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(480)727-6949

Sudhir Kumar, PhD

Director

The Biodesign Institute, Evolutionary Functional Genomics

Professor

College of Liberal Arts and Sciences, School of Life Sciences

Bio

Sudhir Kumar leads a team of interdisciplinary scientists who are developing new computer-based methods of studying and analyzing the tens of thousands of genes in humans and related species, enabling researchers to learn their functions and origins. Dr. Kumar is a renowned expert in the field of evolutionary bioinformatics, who received an Innovation Award in Functional Genomics from the Burroughs Wellcome Fund in 2000. In 2004 he joined the elite ranks of most-cited researchers, being among the top ten in number of citations in the field of computer science over the last decade. Among his more than 70 papers and books are three “Hot Papers,” which were cited among the most of any in their fields.

Dr. Kumar is an interdisciplinary scientist who brings the problem-solving skills from his undergraduate engineering background together with his knowledge of evolutionary genetics from his doctoral work to tackle long-standing problems in functional genomics and evolutionary biology. He has made pioneering efforts in developing bioinformatics tools and databases for the analysis of gene expression patterns from early stages of the fruit fly development. He has also conducted breakthrough work using protein molecular clocks to illuminate the Evolutionary Timescale of Life. Over the last decade, Dr. Kumar has led the team that developed the Molecular Evolutionary Genetics Analysis (MEGA) software in order to make useful methods of comparative sequence analysis easily accessible to the scientific community for research and education. His research is funded by National Institutes of Health and National Science Foundation, among other agencies.

Dr. Kumar is professor of biology at ASU, where he teaches undergraduate-level evolutionary biology and graduate-level evolutionary genomics classes. He is a standing member of the NIH review panel and a member of many journal editorial boards, including Molecular Biology and Evolution, Genome Research, Evolutionary Bioinformatics Online, and Gene: Functional Genomics. Dr. Kumar is currently the webmaster for Society for Molecular Biology and Evolution and American Genetic Association. He received his B.E. in Electrical/Electronics Engineering and M.Sc. in Biological Sciences from Birla Institute of Technology and Sciences in India, and his Ph.D. in Genetics from Pennsylvania State University.

Selected Publications

2008

  • Filipski, A, Kumar, Sudhir. Molecular phylogeny reconstruction. Handbook of Human Molecular Evolution (2008).
  • Kumar, Sudhir, Nei, M., Dudley, J., Tamura, K.. MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics (2008).
  • Kumar, Sudhir, Ye, Jieping, Janardan, R.. Biological image analysis via matrix approximation. Encyclopedia of Data (2008).
  • Kumar, Sudhir, Ye, Jieping, Janardan, R.. Developmental stage annotation of drosophila gene expression pattern images via an entire solution path for LDA. ACM Transactions on Knowledge Discovery from Data (2008).

2007

  • Acquisti, Claudia, Poste, George Henry, Curtiss, David, Kumar, Sudhir. Nullomers: really a matter of natural selection?. PLoS ONE (2007).
  • Clark, Andrew G, Kumar, Sudhir. Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007).
  • Colbourn, C J, Kumar, Sudhir. Lower bounds on multiple sequence alignment using exact 3-way alignment. BMC Bioinformatics (2007).
  • Kumar, Sudhir. InCites (Science Citation Index) 2007 August 2007 http://www.in-cites.com/media/index.html#Sudhir_Kuman0. (2007).
  • Kumar, Sudhir. Bioinform 2007 01 June 2007 http://www.bioinform.com/issues/11_22/expression_profile/140355-1.html. (2007).
  • Kumar, Sudhir, Dudley, J. Bioinformatics software for biologists in the genomics era. Bioinformatics (2007).
  • Kumar, Sudhir, Filipski, Alan J. Multiple sequence alignment: In pursuit of homologous DNA positions. Genome Research (2007).
  • Tamura, K, Dudley, J, Nei, M, Kumar, Sudhir. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution (2007).
  • Zhang, Y., Kumar, Sudhir, Sturgill, D., Parisi, M., Oliver, B.. Constraint and turnover in sex-biased gene expression in the genus Drosophila. Nature (2007).

