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Sudhir Kumar

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TOP 3
Li Liu; Sudhir Kumar
Evolutionary balancing is critical for correctly forecasting disease-associated amino Acid variants.
Mia D Champion; Carl Eberhard; Vanessa Gray; Sudhir Kumar
The evolutionary history of amino acid variations mediating increased resistance of S. aureus identifies reversion mutations in metabolic regulators.
Sudhir Kumar
Editor's Inaugural Message.

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All Publications

2013: Li Liu; Sudhir Kumar
Evolutionary balancing is critical for correctly forecasting disease-associated amino Acid variants.
Molecular biology and evolution 2013;30(6):1252-7.
2013: Mia D Champion; Carl Eberhard; Vanessa Gray; Sudhir Kumar
The evolutionary history of amino acid variations mediating increased resistance of S. aureus identifies reversion mutations in metabolic regulators.
PloS one 2013;8(2):e56466.
2013: Sudhir Kumar
Editor's Inaugural Message.
Molecular biology and evolution 2013;30(1):1-2.
2012: Takahiro Maruki; Sudhir Kumar; Yuseob Kim
Purifying selection modulates the estimates of population differentiation and confounds genome-wide comparisons across single-nucleotide polymorphisms.
Molecular biology and evolution 2012;29(12):3617-23.
2012: Koichiro Tamura; Oscar Murillo; Fabia Ursula Battistuzzi; Paul Billing-Ross; Alan Filipski; Sudhir Kumar
Estimating divergence times in large molecular phylogenies.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(47):19333-8.
2012: Sudhir Kumar; Daniel Peterson; Glen Stecher; Koichiro Tamura
MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis.
Bioinformatics (Oxford, England) 2012;28(20):2685-6.
2012: Sudhir Kumar; Maxwell Sanderford; Jieping Ye; Vanessa E Gray; Li Liu
Evolutionary diagnosis method for variants in personal exomes.
Nature methods 2012;9(9):855-6.
2012: Vanessa E Gray; Kimberly R Kukurba; Sudhir Kumar
Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations.
Bioinformatics (Oxford, England) 2012;28(16):2093-6.
2012: Sudhir Kumar; Fabia U Battistuzzi; Alan J Filipski; Sergei L Kosakovsky Pond; Koichiro Tamura
Statistics and truth in phylogenomics.
Molecular biology and evolution 2012;29(2):457-72.
2012: Lei Yuan; Zhi-Hua Zhou; Shuiwang Ji; Yuan Jiang; Sudhir Kumar; Alexander Woodard; Jieping Ye
Learning sparse representations for fruit-fly gene expression pattern image annotation and retrieval.
BMC bioinformatics 2012;13():107.
2011: Sudhir Kumar; Michael McCutchan; Thomas Brody; Christopher Busick; Kailah T Davis; Kristyn Gerold; Shuiwang Ji; Timothy L Karr; Charlotte Konikoff; Sethuraman Panchanathan; Hector Ramos; Bernard Van Emden; Lin-Wei Wu; Jieping Ye; Stuart J Newfeld
FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis.
Bioinformatics (Oxford, England) 2011;27(23):3319-20.
2011: Koichiro Tamura; Masatoshi Nei; Daniel Peterson; Nicholas Peterson; Glen Stecher; Sudhir Kumar
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.
Molecular biology and evolution 2011;28(10):2731-9.
2011: Sudhir Kumar; Joel T Dudley; Alan Filipski; Li Liu
Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations.
Trends in genetics : TIG 2011;27(9):377-86.
2011: Fabia U Battistuzzi; Paul Billing-Ross; Aditya Paliwal; Sudhir Kumar
Fast and slow implementations of relaxed-clock methods show similar patterns of accuracy in estimating divergence times.
Molecular biology and evolution 2011;28(9):2439-42.
2011: Sudhir Kumar; S Blair Hedges
TimeTree2: species divergence times on the iPhone.
Bioinformatics (Oxford, England) 2011;27(14):2023-4.
2011: M Andreína Pacheco; Fabia U Battistuzzi; Miguel Lentino; Roberto F Aguilar; Sudhir Kumar; Ananias A Escalante
Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders.
Molecular biology and evolution 2011;28(6):1927-42.
2011: Vanessa E Gray; Sudhir Kumar
Rampant purifying selection conserves positions with posttranslational modifications in human proteins.
