Kumar Lab | Publications
Publications
2012
Konikoff C, Karr TL, McCutchan M, Newfeld SJ & Kumar S (2012) Comparison of embryonic expression within multigene families employing the FlyExpress discovery platform reveals significantly more spatial than temporal divergence. Developmental Dynamics 241:150-160. Epub 2011 Sep 29. (Abstract) (Full text) (Google Scholar Citation)
Kumar S, Filipski A, Battistuzzi FU, Kosakovsky Pond SL & Tamura K (2012) Statistics and truth in phylogenomics. Molecular Biology and Evolution 29:457-472. Epub 2011 Sep 26. (Abstract) (Full text) (Google Scholar Citation)
2011
Battistuzzi FU, Billing-Ross P, Paliwal A & Kumar S (2011) Fast and slow implementations of relaxed-clock methods show similar patterns of accuracy in estimating divergence times. Molecular Biology and Evolution 28:2439-2442. Epub 2011 Apr 15. (Abstract) (Full text) (Google Scholar Citation)
Battistuzzi FU, Filipski A & Kumar S (2011) Molecular clock: Testing (version 2.0). Encyclopedia of Life Sciences. John Wiley & Sons, Ltd, Chichester, UK (7pp). (Full text)
Elser JJ, Acquisti C & Kumar S (2011) Stoichiogenomics: the evolutionary ecology of macromolecular elemental composition. Trends in Ecology & Evolution 26:38-44. Epub 2010 Nov 18. (Abstract) (Full text) (Google Scholar Citation)
Gray VE & Kumar S (2011) Rampant purifying selection conserves positions with post-translational modifications in human proteins. Molecular Biology and Evolution 28:1565-1568. (Abstract) (Full text) (Google Scholar Citation)
Kumar S & Hedges SB (2011) TimeTree2: Species divergence times on the iPhone. Bioinformatics 27:2023-2024. Epub 2011 May 26. (Abstract) (Full text) (Google Scholar Citation)
Kumar S, Dudley JT, Filipski A & Liu L (2011) Phylomedicine: An evolutionary telescope to explore and diagnose the universe of disease mutations. Trends in Genetics 27:377-386. Epub 2011 Jul 20. (Abstract) (Full text) (Google Scholar Citation)
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 (2011) FlyExpress: Visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis. Bioinformatics 27:3319-3320. Epub 2011 Oct 12. (Abstract) (Full text) (Google Scholar Citation)
Pacheco MA, Battistuzzi FU, Lentino M, Aguilar R, Kumar S & Escalante AA (2011) Evolution of modern birds revealed by Mitogenomics: timing the radiation and origin of major orders. Molecular Biology & Evolution 28: 1927-1942. (Abstract) (Full text) (Google Scholar Citation)
Tamura K, Peterson D, Peterson N, Stecher G, Nei M & Kumar S (2011) MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28:2731-2739. Epub 2011 May 4. (Abstract) (Full text) (Google Scholar Citation)
2010
Battistuzzi FU, Filipski A, Hedges SB & Kumar S (2010) Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals. Molecular Biology and Evolution 27:1289-1300. (Abstract) (Full text) (Google Scholar Citation)
Kazemian M, Blatti C, Richards A, McCutchan M, Wakabayashi-Ito N, Hammonds AS, Celniker SE, Kumar S, Wolfe SA, Brodsky MH & Sinha S (2010) Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. PLoS Biology 8(8): e1000456. doi:10.1371/journal.pbio.1000456. (Abstract) (Full text) (Google Scholar Citation)
Kumar S (2010) Foreword for the book GENES: Conceptual, Molecular, and Developmental by S Mitra. MacMillan Press, India (In Press).
