Filipski, Alan ; Prohaska, Sonja ; Kumar, Sudhir (2008) Molecular Signatures of Adaptive Evolution Evolutionary Genomics and Proteomics (2008) 241-254

Collins, Sinéad ; de Meaux, Juliette ; Acquisti, Claudia (2007) Adaptive walks toward a moving optimum Genetics. Vol 176. No 2. (2007 Jun) 1089-99

Kumar, Sudhir ; Dudley, Joel (2007) Bioinformatics Software for Biologists in the Genomics Era Bioinformatics. (2007 May 7)

Zhang, Yu ; Sturgill, David ; Parisi, Michael ; Kumar, Sudhir ; Oliver, Brian (2007) Constraint and turnover in sex-biased gene expression in the genus Drosophila Nature. Vol 450. No 7167 (2007 Nov 8) 233-237

Clark, A. G. ; Eisen, M. B. ; Smith, D. R. ; Bergman, C. M. ; Oliver, B. ; Markow, T. A. ; Kaufman, T. C. ; Kellis, M. ; Gelbart, W., [and more] (2007) Evolution of genes and genomes on the Drosophila phylogeny Nature. Vol 450. No 7167 (2007-11-08) 203-218

Perry, George H ; Tito, Raul Y ; Verrelli, Brian C (2007) The Evolutionary History of Human and Chimpanzee Y-Chromosome Gene Loss Mol Biol Evol. (2007 Jan 11)

Colbourn, Charles ; Kumar, Sudhir (2007) Lower Bounds on Multiple Sequence Alignment using Exact 3-way Alignment BMC Bioinformatics. Vol 8. No 1. (2007 Apr 30) p. 140

Tamura, Koichiro ; Dudley, Joel ; Nei, Masatoshi ; Kumar, Sudhir (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0 Mol Biol Evol. (2007 May 7)

Kumar, Sudhir ; Filipski, Alan (2007) Multiple sequence alignment: In pursuit of homologous DNA positions Genome research. Vol 17. No 2. (2007 Feb) p. 127-35

Acquisti, Claudia ; Poste, George ; Curtiss, David ; Kumar, Sudhir (2007) Nullomers: really a matter of natural selection? PLoS ONE. Vol 2. No 10. (2007) e1022

Acquisti, Claudia ; Kleffe, Jürgen ; Collins, Sinéad (2007) Oxygen content of transmembrane proteins over macroevolutionary time scales Nature. Vol 445, No 7123 (2007 Jan 04) p. 47-52

Hudson, Stephanie ; Garrett, Matthew ; Micklem, Gos ; Goldstein, Elliott ; Newfeld, Stuart (2007) Phylogenetic and genome-wide analyses suggest a functional relationship between kayak the Drosophila Fos homolog and fig a predicted PP2C phosphatase nested within a kayak intron Genetics. (2007 Mar 4)

Kim, Yuseob (2007) Rate of adaptive peak shifts with partial genetic robustness Evolution; international journal of organic evolution. Vol 61. No 8. (2007 Aug) 1847-56

Ye, Jieping ; Chen, Jianhui ; Li, Qi ; Kumar, Sudhir (2006) Classification of Drosophila embryonic developmental stage range based on gene expression pattern images Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. (2006) p. 293-8

Ye, J. ; Chen, J. ; Li, Q. ; Kumar, S. (2006) Classification of Drospophila embryonic developmental stage range based on gene expression pattern images Computational systems bioinformatics : CSB2006 conference proceedings, Stanford CA, 14-18 August 2006. (2006) p. 293-298

Xia, Xuhua ; Kumar, Sudhir (2006) Codon-based detection of positive selection can be biased by heterogeneous distribution of polar amino acids along protein sequences Computational systems bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. (2006) p. 335-40

Ye, J. ; Xiong, T. (2006) Computational and Theoretical Analysis of Null Space and Orthogonal Linear Discriminant Analysis The Journal of Machine Learning Research. Vol 7 (2006) 1183-1204

Hedges, S Blair ; Kumar, Sudhir ; van Tuinen, Marcel (2006) Constraining fossil calibrations for molecular clocks Bioessays. Vol 28. No 7. p. 770-771 (2006 Jul 18)

Verrelli, Brian C ; Tishkoff, Sarah A ; Stone, Anne C ; Touchman, Jeffrey W (2006) Contrasting Histories of G6PD Molecular Evolution and Malarial Resistance in Humans and Chimpanzees Mol Biol Evol. Vol 23. No 8. p. 1592-1601 (2006 Aug)

Ye, Jieping ; Xiong, Tao ; Janardan, Ravi (2006) CPM: A covariance-preserving projection method Sixth SIAM International Conference on Data Mining, Apr 20-22 2006. Vol 2006. (2006) p. 24-34

Ye, Jieping ; Xiong, Tao ; Li, Qi ; Janardan, Ravi ; Bi, Jinbo ; Cherkassky, Vladimir ; Kambhamettu, Chandra (2006) Efficient model selection for regularized linear discriminant analysis CIKM 2006 proceedings of the 15th ACM International Conference on Information and Knowledge Management, November 6-11, 2006. (2006) p. 1 CD-ROM