Molecular biology and evolution 2011;28(5):1565-8.
2011: Sudeep Kumar; Sudhir Kumar; Ruchi Gupta; Sher Ali
Molecular mining of alleles in water buffalo Bubalus bubalis and characterization of the TSPY1 and COL6A1 genes.
PloS one 2011;6(9):e24958.
2011: James J Elser; Claudia Acquisti; Sudhir Kumar
Stoichiogenomics: the evolutionary ecology of macromolecular elemental composition.
Trends in ecology & evolution 2011;26(1):38-44.
2010: Anne C Stone; Fabia U Battistuzzi; Laura S Kubatko; George H Perry; Evan Trudeau; Hsiuman Lin; Sudhir Kumar
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 2010;365(1556):3277-88.
2010: Fabia U Battistuzzi; Alan Filipski; S Blair Hedges; Sudhir Kumar
Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals.
Molecular biology and evolution 2010;27(6):1289-300.
2009: Antonio Marco; Charlotte Konikoff; Timothy L Karr; Sudhir Kumar
Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster.
Bioinformatics (Oxford, England) 2009;25(19):2473-7.
2009: Yoshiyuki Suzuki; Takashi Gojobori; Sudhir Kumar
Methods for incorporating the hypermutability of CpG dinucleotides in detecting natural selection operating at the amino acid sequence level.
Molecular biology and evolution 2009;26(10):2275-84.
2009: Sudhir Kumar; Michael P Suleski; Glenn J Markov; Simon Lawrence; Antonio Marco; Alan J Filipski
Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations.
Genome research 2009;19(9):1562-9.
2009: Claudia Acquisti; Sudhir Kumar; James J Elser
Signatures of nitrogen limitation in the elemental composition of the proteins involved in the metabolic apparatus.
Proceedings. Biological sciences / The Royal Society 2009;276(1667):2605-10.
2009: Claudia Acquisti; James J Elser; Sudhir Kumar
Ecological nitrogen limitation shapes the DNA composition of plant genomes.
Molecular biology and evolution 2009;26(5):953-6.
2009: Tokumasa Horiike; Daisuke Miyata; Kazuo Hamada; Satoshi Saruhashi; Takao Shinozawa; Sudhir Kumar; Ranajit Chakraborty; Tomoyoshi Komiyama; Yoshio Tateno
Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs.
Gene 2009;429(1-2):59-64.
2009: Shuiwang Ji; Ying-Xin Li; Zhi-Hua Zhou; Sudhir Kumar; Jieping Ye
A bag-of-words approach for Drosophila gene expression pattern annotation.
BMC bioinformatics 2009;10():119.
2008: Sudhir Kumar; G Rajshekher; Subhashini Prabhakar
Platelet glycoprotein IIb/IIIa inhibitors in acute ischemic stroke.
Neurology India 2008;56(4):399-404.
2008: Shuiwang Ji; Liang Sun; Rong Jin; Sudhir Kumar; Jieping Ye
Automated annotation of Drosophila gene expression patterns using a controlled vocabulary.
Bioinformatics (Oxford, England) 2008;24(17):1881-8.
2008: Sudhir Kumar; Masatoshi Nei; Joel Dudley; Koichiro Tamura
MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences.
Briefings in bioinformatics 2008;9(4):299-306.
2007: Yu Zhang; David Sturgill; Michael Parisi; Sudhir Kumar; Brian Oliver
Constraint and turnover in sex-biased gene expression in the genus Drosophila.
Nature 2007;450(7167):233-7.
