Sudhir Kumar - Publications

Affiliations: 
Arizona State University, Tempe, AZ, United States 
Area:
Molecular Evolution, Bioinformatics

70 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, 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
2019 Tao Q, Tamura K, Battistuzzi F, Kumar S. A new method for detecting autocorrelation of evolutionary rates in large phylogenies. Molecular Biology and Evolution. PMID 30689923 DOI: 10.1093/molbev/msz014  0.68
2019 Liu L, Sanderford MD, Patel R, Chandrashekar P, Gibson G, Kumar S. Biological relevance of computationally predicted pathogenicity of noncoding variants. Nature Communications. 10: 330. PMID 30659175 DOI: 10.1038/s41467-018-08270-y  0.36
2018 Miura S, Huuki LA, Buturla T, Vu T, Gomez K, Kumar S. Computational enhancement of single-cell sequences for inferring tumor evolution. Bioinformatics (Oxford, England). 34: i917-i926. PMID 30423071 DOI: 10.1093/bioinformatics/bty571  0.6
2018 Hedges SB, Tao Q, Walker M, Kumar S. Accurate timetrees require accurate calibrations. Proceedings of the National Academy of Sciences of the United States of America. PMID 30266795 DOI: 10.1073/pnas.1812558115  0.64
2018 Miura S, Gomez K, Murillo O, Huuki LA, Vu T, Buturla T, Kumar S. Predicting clone genotypes from tumor bulk sequencing of multiple samples. Bioinformatics (Oxford, England). PMID 29931046 DOI: 10.1093/bioinformatics/bty469  0.68
2018 Tamura K, Tao Q, Kumar S. Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates. Molecular Biology and Evolution. 35: 1770-1782. PMID 29893954 DOI: 10.1093/molbev/msy044  0.68
2018 Battistuzzi FU, Tao Q, Jones L, Tamura K, Kumar S. RelTime relaxes the strict molecular clock throughout the phylogeny. Genome Biology and Evolution. PMID 29878203 DOI: 10.1093/gbe/evy118  0.68
2018 Patel R, Scheinfeldt LB, Sanderford MD, Lanham TR, Tamura K, Platt A, Glicksberg BS, Xu K, Dudley JT, Kumar S. Adaptive landscape of protein variation in human exomes. Molecular Biology and Evolution. PMID 29846678 DOI: 10.1093/molbev/msy107  0.68
2018 Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution. PMID 29722887 DOI: 10.1093/molbev/msy096  0.68
2018 Gomez K, Miura S, Huuki LA, Spell BS, Townsend JP, Kumar S. Somatic evolutionary timings of driver mutations. Bmc Cancer. 18: 85. PMID 29347918 DOI: 10.1186/s12885-017-3977-y  0.6
2017 Kumar S, Konikoff C, Sanderford M, Liu L, Newfeld S, Ye J, Kulathinal RJ. FlyExpress 7: An Integrated Discovery Platform To Study Co-expressed Genes Using In Situ Hybridization Images in Drosophila. G3 (Bethesda, Md.). PMID 28667017 DOI: 10.1534/g3.117.040345  0.8
2017 Kavoor AR, Mitra S, Kumar S, Sisodia AK, Jain R. Lipids, aggression, suicidality and impulsivity in drug-naïve/drug-free patients of schizophrenia. Asian Journal of Psychiatry. 27: 129-136. PMID 28558886 DOI: 10.1016/j.ajp.2017.03.002  0.44
2017 Kumar S, Stecher G, Suleski M, Blair Hedges S. TimeTree: A resource for timelines, timetrees, and divergence times. Molecular Biology and Evolution. PMID 28387841 DOI: 10.1093/molbev/msx116  0.36
2017 Karim S, Nour Eldin HF, Abusamra H, Salem N, Alhathli E, Dudley J, Sanderford M, Scheinfeldt LB, Chaudhary AG, Al-Qahtani MH, Kumar S. Erratum to: e-GRASP: an integrated evolutionary and GRASP resource for exploring disease associations. Bmc Genomics. 18: 281. PMID 28385147 DOI: 10.1186/s12864-017-3647-0  0.36
2017 Katsura Y, Stanley CE, Kumar S, Nei M. The Reliability and Stability of an Inferred Phylogenetic Tree from Empirical Data. Molecular Biology and Evolution. PMID 28100791 DOI: 10.1093/molbev/msw272  0.56
2016 Mello B, Tao Q, Tamura K, Kumar S. Fast and accurate estimates of divergence times from big data. Molecular Biology and Evolution. PMID 27836983 DOI: 10.1093/molbev/msw247  0.68