Li Y-X, Ji S, Kumar S, Ye J & Zhou Z-H (2010) Drosophila Gene Expression Pattern Annotation through Multi-Instance Multi-Label Learning. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2009:1445-1450. (Abstract) (Full text) (Google Scholar Citation)
Stone AC, Battistuzzi FU, Kubatko LS, Perry GH Jr, Trudeau E, Lin H & Kumar S (2010) More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure. Philosophical Transactions of Royal Society B 365:3277-3288. (Abstract) (Full text) (Google Scholar Citation)
2009
Acquisti CA, Elser JJ & Kumar S (2009) Ecological nitrogen-limitation shapes the DNA composition of plant genomes. Molecular Biology and Evolution 26:953-956. (Abstract) (Full text) (Google Scholar Citation)
Acquisti CA, Kumar S & Elser JJ (2009) Signatures of nitrogen limitation in the elemental composition of the proteins involved in the metabolic apparatus. Proceedings of the Royal Society of London Series B-Biological Sciences 276:2605-2610. (Abstract) (Full text)
Goering LM, Hunt PK, Heighington C, Busick C, Pennings P, Hermisson J, Kumar S & Gibson G (2009) Association of orthodenticle with natural variation for early embryonic patterning in Drosophila melanogaster. Journal of Experimental Zoology (Molecular & Developmental Evolution) 312B:841-854. (Abstract) (Full text)
Hedges SB & Kumar (2009) The Timetree of Life. Oxford University Press . (Google Scholar Citation)
Hedges SB & Kumar S (2009) Discovering the timetree of life. The Timetree of Life (book) 3-18. (Full text)
Horiike T, Miyata D, Hamada K, Saruhashi S, Shinozawa T, Kumar S, Chakraborty R, Komiyama T & Tateno Y (2009) Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs. Gene 429:59-64. (Abstract) (Full text) (Google Scholar Citation)
Ji S, Li Y-X, Zhou Z-H, Kumar S & Ye J (2009) A bag-of-words approach for Drosophila gene expression pattern annotation. BMC Bioinformatics 10:119. (Abstract) (Full text) (Google Scholar Citation)
Ji S, Yuan L, Li Y-X, Zhou Z-H, Kumar S & Ye J (2009) Drosophila gene expression pattern annotation using sparse features and term-term interactions. ACM SIGKDD International Conference on Knowledge Discovery and Data Mining 407-416. (Abstract) (Full text) (Google Scholar Citation)
Kumar S, Suleski M, Markov GJ, Lawrence S, Marco A & Filipski AJ (2009) Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations. Genome Research 19:1562-1569. (Abstract) (Full text) (Google Scholar Citation)
Li Y-X, Ji S, Kumar S, Ye J & Zhou Z-H (2009) Drosophila gene expression pattern annotation by multi-instance multi-label learning. International Joint Conference on Artificial Intelligence 1445-1450. (Abstract) (Full text) (Google Scholar Citation)
Marco A, Konikoff C, Karr TL & Kumar S (2009) Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster. Bioinformatics 25:2473-2477. (Abstract) (Full text)
Mikhailov KV, Konstantinova AV, Nikitin MA, Troshin PV, Rusin LY, Lyubetsky VA, Panchin YV, Mylnikov AP, Moroz LL, Kumar S & Aleoshin VV (2009) The origin of Metazoa: a transition from temporal to spatial cell differentiation. BioEssays 31:758-68. (Abstract) (Full text)
Suzuki Y, Gojobori T & Kumar S (2009) Methods for incorporating the hypermutability of CpG dinucleotides in detecting natural selection operating at the amino acid sequence level. Molecular Biology and Evolution 26:2275-2284. (Abstract) (Full text)
2008
Ji S, Sun L, Jin R, Kumar S & Ye J (2008) Automated annotation of Drosophila gene expression patterns using a controlled vocabulary. Bioinformatics 24:1881-1888. (Abstract) (Full text) (Google Scholar Citation)
Kumar S & Filipski A (2008) Molecular phylogeny reconstruction. Encyclopedia of Life Sciences . (Full text) (Google Scholar Citation)
Kumar S, Dudley J, Nei M & Tamura K (2008) MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics 9:299-306. (Abstract) (Full text) (Google Scholar Citation)
Ye J, Chen J, Janardan R & Kumar S (2008) Developmental stage annotation of Drosophila gene expression pattern images via an entire solution path for LDA. ACM Transactions on Knowledge Discovery from Data 2:1-21. Abstract Full text Google Scholar Citation