2006

  • Elser, James Joseph, Fagan, W F, Subramanian, S, Kumar, Sudhir. Signatures of ecological resource availability in the animal and plant proteomes. Molecular Biology and Evolution (2006).
  • Hedges, S B, Dudley, J, Kumar, Sudhir. TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics (2006).
  • Hedges, S B, Kumar, Sudhir, van Tuinen, M. Constraining fossil calibrations for molecular clocks. BioEssays (2006).
  • Kumar, Sudhir. A web-accessible database containing published times of tetrapod species divergence inferred using molecular data (Version 1). (2006).
  • Kumar, Sudhir. A database of spatial gene expression patterns in the fruit fly embryos, with an ability to find the overlapping patterns of gene expression by means of image-analysis (Version 1). (2006).
  • Kumar, Sudhir, Filiski, A. Multiple sequence alignment: in pursuit of homologous DNA positions. Genome Research (in press) (2006).
  • Subramanian, S, Kumar, Sudhir. Higher intensity of natural selection on >90% of the human genes revealed by the intrinsic replacement mutation rates. Molecular Biology and Evolution (2006).
  • Subramanian, S, Kumar, Sudhir. Evolutionary anatomies of positions and types of disease-associated and neutral amino acid mutations in the human genome. BMC Genomics (2006).
  • Xia, X, Kumar, Sudhir. Codon-based detection of positive selection can be biased by heterogeneous distribution of polar amino acids along protein sequences. Advances in Bioinformatics and Computational Biology (2006).
  • Ye, J, Chen, J, Li, Q, Kumar, Sudhir. Classification of Drosophila embryonic developmental stage range based on gene expression pattern images. Advances in Bioinformatics and Computational Biology (2006).

2005

  • Filipski, A, Kumar, Sudhir. Comparative Genomics in Eukaryotes. The Evolution of the Genome (2005).
  • Filipski, A, Kumar, Sudhir. Comparative Genomics in Eukaryotes. The Evolution of the Genome (2005).
  • Gadagkar, S R, Kumar, Sudhir. Maximum Likelihood Outperforms Maximum Parsimony even when Evolutionary Rates are Heterotachous. Molecular Biology and Evolution (2005).
  • Gadagkar, S R, Rosenberg, M S, Kumar, Sudhir. Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree. Journal of Experimental Zoology (Molecular & Developmental Evolution) (2005).
  • Gargesha, M, Yang, J, Emden, B Van, Panchanathan, S, Kumar, Sudhir. Automatic annotation techniques for gene expression images of the fruit fly embryo. Proceedings of Society of Photo-optical Instrumentation Engineers (Visual Communications and Image Processing 2005) (2005).
  • Gargesha, M, Yang, J, Van Emden, B, Panchanathan, S, Kumar, Sudhir. Automatic Annotation Techniques for Gene Expression Images of the Fruit Fly Embryo. Proceedings of SPIE (Visual Communications and Image Processing 2005) (2005).
  • Kumar, Sudhir. Molecular Clocks: four decades of evolution. Nature Reviews Genetics (2005).
  • Kumar, Sudhir, Filipski, A. Reconstructing Vertebrate Phylogeny. Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics (2005).
  • Kumar, Sudhir, Filipski, A, Swarna, V, Walker, A, Hedges, S B. Placing confidence limits on the molecular age of the human-chimpanzee divergence. Proceedings of the National Academy of Sciences (USA) (2005).
  • Kumar, Sudhir, Hedges, S B. Pushing back the expansion of introns in animal genomes. Cell (2005).
  • Kumar, Sudhir, Hedges, S B. Pushing Back the expansion of Introns in Animal Genomes. (2005).

