinformatics 2022
Exploring ribosome-positioning on translating transcripts with ribosome-profiling.
Cope et al. MiMB 2021
Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli.
Skalenko et al. PNAS 2021
The gastrin-releasing peptide regulates stress-enhanced fear and dopamine signaling.
Morishita et al. bioRxiv 2021
Ribosomal stalk proteins RPLP1 and RPLP2 promote biogenesis of flaviviral and cellular multi-pass transmembrane proteins.
Campos et al. Nucl. Acids Res. 2020
XACT-seq comprehensively defines the promoter-position and promoter-sequence determinants for initial-transcription pausing.
Winkelman et al. Mol. Cell 2020
A tRNA modification balances carbon and nitrogen metabolism by regulating phosphate homeostasis, to couple metabolism to cell cycle progression.
Gupta et al. eLife 2019
Simultaneous ribosome profiling of human host cells infected with Toxoplasma gondii.
Holmes et al. mSphere 2019
O-GlcNAcylation alters the selection of mRNAs for translation and promotes 4E-BP1–dependent mitochondrial dysfunction in the retina.
Dierschke et al. Jour Biol Chem 2019
Post-transcriptional regulation of colonic epithelial repair by RNA binding protein IMP1/IGF2BP1.
Chatterji et al. EMBO reports 2019
The LIN28B–IMP1 post-transcriptional regulon has opposing effects on oncogenic signaling in the intestine.
Chatterji et al. Genes & Development 2018
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
