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Premal Shah, Ph.D. - Publications

Affiliations: 
2006-2011 Ecology and Evolutionary Biology University of Tennessee, Knoxville, Knoxville, TN, United States 
 2011-2015 Biology University of Pennsylvania, Philadelphia, PA, United States 
 2016- Genetics Rutgers University, New Brunswick, New Brunswick, NJ, United States 
Area:
translation, codon bias, population genetics, epistasis
Website:
theshahlab.org
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38 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Favate JS, Skalenko KS, Chiles E, Su X, Yadavalli SS, Shah P. Linking genotypic and phenotypic changes in the long-term evolution experiment using metabolomics. Elife. 12. PMID 37991493 DOI: 10.7554/eLife.87039  0.768
2023 Salamon I, Park Y, Miškić T, Kopić J, Matteson P, Page NF, Roque A, McAuliffe GW, Favate J, Garcia-Forn M, Shah P, Judaš M, Millonig JH, Kostović I, De Rubeis S, et al. Celf4 controls mRNA translation underlying synaptic development in the prenatal mammalian neocortex. Nature Communications. 14: 6025. PMID 37758766 DOI: 10.1038/s41467-023-41730-8  0.772
2023 Das S, Singh A, Shah P. Evaluating single-cell variability in proteasomal decay. Biorxiv : the Preprint Server For Biology. PMID 37662347 DOI: 10.1101/2023.08.22.554358  0.677
2023 Vora M, Pyonteck SM, Popovitchenko T, Matlack TL, Prashar A, Kane NS, Favate J, Shah P, Rongo C. Reply to: Potential contribution of PEP carboxykinase-dependent malate dismutation to the hypoxia response in C. elegans. Nature Communications. 14: 3937. PMID 37402706 DOI: 10.1038/s41467-023-39511-4  0.729
2023 Sharma S, Yang J, Favate J, Shah P, Kiledjian M. NADcapPro and circNC: methods for accurate profiling of NAD and non-canonical RNA caps in eukaryotes. Communications Biology. 6: 406. PMID 37055518 DOI: 10.1038/s42003-023-04774-6  0.779
2023 Favate JS, Skalenko KS, Chiles E, Su X, Yadavalli SS, Shah P. Linking genotypic and phenotypic changes in the LTEE using metabolomics. Biorxiv : the Preprint Server For Biology. PMID 36874203 DOI: 10.1101/2023.02.15.528756  0.773
2022 Vora M, Pyonteck SM, Popovitchenko T, Matlack TL, Prashar A, Kane NS, Favate J, Shah P, Rongo C. The hypoxia response pathway promotes PEP carboxykinase and gluconeogenesis in C. elegans. Nature Communications. 13: 6168. PMID 36257965 DOI: 10.1038/s41467-022-33849-x  0.763
2022 Favate JS, Liang S, Cope AL, Yadavalli SS, Shah P. The landscape of transcriptional and 1translational changes over 22 years of bacterial adaptation. Elife. 11. PMID 36214449 DOI: 10.7554/eLife.81979  0.757
2022 Kuhn M, Zhang Y, Favate J, Morita M, Blucher A, Das S, Liang S, Preet R, Parham LR, Williams KN, Molugu S, Armstrong RJ, Zhang W, Yang J, Hamilton KE, ... ... Shah P, et al. IMP1/IGF2BP1 in human colorectal cancer extracellular vesicles. American Journal of Physiology. Gastrointestinal and Liver Physiology. PMID 36194131 DOI: 10.1152/ajpgi.00121.2022  0.778
2022 Cope AL, Shah P. Intragenomic variation in non-adaptive nucleotide biases causes underestimation of selection on synonymous codon usage. Plos Genetics. 18: e1010256. PMID 35714134 DOI: 10.1371/journal.pgen.1010256  0.767
2022 Nikonorova IA, Wang J, Cope AL, Tilton PE, Power KM, Walsh JD, Akella JS, Krauchunas AR, Shah P, Barr MM. Isolation, profiling, and tracking of extracellular vesicle cargo in Caenorhabditis elegans. Current Biology : Cb. PMID 35334227 DOI: 10.1016/j.cub.2022.03.005  0.769