2007: andrew clark; Michael B Eisen; Douglas R Smith; Casey M Bergman; Brian Oliver; Therese A Markow; Thomas C Kaufman; Manolis Kellis; William Gelbart; Venky N Iyer; Daniel A Pollard; Timothy B Sackton; Amanda M Larracuente; Nadia D Singh; Jose P Abad; Dawn N Abt; Boris Adryan; Montserrat Aguade; Hiroshi Akashi; Wyatt W Anderson; Charles F Aquadro; David H Ardell; Roman Arguello; Carlo G Artieri; Daniel A Barbash; Daniel Barker; Paolo Barsanti; Phil Batterham; Serafim Batzoglou; Dave Begun; Arjun Bhutkar; Enrico Blanco; Stephanie A Bosak; Robert K Bradley; Adrianne D Brand; Michael R Brent; Angela N Brooks; Randall H Brown; Roger K Butlin; Corrado Caggese; Brian R. Calvi; A Bernardo de Carvalho; Anat Caspi; Sergio Castrezana; Susan E Celniker; Jean L Chang; Charles Chapple; Sourav Chatterji; Asif Chinwalla; Alberto Civetta; Sandra W Clifton; Josep M Comeron; James C Costello; Jerry A Coyne; Jennifer Daub; Robert G David; Arthur L Delcher; Kim Delehaunty; Chuong B Do; Heather Ebling; Kevin Edwards; Thomas Eickbush; Jay Evans; Alan Filipski; Sven Findeiss; Eva Freyhult; Lucinda Fulton; Robert Fulton; Ana C L Garcia; Anastasia Gardiner; David A Garfield; Barry E Garvin; Greg Gibson; Donald G Gilbert; Sante Gnerre; Jennifer Godfrey; Robert Good; Valer Gotea; Brenton Gravely; Anthony J Greenberg; Sam Griffiths-Jones; Samuel Gross; Roderic Guigo; Erik A Gustafson; Wilfried Haerty; Matthew W Hahn; Daniel L Halligan; Aaron L Halpern; Gillian M Halter; Mira V Han; Andreas Heger; LaDeana Hillier; Angie S Hinrichs; Ian Holmes; Roger A Hoskins; Melissa J Hubisz; Dan Hultmark; Melanie A Huntley; David B Jaffe; Santosh Jagadeeshan; William R Jeck; Justin Johnson; Corbin D Jones; William C Jordan; Gary Karpen; Eiko Kataoka; Peter D Keightley; Pouya Kheradpour; Ewen F Kirkness; Leonardo B Koerich; Karsten Kristiansen; Dave Kudrna; Rob J Kulathinal; Sudhir Kumar; Roberta Kwok; Eric Lander; Charles H Langley; Richard Lapoint; Brian P Lazzaro; So-Jeong Lee; Lisa Levesque; Ruiqiang Li; Chiao-Feng Lin; Michael F Lin; Kerstin Lindblad-Toh; Ana Llopart; Manyuan Long; Lloyd Low; Elena Lozovsky; Jian Lu; Meizhong Luo; Carlos A Machado; Wojciech Makalowski; Mar Marzo; Muneo Matsuda; Luciano Matzkin; Bryant McAllister; Carolyn S McBride; Brendan McKernan; Kevin McKernan; Maria Mendez-Lago; Patrick Minx; Michael U Mollenhauer; Kristi Montooth; Steve Mount; Xu Mu; Eugene Myers; Barbara Negre; Stuart Newfeld; Rasmus Nielsen; Mohamed A F Noor; Patrick O'Grady; Lior Pachter; Montserrat Papaceit; Matthew J Parisi; Michael Parisi; Leopold Parts; Jakob S Pedersen; Graziano Pesole; Adam M Phillippy; Chris P Ponting; Mihai Pop; Damiano Porcelli; Jeffrey R Powell; Sonja J Prohaska; Kim Pruitt; Marta Puig; Hadi Quesneville; Kristipati Ravi Ram; David Rand; Matthew D Rasmussen; Laura K Reed; Robert Reenan; Amy Reily; Karin A Remington; Tania T Rieger; Michael G Ritchie; Charles Robin; Yu-Hui Rogers; Claudia Rohde; Julio Rozas; Marc J Rubenfield; Alfredo Ruiz; Susan Russo; Steven L Salzberg; Alejandro Sanchez-Gracia; David J Saranga; Hajime Sato; Stephen W Schaeffer; Michael C Schatz; Todd Schlenke; Russell Schwartz; Carmen Segarra; Rama S Singh; Laura K Sirot; Marina Sirota; Nicholas B Sisneros; Chris D Smith; Temple F Smith; John Spieth; Deborah E Stage; Alexander Stark; Wolfgang Stephan; Robert L