Publications
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        2012
127 PubMed PDF Dudley JT, Chen R, Sanderford M, Butte AJ & Kumar S (2012) Evolutionary meta-analysis of association studies reveals ancient constraints affecting disease marker discovery . Molecular Biology and Evolution doi: 10.1093/molbev/mss079 [Download PDF]
126 PubMed PDF 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. [Download PDF]
125 PubMed PDF 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. [Download PDF]
         
        2011
124 PubMed PDF 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. [Download PDF]
123 PubMed PDF 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. [Download PDF]
122 PubMed PDF Kumar S & Hedges SB (2011) TimeTree2: Species divergence times on the iPhone. Bioinformatics 27:2023-2024. Epub 2011 May 26. [www.timetree.org]
121 PubMed PDF 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. [Download PDF]
120 PubMed PDF 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. [www.megasoftware.net]
119 PubMed PDF 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. [Download PDF]
118 PubMed PDF Gray VE & Kumar S (2011) Rampant purifying selection conserves positions with posttranslational modifications in human proteins. Molecular Biology and Evolution 28:1565-1568. Epub 2011 Jan 27. [Download PDF]
117 PDF Battistuzzi FU, Filipski A & Kumar S (2011) Molecular clock: Testing (version 2.0). Encyclopedia of Life Sciences. John Wiley & Sons, Ltd, Chichester, UK (7pp). [Download PDF]
116 PubMed PDF Pacheco MA, Battistuzzi FU, Lentino M, Aguilar RF, Kumar S & Escalante AA (2011) Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders. Molecular Biology and Evolution 28:1927-1942. Epub 2011 Jan 17. [Download PDF]
         
        2010
115 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. Epub 2010 Jan 21. [Download PDF]
114 PubMed PDF 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. [Download PDF]
113 PubMed PDF Li YX, 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 (US) 2009: 1445-1450. [Download PDF]
112 PubMed PDF 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. [Download PDF]
111       Kumar S (2010) Foreword for the book GENES: conceptual, molecular, and developmental by S Mitra. MacMillan Press, India. (In Press)
         
        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. Epub 2009 Jul 24. [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. Epub 2009 Jul 6. [Download PDF]
108 PubMed PDF Kumar S, Suleski MP, 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. Epub 2009 Jun 22. [Download PDF]
107 PubMed PDF Goering LM, Hunt PK, Heighington C, Busick C, Pennings PS, 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 Ji S, Yuan L, Li YX, Zhou ZH, 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 Ji S, Li YX, Zhou ZH, 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 Li YX, Ji S, Kumar S, Ye J & Zhou ZH (2009) Drosophila gene expression pattern annotation through 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 C, 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. Epub 2009 Apr 15. [Download PDF]
101 PubMed PDF Acquisti C, Elser JJ & Kumar S (2009) Ecological nitrogen limitation shapes the DNA composition of plant genomes. Molecular Biology and Evolution 26:953-956. Epub 2009 Mar 2. [Download PDF]
100 PubMed 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. Epub 2008 Oct 21. [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 Hedges SB & Kumar S (2009) The Timetree of Life. Oxford University Press, New York, (551 pp). [Download Book Chapter]
         
        2008
97
 PubMed 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
 PubMed PDF 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 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 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 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., Massachusetts, 241-254. [Download PDF]
91
 PubMed PDF Drosophila 12 Genomes Consortium (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218. [Download PDF]
90
 PubMed PDF 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 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 Kumar S & Dudley J (2007) Bioinformatics software for biologists in the genomics era. Bioinformatics 23:1713-1717. [Download PDF]
87
 PubMed PDF 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 Kumar S & Filipski A (2007) Multiple sequence alignment: In pursuit of homologous DNA positions. Genome Research 17:127-135. [Download PDF]
85
 PubMed PDF 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 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 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 Subramanian S & Kumar S (2006) Higher intensity of purifying 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 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 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 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 Hedges SB, Kumar S & van Tuinen M (2006) Constraining fossil calibrations for molecular clocks. BioEssays 28:770-771. [Download PDF]
         
        2005
77
 PubMed PDF Kumar S & Hedges SB (2005) Pushing back the expansion of introns in animal genomes. Cell 123:1182-1184. [Download PDF]
76
 PubMed PDF 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 Kumar S (2005) Molecular clocks: Four decades of evolution. Nature Reviews Genetics 6:654-662. [Download PDF]
74
 PubMed PDF 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 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 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 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 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 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 Hedges SB & Kumar S (2004) Precision of molecular time estimates. Trends in Genetics 20:242-247. [Download PDF]
66
 PubMed PDF 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 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 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 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 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 Hedges SB & Kumar S (2003) Genomic clocks and evolutionary timescales. Trends in Genetics 19:200-206. [Download PDF]
58
 PubMed 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
 PubMed PDF Rosenberg MS & Kumar S (2003) Taxon sampling, bioinformatics, and phylogenomics. Systematic Biology 52:119-124. [Download PDF]
56
 PubMed PDF 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 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 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 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 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 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 Hedges SB & Kumar S (2002) Vertebrate genomes compared. Science 297:1283-1285. [Download PDF]
48
 PubMed 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
 PubMed PDF 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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   Nei M & Kumar S (2000) Molecular Evolution and Phylogenetics. Oxford University Press, New York (333 pp). [Translated in Russian, Chinese & Japanese]
27
 PubMed PDF 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]