Publications
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        2010
113     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. (Accepted)
112   PDF   Stone AC, Battistuzzi F, Kubatko LS, Perry GH, 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 (In Press - Oct 2010, Advance Access - Sep 2010). [Download PDF]
111 PubMed PDF   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. [Download PDF]
         
        2009
110 PubMed PDF   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. [Download PDF]
109 PubMed PDF   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. [Download PDF]
108 PubMed PDF Google 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. [Download PDF]
107 PubMed PDF   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. [Download PDF]
106 PubMed PDF Google 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. [Download PDF]
105 PubMed PDF Google 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. [Download PDF]
104 PubMed PDF Google 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. [Download PDF]
103 PubMed PDF   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. [Download PDF]
102 PubMed PDF   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. [Download PDF]
101 PubMed PDF Google Acquisti CA, Elser JJ & Kumar S (2009) Ecological nitrogen-limitation shapes the DNA composition of plant genomes. Molecular Biology and Evolution 26:953-956. [Download PDF]
100
 PubMed PDF Google 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. [Download PDF]
99
 Book PDF   Hedges SB & Kumar S (2009) Discovering the timetree of life. The Timetree of Life edited by Hedges SB & Kumar S. Oxford University Press, New York, 3-18. [Download PDF]
98
 Book Google Hedges SB & Kumar S (2009) The Timetree of Life. Oxford University Press, New York, (551 pp). [Download Book Chapter]
         
        2008
97
 PubMed PDF Google 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. [Download PDF]
96
 PubMed PDF Google 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. [Download PDF]
95
 Book PDF Google Kumar S & Filipski A (2008) Molecular phylogeny reconstruction. Encyclopedia of Life Sciences. Macmillan Reference Ltd, Oxford, Nature Publishing Group, UK. [Download PDF]
94
 PubMed PDF Google 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. [Download PDF]
93
 PDF   Ye J, Janardan R & Kumar S (2008) Biological image analysis via matrix approximation. Encyclopedia of Data Warehousing and Mining (2nd Ed.) edited by John Wang, Idea Group, Inc., Pennsylvania, 166-170. [Download PDF]
         
        2007
92
 Book PDF Google Filipski A, Prohaska S & Kumar S (2007) Molecular signatures of adaptive evolution. Evolutionary Genomics and Proteomics edited by Pagel M & Pomiankowski A. Sinauer Associates, Inc., Massachussets, 241-254. [Download PDF]
91
 PubMed PDF Google Drosophila 12 Genomes Consortium (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218. [Download PDF]
90
 PubMed PDF Google 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. [Download PDF]
89
 PubMed PDF Google Acquisti C, Poste G, Curtiss D & Kumar S (2007) Nullomers: Really a matter of natural selection? PLoS ONE 2 (3 pp). [Download PDF]
88
 PubMed PDF Google Kumar S & Dudley J (2007) Bioinformatics software for biologists in the genomics era. Bioinformatics 23:1713-1717. [Download PDF]
87
 PubMed PDF Google Tamura K, Dudley J, Nei M & Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24:1596-1599. [www.megasoftware.net] [Download PDF]
86
 PubMed PDF Google Kumar S & Filipski A (2007) Multiple sequence alignment: In pursuit of homologous DNA positions. Genome Research 17:127-135. [Download PDF]
85
 PubMed PDF Google Colbourn CJ & Kumar S (2007) Lower bounds on multiple sequence alignment using exact 3-way alignment. BMC Bioinformatics 8:140 (8 pp). [Download PDF]
         
        2006
84
 PubMed PDF Google 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 (9 pp). [Download PDF]
83
 PubMed PDF Google Hedges SB, Dudley J & Kumar S (2006) TimeTree: A public knowledge-base of divergence times among organisms. Bioinformatics 22:2971-2972. [Download PDF]
82
 PubMed PDF Google 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. [Download PDF]
81
 PubMed PDF Google 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. [Download PDF]
80
 PubMed PDF Google 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. [Download PDF]
79
 PubMed PDF Google 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. [Download PDF]
78
 PubMed PDF Google Hedges SB, Kumar S & van Tuinen M (2006) Constraining fossil calibrations for molecular clocks. BioEssays 28:770-771. [Download PDF]
         
        2005
77
 PubMed PDF Google Kumar S & Hedges SB (2005) Pushing back the expansion of introns in animal genomes. Cell 123:1182-1184. [Download PDF]
76
 PubMed PDF Google 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. [Download PDF]
75
 PubMed PDF Google Kumar S (2005) Molecular clocks: Four decades of evolution. Nature Reviews Genetics 6:654-662. [Download PDF]
74
 PubMed PDF Google 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. [Download PDF]
73
 PubMed PDF Google Gadagkar SR & Kumar S (2005) Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous. Molecular Biology and Evolution 22:2139-2141. [Download PDF]
72
 Book PDF Google Filipski A & Kumar S (2005) Comparative genomics in eukaryotes.The Evolution of the Genome edited by Ryan TG. Elsevier, San Diego, 521-583. [Download PDF]
71
 PDF Google 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. [Download PDF]
70
 Book     Kumar S & Filipski A (2005) Reconstructing vertebrate phylogeny. Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics edited by Subramaniam S. John Wiley & Sons, New York.
         