Strausberg; Sebastian Strempel; David Sturgill; Granger Sutton; Granger G Sutton; Wei Tao; Sarah Teichmann; Yoshiko N Tobari; Yoshihiko Tomimura; Jason M Tsolas; Vera L S Valente; Eli Venter; J Craig Venter; Saverio Vicario; Filipe G Vieira; Albert J Vilella; Alfredo Villasante; Brian Walenz; Jun Wang; Marvin Wasserman; Thomas Watts; Derek Wilson; Richard K Wilson; Rod A Wing; Mariana F Wolfner; Alex Wong; Gane Ka-Shu Wong; Chung-I Wu; Gabriel Wu; Daisuke Yamamoto; Hsiao-Pei Yang; Shiaw-Pyng Yang; James A. Yorke; Kiyohito Yoshida; Evgeny Zdobnov; Peili Zhang; Yu Zhang; Aleksey V Zimin; Jennifer Baldwin; Amr Abdouelleil; Jamal Abdulkadir; Adal Abebe; Brikti Abera; Justin Abreu; St Christophe Acer; Lynne Aftuck; Allen Alexander; Peter An; Erica Anderson; Scott Anderson; Harindra Arachi; Marc Azer; Pasang Bachantsang; Andrew Barry; Tashi Bayul; Aaron Berlin; Daniel Bessette; Toby Bloom; Jason Blye; Leonid Boguslavskiy; Claude Bonnet; Boris Boukhgalter; Imane Bourzgui; Adam Brown; Patrick Cahill; Sheridon Channer; Yama Cheshatsang; Lisa Chuda; Mieke Citroen; Alville Collymore; Patrick Cooke; Maura Costello; Katie D'Aco; Riza Daza; Georgius De Haan; Stuart DeGray; Christina DeMaso; Norbu Dhargay; Kimberly Dooley; Erin Dooley; Missole Doricent; Passang Dorje; Kunsang Dorjee; Alan Dupes; Richard Elong; Jill Falk; Abderrahim Farina; Susan Faro; Diallo Ferguson; Sheila Fisher; Chelsea D Foley; Alicia Franke; Dennis Friedrich; Loryn Gadbois; Gary Gearin; Christina R Gearin; Georgia Giannoukos; Tina Goode; Joseph Graham; Edward Grandbois; Sharleen Grewal; Kunsang Gyaltsen; Nabil Hafez; Birhane Hagos; Jennifer Hall; Charlotte Henson; Andrew Hollinger; Tracey Honan; Monika D Huard; Leanne Hughes; Brian Hurhula; M Erii Husby; Asha Kamat; Ben Kanga; Seva Kashin; Dmitry Khazanovich; Peter Kisner; Krista Lance; Marcia Lara; William Lee; Niall Lennon; Frances Letendre; Rosie LeVine; Alex Lipovsky; Xiaohong Liu; Jinlei Liu; Shangtao Liu; Tashi Lokyitsang; Yeshi Lokyitsang; Rakela Lubonja; Annie Lui; Pen MacDonald; Vasilia Magnisalis; Kebede Maru; Charles Matthews; William McCusker; Susan McDonough; Teena Mehta; James Meldrim; Louis Meneus; Oana Mihai; Atanas Mihalev; Tanya Mihova; Rachel Mittelman; Valentine Mlenga; Anna Montmayeur; Leonidas Mulrain; Adam Navidi; Jerome Naylor; Tamrat Negash; Thu Nguyen; Nga Nguyen; Robert Nicol; Choe Norbu; Nyima Norbu; Nathaniel Novod; Barry O'Neill; Sahal Osman; Eva Markiewicz; Otero L Oyono; Christopher Patti; Pema Phunkhang; Fritz Pierre; Margaret Priest; Sujaa Raghuraman; Filip Rege; Rebecca Reyes; Cecil Rise; Peter Rogov; Keenan Ross; Elizabeth Ryan; Sampath Settipalli; Terry Shea; Ngawang Sherpa; Lu Shi; Diana Shih; Todd Sparrow; Jessica Spaulding; John Stalker; Nicole Stange-Thomann; Sharon Stavropoulos; Catherine Stone; Christopher Strader; Senait Tesfaye; Talene Thomson; Yama Thoulutsang; Dawa Thoulutsang; Kerri Topham; Ira Topping; Tsamla Tsamla; Helen Vassiliev; Andy Vo; Tsering Wangchuk; Tsering Wangdi; Michael Weiand; Jane Wilkinson; Adam Wilson; Shailendra Yadav; Geneva Young; Qing Yu; Lisa Zembek; Danni Zhong; Andrew Zimmer; Zac Zwirko; David B Jaffe; Pablo Alvarez; Will Brockman; Jonathan Butler; CheeWhye Chin; Sante Gnerre; Manfred Grabherr; Michael Kleber; Evan Mauceli; Iain MacCallum
Evolution of genes and genomes on the Drosophila phylogeny.