2016 Karim S, NourEldin HF, Abusamra H, Salem N, Alhathli E, Dudley J, Sanderford M, Scheinfeldt LB, Kumar S. e-GRASP: an integrated evolutionary and GRASP resource for exploring disease associations. Bmc Genomics. 17: 770. PMID 27766955 DOI: 10.1186/s12864-016-3088-1  0.36
2016 Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution. PMID 27004904 DOI: 10.1093/molbev/msw054  0.68
2016 Kumar S, Hedges SB. Advances in time estimation methods for molecular data. Molecular Biology and Evolution. PMID 26882983 DOI: 10.1093/molbev/msw026  0.64
2015 Kumar S. MBE Citation Classics (2016 Edition). Molecular Biology and Evolution. PMID 26709393 DOI: 10.1093/molbev/msv279  1
2015 Miura S, Tate S, Kumar S. Using Disease-Associated Coding Sequence Variation to Investigate Functional Compensation by Human Paralogous Proteins. Evolutionary Bioinformatics Online. 11: 245-251. PMID 26604664 DOI: 10.4137/EBO.S30594  1
2015 Liu L, Tamura K, Sanderford M, Gray VE, Kumar S. A Molecular Evolutionary Reference for the Human Variome. Molecular Biology and Evolution. PMID 26464126 DOI: 10.1093/molbev/msv198  1
2015 Sanderson MJ, Copetti D, Búrquez A, Bustamante E, Charboneau JL, Eguiarte LE, Kumar S, Lee HO, Lee J, McMahon M, Steele K, Wing R, Yang TJ, Zwickl D, Wojciechowski MF. Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea): Loss of the ndh gene suite and inverted repeat. American Journal of Botany. 102: 1115-27. PMID 26199368 DOI: 10.3732/ajb.1500184  1
2015 Gerek NZ, Liu L, Gerold K, Biparva P, Thomas ED, Kumar S. Evolutionary Diagnosis of non-synonymous variants involved in differential drug response. Bmc Medical Genomics. 8: S6. PMID 25952014 DOI: 10.1186/1755-8794-8-S1-S6  0.36
2015 Filipski A, Tamura K, Billing-Ross P, Murillo O, Kumar S. Phylogenetic placement of metagenomic reads using the minimum evolution principle. Bmc Genomics. 16: S13. PMID 25923672 DOI: 10.1186/1471-2164-16-S1-S13  1
2015 Battistuzzi FU, Billing-Ross P, Murillo O, Filipski A, Kumar S. A Protocol for Diagnosing the Effect of Calibration Priors on Posterior Time Estimates: A Case Study for the Cambrian Explosion of Animal Phyla. Molecular Biology and Evolution. 32: 1907-12. PMID 25808541 DOI: 10.1093/molbev/msv075  1
2015 Hedges SB, Marin J, Suleski M, Paymer M, Kumar S. Tree of life reveals clock-like speciation and diversification. Molecular Biology and Evolution. 32: 835-45. PMID 25739733 DOI: 10.1093/molbev/msv037  1
2015 Butler BM, Gerek ZN, Kumar S, Ozkan SB. Conformational dynamics of nonsynonymous variants at protein interfaces reveals disease association. Proteins. 83: 428-35. PMID 25546381 DOI: 10.1002/prot.24748  1
2015 Kumar S. MBE citation classics (2015 edition). Molecular Biology and Evolution. 32: 1-3. PMID 25527615 DOI: 10.1093/molbev/msu339  1
2014 Kumar S. Society for Molecular Biology and Evolution a report by Editor-in-Chief MBE Volume 30. Molecular Biology and Evolution. 31: 3373-4. PMID 25323574 DOI: 10.1093/molbev/msu274  1
2014 Kumar S, Ye J, Liu L. Reply to: "Proper reporting of predictor performance". Nature Methods. 11: 781-2. PMID 25075901 DOI: 10.1038/nmeth.3039  1
2014 Filipski A, Murillo O, Freydenzon A, Tamura K, Kumar S. Prospects for building large timetrees using molecular data with incomplete gene coverage among species. Molecular Biology and Evolution. 31: 2542-50. PMID 24974376 DOI: 10.1093/molbev/msu200  1
2014 Kumar S, Liu L. No positive selection for G allele in a p53 response element in Europeans. Cell. 157: 1497-9. PMID 24949959 DOI: 10.1016/j.cell.2014.05.033  1
2014 Gray VE, Liu L, Nirankari R, Hornbeck PV, Kumar S. Signatures of natural selection on mutations of residues with multiple posttranslational modifications. Molecular Biology and Evolution. 31: 1641-5. PMID 24739307 DOI: 10.1093/molbev/msu137  1
2014 Stecher G, Liu L, Sanderford M, Peterson D, Tamura K, Kumar S. MEGA-MD: molecular evolutionary genetics analysis software with mutational diagnosis of amino acid variation. Bioinformatics (Oxford, England). 30: 1305-7. PMID 24413669 DOI: 10.1093/bioinformatics/btu018  1
