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| 99 |
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Kumar S & Hedges SB (2009) Discovering the timetree of life. The Timetree of Life edited by Hedges SB & Kumar S. Oxford University Press, New York, In press. |
| 98 |
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Hedges SB & Kumar S (2009) The Timetree of Life. Oxford University Press, New York (480 pages; in press). |
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| 97 |
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Ji S, Sun L, Jin R, Kumar S & Ye J (2008) Automated annotation of Drosophila gene expression patterns using a controlled vocabulary. Bioinformatics (doi: 10.1093/bioinformatics/btn347). |
| 96 |
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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. |
| 95 |
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Kumar S & Filipski A (2008) Molecular phylogeny reconstruction. Encyclopedia of Life Sciences. Macmillan Reference Ltd, Oxford, Nature Publishing
Group, UK. |
| 94 |
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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. |
| 93 |
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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. |
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| 92 |
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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. |
| 91 |
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Drosophila 12 Genomes Consortium (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218. |
| 90 |
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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. |
| 89 |
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Acquisti C, Poste G, Curtiss D & Kumar S (2007) Nullomers: Really a matter of
natural selection? PLoS ONE 2 (3 pp). |
| 88 |
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Kumar S & Dudley J (2007)
Bioinformatics software for biologists in the genomics era. Bioinformatics 23:1713-1717. |
| 87 |
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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] |
| 86 |
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Kumar S & Filipski A (2007)
Multiple sequence alignment: In pursuit of homologous DNA positions. Genome
Research 17:127-135. |
| 85 |
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Colbourn CJ & Kumar S (2007)
Lower bounds on multiple sequence alignment using exact 3-way alignment. BMC Bioinformatics 8:140 (8 pp). |
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| 84 |
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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). |
| 83 |
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Hedges SB, Dudley J & Kumar S (2006)
TimeTree: A public knowledge-base of divergence times among
organisms. Bioinformatics 22:2971-2972. |
| 82 |
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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. |
| 81 |
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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. |
| 80 |
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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. |
| 79 |
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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. |
| 78 |
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Hedges SB, Kumar S & van Tuinen
M (2006)
Constraining fossil calibrations for molecular clocks. BioEssays 28:770-771. |
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| 77 |
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Kumar S & Hedges SB (2005)
Pushing back the expansion of introns in animal genomes. Cell 123:1182-1184. |
| 76 |
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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. |
| 75 |
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Kumar S (2005) Molecular
clocks: Four decades of evolution. Nature
Reviews Genetics 6:654-662. |
| 74 |
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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. |
| 73 |
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Gadagkar SR & Kumar
S (2005) Maximum likelihood outperforms maximum parsimony
even when evolutionary rates are heterotachous. Molecular
Biology and Evolution 22:2139-2141. |
| 72 |
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Filipski A & Kumar
S (2005) Comparative genomics in eukaryotes.The
Evolution of the Genome edited by Ryan TG. Elsevier, San Diego, 521-583. |
| 71 |
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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. |
| 70 |
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Kumar S & Filipski
A (2005) Reconstructing vertebrate phylogeny. Encyclopedia
of Genetics, Genomics, Proteomics, and Bioinformatics edited
by Subramaniam S. John Wiley & Sons, New York. |
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| 69 |
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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] |
| 68 |
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Subramanian S & Kumar
S (2004) Gene expression intensity shapes evolutionary
rates of the proteins encoded by the vertebrate genome. Genetics 168:373-381. |
| 67 |
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Hedges SB & Kumar S (2004) Precision of molecular time estimates. Trends in Genetics 20:242-247. |
| 66 |
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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. |
| 65 |
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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. |
| 64 |
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Briscoe AD, Gaur C & Kumar S (2004) The spectrum of human rhodopsin disease mutations through the lens of interspecific variation. Gene 332:107-118. |
| 63 |
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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). |
| 62 |
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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 |
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Kumar S & Filipski A (2004) Phylogenetic Analysis. Dictionary of Bioinformatics and Computational Biology edited by Hancock J & Zvelebil M, Wiley-Liss, New York. |
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| 60 |
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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. |
| 59 |
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Hedges SB & Kumar S (2003) Genomic clocks and evolutionary timescales. Trends in Genetics 19:200-206. |
| 58 |
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Rosenberg MS & Kumar S (2003) Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference. Molecular Biology and Evolution 20:610-621. |
| 57 |
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Rosenberg MS & Kumar S (2003) Taxon sampling, bioinformatics, and phylogenomics. Systematic Biology 52:119-124. |
| 56 |
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Rosenberg MS, Subramanian S & Kumar S (2003) Patterns of transitional mutation biases within and among mammalian genomes. Molecular Biology and Evolution 20:988-993. |
| 55 |
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Miller MP, Parker JD, Rissing SW & Kumar S (2003) Quantifying the intragenic distribution of human disease mutations. Annals of Human Genetics 67:567-579. |
| 54 |
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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. |
| 53 |
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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. |
| 52 |
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Lorson C & Kumar S (2003) A review of the book Genomes (second edition) by Brown TA, The Quarterly Review of Biology 78:225. |
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| 51 |
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Kumar S & Subramanian S (2002) Mutation rates in mammalian genomes. Proceedings of the National Academy of Sciences (USA) 99:803-808. |
| 50 |
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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. |
| 49 |
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Hedges SB & Kumar S (2002) Vertebrate genomes compared. Science 297:1283-1285. |
| 48 |
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Tamura K & Kumar S (2002) Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Molecular Biology and Evolution 19:1727-1736. |
| 47 |
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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. |
| 46 |
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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. |
| 45 |
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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. |
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| 44 |
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Kumar S, Tamura K, Jakobsen
IB & Nei M (2001) MEGA2: Molecular Evolutionary Genetics
Analysis software. Bioinformatics 17:1244-1245.
[www.megasoftware.net] |
| 43 |
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Kumar S, Gadagkar SR, Filipski A & Gu X (2001) Determination of the number of conserved chromosomal segments between species. Genetics 157:1387-1395. |
| 42 |
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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 . |
| 41 |
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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. |
| 40 |
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Rosenberg MS & Kumar S (2001) Traditional phylogenetic reconstruction methods reconstruct shallow and deep evolutionary relationships equally well. Molecular Biology and Evolution 18:1823-1827. |
| 39 |
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Miller MP & Kumar S (2001) Understanding human disease mutations through the use of interspecific genetic variation. Human Molecular Genetics 21:2319-2328. |
| 38 |
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Hedrick P & Kumar S (2001) Mutation and linkage disequilibrium in human mtDNA. European Journal of Human Genetics 9:969-972. |
37 |
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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). |
| 36 |
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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. |
| 35 |
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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. |
| 34 |
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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. |
| 33 |
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Kumar S & Filipski
A (2001) Molecular phylogeny reconstruction. Encyclopedia
of Life Sciences. Macmillan Reference Ltd, Oxford, Nature Publishing
Group, UK (4 pp). |
| 32 |
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Kumar S & Filipski
A (2001) Molecular clock: Testing. Encyclopedia
of Life Sciences. Macmillan Reference Ltd, Oxford, Nature Publishing
Group, UK (5 pp). |
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| 31 |
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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. |
| 30 |
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Kumar S, Hedrick P, Dowling T & Stoneking M (2000) Questioning evidence for recombination in human mitochondrial DNA. Science 288:1931a. |
| 29 |
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