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Research Output 2009 2019

  • 780 Citations
  • 11 h-Index
  • 21 Article
  • 1 Comment/debate
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Article
2019
2 Citations (Scopus)

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
Transfer RNA
Metabolism
Homeostasis
Nitrogen
Carbon

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., Jan 1 2019, In : Journal of Biological Chemistry. 294, 14, p. 5508-5520 13 p.

Research output: Contribution to journalArticle

Protein Biosynthesis
Retina
Messenger RNA
Ribosomes
Eukaryotic Initiation Factors
1 Citation (Scopus)

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

RNA-Binding Proteins
Repair
Enhanced recovery
Autophagy
Dextran Sulfate

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
Toxoplasma
Ribosomes
Parasites
Gene Expression
Foreskin
2018
5 Citations (Scopus)

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

Regulon
RNA-Binding Proteins
Intestines
Carcinogenesis
Homeostasis
2017
9 Citations (Scopus)

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

Profiling
Ribosomes
Visualization
Genes
Web Application
2016
4 Citations (Scopus)

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

codons
Codon
substitution
Nucleotides
nucleotides
18 Citations (Scopus)

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

Molecular Evolution
Amino Acid Substitution
Amino Acids
Mutation
Proteins
115 Citations (Scopus)

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

Ribosomes
Yeast
Yeasts
Messenger RNA
Genes
2015
60 Citations (Scopus)

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

Mutation
Proteins
Alleles
Thermodynamics
Carrier Proteins
9 Citations (Scopus)

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., Jan 1 2015, In : Genome biology and evolution. 7, 6, p. 1559-1579 21 p.

Research output: Contribution to journalArticle

Selection Bias
codons
Codon
gene expression
mutation
2014
4 Citations (Scopus)

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

Mathematical Computing
Statistical Distributions
phylogenetics
phylogeny
Random Allocation
2013
10 Citations (Scopus)

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

Plethodon
phylogenetics
phylogeny
Urodela
salamanders and newts
47 Citations (Scopus)

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

rhodopsin
Rhodopsin
cave
caves
mutation
91 Citations (Scopus)

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., Jan 1 2013, In : Nature. 495, 7439, p. 116-120 5 p.

Research output: Contribution to journalArticle

Circadian Clocks
Codon
Periodicity
Temperature
Genetic Selection
208 Citations (Scopus)

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

Fungal Proteins
Protein Biosynthesis
Ribosomes
Yeast
Messenger RNA
2012
11 Citations (Scopus)

Weak 5′-mRNA secondary structures in short eukaryotic genes

Ding, Y., Shah, P. & Plotkin, J. B., Dec 1 2012, In : Genome biology and evolution. 4, 10, p. 1046-1053 8 p.

Research output: Contribution to journalArticle

secondary structure
Messenger RNA
gene
Genes
genes
2011
73 Citations (Scopus)
Genetic Drift
Codon
Mutation
Population Genetics
Protein Biosynthesis
2010
59 Citations (Scopus)

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

Shah, P. & Gilchrist, M. A., Sep 1 2010, In : PLoS genetics. 6, 9, e1001128.

Research output: Contribution to journalArticle

Transfer RNA
codons
Codon
translation (genetics)
genetic code
5 Citations (Scopus)

Is thermosensing property of RNA thermometers unique?

Shah, P. & Gilchrist, M. A., Aug 13 2010, In : PloS one. 5, 7, e11308.

Research output: Contribution to journalArticle

Thermosensing
Thermometers
thermometers
melting
Freezing
2009
22 Citations (Scopus)

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

Protein Biosynthesis
Codon
Costs and Cost Analysis
Alleles
Genetic Selection