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Research Output

  • 866 Citations
  • 12 h-Index
  • 21 Article
  • 1 Comment/debate
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Article
2019

A tRNA modification balances carbon and nitrogen metabolism by regulating phosphate homeostasis

Gupta, R., Walvekar, A. S., Liang, S., Rashida, Z., Shah, P. & Laxman, S., Jul 2019, In : eLife. 8, e44795.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

O-GlcNAcylation alters the selection of mRNAs for translation and promotes 4E-BP1 dependent mitochondrial dysfunction in the retina

Dierschke, S. K., Miller, W. P., Favate, J. S., Shah, P., Kawasawa, Y. I., Salzberg, A. C., Kimball, S. R., Jefferson, L. S. & Dennis, M. D., Apr 5 2019, In : Journal of Biological Chemistry. 294, 14, p. 5508-5520 13 p.

Research output: Contribution to journalArticle

1 Scopus citations

Posttranscriptional regulation of colonic epithelial repair by RNA binding protein IMP1/IGF2BP1

Chatterji, P., Williams, P. A., Whelan, K. A., Samper, F. C., Andres, S. F., Simon, L. A., Parham, L. R., Mizuno, R., Lundsmith, E. T., Lee, D. S. M., Liang, S., Wijeratne, HR. S., Marti, S., Chau, L., Giroux, V., Wilkins, B. J., Wu, G. D., Shah, P., Tartaglia, G. G. & Hamilton, K. E., Jun 2019, In : EMBO Reports. 20, 6, e47074.

Research output: Contribution to journalArticle

1 Scopus citations

Simultaneous ribosome profiling of human host cells infected with Toxoplasma gondii

Holmes, M. J., Shah, P., Wek, R. C. & Sullivan, W. J., May 1 2019, In : mSphere. 4, 3, e00292-19.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations
2018

The LIN28B–IMP1 post-transcriptional regulon has opposing effects on oncogenic signaling in the intestine

Chatterji, P., Hamilton, K. E., Liang, S., Andres, S. F., Wijeratne, H. R. S., Mizuno, R., Simon, L. A., Hicks, P. D., Foley, S. W., Pitarresi, J. R., Klein-Szanto, A. J., Mah, A. T., van Landeghem, L., Gregory, B. D., Lengner, C. J., Madison, B. B., Shah, P. & Rustgi, A. K., Aug 1 2018, In : Genes and Development. 32, 15-16, p. 1020-1034 15 p.

Research output: Contribution to journalArticle

6 Scopus citations
2017

Riboviz: Analysis and visualization of ribosome profiling datasets

Carja, O., Xing, T., Wallace, E. W. J., Plotkin, J. B. & Shah, P., Oct 25 2017, In : BMC Bioinformatics. 18, 1, 461.

Research output: Contribution to journalArticle

14 Scopus citations
2016

A codon model of nucleotide substitution with selection on synonymous codon usage

Kubatko, L., Shah, P., Herbei, R. & Gilchrist, M. A., Jan 1 2016, In : Molecular Phylogenetics and Evolution. 94, p. 290-297 8 p.

Research output: Contribution to journalArticle

4 Scopus citations

Epistasis and the dynamics of reversion in molecular evolution

McCandlish, D. M., Shah, P. & Plotkin, J. B., Jul 2016, In : Genetics. 203, 3, p. 1335-1351 17 p.

Research output: Contribution to journalArticle

22 Scopus citations

Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation

Weinberg, D. E., Shah, P., Eichhorn, S. W., Hussmann, J. A., Plotkin, J. B. & Bartel, D. P., Feb 23 2016, In : Cell Reports. 14, 7, p. 1787-1799 13 p.

Research output: Contribution to journalArticle

135 Scopus citations
2015

Contingency and entrenchment in protein evolution under purifying selection

Shah, P., McCandlish, D. M. & Plotkin, J. B., Jun 23 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 25, p. E3226-E3235

Research output: Contribution to journalArticle

67 Scopus citations

Estimating gene expression and codon-specific translational efficiencies, mutation biases, and selection coefficients from genomic data alone

Gilchrist, M. A., Chen, W. C., Shah, P., Landerer, C. L. & Zaretzki, R., 2015, In : Genome biology and evolution. 7, 6, p. 1559-1579 21 p.

Research output: Contribution to journalArticle

14 Scopus citations
2014

iteRates: An R package for implementing a parametric rate comparison on phylogenetic trees

Fordyce, J. A., Shah, P. & Fitzpatrick, B. M., Aug 3 2014, In : Evolutionary Bioinformatics. 10, p. 127-130 4 p.

Research output: Contribution to journalArticle

4 Scopus citations
2013

A parametric method for assessing diversification-rate variation in phylogenetic trees

Shah, P., Fitzpatrick, B. M. & Fordyce, J. A., Feb 1 2013, In : Evolution. 67, 2, p. 368-377 10 p.

Research output: Contribution to journalArticle

10 Scopus citations

Evidence for repeated loss of selective constraint in rhodopsin of amblyopsid cavefishes (teleostei: Amblyopsidae)

Niemiller, M. L., Fitzpatrick, B. M., Shah, P., Schmitz, L. & Near, T. J., Mar 1 2013, In : Evolution. 67, 3, p. 732-748 17 p.

Research output: Contribution to journalArticle

51 Scopus citations

Non-optimal codon usage is a mechanism to achieve circadian clock conditionality

Xu, Y., Ma, P., Shah, P., Rokas, A., Liu, Y. & Johnson, C. H., Mar 2013, In : Nature. 495, 7439, p. 116-120 5 p.

Research output: Contribution to journalArticle

97 Scopus citations

XRate-limiting steps in yeast protein translation

Shah, P., Ding, Y., Niemczyk, M., Kudla, G. & Plotkin, J. B., Jun 20 2013, In : Cell. 153, 7, 1 p.

Research output: Contribution to journalArticle

228 Scopus citations
2012

Weak 5′-mRNA secondary structures in short eukaryotic genes

Ding, Y., Shah, P. & Plotkin, J. B., 2012, In : Genome biology and evolution. 4, 10, p. 1046-1053 8 p.

Research output: Contribution to journalArticle

12 Scopus citations
2011
77 Scopus citations
2010

Effect of Correlated tRNA abundances on translation errors and evolution of codon usage bias

Shah, P. & Gilchrist, M. A., Sep 2010, In : PLoS genetics. 6, 9, e1001128.

Research output: Contribution to journalArticle

60 Scopus citations

Is thermosensing property of RNA thermometers unique?

Shah, P. & Gilchrist, M. A., 2010, In : PloS one. 5, 7, e11308.

Research output: Contribution to journalArticle

5 Scopus citations
2009

Measuring and detecting molecular adaptation in codon usage against nonsense errors during protein translation

Gilchrist, M. A., Shah, P. & Zaretzki, R., Dec 1 2009, In : Genetics. 183, 4, p. 1493-1505 13 p.

Research output: Contribution to journalArticle

22 Scopus citations