Research
Molecular Evolution
R Package
Genomic Data
Gene Expression, Gene Expressions
Mutation Biases
Mutation Bias
Translation Errors
Protein Translation
Molecular Adaptation
List of Publications (16)
In 2016
16
Epistasis and the dynamics of reversion in molecular evolution. DM McCandlish, P Shah, JB Plotkin Genetics, genetics. 116.188961, 2016.
Found on Publication Page
15
Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation. DE Weinberg*, P Shah*, SW Eichhorn, JA Hussmann, JB Plotkin, ... Cell Reports 14 (7), 1787-1799, 2016.
Found on Publication Page
14
A codon model of nucleotide substitution with selection on synonymous codon usage. L Kubatko, P Shah, R Herbei, MA Gilchrist Molecular Phylogenetics and Evolution 94, 290-297, 2016.
Found on Publication Page
In 2015
13
Contingency and entrenchment in protein evolution under purifying selection. P Shah, DM McCandlish, JB Plotkin PNAS 112 (25), E3226-E3235, 2015.
Found on Publication Page
12
Estimating Gene Expression and Codon-Specific Translational Efficiencies, Mutation Biases, and Selection Coefficients from Genomic Data Alone. MA Gilchrist, WC Chen, P Shah, CL Landerer, R Zaretzki Genome biology and evolution 7 (6), 1559-1579, 2015.
Found on Publication Page
In 2014
11
iteRates: An R package for implementing a parametric rate comparison on phylogenetic trees. JA Fordyce, P Shah, BM Fitzpatrick Evolutionary Bioinformatics 10, 127, 2014.
Found on Publication Page
In 2013
10
A parametric method for assessing diversificationrate variation in phylogenetic trees. P Shah, BM Fitzpatrick, JA Fordyce Evolution 67 (2), 368-377, 2013.
Found on Publication Page
9
The role of epistasis in protein evolution. DM McCandlish, E Rajon, P Shah, Y Ding, JB Plotkin Nature 497 (7451), E1-E2, 2013.
Found on Publication Page
8
Evidence for repeated loss of selective constraint in rhodopsin of amblyopsid cavefishes (Teleostei: Amblyopsidae). ML Niemiller, BM Fitzpatrick, P Shah, L Schmitz, TJ Near Evolution 67 (3), 732-748, 2013.
Found on Publication Page
7
Rate-limiting steps in yeast protein translation. P Shah, Y Ding, M Niemczyk, G Kudla, JB Plotkin Cell 153 (7), 1589-1601, 2013.
Found on Publication Page
6
Non-optimal codon usage is a mechanism to achieve circadian clock conditionality. Y Xu, P Ma, P Shah, A Rokas, Y Liu, CH Johnson Nature 495, 116-120, 2013.
Found on Publication Page
In 2012
5
Weak 5-mRNA secondary structures in short eukaryotic genes. Y Ding, P Shah, JB Plotkin Genome biology and evolution 4 (10), 1046-1053, 2012.
Found on Publication Page
In 2011
4
Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift. P Shah, MA Gilchrist PNAS 108 (25), 10231, 2011.
Found on Publication Page
In 2010
3
Is thermosensing property of RNA thermometers unique?. P Shah, MA Gilchrist PLoS ONE 5 (7), e11308, 2010.
Found on Publication Page
2
Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias. P Shah, MA Gilchrist PLoS Genetics 6 (9), e1001128, 2010.
Found on Publication Page
In 2009
1
Measuring and detecting molecular adaptation in codon usage against nonsense errors during protein translation. MA Gilchrist, P Shah, R Zaretzki Genetics 183 (4), 1493-1505, 2009.
Found on Publication Page