Nature 2007;450(7167):203-18.
2007: Koichiro Tamura; Joel Dudley; Masatoshi Nei; Sudhir Kumar
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.
Molecular biology and evolution 2007;24(8):1596-9.
2007: Sudhir Kumar; Joel Dudley
Bioinformatics software for biologists in the genomics era.
Bioinformatics (Oxford, England) 2007;23(14):1713-7.
2007: Sudhir Kumar; Alan Filipski
Multiple sequence alignment: in pursuit of homologous DNA positions.
Genome research 2007;17(2):127-35.
2007: Claudia Acquisti; George Poste; David Curtiss; Sudhir Kumar
Nullomers: really a matter of natural selection?
PloS one 2007;2(10):e1022.
2007: Charles J Colbourn; Sudhir Kumar
Lower bounds on multiple sequence alignment using exact 3-way alignment.
BMC bioinformatics 2007;8():140.
2006: S Blair Hedges; Joel Dudley; Sudhir Kumar
TimeTree: a public knowledge-base of divergence times among organisms.
Bioinformatics (Oxford, England) 2006;22(23):2971-2.
2006: Sankar Subramanian; Sudhir Kumar
Higher intensity of purifying selection on >90% of the human genes revealed by the intrinsic replacement mutation rates.
Molecular biology and evolution 2006;23(12):2283-7.
2006: James J Elser; William F Fagan; Sankar Subramanian; Sudhir Kumar
Signatures of ecological resource availability in the animal and plant proteomes.
Molecular biology and evolution 2006;23(10):1946-51.
2006: S Blair Hedges; Sudhir Kumar; Marcel van Tuinen
Constraining fossil calibrations for molecular clocks.
BioEssays : news and reviews in molecular, cellular and developmental biology 2006;28(7):770-1; author reply 772-3.
2006: Jieping Ye; Jianhui Chen; Qi Li; Sudhir Kumar
Classification of Drosophila embryonic developmental stage range based on gene expression pattern images.
Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference 2006;():293-8.
2006: Sankar Subramanian; Sudhir Kumar
Evolutionary anatomies of positions and types of disease-associated and neutral amino acid mutations in the human genome.
BMC genomics 2006;7():306.
2005: Sudhir Kumar; S Blair Hedges
Pushing back the expansion of introns in animal genomes.
Cell 2005;123(7):1182-4.
2005: Sudhir Kumar; Alan Filipski; Vinod Swarna; Alan Walker; S Blair Hedges
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 2005;102(52):18842-7.
2005: Sudhindra R Gadagkar; Sudhir Kumar
Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous.
Molecular biology and evolution 2005;22(11):2139-41.
2005: Sudhir Kumar
Molecular clocks: four decades of evolution.
Nature reviews. Genetics 2005;6(8):654-62.
2005: Sudhindra R Gadagkar; Michael S Rosenberg; Sudhir Kumar
Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree.
Journal of experimental zoology. Part B, Molecular and developmental evolution 2005;304(1):64-74.
2004: Sankar Subramanian; Sudhir Kumar
Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome.
Genetics 2004;168(1):373-81.
2004: Koichiro Tamura; Masatoshi Nei; Sudhir Kumar
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 2004;101(30):11030-5.
2004: Sudhir Kumar; Koichiro Tamura; Masatoshi Nei
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment.
Briefings in bioinformatics 2004;5(2):150-63.
2004: Adriana D Briscoe; Charu Gaur; Sudhir Kumar
The spectrum of human rhodopsin disease mutations through the lens of interspecific variation.
Gene 2004;332():107-18.
2004: S Blair Hedges; Sudhir Kumar
Precision of molecular time estimates.
Trends in genetics : TIG 2004;20(5):242-7.
2004: Rajalakshmi Gurunathan; Bernard Van Emden; Sethuraman Panchanathan; Sudhir Kumar
Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations.
BMC bioinformatics 2004;5():202.
2004: Koichiro Tamura; Sankar Subramanian; Sudhir Kumar
Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks.
Molecular biology and evolution 2004;21(1):36-44.
2003: James K Jancovich; Jinghe Mao; V Gregory Chinchar; Christopher Wyatt; Steven T Case; Sudhir Kumar; Graziela Valente; Sankar Subramanian; Elizabeth W Davidson; James P Collins; Bertram L Jacobs
Genomic sequence of a ranavirus (family Iridoviridae) associated with salamander mortalities in North America.