Subramanian, Sankar ; Kumar, Sudhir (2006) Evolutionary anatomies of positions and types of disease-associated and neutral amino acid mutations in the human genome BMC genomics. Vol 7. (2006) p. 306

Ye, Jieping ; Janardan, Ravi ; Li, Qi ; Park, Haesun (2006) Feature reduction via generalized uncorrelated linear discriminant analysis IEEE Transactions on Knowledge and Data Engineering. Vol 18. No 10. (2006) p. 1312-1322

Stone, Anne C ; Verrelli, Brian C (2006) Focusing on comparative ape population genetics in the post-genomic age . (2006 Sep 27) p.

Hedrick, Philip W ; Verrelli, Brian C (2006) "Ground truth" for selection on CCR5-Delta32. Trends in genetics : TIG. Vol 22. No 6. p. 293-6 (2006 Jun)

Subramanian, Sankar ; Kumar, Sudhir (2006) Higher Intensity of Purifying Selection on >90% of the Human Genes Revealed by the Intrinsic Replacement Mutation Rates . (2006 Sep 18) p.

Ogden, T Heath ; Rosenberg, Michael S (2006) How should gaps be treated in parsimony? A comparison of approaches using simulation Mol Phylogenet Evol (2006 Aug 22)

Xiong, Tao ; Ye, Jieping ; Cherkassky, Vladimir (2006) Kernel uncorrelated and orthogonal discriminant analysis: A unified approach 2006 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, CVPR 2006. Vol 1. (2006-06-17) p. 125-131

Anderson, Douglas M ; Arredondo, Jennifer ; Hahn, Katherine ; Valente, Graziela ; Martin, James F ; Wilson-Rawls, Jeanne ; Rawls, Alan (2006) Mohawk is a novel homeobox gene expressed in the developing mouse embryo Developmental dynamics : an official publication of the American Association of Anatomists. Vol 235. No 3. p. 792-801 (2006 Mar)

Perry, George H ; Verrelli, Brian C ; Stone, Anne C (2006) Molecular evolution of the primate developmental genes MSX1 and PAX9 Molecular biology and evolution. Vol 23. No 3. p. 644-54 (2006 Mar)

Ogdenw, T Heath ; Rosenberg, Michael S (2006) Multiple sequence alignment accuracy and phylogenetic inference Systematic biology. Vol 55. No 2. p. 314-28 (2006 Apr)

Ye, J. P. ; Ilinkin, I. ; Janardan, R. ; Isom, A. (2006) Multiple structure alignment and consensus identification for proteins Algorithms in Bioinformatics, Proceedings. Vol 4175. (2006) p. 115-125

Ye, Jieping ; Xiong, Tao (2006) Null space versus orthogonal linear discriminant analysis Proceedings of the 23rd International Conference on Machine Learning : Pittsburgh, Pennsylvania : June 25-29, 2006. (2006) p. 1073-1080

Ye, Jieping ; Wan, Tie (2006) Regularized Discriminant Analysis for high dimensional, low sample size data KDD-2006 : proceedings of the Twelfth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining : August 20-23, 2006, Philadelphia, PA, USA. (2006) p. 454-463

Elser, James J ; Fagan, William F ; Subramanian, Sankar ; Kumar, Sudhir (2006) Signatures of Ecological Resource Availability in the Animal and Plant Proteomes Mol Biol Evol (2006 Jul 26)

Li, Qi ; Ye, Jieping ; Kambhamettu, C. (2006) Spatial interest pixels (SIPs): useful low-level features of visual media data Multimedia Tools and Applications. Vol 30. No 1. (2006) p. 89-108

Hedges, S Blair ; Dudley, Joel ; Kumar, Sudhir (2006) TimeTree: a public knowledge-base of divergence times among organisms Bioinformatics (Oxford, England). Vol 22. No 23. (2006 Dec 1) p. 2971-2

Gargesha, Madhusudhana ; Yang, Jian ; Van Emden, Bernard ; Panchanathan, Sethuraman ; Kumar, Sudhir (2005) Automatic annotation techniques for gene expression images of the fruit fly embryo Medical Imaging; Proceedings of the SPIE. Vol 5960. p. 576-583 (2005)

Perry, George H ; Verrelli, Brian C ; Stone, Anne C (2005) Comparative analyses reveal a complex history of molecular evolution for human MYH16 Molecular biology and evolution. Vol 22. No 3. p. 379-82 (2005 Mar)

Ye, Jieping ; Xiong, Tao (2005) Computational and theoretical analysis of null space and orthogonal linear discriminant analysis Journal of Machine Learning Research. Vol 7. (2005) p. 1183-1204

Rosenberg, Michael S (2005) Evolutionary distance estimation and fidelity of pair wise sequence alignment BMC bioinformatics [electronic resource]. Vol 102 (2005)

