NADcapPro and circNC: methods for accurate profiling of NAD and non-canonical RNA caps in eukaryotes.

Sharma et al. Commun Biol 2023

METTL3 is essential for small intestinal epithelial proliferation via regulation of growth factor signaling including KRAS.

Danan et al. bioRxiv 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