        2004
69
 PubMed PDF Google Kumar S, Tamura K & Nei M (2004) MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Briefings in Bioinformatics 5:150-163. [www.megasoftware.net] [Download PDF]
68
 PubMed PDF Google Subramanian S & Kumar S (2004) Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome. Genetics 168:373-381. [Download PDF]
67
 PubMed PDF Google Hedges SB & Kumar S (2004) Precision of molecular time estimates. Trends in Genetics 20:242-247. [Download PDF]
66
 PubMed PDF Google 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. [Download PDF]
65
 PubMed PDF Google 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. [Download PDF]
64
 PubMed PDF Google Briscoe AD, Gaur C & Kumar S (2004) The spectrum of human rhodopsin disease mutations through the lens of interspecific variation. Gene 332:107-118. [Download PDF]
63
 PubMed PDF Google 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 (13 pp). [Download PDF]
62
       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).
61
 Book     Kumar S & Filipski A (2004) Phylogenetic Analysis. Dictionary of Bioinformatics and Computational Biology edited by Hancock J & Zvelebil M, Wiley-Liss, New York.
         
        2003
60
 PubMed PDF Google 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. [Download PDF]
59
 PubMed PDF Google Hedges SB & Kumar S (2003) Genomic clocks and evolutionary timescales. Trends in Genetics 19:200-206. [Download PDF]
58
 PubMed PDF Google Rosenberg MS & Kumar S (2003) Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference. Molecular Biology and Evolution 20:610-621. [Download PDF]
57
 PubMed PDF Google Rosenberg MS & Kumar S (2003) Taxon sampling, bioinformatics, and phylogenomics. Systematic Biology 52:119-124. [Download PDF]
56
 PubMed PDF Google Rosenberg MS, Subramanian S & Kumar S (2003) Patterns of transitional mutation biases within and among mammalian genomes. Molecular Biology and Evolution 20:988-993. [Download PDF]
55
 PubMed PDF Google Miller MP, Parker JD, Rissing SW & Kumar S (2003) Quantifying the intragenic distribution of human disease mutations. Annals of Human Genetics 67:567-579. [Download PDF]
54
 PubMed PDF Google Jancovich JK, Mao J, Chinchar VG, Wyatt C, Case ST, Kumar S, Valente G, Subramanian S, Davidson EW, Collins JP & Jacobs BL (2003) Genomic sequence of a ranavirus (family Iridoviridae) associated with salamander mortalities in North America. Virology 316:90-103. [Download PDF]
53
 Book PDF Google 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. [Download PDF]
52
 Book PDF   Lorson C & Kumar S (2003) A review of the book Genomes (second edition) by Brown TA, The Quarterly Review of Biology 78:225. [Download PDF]
         
        2002
51
 PubMed PDF Google Kumar S & Subramanian S (2002) Mutation rates in mammalian genomes. Proceedings of the National Academy of Sciences (USA) 99:803-808. [Download PDF]
50
 PubMed PDF Google 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. [Download PDF]
49
 PubMed PDF Google Hedges SB & Kumar S (2002) Vertebrate genomes compared. Science 297:1283-1285. [Download PDF]
48
 PubMed PDF Google Tamura K & Kumar S (2002) Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Molecular Biology and Evolution 19:1727-1736. [Download PDF]
47
 PubMed PDF Google 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. [Download PDF]
46
 Book PDF   Kumar S & Newfeld SJ (2002) A review of the book Modern Genetic Analysis: Integrating Genes and Genomes (second edition) by Griffiths AJF, Gelbart WM, Lewontin RC, & Miller JH. The Quarterly Review of Biology 77:456-457. [Download PDF]
45
 Book PDF   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. [Download PDF]
         
        2001
44
 PubMed PDF Google Kumar S, Tamura K, Jakobsen IB & Nei M (2001) MEGA2: Molecular Evolutionary Genetics Analysis software. Bioinformatics 17:1244-1245. [www.megasoftware.net] [Download PDF]
43
 PubMed PDF Google Kumar S, Gadagkar SR, Filipski A & Gu X (2001) Determination of the number of conserved chromosomal segments between species. Genetics 157:1387-1395. [Download PDF]
42
 PubMed PDF Google 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. (See expanded proof in Genetics ) [Download PDF]
41
 PubMed PDF Google 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. [Download PDF]
40
 PubMed PDF Google Rosenberg MS & Kumar S (2001) Traditional phylogenetic reconstruction methods reconstruct shallow and deep evolutionary relationships equally well. Molecular Biology and Evolution 18:1823-1827. [Download PDF]
39
 PubMed PDF Google Miller MP & Kumar S (2001) Understanding human disease mutations through the use of interspecific genetic variation. Human Molecular Genetics 21:2319-2328. [Download PDF]
38
 PubMed PDF Google Hedrick P & Kumar S (2001) Mutation and linkage disequilibrium in human mtDNA. European Journal of Human Genetics 9:969-972. [Download PDF]
37
 PubMed PDF Google 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). [Download PDF]
36
 PDF Google 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. [Download PDF]
35
 PubMed PDF Google 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. [Download PDF]
34
 SPIE PDF Google 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. [Download PDF]
33
 Book PDF Google Kumar S & Filipski A (2001) Molecular phylogeny reconstruction. Encyclopedia of Life Sciences. Macmillan Reference Ltd, Oxford, Nature Publishing Group, UK (4 pp). [Download PDF]
32
 Book PDF   Kumar S & Filipski A (2001) Molecular clock: Testing. Encyclopedia of Life Sciences. Macmillan Reference Ltd, Oxford, Nature Publishing Group, UK (5 pp). [Download PDF]
         
