Sudhir Kumar - Publications

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

72 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
2022 Huzar J, Kim H, Kumar S, Miura S. MOCA for Integrated Analysis of Gene Expression and Genetic Variation in Single Cells. Frontiers in Genetics. 13: 831040. PMID 35432484 DOI: 10.3389/fgene.2022.831040  0.314
2022 Caraballo-Ortiz MA, Miura S, Sanderford M, Dolker T, Tao Q, Weaver S, Pond SLK, Kumar S. TopHap: Rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity. Bioinformatics (Oxford, England). PMID 35325058 DOI: 10.1093/bioinformatics/btac186  0.306
2021 Caraballo-Ortiz MA, Miura S, Sanderford M, Dolker T, Tao Q, Weaver S, Pond SLK, Kumar S. TopHap: Rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity. Biorxiv : the Preprint Server For Biology. PMID 34931186 DOI: 10.1101/2021.12.13.472454  0.57
2021 Townsend JP, Hassler HB, Wang Z, Miura S, Singh J, Kumar S, Ruddle NH, Galvani AP, Dornburg A. The durability of immunity against reinfection by SARS-CoV-2: a comparative evolutionary study. The Lancet. Microbe. PMID 34632431 DOI: 10.1016/S2666-5247(21)00219-6  0.464
2021 Chroni A, Miura S, Oladeinde O, Aly V, Kumar S. Migrations of cancer cells through the lens of phylogenetic biogeography. Scientific Reports. 11: 17184. PMID 34433859 DOI: 10.1038/s41598-021-96215-9  0.529
2021 Kumar S, Sharma S. Evolutionary Sparse Learning for Phylogenomics. Molecular Biology and Evolution. PMID 34343318 DOI: 10.1093/molbev/msab227  0.331
2021 Kumar S, Tao Q, Weaver S, Sanderford M, Caraballo-Ortiz MA, Sharma S, Pond SLK, Miura S. An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic. Molecular Biology and Evolution. PMID 33942847 DOI: 10.1093/molbev/msab118  0.535
2021 Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Molecular Biology and Evolution. PMID 33892491 DOI: 10.1093/molbev/msab120  0.348
2020 Kumar S, Chroni A, Tamura K, Sanderford M, Oladeinde O, Aly V, Vu T, Miura S. PathFinder: Bayesian inference of clone migration histories in cancer. Bioinformatics (Oxford, England). 36: i675-i683. PMID 33381835 DOI: 10.1093/bioinformatics/btaa795  0.485
2020 Barba-Montoya J, Tao Q, Kumar S. Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated. Bioinformatics (Oxford, England). 36: i884-i894. PMID 33381826 DOI: 10.1093/bioinformatics/btaa820  0.323
2020 Kumar S, Tao Q, Weaver S, Sanderford M, Caraballo-Ortiz MA, Sharma S, Pond SLK, Miura S. An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic. Biorxiv : the Preprint Server For Biology. PMID 32995781 DOI: 10.1101/2020.09.24.311845  0.542
2020 Miura S, Vu T, Deng J, Buturla T, Oladeinde O, Choi J, Kumar S. Power and pitfalls of computational methods for inferring clone phylogenies and mutation orders from bulk sequencing data. Scientific Reports. 10: 3498. PMID 32103044 DOI: 10.1038/S41598-020-59006-2  0.538
2020 Miura S, Tamura K, Tao Q, Huuki LA, Kosakovsky Pond SL, Priest J, Deng J, Kumar S. A new method for inferring timetrees from temporally sampled molecular sequences. Plos Computational Biology. 16: e1007046. PMID 31951607 DOI: 10.1371/Journal.Pcbi.1007046  0.585
2019 Chroni A, Vu T, Miura S, Kumar S. Delineation of Tumor Migration Paths by Using a Bayesian Biogeographic Approach. Cancers. 11. PMID 31783570 DOI: 10.3390/Cancers11121880  0.492
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  0.747
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  0.522
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  0.542
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  0.312
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  0.719
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  0.486
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 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  0.474
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  0.303
2016 Kumar S, Hedges SB. Advances in time estimation methods for molecular data. Molecular Biology and Evolution. PMID 26882983 DOI: 10.1093/molbev/msw026  0.343
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  0.559
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  0.724
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  0.774
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  0.741
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  0.792
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  0.795
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  0.716
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  0.798
2012 Kumar S, Stecher G, Peterson D, Tamura K. MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis. Bioinformatics (Oxford, England). 28: 2685-6. PMID 22923298 DOI: 10.1093/bioinformatics/bts507  0.306
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  0.802