2004

  • Briscoe, A, Gaur, C, Kumar, Sudhir. The spectrum of human rhodopsin disease mutations through the lens of interspecific variation. Gene (2004).
  • Gargesha, M, Antin, P, Van Emden, B, Panchanathan, S, Kumar, Sudhir. Image Registration and Similarity Computation for Chicken Gene Expression Patterns. Workshop on Genomic Signal Processing and Statistics (GENSIPS), IEEE Signal Processing Society (2004).
  • Gurunathan, R, Van Emden, B, Panchanathan, S, Kumar, Sudhir. Identifying Spatially Similar Gene Expression Patterns in Early Stage Fruit Fly Embryo Images: Binary Feature Versus Invariant Moment Digital Representations. BMC Bioinformatics (2004).
  • Hedges, S B, Dudley, J, Pisani, D, Swarma, V, Kumar, Sudhir. Timescale: evolutionary timescale database version 1.0. (2004).
  • Hedges, S B, Kumar, Sudhir. Precision of Molecular Time Estimates. Trends in Genetics (2004).
  • Kumar, Sudhir. American Genetic Association 2004 2004 http://www.theaga.org. (2004).
  • Kumar, Sudhir. A website for the Society for Molecular Biology and Evolution. (2004).
  • Kumar, Sudhir, Dudley, J. EF Navigator: A Database of Evolutionary Footprints in multigene families; Vesion 1.0. (2004).
  • Kumar, Sudhir, Filipski, A. Phylogenetic Analysis. Dictionary of Bioinformatics and Computational Biology (2004).
  • Kumar, Sudhir, Filipski, A. Phylogenetic Analysis. Dictionary of Bioinformatics (2004).
  • Kumar, Sudhir, Tamura, K, Nei, M. MEGA3: A website for downloading Molecular Evolutionary Genetics Analysis Software version 3.0. (2004).
  • Kumar, Sudhir, Tamura, K, Nei, M. MEGA3: Integrated Software for Molecular Evolutionary Genetics Analysis and Sequence Alignment. Briefings in Bioinformatics (2004).
  • Subramanian, S, Kumar, Sudhir. Gene Expression Intensity Shapes Evolutionary Rates of the Proteins Encoded by the Vertebrate Genome. Genetics (2004).
  • Tamura, K, Nei, M, Kumar, Sudhir. Prospects for Inferring Very Large Phylogenies by Using the Neighbor-Joining Method. Proceedings of the National Academy of Sciences (USA) (2004).
  • Tamura, K, Subramanian, S, Kumar, Sudhir. Temporal Patterns of Fruit Fly Evolution Revealed by Mutation Clocks. Molecular Biology and Evolution (2004).

2003

  • Hedges, S B, Kumar, Sudhir. Genomic Clocks and Evolutionary Timescales. Trends in Genetics (2003).
  • Jancovich, J K, Mao, J, Chinchar, V G, Wyatt, C, Case, S T, Kumar, Sudhir, Valente, G, Subramanian, S, Davidson, E W, Collind, J P, Jacobs, Bertram Lewis. Genomic Sequence of a Ranavirus (Family Iridoviridae) Associated with Salamander Mortalities in North America. Virology (2003).
  • Kumar, Sudhir. Review of A Review of Genomes (Second Edition) by Brown TA The Quarterly Review of Biology 2003 2003 . Review of A Review of Genomes (Second Edition) by Brown TA (2003).
  • Kumar, Sudhir. Review of MacTrees Made Easy Molecular Phylogenetics & Evolution 2003 2003 . Review of MacTrees Made Easy (2003).
  • Miller, M P, Parker, J D, Rissing, S W, Kumar, Sudhir. Quantifying the Inragenic Distribution of Disease Mutations. Annals of Human Genetics (2003).
  • Rosenberg, M S, Kumar, Sudhir. Herogeneity of Nucleotide Frequencies Among Evolutionary Lineages and Phylogenetic Inference. Molecular Biology and Evolution (2003).
  • Rosenberg, M S, Subramanian, S, Kumar, Sudhir. Patterns of Mutational Biases Within and Among Mammalian Genomes. Molecular Biology and Evolution (2003).
  • Rosenberg, Michael, Kumar, Sudhir. Taxon sampling, bioinformatics, and phylogenomics. Systematic Biology (2003).
  • Subramanian, S, Kumar, Sudhir. Neutral Substitutions Occur at a Faster Rate in Exons Than in Noncoding DNA in Primate Genomes. Genome Research (2003).