Rosenberg, Michael S (2005) The file-drawer problem revisited: a general weighted method for calculating fail-safe numbers in meta-analysis Evolution; international journal of organic evolution. Vol 59. No 2. p. 464-8 (2005 Feb)

Gadagkar, Sudhindra R ; Rosenberg, Michael S ; Kumar, Sudhir (2005) Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree Journal of experimental zoology. Part B. Molecular and developmental evolution. Vol 304. No 1. p. 64-74 (2005 Jan 15)

Gadagkar, Sudhindra R ; Kumar, Sudhir (2005) Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous Molecular biology and evolution. Vol 22. No 11. p. 2139-41 (2005 Nov)

Kumar, Sudhir (2005) Molecular clocks: four decades of evolution Nature reviews. Genetics. Vol 6. No 8. p. 654-62 (2005 Aug)

Rosenberg, Michael S (2005) Multiple sequence alignment accuracy and evolutionary distance estimation BMC bioinformatics [electronic resource]. 278 (2005)

Rosenberg, Michael S. (2005) MySSP: Non-stationary evolutionary sequence simulation, including indels Evolutionary Bioinformatics Online. Vol 1. p. 51-53 (2005)

Kumar, Sudhir ; Filipski, Alan ; Swarna, Vinod ; Walker, Alan ; Hedges, S Blair (2005) Placing confidence limits on the molecular age of the human-chimpanzee divergence Proceedings of the National Academy of Sciences of the United States of America. Vol 102. No 52. p. 18842-7 (2005 Dec 27)

Subramanian, Sankar ; Kumar, Sudhir (2004) Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome Genetics. Vol 168. No 1. p. 373-81 (2004 Sep)

Gurunathan, Rajalakshmi ; Van Emden, Bernard ; Panchanathan, Sethuraman ; Kumar, Sudhir (2004) Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations BMC bioinformatics [electronic resource]. Vol 5. No 1. p. 202 (2004)

Kumar, Sudhir ; Tamura, Koichiro ; Nei, Masatoshi (2004) MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment Briefings in bioinformatics. Vol 5. No 2. p. 150-63 (2004 Jun)

Kumar, Sudhir ; Filipski, Alan (2004) Phylogenetic Analysis Dictionary of bioinformatics and computational biology. (2004)

Hedges, S Blair ; Kumar, Sudhir (2004) Precision of molecular time estimates Trends in genetics : TIG. Vol 20. No 5. p. 242-7 (2004 May)

Tamura, Koichiro ; Nei, Masatoshi ; Kumar, Sudhir (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method Proceedings of the National Academy of Sciences of the United States of America. Vol 101. No 30. p. 11030-5 (2004 Jul 27)

Verrelli, Brian C ; Tishkoff, Sarah A (2004) Signatures of selection and gene conversion associated with human color vision variation American journal of human genetics. Vol 75. No 3. p. 363-75 (2004 Sep)

Briscoe, Adriana D. ; Gaur, Charu ; Kumar, Sudhir (2004) The spectrum of human rhodopsin disease mutations through the lens of interspecific variation Gene (Amsterdam). Vol 332. No May 12. p. 107-118 (2004)

Tamura, Koichiro ; Subramanian, Sankar ; Kumar, Sudhir (2004) Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks Molecular biology and evolution. Vol 21. No 1. p. 36-44 (2004 Jan)

Blair Hedges, S ; Kumar, Sudhir (2003) Genomic clocks and evolutionary timescales Trends in genetics : TIG. Vol 19. No 4. p. 200-6 (2003 Apr)

Jancovich, James K ; Mao, Jinghe ; Chinchar, V Gregory ; Wyatt, Christopher ; Case, Steven T ; Kumar, Sudhir ; Valente, Graziela ; Subramanian, Sankar ; Davidson, Elizabeth W, [and more] (2003) Genomic sequence of a ranavirus (family Iridoviridae) associated with salamander mortalities in North America Virology. Vol 316. No 1. p. 90-103 (2003 Nov 10)

Rosenberg, Michael S ; Kumar, Sudhir (2003) Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference Molecular biology and evolution. Vol 20. No 4. p. 610-21 (2003 Apr)

Subramanian, Sankar ; Kumar, Sudhir (2003) Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes Genome research. Vol 13. No 5. p. 838-44 (2003 May)

Rosenberg, Michael S ; Subramanian, Sankar ; Kumar, Sudhir (2003) Patterns of transitional mutation biases within and among mammalian genomes Molecular biology and evolution. Vol 20. No 6. p. 988-93 (2003 Jun)

Miller, M P ; Parker, J D ; Rissing, S W ; Kumar, S (2003) Quantifying the intragenic distribution of human disease mutations Annals of human genetics. Vol 67. No Pt 6. p. 567-79 (2003 Nov)

Kumar, Sudhir ; Jayaraman, Karthik ; Panchanathan, Sethuraman ; Gurunathan, Rajalakshmi ; Marti-Subirana, Ana ; Newfeld, Stuart J (2002) BEST: a novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development Genetics. Vol 162. No 4. p. 2037-47 (2002 Dec)