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  0.788
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  0.793
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  0.718
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  0.589
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  0.738
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  0.769
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  0.734
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  0.794
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  0.785
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  0.761
2009 Horiike T, Miyata D, Hamada K, Saruhashi S, Shinozawa T, Kumar S, Chakraborty R, Komiyama T, Tateno Y. Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs. Gene. 429: 59-64. PMID 19000750 DOI: 10.1016/j.gene.2008.10.006  0.306
2008 Ye J, Chen J, Janardan R, Kumar S. Developmental Stage Annotation of Drosophila Gene Expression Pattern Images via an Entire Solution Path for LDA. Acm Transactions On Knowledge Discovery From Data. 2. PMID 18769656 DOI: 10.1145/1342320.1342324  0.304
2008 Ji S, Sun L, Jin R, Kumar S, Ye J. Automated annotation of Drosophila gene expression patterns using a controlled vocabulary. Bioinformatics (Oxford, England). 24: 1881-8. PMID 18632750 DOI: 10.1093/Bioinformatics/Btn347  0.318
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  0.575
2007 Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, ... ... Kumar S, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/Nature06341  0.789
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  0.591
2007 Kumar S, Dudley J. Bioinformatics software for biologists in the genomics era Bioinformatics. 23: 1713-1717. PMID 17485425 DOI: 10.1093/Bioinformatics/Btm239  0.315
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  0.717
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  0.716
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  0.601
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  0.757
2004 Subramanian S, Kumar S. Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome Genetics. 168: 373-381. PMID 15454550 DOI: 10.1534/Genetics.104.028944  0.336
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 DOI: 10.1093/Bib/5.2.150  0.596
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  0.579
2004 Tamura K, Subramanian S, Kumar S. Temporal Patterns of Fruit Fly (Drosophila) Evolution Revealed by Mutation Clocks Molecular Biology and Evolution. 21: 36-44. PMID 12949132 DOI: 10.1093/Molbev/Msg236  0.329
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  0.557
2003 Blair Hedges S, Kumar S. Genomic clocks and evolutionary timescales. Trends in Genetics : Tig. 19: 200-6. PMID 12683973 DOI: 10.1016/S0168-9525(03)00053-2  0.372
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  0.547
2003 Rosenberg MS, Kumar S. Taxon sampling, bioinformatics, and phylogenomics. Systematic Biology. 52: 119-24. PMID 12554445 DOI: 10.1080/10635150390132894  0.543
2003 Tamura K, Kumar S. Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Molecular Biology and Evolution. 19: 1727-36. PMID 12270899 DOI: 10.1093/OXFORDJOURNALS.MOLBEV.A003995  0.333
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  0.766
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  0.7
2001 Rosenberg MS, Kumar S. Incomplete taxon sampling is not a problem for phylogenetic inference. Proceedings of the National Academy of Sciences of the United States of America. 98: 10751-6. PMID 11526218 DOI: 10.1073/Pnas.191248498  0.444
2001 Rosenberg MS, Kumar S. Traditional phylogenetic reconstruction methods reconstruct shallow and deep evolutionary relationships equally well. Molecular Biology and Evolution. 18: 1823-7. PMID 11504861 DOI: 10.1093/Oxfordjournals.Molbev.A003969  0.444
1998 Nei M, Kumar S, Takahashi K. The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small. Proceedings of the National Academy of Sciences of the United States of America. 95: 12390-7. PMID 9770497 DOI: 10.1073/pnas.95.21.12390  0.505
1997 Zhang J, Kumar S, Nei M. Small-sample tests of episodic adaptive evolution: a case study of primate lysozymes. Molecular Biology and Evolution. 14: 1335-8. PMID 9402743 DOI: 10.1093/Oxfordjournals.Molbev.A025743  0.547
1997 Zhang J, Kumar S. Detection of convergent and parallel evolution at the amino acid sequence level. Molecular Biology and Evolution. 14: 527-36. PMID 9159930 DOI: 10.1093/OXFORDJOURNALS.MOLBEV.A025789  0.474
1995 Rzhetsky A, Kumar S, Nei M. Four-cluster analysis: a simple method to test phylogenetic hypotheses. Molecular Biology and Evolution. 12: 163-7. PMID 7877491 DOI: 10.1093/OXFORDJOURNALS.MOLBEV.A040185  0.465
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