Virology 2003;316(1):90-103.
2003: M P Miller; Joel D Parker; Steven W Rissing; Sudhir Kumar
Quantifying the intragenic distribution of human disease mutations.
Annals of human genetics 2003;67(Pt 6):567-79.
2003: Michael S Rosenberg; Sankar Subramanian; Sudhir Kumar
Patterns of transitional mutation biases within and among mammalian genomes.
Molecular biology and evolution 2003;20(6):988-93.
2003: Sankar Subramanian; Sudhir Kumar
Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes.
Genome research 2003;13(5):838-44.
2003: S Blair Hedges; Sudhir Kumar
Genomic clocks and evolutionary timescales.
Trends in genetics : TIG 2003;19(4):200-6.
2003: Michael S Rosenberg; Sudhir Kumar
Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference.
Molecular biology and evolution 2003;20(4):610-21.
2003: Michael S Rosenberg; Sudhir Kumar
Taxon sampling, bioinformatics, and phylogenomics.
Systematic biology 2003;52(1):119-24.
2002: Sudhir Kumar; Karthik Jayaraman; Sethuraman Panchanathan; Rajalakshmi Gurunathan; Ana Marti-Subirana; Stuart J Newfeld
BEST: a novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development.
Genetics 2002;162(4):2037-47.
2002: Koichiro Tamura; Sudhir Kumar
Evolutionary distance estimation under heterogeneous substitution pattern among lineages.
Molecular biology and evolution 2002;19(10):1727-36.
2002: S Blair Hedges; Sudhir Kumar
Genomics. Vertebrate genomes compared.
Science (New York, N.Y.) 2002;297(5585):1283-5.
2002: Zhihua Jiang; Jenna S Melville; Honghe Cao; Sudhir Kumar; Alan Filipski; Ann M Verrinder Gibbins
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 2002;45(4):769-76.
2002: Sudhir Kumar; Sankar Subramanian
Mutation rates in mammalian genomes.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(2):803-8.
2001: Sudhir Kumar; K Tamura; Ingrid Jakobsen; M Nei
MEGA2: molecular evolutionary genetics analysis software.
Bioinformatics (Oxford, England) 2001;17(12):1244-5.
2001: M P Miller; Sudhir Kumar
Understanding human disease mutations through the use of interspecific genetic variation.
Human molecular genetics 2001;10(21):2319-28.
2001: Michael S Rosenberg; Sudhir Kumar
Incomplete taxon sampling is not a problem for phylogenetic inference.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(19):10751-6.
2001: M S Rosenberg; Sudhir Kumar
Traditional phylogenetic reconstruction methods reconstruct shallow and deep evolutionary relationships equally well.
Molecular biology and evolution 2001;18(9):1823-7.
2001: Sudhir Kumar; SR Gadagkar
Disparity index: a simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences.
Genetics 2001;158(3):1321-7.
2001: Sudhir Kumar; SR Gadagkar; Alan Filipski; X Gu
Determination of the number of conserved chromosomal segments between species.
Genetics 2001;157(3):1387-95.
2001: A S Gerber; R Loggins; Sudhir Kumar; Thomas E Dowling
Does nonneutral evolution shape observed patterns of DNA variation in animal mitochondrial genomes?
Annual review of genetics 2001;35():539-66.
2001: S Blair Hedges; H Chen; Sudhir Kumar; D Y Wang; A S Thompson; H Watanabe
A genomic timescale for the origin of eukaryotes.
BMC evolutionary biology 2001;1():4.
2000: Sudhir Kumar; SR Gadagkar
Efficiency of the neighbor-joining method in reconstructing deep and shallow evolutionary relationships in large phylogenies.
Journal of molecular evolution 2000;51(6):544-53.
2000: Sudhir Kumar; Philip W Hedrick; Thomas E Dowling; M Stoneking
Questioning evidence for recombination in human mitochondrial DNA.
Science (New York, N.Y.) 2000;288(5473):1931.
2000: Sudhir Kumar; C Mitnik; G Valente; G Floyd-Smith
Expansion and molecular evolution of the interferon-induced 2'-5' oligoadenylate synthetase gene family.
Molecular biology and evolution 2000;17(5):738-50.