Ye J, Janardan R & Kumar S (2008) Biological image analysis via matrix approximation. Encyclopedia of Data Warehousing and Mining (2nd Ed.) 166-170. (Full text)
2007
Drosophila 12 Genomes Consortium (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218. (Abstract) (Full text) (Google Scholar Citation)
Acquisti C, Poste G, Curtiss D & Kumar S (2007) Nullomers: Really a matter of natural selection?. PLoS ONE 2 (3 pp). (Abstract) (Full text) (Google Scholar Citation)
Colbourn CJ & Kumar S (2007) Lower bounds on multiple sequence alignment using exact 3-way alignment. BMC Bioinformatics 8:140. (Abstract) (Full text) (Google Scholar Citation)
Filipski A, Prohaska S & Kumar S (2007) Molecular signatures of adaptive evolution. Evolutionary Genomics and Proteomics 241-254. (Abstract) (Full text) (Google Scholar Citation)
Kumar S & Dudley J (2007) Bioinformatics software for biologists in the genomics era. Bioinformatics 23:1713-1717. (Abstract) (Full text) (Google Scholar Citation)
Kumar S & Filipski A (2007) Multiple sequence alignment: In pursuit of homologous DNA positions. Genome Research 17:127-135. (Abstract) (Full text) (Google Scholar Citation)
Tamura K, Dudley J, Nei M & Kumar S (2007) Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24:1596-1599. (Abstract) (Full text) (Google Scholar Citation)
Zhang Y, Sturgill D, Parisi M, Kumar S & Oliver B (2007) Constraint and turnover in sex-biased gene expression in the genus Drosophila. Nature 450:233-237. (Abstract) (Full text) (Google Scholar Citation)
2006
Elser JJ, Fagan WF, Subramanian S & Kumar S (2006) Signatures of ecological resource availability in the animal and plant proteomes. Molecular Biology and Evolution 23:1946-1951. (Abstract) (Full text) (Google Scholar Citation)
Hedges SB, Dudley J & Kumar S (2006) TimeTree: A public knowledge-base of divergence times among organisms. Bioinformatics 22:2971-2972. (Abstract) (Full text) (Google Scholar Citation)
Hedges SB, Kumar S & van Tuinen M (2006) Constraining fossil calibrations for molecular clocks. BioEssays 28:770-771. (Abstract) (Full text) (Google Scholar Citation)
Subramanian S & Kumar S (2006) Evolutionary anatomies of positions and types of disease-associated and neutral amino acid mutations in the human genome. BMC Genomics 7:306. (Abstract) (Full text) (Google Scholar Citation)
Subramanian S & Kumar S (2006) Higher intensity of natural selection on >90% of the human genes revealed by the intrinsic replacement mutation rates. Molecular Biology and Evolution 23:2283-2287. (Abstract) (Full text) (Google Scholar Citation)
Xia X & Kumar S (2006) Codon-based detection of positive selection can be biased by heterogeneous distribution of polar amino acids along protein sequences. Computational Systems Bioinformatics Conference 4:335-340. (Abstract) (Full text) (Google Scholar Citation)
Ye J , Chen J, Li Q & Kumar S (2006) Classification of Drosophila embryonic developmental stage range based on gene expression pattern images. Computational Systems Bioinformatics Conference 4:293-298. (Abstract) (Full text) (Google Scholar Citation)
2005
Filipski A & Kumar S (2005) Comparative genomics in eukaryotes. The Evolution of the Genome 521-583. (Full text) (Google Scholar Citation)
Gadagkar SR & Kumar S (2005) Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous. Molecular Biology and Evolution 22:2139-2141. (Abstract) (Full text) (Google Scholar Citation)
Gadagkar SR, Rosenberg MS & Kumar S (2005) Inferring species phylogenies from multiple genes: Concatenated sequence tree versus consensus gene tree. Journal of Experimental Zoology (Molecular & Developmental Evolution) 304B:64-74. (Abstract) (Full text) (Google Scholar Citation)
Gargesha M, Yang J, Van Emden B, Panchanathan S & Kumar S (2005) Automatic annotation techniques for gene expression images of the fruit fly embryo. Proceedings of SPIE (Visual Communications and Image Processing 2005) 5960:576-583. (Full text) (Google Scholar Citation)
Kumar S (2005) Molecular clocks: Four decades of evolution. Nature Reviews Genetics 6:654-662. (Abstract) (Full text) (Google Scholar Citation)
Kumar S & Filipski A (2005) Reconstructing vertebrate phylogeny. Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics .
Kumar S & Hedges SB (2005) Pushing back the expansion of introns in animal genomes. Cell 123:1182-1184. (Abstract) (Full text) (Google Scholar Citation)
Kumar S, Filipski A, Swarna V, Walker A & Hedges SB (2005) Placing confidence limits on the molecular age of the human-chimpanzee divergence. Proceedings of the National Academy of Sciences (USA) 102:18842-18847. (Abstract) (Full text) (Google Scholar Citation)
2004
Briscoe AD, Gaur C & Kumar S (2004) The spectrum of human rhodopsin disease mutations through the lens of interspecific variation. Gene 332:107-118. (Abstract) (Full text) (Google Scholar Citation)
Gargesha M, Antin P, Van Emden B, Panchanathan S & Kumar S (2004) Image registration and similarity computation for chicken gene expression patterns. Genomic Signal Processing and Statistics (GENSIPS), IEEE Signal Processing Society (4 pp).
Gurunathan R, Van Emden B, Panchanathan S, & Kumar S (2004) Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations. BMC Bioinformatics 5:202 . (Abstract) (Full text) (Google Scholar Citation)
Hedges SB & Kumar S (2004) Precision of molecular time estimates. Trends in Genetics 20:242-247. (Abstract) (Full text) (Google Scholar Citation)
Kumar S & Filipski A (2004) Phylogenetic Analysis. Dictionary of Bioinformatics and Computational Biology, edited by Hancock J & Zvelebil M, Wiley-Liss, New York . (Full text)
Kumar S, Tamura K & Nei M (2004) MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Briefings in Bioinformatics 5:150-163. (Abstract) (Full text) (Google Scholar Citation)
Subramanian S & Kumar S (2004) Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome. Genetics 168:373-381. (Abstract) (Full text) (Google Scholar Citation)
Tamura K, Nei M & Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proceedings of the National Academy of Sciences (USA) 101:11030-11035. (Abstract) (Full text) (Google Scholar Citation)
Tamura K, Subramanian S & Kumar S (2004) Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Molecular Biology and Evolution 21:36-44. (Abstract) (Full text) (Google Scholar Citation)
2003
Hedges SB & Kumar S (2003) Genomic clocks and evolutionary timescales. Trends in Genetics 19:200-206. (Abstract) (Full text) (Google Scholar Citation)
Kumar S (2003) MacTrees made easy, a review of the book Phylogenetic trees made easy: a how-to-manual for molecular biologists by Hall BG. Molecular Phylogenetics and Evolution 27:165-167. (Abstract) (Full text) (Google Scholar Citation)
Lorson C & Kumar S (2003) A review of the book Genomes (second edition) by Brown TA. The Quarterly Review of Biology 78:225. (Abstract) (Full text)
Miller MP, Parker JD, Rissing SW & Kumar S (2003) Quantifying the intragenic distribution of human disease mutations. Annals of Human Genetics 67:567-579. (Abstract) (Full text) (Google Scholar Citation)
Rosenberg MS & Kumar S (2003) Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference. Molecular Biology and Evolution 20:610-621. (Abstract) (Full text) (Google Scholar Citation)
Rosenberg MS & Kumar S (2003) Taxon sampling, bioinformatics, and phylogenomics. Systematic Biology 52:119-124. (Abstract) (Full text) (Google Scholar Citation)
Rosenberg MS, Subramanian S & Kumar S (2003) Patterns of transitional mutation biases within and among mammalian genomes. Molecular Biology and Evolution 20:988-993. (Abstract) (Full text) (Google Scholar Citation)
Subramanian S & Kumar S (2003) Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes. Genome Research 13:838-844. (Abstract) (Full text) (Google Scholar Citation)
2002