2014 Montiel I, Konikoff C, Braun B, Packard M, Gramates SL, Sun Q, Ye J, Kumar S. myFX: a turn-key software for laboratory desktops to analyze spatial patterns of gene expression in Drosophila embryos. Bioinformatics (Oxford, England). 30: 1319-21. PMID 24413523 DOI: 10.1093/bioinformatics/btu007  1
2014 Yuan L, Pan C, Ji S, McCutchan M, Zhou ZH, Newfeld SJ, Kumar S, Ye J. Automated annotation of developmental stages of Drosophila embryos in images containing spatial patterns of expression. Bioinformatics (Oxford, England). 30: 266-73. PMID 24300439 DOI: 10.1093/bioinformatics/btt648  1
2014 Kumar S. Editor's message for 2014. Molecular Biology and Evolution. 31: 4-5. PMID 24273321 DOI: 10.1093/molbev/mst216  1
2013 Zhang W, Feng D, Li R, Chernikov A, Chrisochoides N, Osgood C, Konikoff C, Newfeld S, Kumar S, Ji S. A mesh generation and machine learning framework for Drosophila gene expression pattern image analysis. Bmc Bioinformatics. 14: 372. PMID 24373308 DOI: 10.1186/1471-2105-14-372  1
2013 Sun Q, Muckatira S, Yuan L, Ji S, Newfeld S, Kumar S, Ye J. Image-level and group-level models for Drosophila gene expression pattern annotation. Bmc Bioinformatics. 14: 350. PMID 24299119 DOI: 10.1186/1471-2105-14-350  1
2013 Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution. 30: 2725-9. PMID 24132122 DOI: 10.1093/molbev/mst197  1
2013 Gilbert JDJ, Acquisti C, Martinson HM, Elser JJ, Kumar S, Fagan WF. GRASP [Genomic Resource Access for Stoichioproteomics]: Comparative explorations of the atomic content of 12 Drosophila proteomes Bmc Genomics. 14. PMID 24007337 DOI: 10.1186/1471-2164-14-599  1
2013 Wellensiek BP, Larsen AC, Stephens B, Kukurba K, Waern K, Briones N, Liu L, Snyder M, Jacobs BL, Kumar S, Chaput JC. Genome-wide profiling of human cap-independent translation-enhancing elements. Nature Methods. 10: 747-50. PMID 23770754 DOI: 10.1038/nmeth.2522  1
2013 Nevin Gerek Z, Kumar S, Banu Ozkan S. Structural dynamics flexibility informs function and evolution at a proteome scale. Evolutionary Applications. 6: 423-33. PMID 23745135 DOI: 10.1111/eva.12052  1
2013 Liu L, Kumar S. Evolutionary balancing is critical for correctly forecasting disease-associated amino acid variants. Molecular Biology and Evolution. 30: 1252-7. PMID 23462317 DOI: 10.1093/molbev/mst037  1
2012 Tamura K, Battistuzzi FU, Billing-Ross P, Murillo O, Filipski A, Kumar S. Estimating divergence times in large molecular phylogenies. Proceedings of the National Academy of Sciences of the United States of America. 109: 19333-8. PMID 23129628 DOI: 10.1073/pnas.1213199109  1
2012 Konikoff CE, Karr TL, McCutchan M, Newfeld SJ, Kumar S. Comparison of embryonic expression within multigene families using the FlyExpress discovery platform reveals more spatial than temporal divergence. Developmental Dynamics : An Official Publication of the American Association of Anatomists. 241: 150-60. PMID 21960044 DOI: 10.1002/dvdy.22749  1
2012 Kumar S, Filipski AJ, Battistuzzi FU, Kosakovsky Pond SL, Tamura K. Statistics and truth in phylogenomics. Molecular Biology and Evolution. 29: 457-72. PMID 21873298 DOI: 10.1093/molbev/msr202  1
2011 Kumar S, Konikoff C, Van Emden B, Busick C, Davis KT, Ji S, Wu LW, Ramos H, Brody T, Panchanathan S, Ye J, Karr TL, Gerold K, McCutchan M, Newfeld SJ. FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis. Bioinformatics (Oxford, England). 27: 3319-20. PMID 21994220 DOI: 10.1093/bioinformatics/btr567  1
2011 Kumar S, Dudley JT, Filipski A, Liu L. Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations. Trends in Genetics : Tig. 27: 377-86. PMID 21764165 DOI: 10.1016/j.tig.2011.06.004  1
2011 Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution. 28: 2731-9. PMID 21546353 DOI: 10.1093/molbev/msr121  1