2002

  • Hedges, S B, Chen, H, Kumar, Sudhir, Wang, DY-C, Thompson, A S, Watanabe, H. A genomic timescale for the origin of eukaryotes. BMC Evolutionary Biology (2002).
  • Hedges, S B, Kumar, Sudhir. Vertebrate genomes compared. Science (2002).
  • Jiang, Z, Melville, J S, Cao, H, Kumar, Sudhir, Filipski, A, Gibbins, AM Verrinder. Measuring conservation of contiguous sets of autosomal markers on bovine and porcine genomes in relation to the map of the human genome. Genome (2002).
  • Kumar, Sudhir, Newfeld, S J. Review of Modern Genetic Analysis: Integrating Genes and Genomes The Quarterly Review of Biology 2002 2002 . Review of Modern Genetic Analysis: Integrating Genes and Genomes (2002).
  • Kumar, Sudhir, Subramanian, S. Mutation rates in mammalian genomes. Proceedings of the National Academy of Sciences (USA) (2002).
  • Rawls, A, Kumar, Sudhir. Review of Genomic Regulatory Systems: Development and Evolution The Quarterly Review of Biology 2002 2002 . Review of Genomic Regulatory Systems: Development and Evolution (2002).
  • Tamura, K, Kumar, Sudhir. Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Molecular Biology Evolution (2002).

2001

  • Gerber, A S, Loggins, R, Kumar, Sudhir, Dowling, T E. Does nonneutral evolution shape observed patterns of DNA variation in animal mitochondrial genomes?. Annual Review of Genetics (2001).
  • Hedrick, P, Kumar, Sudhir. Mutation and linkage disequilibrium in human mtDNA. European Journal of Human Genetics (2001).
  • Jayaraman, K, Panchanathan, S, Kumar, Sudhir. Classification and indexing of gene expression images. Proceedings of Society of Photo-optical Instrumentation Engineers (2001).
  • Kumar, Sudhir, Filipski, A. Molecular Clock Testing. Encyclopedia of Life Sciences (2001).
  • Kumar, Sudhir, Filipski, A. Molecular Phylogeny Reconstruction. Encyclopedia of Life Sciences (2001).
  • Kumar, Sudhir, Gadagkar, S R. Disparity Index: A simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences. Genetics (2001).
  • Kumar, Sudhir, Gadagkar, S R, Filipski, A, Gu, X. Determination of the number of conserved chromosomal segments between species. Genetics (2001).
  • Kumar, Sudhir, Panchanathan, S. Elucidating gene interaction networks based on gene expression pattern image analysis. Proceedings of the International Conference on Biomedical Engineering (2001).
  • Kumar, Sudhir, Tamura, K, Jakobsen, I B, Nei, M. MEGA2: Molecular Evolutionary Genetics Analysis software. Bioinformatics (2001).
  • Miller, M P, Kumar, Sudhir. Understanding human disease mutations through the use of interspecific genetic variation. Human Molecular Genetics (2001).
  • Rosenberg, M S, Kumar, Sudhir. Traditional phylogenetic reconstruction methods reconstruct shallow and deep evolutionary relationships equally well. Molecular Biology & Evolution (2001).
  • Rosenberg, M S, Kumar, Sudhir. Incomplete taxon sampling is not a problem for phylogenetic inference. Proceedings of the National Academy of Sciences (USA) (2001).

2000

  • Kumar, Sudhir. LDA: Linkage Disequilibrium Analysis of Bi-allelic Sites in Molecular Sequence Data. Version 1.0. (2000).
  • Kumar, Sudhir. Review of Genomes The Quarterly Review of Biology 2000 2000 . Review of Genomes (2000).
  • Kumar, Sudhir, Gadagkar, S R. Efficiency of the neighbor-joining method in reconstructing deep and shallow evolutionary relationships in large phylogenies. Journal of Molecular Evolution (2000).
  • Kumar, Sudhir, Hedrick, P, Dowling, T, Stoneking, M. Questioning evidence for recombination in human mitochondrial DNA. Science (2000).
  • Kumar, Sudhir, Mitnik, C, Valente, G, Floyd-Smith, G. Expansion and molecular evolution of the interferon-induced 2'-5' oligoadenylate synthetase gene family. Molecular Biology & Evolution (2000).
  • Nei, M, Kumar, Sudhir. Molecular Evolution and Phylogenetics. (2000).
  • Purdom, P W, Bradford, P G, Tamura, K, Kumar, Sudhir. Single column discrepancy and dynamic max-mini optimizations for quickly finding the most parsimonious evolutionary trees. Bioinformatics (2000).