2022 Cope AL, Anderson F, Favate J, Jackson M, Mok A, Kurowska A, Liu J, MacKenzie E, Shivakumar V, Tilton P, Winterbourne SM, Xue S, Kavoussanakis K, Lareau LF, Shah P, et al. riboviz 2: A flexible and robust ribosome profiling data analysis and visualization workflow. Bioinformatics (Oxford, England). PMID 35157051 DOI: 10.1093/bioinformatics/btac093  0.743
2022 Cope AL, Vellappan S, Favate JS, Skalenko KS, Yadavalli SS, Shah P. Exploring Ribosome-Positioning on Translating Transcripts with Ribosome Profiling. Methods in Molecular Biology (Clifton, N.J.). 2404: 83-110. PMID 34694605 DOI: 10.1007/978-1-0716-1851-6_5  0.749
2021 Skalenko KS, Li L, Zhang Y, Vvedenskaya IO, Winkelman JT, Cope AL, Taylor DM, Shah P, Ebright RH, Kinney JB, Zhang Y, Nickels BE. Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in . Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34187896 DOI: 10.1073/pnas.2106388118  0.774
2020 Campos RK, Wijeratne HRS, Shah P, Garcia-Blanco MA, Bradrick SS. Ribosomal stalk proteins RPLP1 and RPLP2 promote biogenesis of flaviviral and cellular multi-pass transmembrane proteins. Nucleic Acids Research. PMID 32890404 DOI: 10.1093/Nar/Gkaa717  0.402
2020 Winkelman JT, Pukhrambam C, Vvedenskaya IO, Zhang Y, Taylor DM, Shah P, Ebright RH, Nickels BE. XACT-Seq Comprehensively Defines the Promoter-Position and Promoter-Sequence Determinants for Initial-Transcription Pausing. Molecular Cell. PMID 32750314 DOI: 10.1016/J.Molcel.2020.07.006  0.371
2020 Andres SF, Preet R, Zhang W, Yang J, Das S, Chatterji P, Liang S, Rodriguez H, Moreira L, Shah P, Dixon DA, Guo W, Rustgi A. Su1169 RNA BINDING PROTEIN IMP1 MODULATES EXOSOME BIOLOGY IN COLON CANCER Gastroenterology. 158. DOI: 10.1016/S0016-5085(20)32018-7  0.7
2019 Chatterji P, Williams PA, Whelan KA, Samper FC, Andres SF, Simon LA, Parham LR, Mizuno R, Lundsmith ET, Lee DS, Liang S, Wijeratne HS, Marti S, Chau L, Giroux V, ... ... Shah P, et al. Posttranscriptional regulation of colonic epithelial repair by RNA binding protein IMP1/IGF2BP1. Embo Reports. PMID 31061170 DOI: 10.15252/Embr.201847074  0.32
2019 Dierschke SK, Miller WP, Favate JS, Shah P, Imamura Kawasawa Y, Salzberg AC, Kimball SR, Jefferson LS, Dennis MD. O-GlcNAcylation alters the selection of mRNAs for translation and promotes 4E-BP1-dependent mitochondrial dysfunction in retina. The Journal of Biological Chemistry. PMID 30733333 DOI: 10.1074/Jbc.Ra119.007494  0.771
2019 Andres SF, Preet R, Das S, Yang J, Chatterji P, Liang S, Mizuno R, Williams K, Moreira L, Guo W, Shah P, Dixon DA, Rustgi A. 854 – Rna Binding Protein Imp1 Promotes Exosome Production in Colon Cancer Gastroenterology. 156: S-188. DOI: 10.1016/S0016-5085(19)37263-4  0.699
2018 Chatterji P, Hamilton KE, Liang S, Andres SF, Wijeratne HRS, Mizuno R, Simon LA, Hicks PD, Foley SW, Pitarresi JR, Klein-Szanto AJ, Mah AT, Van Landeghem L, Gregory BD, Lengner CJ, ... ... Shah P, et al. The LIN28B-IMP1 post-transcriptional regulon has opposing effects on oncogenic signaling in the intestine. Genes & Development. 32: 1020-1034. PMID 30068703 DOI: 10.1101/Gad.314369.118  0.391
2017 Carja O, Xing T, Wallace EWJ, Plotkin JB, Shah P. riboviz: analysis and visualization of ribosome profiling datasets. Bmc Bioinformatics. 18: 461. PMID 29070028 DOI: 10.1186/S12859-017-1873-8  0.771