2011 Battistuzzi FU, Billing-Ross P, Paliwal A, Kumar S. Fast and slow implementations of relaxed-clock methods show similar patterns of accuracy in estimating divergence times. Molecular Biology and Evolution. 28: 2439-42. PMID 21498604 DOI: 10.1093/molbev/msr100  1
2011 Pacheco MA, Battistuzzi FU, Lentino M, Aguilar RF, Kumar S, Escalante AA. Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders. Molecular Biology and Evolution. 28: 1927-42. PMID 21242529 DOI: 10.1093/molbev/msr014  1
2010 Stone AC, Battistuzzi FU, Kubatko LS, Perry GH, Trudeau E, Lin H, Kumar S. More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365: 3277-88. PMID 20855302 DOI: 10.1098/rstb.2010.0096  1
2010 Battistuzzi FU, Filipski A, Hedges SB, Kumar S. Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals. Molecular Biology and Evolution. 27: 1289-300. PMID 20093431 DOI: 10.1093/molbev/msq014  1
2009 Marco A, Konikoff C, Karr TL, Kumar S. Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster. Bioinformatics (Oxford, England). 25: 2473-7. PMID 19633094 DOI: 10.1093/bioinformatics/btp462  1
2009 Kumar S, Suleski MP, Markov GJ, Lawrence S, Marco A, Filipski AJ. Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations. Genome Research. 19: 1562-9. PMID 19546171 DOI: 10.1101/gr.091991.109  1
2008 Kumar S, Nei M, Dudley J, Tamura K. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics. 9: 299-306. PMID 18417537 DOI: 10.1093/bib/bbn017  1
2007 Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution. 24: 1596-9. PMID 17488738 DOI: 10.1093/molbev/msm092  1
2007 Kumar S, Filipski A. Multiple sequence alignment: in pursuit of homologous DNA positions. Genome Research. 17: 127-35. PMID 17272647 DOI: 10.1101/gr.5232407  1
2005 Kumar S, Filipski A, Swarna V, Walker A, Hedges SB. Placing confidence limits on the molecular age of the human-chimpanzee divergence. Proceedings of the National Academy of Sciences of the United States of America. 102: 18842-7. PMID 16365310 DOI: 10.1073/pnas.0509585102  1
2005 Gadagkar SR, Rosenberg MS, Kumar S. Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 304: 64-74. PMID 15593277 DOI: 10.1002/jez.b.21026  1
2004 Gurunathan R, Van Emden B, Panchanathan S, Kumar S. Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations. Bmc Bioinformatics. 5: 202. PMID 15603586 DOI: 10.1186/1471-2105-5-202  1
2004 Kumar S, Tamura K, Nei M. MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Briefings in Bioinformatics. 5: 150-63. PMID 15260895  1
2004 Tamura K, Nei M, Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proceedings of the National Academy of Sciences of the United States of America. 101: 11030-5. PMID 15258291 DOI: 10.1073/pnas.0404206101  1
2003 Rosenberg MS, Subramanian S, Kumar S. Patterns of transitional mutation biases within and among mammalian genomes. Molecular Biology and Evolution. 20: 988-93. PMID 12716982 DOI: 10.1093/molbev/msg113  1
2003 Rosenberg MS, Kumar S. Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference. Molecular Biology and Evolution. 20: 610-21. PMID 12679548 DOI: 10.1093/molbev/msg067  1
2003 Rosenberg MS, Kumar S. Taxon sampling, bioinformatics, and phylogenomics. Systematic Biology. 52: 119-24. PMID 12554445  1
2002 Kumar S, Jayaraman K, Panchanathan S, Gurunathan R, Marti-Subirana A, Newfeld SJ. BEST: a novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development. Genetics. 162: 2037-47. PMID 12524369  1
2002 Jiang Z, Melville JS, Cao H, Kumar S, Filipski A, Gibbins AM. Measuring conservation of contiguous sets of autosomal markers on bovine and porcine genomes in relation to the map of the human genome. Genome / National Research Council Canada = GéNome / Conseil National De Recherches Canada. 45: 769-76. PMID 12175081 DOI: 10.1139/g02-038  1
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