Hedges SB & Kumar S (2002) Vertebrate genomes compared. Science 297:1283-1285. (Abstract) (Full text) (Google Scholar Citation)
Jiang Z, Melville JS, Cao H, Kumar S, Filipski A & Verrinder Gibbins AM (2002) Measuring conservation of contiguous sets of autosomal markers on bovine and porcine genomes in relation to the map of the human genome. Genome 45:769-776. (Abstract) (Full text) (Google Scholar Citation)
Kumar S & Subramanian S (2002) Mutation rates in mammalian genomes. Proceedings of the National Academy of Sciences (USA) 99:803-808. (Abstract) (Full text) (Google Scholar Citation)
Kumar S, Jayaraman K, Panchanathan S, Gurunathan R, Marti-Subirana A & Newfeld SJ (2002) BEST: A novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development. Genetics 162:2037-2047. (Abstract) (Full text) (Google Scholar Citation)
Rawls A & Kumar S (2002) A review of the book Genomic Regulatory Systems: Development and Evolution by Davidson EH. The Quarterly Review of Biology 77:456. (Abstract) (Full text)
Tamura K & Kumar S (2002) Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Molecular Biology and Evolution 19:1727-1736. (Abstract) (Full text) (Google Scholar Citation)
2001
Gerber AS, Loggins R, Kumar S & Dowling TE (2001) Does nonneutral evolution shape observed patterns of DNA variation in animal mitochondrial genomes?. Annual Review of Genetics 35:539-566. (Abstract) (Full text) (Google Scholar Citation)
Hedges SB, Chen H, Kumar S, Wang DY-C, Thompson AS & Watanabe H (2001) A genomic timescale for the origin of eukaryotes. BMC Evolutionary Biology 1:4 (10 pp). (Abstract) (Full text) (Google Scholar Citation)
Hedrick P & Kumar S (2001) Mutation and linkage disequilibrium in human mtDNA. European Journal of Human Genetics 9:969-972. (Abstract) (Full text) (Google Scholar Citation)
Jayaraman K, Panchanathan S & Kumar S (2001) Classification and indexing of gene expression images. Proceedings of SPIE (Applications of Digital Image Processing XXIV) 4472:471-481. (Abstract) (Full text) (Google Scholar Citation)
Kumar S & Filipski A (2001) Molecular phylogeny reconstruction. Encyclopedia of Life Sciences 4 pp. (Abstract) (Full text) (Google Scholar Citation)
Kumar S & Filipski A (2001) Molecular clock: Testing. Encyclopedia of Life Sciences 5 pp. (Abstract) (Full text)
Kumar S & Gadagkar SR (2001) Disparity Index: A simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences. Genetics 158:1321-1327. (Abstract) (Full text) (Google Scholar Citation)
Kumar S & Panchanathan S (2001) Elucidating gene interaction networks based on gene expression pattern image analysis. Proceedings of the International Conference on Biomedical Engineering 5A:232-234. (Full text) (Google Scholar Citation)
Kumar S, Gadagkar SR, Filipski A & Gu X (2001) Determination of the number of conserved chromosomal segments between species. Genetics 157:1387-1395. (Abstract) (Full text) (Google Scholar Citation)
Kumar S, Tamura K, Jakobsen IB & Nei M (2001) MEGA2: Molecular Evolutionary Genetics Analysis software. Bioinformatics 17:1244-1245. (Abstract) (Full text) (Google Scholar Citation)
Miller MP & Kumar S (2001) Understanding human disease mutations through the use of interspecific genetic variation. Human Molecular Genetics 21:2319-2328. (Abstract) (Full text) (Google Scholar Citation)
Rosenberg MS & Kumar S (2001) Incomplete taxon sampling is not a problem for phylogenetic inference. Proceedings of the National Academy of Sciences (USA) 98:10751-10756. (Abstract) (Full text) (Google Scholar Citation)