        2000
31
 PubMed PDF Google 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. [Download PDF]
30
 PubMed PDF Google Kumar S, Hedrick P, Dowling T & Stoneking M (2000) Questioning evidence for recombination in human mitochondrial DNA. Science 288:1931a. [Download PDF]
29
 PubMed PDF Google 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. [Download PDF]
28
 Book   Google Nei M & Kumar S (2000) Molecular Evolution and Phylogenetics. Oxford University Press, New York (333 pp). [Translated in Russian, Chinese & Japanese]
27
 PubMed PDF Google 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. [Download PDF]
26
 Book PDF   Kumar S (2000) A review of the book Genomes by Brown TA. The Quarterly Review of Biology 75:316-317. [Download PDF]
25
       Kumar S (2000) LDA: Linkage Disequilibrium Analysis of Bi-Allelic Sites in Molecular Sequence Data. Version 1.0. Arizona State University, Tempe, Arizona. [Download LDA]
         
        1999
24
 PubMed PDF Google 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. [Download PDF]
23
 PDF Google Hedges SB & Kumar S (1999) Divergence times of eutherian mammals. Science 285:2031a (6 pp). [Download PDF]
22
 PubMed PDF Google 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. [Download PDF]
21
 PubMed PDF Google 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. [Download PDF]
         
        1998
20
 PubMed PDF Google Kumar S & Hedges SB (1998) A molecular timescale for vertebrate evolution. Nature 392:917-920. [Download PDF]
19
 PubMed PDF Google 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. [Download PDF]
         
        1997
18
 PubMed PDF Google Zhang J & Kumar S (1997) Detection of convergent and parallel evolution at the amino acid sequence level. Molecular Biology and Evolution 14:527-536. [Download PDF]
17
 PubMed PDF Google 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. [Download PDF]
16
 PubMed PDF Google 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. [Download PDF]
15
 PubMed PDF Google 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. [Download PDF]
14
 PubMed PDF Google 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. [Download PDF]
         
        1996
13
 PubMed PDF Google Kumar S (1996) Patterns of nucleotide substitution in mitochondrial protein coding genes of vertebrates. Genetics 143:537-548. [Download PDF]
12
 PubMed PDF Google Kumar S (1996) A stepwise algorithm for finding minimum evolution trees. Molecular Biology and Evolution 13:584-593. [Download PDF]
11
 PubMed PDF Google Kumar S & Rzhetsky A (1996) Evolutionary relationships of eukaryotic kingdoms. Journal of Molecular Evolution 42:183-193. [Download PDF]
10
 PubMed PDF Google Kumar S, Balczarek KA & Lai Z-C (1996) Evolution of the hedgehog gene family. Genetics 142:965-972. [Download PDF]
9
 PubMed PDF Google 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. [Download PDF]
8
 PubMed PDF Google Hedges SB, Parker PH, Sibley CG & Kumar S (1996) Continental breakup and the ordinal diversification of birds and mammals. Nature 381:226-229. [Download PDF]
7
   Google Kumar S (1996) PHYLTEST: Phylogenetic Hypothesis Testing Software. Version 2.0. Pennsylvania State University, University Park, Pennsylvania. [Download PHYLTEST]
         
        1995
6
 PubMed PDF Google Yang Z, Kumar S & Nei M (1995) A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641-1650. [Download PDF]
5
 PubMed PDF Google Rzhetsky A, Kumar S & Nei M (1995) Four-cluster analysis: A simple method to test phylogenetic hypotheses. Molecular Biology and Evolution 12:163-167. [Download PDF]
4
 PubMed PDF Google 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. [Download PDF]
         
        1994
3
 PubMed PDF Google Kumar S, Tamura K & Nei M (1994) MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. Computer Applications in Biosciences 10:189-191. [Download MEGA for DOS] [Download PDF]
         
        1993
2
     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
1
 PubMed PDF Google Hedges SB, Kumar S, Tamura K & Stoneking M (1992) Human origins and analysis of mitochondrial DNA sequences. Science 255:737-739. [Download PDF]