2016 McCandlish DM, Shah P, Plotkin JB. Epistasis and the Dynamics of Reversion in Molecular Evolution. Genetics. PMID 27194749 DOI: 10.1534/Genetics.116.188961  0.582
2016 Weinberg DE, Shah P, Eichhorn SW, Hussmann JA, Plotkin JB, Bartel DP. Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation. Cell Reports. PMID 26876183 DOI: 10.1016/J.Celrep.2016.01.043  0.642
2015 Kubatko L, Shah P, Herbei R, Gilchrist MA. A codon model of nucleotide substitution with selection on synonymous codon usage. Molecular Phylogenetics and Evolution. PMID 26358614 DOI: 10.1016/J.Ympev.2015.08.026  0.766
2015 Shah P, McCandlish DM, Plotkin JB. Contingency and entrenchment in protein evolution under purifying selection. Proceedings of the National Academy of Sciences of the United States of America. 112: E3226-35. PMID 26056312 DOI: 10.1073/Pnas.1412933112  0.62
2015 Gilchrist MA, Chen WC, Shah P, Landerer CL, Zaretzki R. Estimating Gene Expression and Codon-Specific Translational Efficiencies, Mutation Biases, and Selection Coefficients from Genomic Data Alone. Genome Biology and Evolution. 7: 1559-79. PMID 25977456 DOI: 10.1093/Gbe/Evv087  0.786
2014 Fordyce JA, Shah P, Fitzpatrick BM. iteRates: An R Package for Implementing a Parametric Rate Comparison on Phylogenetic Trees. Evolutionary Bioinformatics Online. 10: 127-30. PMID 25125968 DOI: 10.4137/Ebo.S16487  0.704
2013 Shah P, Ding Y, Niemczyk M, Kudla G, Plotkin JB. Rate-limiting steps in yeast protein translation. Cell. 153: 1589-601. PMID 23791185 DOI: 10.1016/J.Cell.2013.05.049  0.651
2013 McCandlish DM, Rajon E, Shah P, Ding Y, Plotkin JB. The role of epistasis in protein evolution. Nature. 497: E1-2; discussion E2-. PMID 23719465 DOI: 10.1038/Nature12219  0.602
2013 Niemiller ML, Fitzpatrick BM, Shah P, Schmitz L, Near TJ. Evidence for repeated loss of selective constraint in rhodopsin of amblyopsid cavefishes (Teleostei: Amblyopsidae). Evolution; International Journal of Organic Evolution. 67: 732-48. PMID 23461324 DOI: 10.1111/J.1558-5646.2012.01822.X  0.635
2013 Xu Y, Ma P, Shah P, Rokas A, Liu Y, Johnson CH. Non-optimal codon usage is a mechanism to achieve circadian clock conditionality. Nature. 495: 116-20. PMID 23417065 DOI: 10.1038/Nature11942  0.361
2013 Shah P, Fitzpatrick BM, Fordyce JA. A parametric method for assessing diversification-rate variation in phylogenetic trees. Evolution; International Journal of Organic Evolution. 67: 368-77. PMID 23356610 DOI: 10.1111/J.1558-5646.2012.01791.X  0.703
2012 Ding Y, Shah P, Plotkin JB. Weak 5'-mRNA secondary structures in short eukaryotic genes. Genome Biology and Evolution. 4: 1046-53. PMID 23034215 DOI: 10.1093/Gbe/Evs082  0.609
2011 Shah P, Gilchrist MA. Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift. Proceedings of the National Academy of Sciences of the United States of America. 108: 10231-6. PMID 21646514 DOI: 10.1073/Pnas.1016719108  0.791
2010 Shah P, Gilchrist MA. Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias. Plos Genetics. 6: e1001128. PMID 20862306 DOI: 10.1371/Journal.Pgen.1001128  0.767
2010 Shah P, Gilchrist MA. Is thermosensing property of RNA thermometers unique? Plos One. 5: e11308. PMID 20625392 DOI: 10.1371/Journal.Pone.0011308  0.784
2009 Gilchrist MA, Shah P, Zaretzki R. Measuring and detecting molecular adaptation in codon usage against nonsense errors during protein translation. Genetics. 183: 1493-505. PMID 19822731 DOI: 10.1534/Genetics.109.108209  0.769
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