Rosenberg MS & Kumar S (2001) Traditional phylogenetic reconstruction methods reconstruct shallow and deep evolutionary relationships equally well. Molecular Biology and Evolution 18:1823-1827. (Abstract) (Full text) (Google Scholar Citation)
2000
Kumar S (2000) A review of the book Genomes by Brown TA. The Quarterly Review of Biology 75:316-317. (Abstract) (Full text)
Kumar S (2000) LDA: Linkage Disequilibrium Analysis of Bi-Allelic Sites in Molecular Sequence Data. Version 1. Arizona State University, Tempe, AZ . (Full text)
Kumar S & Gadagkar SR (2000) Efficiency of the neighbor-joining method in reconstructing deep and shallow evolutionary relationships in large phylogenies. Journal of Molecular Evolution 51:544-553. (Abstract) (Full text) (Google Scholar Citation)
Kumar S, Hedrick P, Dowling T & Stoneking M (2000) Questioning evidence for recombination in human mitochondrial DNA. Science 288:1931a. (Abstract) (Full text) (Google Scholar Citation)
Kumar S, Mitnik C, Valente G & Floyd-Smith G (2000) Expansion and molecular evolution of the interferon-induced 2'-5' oligoadenylate synthetase gene family. Molecular Biology and Evolution 17:738-750. (Abstract) (Full text) (Google Scholar Citation)
Nei M & Kumar S (2000) Molecular Evolution and Phylogenetics. Oxford University Press, New York 333 pp. (Abstract) (Google Scholar Citation)
Purdom PW, Bradford PG, Tamura K & Kumar S (2000) Single column discrepancy and dynamic max-mini optimizations for quickly finding the most parsimonious evolutionary trees. Bioinformatics 16:140-151. (Abstract) (Full text) (Google Scholar Citation)
1999
Hedges SB & Kumar S (1999) Divergence times of eutherian mammals. Science 285:2031a (6 pp).. (Full text) (Google Scholar Citation)
Newfeld SJ, Wisotzkey RG & Kumar S (1999) Molecular evolution of a development pathway: Phylogenetic analyses of transforming growth factor-ß family ligands, receptors, and Smad signal transducers. Genetics 152:783-795. (Abstract) (Full text) (Google Scholar Citation)
O'Brien S, Eisenberg JF, Miyamoto M, Hedges SB, Kumar S & Wilson DE (1999) Genome Maps 10. Comparative Genomics. Mammalian radiations. Wall Chart. Science 286:463-478. (Abstract) (Full text) (Google Scholar Citation)
Wang DY, Kumar S & Hedges SB (1999) Divergence time estimates for the early history of animal phyla and the origin of plants, animals, and fungi. Proceedings of the Royal Society, London B266:163-171. (Abstract) (Full text) (Google Scholar Citation)
1998
Kumar S & Hedges SB (1998) A molecular timescale for vertebrate evolution. Nature 392:917-920. (Abstract) (Full text) (Google Scholar Citation)
Nei M, Kumar S & Takahashi K (1998) 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 (USA) 95:12390-12397. (Abstract) (Full text) (Google Scholar Citation)
1997
Balczarek KA, Lai Z-C & Kumar S (1997) Evolution and functional diversification of the paired box (Pax) DNA-binding domains. Molecular Biology and Evolution 14:829-842. (Abstract) (Full text) (Google Scholar Citation)
Leitner T, Kumar S & Albert J (1997) 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 71:4761-4770. (Abstract) (Full text) (Google Scholar Citation)
Yeager M, Kumar S & Hughes AL (1997) Sequence convergence in the peptide-binding region of primate and rodent MHC class Ib molecules. Molecular Biology and Evolution 14:1035-1041. (Abstract Full text) (Google Scholar Citation)
Abstract Full text Google Scholar Citation Zhang J & Kumar S (1997) Detection of convergent and parallel evolution at the amino acid sequence level. Molecular Biology and Evolution 14:527-536.
