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Website, = Citations
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. doi:10.1371/journal.pbio.1000456
112
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
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
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
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
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]
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]
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
Hedges SB & Kumar S (2009) Discovering the timetree of life. The Timetree of Lifeedited by Hedges SB & Kumar S. Oxford University Press, New York, 3-18. [Download PDF]
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
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
Kumar S & Filipski A (2008) Molecular phylogeny reconstruction. Encyclopedia of Life Sciences. Macmillan Reference Ltd, Oxford, Nature Publishing
Group, UK. [Download 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
Filipski A, Prohaska S & Kumar
S (2007) Molecular signatures of adaptive evolution. Evolutionary Genomics and Proteomicsedited
by Pagel M & Pomiankowski
A. Sinauer Associates, Inc., Massachussets, 241-254. [Download PDF]
91
Drosophila 12 Genomes Consortium (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218. [Download PDF]
90
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
Acquisti C, Poste G, Curtiss D & Kumar S (2007) Nullomers: Really a matter of
natural selection? PLoS ONE 2 (3 pp). [Download PDF]
88
Kumar S & Dudley J (2007)
Bioinformatics software for biologists in the genomics era. Bioinformatics 23:1713-1717. [Download PDF]
Kumar S & Filipski A (2007)
Multiple sequence alignment: In pursuit of homologous DNA positions. Genome
Research 17:127-135. [Download PDF]
85
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
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
Hedges SB, Dudley J & Kumar S (2006)
TimeTree: A public knowledge-base of divergence times among
organisms. Bioinformatics 22:2971-2972. [Download PDF]
82
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
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]
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]
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]
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
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
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).
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]
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
Rosenberg MS & Kumar S (2003) Taxon sampling, bioinformatics, and phylogenomics. Systematic Biology 52:119-124. [Download PDF]
56
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
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
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
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]
Tamura K & Kumar S (2002) Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Molecular Biology and Evolution 19:1727-1736. [Download PDF]
47
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
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]
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
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]
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
Miller MP & Kumar S (2001) Understanding human disease mutations through the use of interspecific genetic variation. Human Molecular Genetics 21:2319-2328. [Download PDF]
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]
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]
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
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
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
Kumar S, Hedrick P, Dowling T & Stoneking M (2000) Questioning evidence for recombination in human mitochondrial DNA. Science 288:1931a. [Download PDF]
29
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
Nei M & Kumar S (2000)Molecular
Evolution and Phylogenetics. Oxford University Press, New
York (333 pp). [Translated in Russian, Chinese & Japanese]
27
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]
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
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
Hedges SB & Kumar S (1999) Divergence
times of eutherian mammals. Science 285:2031a
(6 pp). [Download PDF]
22
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
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
Kumar S & Hedges SB (1998) A molecular timescale for vertebrate evolution. Nature 392:917-920. [Download PDF]
19
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]
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
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
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
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
Kumar S (1996) Patterns of nucleotide substitution in mitochondrial protein coding genes of vertebrates. Genetics 143:537-548. [Download PDF]
Kumar S, Balczarek KA & Lai Z-C (1996) Evolution of the hedgehog gene family. Genetics 142:965-972. [Download PDF]
9
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
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
Kumar S (1996) PHYLTEST:
Phylogenetic Hypothesis Testing Software. Version 2.0. Pennsylvania
State University, University Park, Pennsylvania. [Download PHYLTEST]
1995
6
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]
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]
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
Hedges SB, Kumar S, Tamura K & Stoneking M (1992) Human origins and analysis of mitochondrial DNA sequences. Science 255:737-739. [Download PDF]
=
Abstract, 
= Reprint, 
= Book
Website, 
= Citations 