2000: P W Purdom; P G Bradford; K Tamura; Sudhir Kumar
Single column discrepancy and dynamic max-mini optimizations for quickly finding the most parsimonious evolutionary trees.
Bioinformatics (Oxford, England) 2000;16(2):140-51.
1999: Stuart J Newfeld; Robert G Wisotzkey; Sudhir Kumar
Molecular evolution of a developmental pathway: phylogenetic analyses of transforming growth factor-beta family ligands, receptors and Smad signal transducers.
Genetics 1999;152(2):783-95.
1999: X Lin; D E Wells; W J Kimberling; Sudhir Kumar
Human NDUFB9 gene: genomic organization and a possible candidate gene associated with deafness disorder mapped to chromosome 8q13.
Human heredity 1999;49(2):75-80.
1999: D Y Wang; Sudhir Kumar; S Blair Hedges
Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi.
Proceedings. Biological sciences / The Royal Society 1999;266(1415):163-71.
1998: Masatoshi Nei; Sudhir Kumar; K Takahashi
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 1998;95(21):12390-7.
1998: Sudhir Kumar; S Blair Hedges
A molecular timescale for vertebrate evolution.
Nature 1998;392(6679):917-20.
1997: jianzhi zhang; Sudhir Kumar; M Nei
Small-sample tests of episodic adaptive evolution: a case study of primate lysozymes.
Molecular biology and evolution 1997;14(12):1335-8.
1997: M Yeager; Sudhir Kumar; Austin Hughes
Sequence convergence in the peptide-binding region of primate and rodent MHC class Ib molecules.
Molecular biology and evolution 1997;14(10):1035-41.
1997: K A Balczarek; Zhi-Chun Lai; Sudhir Kumar
Evolution of functional diversification of the paired box (Pax) DNA-binding domains.
Molecular biology and evolution 1997;14(8):829-42.
1997: Thomas Leitner; Sudhir Kumar; J Albert
Tempo and mode of nucleotide substitutions in gag and env gene fragments in human immunodeficiency virus type 1 populations with a known transmission history.
Journal of virology 1997;71(6):4761-70.
1997: Jian Zhang; Sudhir Kumar
Detection of convergent and parallel evolution at the amino acid sequence level.
Molecular biology and evolution 1997;14(5):527-36.
1996: S Blair Hedges; P H Parker; C G Sibley; Sudhir Kumar
Continental breakup and the ordinal diversification of birds and mammals.
Nature 1996;381(6579):226-9.
1996: Sudhir Kumar
Patterns of nucleotide substitution in mitochondrial protein coding genes of vertebrates.
Genetics 1996;143(1):537-48.
1996: Z Yang; Sudhir Kumar
Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites.
Molecular biology and evolution 1996;13(5):650-9.
1996: Sudhir Kumar
A stepwise algorithm for finding minimum evolution trees.
Molecular biology and evolution 1996;13(4):584-93.
1996: Sudhir Kumar; K A Balczarek; Zhi-Chun Lai
Evolution of the hedgehog gene family.
Genetics 1996;142(3):965-72.
1996: Sudhir Kumar; Andrey Rzhetsky
Evolutionary relationships of eukaryotic kingdoms.
Journal of molecular evolution 1996;42(2):183-93.
1995: Z Yang; Sudhir Kumar; Masatoshi Nei
A new method of inference of ancestral nucleotide and amino acid sequences.
Genetics 1995;141(4):1641-50.
1995: BM Winnepenninckx; Thierry Backeljau; L Y Mackey; J M Brooks; Rupert De Wachter; Sudhir Kumar; J R Garey
18S rRNA data indicate that Aschelminthes are polyphyletic in origin and consist of at least three distinct clades.
Molecular biology and evolution 1995;12(6):1132-7.
1995: Andrey Rzhetsky; Sudhir Kumar; Masatoshi Nei
Four-cluster analysis: a simple method to test phylogenetic hypotheses.
Molecular biology and evolution 1995;12(1):163-7.
1994: Sudhir Kumar; K Tamura; Masatoshi Nei
MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers.
Computer applications in the biosciences : CABIOS 1994;10(2):189-91.
1992: S B Hedges; Sudhir Kumar; K Tamura; M Stoneking
Human origins and analysis of mitochondrial DNA sequences.
Science (New York, N.Y.) 1992;255(5045):737-9.