Zhang J, Kumar S & Nei M (1997) Small-sample tests of episodic adaptive evolution: A case study of primate lysozymes. Molecular Biology and Evolution 14:1335-1338. (Abstract) (Full text) (Google Scholar Citation)
1996
Hedges SB, Parker PH, Sibley CG & Kumar S (1996) Continental breakup and the ordinal diversification of birds and mammals. Nature 381:226-229. (Abstract) (Full text) (Google Scholar Citation)
Kumar S (1996) Patterns of nucleotide substitution in mitochondrial protein coding genes of vertebrates. Genetics 143:537-548. (Abstract) (Full text) (Google Scholar Citation)
Kumar S (1996) A stepwise algorithm for finding minimum evolution trees. Molecular Biology and Evolution 13:584-593. (Abstract) Full text) (Google Scholar Citation)
Kumar S (1996) PHYLTEST: Phylogenetic Hypothesis Testing Software. Version 2.0. Pennsylvania State University, University Park, Pennsylvania . (Full text) (Google Scholar Citation)
Kumar S & Rzhetsky A (1996) Evolutionary relationships of eukaryotic kingdoms. Journal of Molecular Evolution 42:183-193. (Abstract) (Full text) (Google Scholar Citation)
Kumar S, Balczarek KA & Lai Z-C (1996) Evolution of the hedgehog gene family. Genetics 142:965-972. (Abstract) (Full text) (Google Scholar Citation)
Yang Z & Kumar S (1996) Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites. Molecular Biology and Evolution 13:650-659. (Abstract) (Full text) (Google Scholar Citation)
1995
Rzhetsky A, Kumar S & Nei M (1995) Four-cluster analysis: A simple method to test phylogenetic hypotheses. Molecular Biology and Evolution 12:163-167. (Abstract) (Full text) (Google Scholar Citation)
Winnepenninckx W, Backeljau T, Mackey LY, Brooks JM, De-Wachter R, Kumar S & Garey JR (1995) 18S rRNA data indicate that Aschelminthes are polyphyletic in origin and consist of at least three distinct clades. Molecular Biology and Evolution 12:1132-1137. (Abstract) (Full text) (Google Scholar Citation)
Yang Z, Kumar S & Nei M (1995) A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641-1650. (Abstract) (Full text) (Google Scholar Citation)
1994
Kumar S, Tamura K & Nei M (1994) MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. Computer Applications in Biosciences 10:189-191. (Abstract) (Full text) (Google Scholar Citation)
1993
Kumar S, Tamura K & Nei M (1993) A Guide to Molecular Evolutionary Genetics Analysis Program for Microcomputers . Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, Pennsylvania (140 pp).
1992
Hedges SB, Kumar S, Tamura K & Stoneking M (1992) Human origins and analysis of mitochondrial DNA sequences. Science 255:737-739. (Abstract) (Full text) (Google Scholar Citation)
Submitted
Konikoff C, McCutchan M, Van Emden B, Busick C, Davis KT, Ji S, Wu L, Ramos H, Brody T, Panchanathan S, Ye J, Karr TL, Newfeld SJ & Kumar S (Submitted) FlyExpress: Discovering co-expressed genes by comparative analysis of spatial patterns in images of Drosophila embryogenesis. (Submitted) .
