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Sudhir Kumar

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Adjunct Faculty
Faculty, Tempe Campus,
Biography

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.

Publications
  • Kumar S. Editor's Message for 2014. Molecular Biology and Evolution (2014).
  • Kumar S. MBE Citation Classics (2014 Edition). Molecular Biology and Evolution (2014).
  • Champion MD, Gray V, Eberhard C, Kumar S. The evolutionary history of amino acid variations mediating increased resistance of S. Aureus identifies reversion mutations in metabolic regulators. PLoS ONE (2013).
  • Gerek ZN, Kumar S, Ozkan SB. Structural dynamics flexibility informs function and evolution at a proteome scale. Evolutionary Applications (2013).
  • Gilbert JDJ, Acquisti C, Martinson HM, Elser JJ, Kumar S, Fagan F. GRASP [Genomic Resource Access for Stoichioproteomics]: comparative explorations of the atomic content of 12 Drosophila proteomes. BMC Genomics (2013).
  • Kumar S. MBE Citation Classics. Molecular Biology and Evolution (2013).
  • Kumar S. MBE Editor's Inaugural Message. Molecular Biology and Evolution (2013).
  • Liu L, Kumar S. Evolutionary balancing is critical for correctly forecasting disease associated amino acid variants. Molecular Biology and Evolution (2013).
  • Sun Q, Muckatira S, Yuan L, Ji S, Newfeld S, Kumar S, Ye J. Image-level and group-level models for Drosophila gene expression pattern annotation. BMC Bioinformatics (2013).
  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution (2013).
  • Wellensiek BP, Larsen AC, Stephens B, Kukurba K, Waern K, Briones N, Liu L, Snyder M, Jacobs BL, Kumar S, Chaput JC. Genome-wide profiling of cap-independent translation enhancing elements in the human genome. Nature Methods (2013).
  • Zhang W, Feng D, Li R, Chernikov A, Chrisochoides N, Osgood C, Koinkoff C, Newfeld S, Kumar S, Ji S. A mesh generation and machine learning framework for Drosophila gene expression pattern image analysis. BMC Bioinformatics (2013).
  • Dudley JT, Chen R, Sanderford M, Butte AJ, Kumar S. Evolutionary Meta-analysis of Association Studies Reveals Ancient Constraints Affecting Disease Marker Discovery. Molecular Biology and Evolution (2012).
  • Gray VE, Kukurba KR, Kumar S. Performance of Computational Tools in Evaluating the Functional Impact of Laboratory-Induced Amino Acid Mutations. Bioinformatics (2012).
  • Konikoff CE, Karr TL, McCutchan M, Newfeld SJ, Kumar S. Comparison of Embryonic Expression Within Multigene Families Employing the FlyExpress Discovery Platform Reveals Significantly More Spatial Than Temporal Divergence. Developmental Dynamics (2012).
  • Kumar S, Boccia K, McCutchan M, Ye J. Exploring Spatial Patterns of Gene Expression from Fruit Fly Embryogenesis on the IPhone. Bioinformatics (2012).
  • Kumar S, Sanderford M, Gray VE, Ye J, Liu L. Evolutionary Diagnosis Methods for Variants in Personal Exomes. Nature Methocs (2012).
  • Kumar S, Stecher G, Peterson D, Tamura K. MEGA-CC: Computing Core of Molecular Evolutionary Genetics Analysis Program for Automated and Iterative Data Analysis. Bioinformatics (2012).
  • Li YX, Ji S, Kumar S, Ye J, Zhou ZH. Drosophila Gene Expression Pattern Annotation Through Multi-instance Multi-label Learning. ACM/IEEE Transactions on Computational Biology and Bioinformatics (2012).
  • Maruki T, Kumar S, Kim Y. Purifying Selection Modulates the Estimates of population Differentiation and Confounds Genome-Wide Comparisons Across Single Nucleotide Polymorphisms. Molecular Biology and Evolution (2012).
  • Stoltzfus SA, O'Meara B, Whitacre J, Mounce R, Gillespie EL, Kumar S, Rosauer DF, Vos RA. Sharing and Re-use of Phylogenetic Trees (and Associated Data) to Facilitate Synthesis. BMC Research Notes (2012).
  • Tamura K, Battistuzzi FU, Billing-Ross P, Murillo O, Filipski A, Kumar S. Estimating Divergence Times in Large Molecular Phylogenies. Proceedings of the National Academy of Sciences 109:19333-19338 (2012).
  • Yuan L, Woodard A, Ji S, Jiang Y, Zhou ZH, Kumar S, Ye J. Learning Sparse Representations for Fruit-Fly Gene Expression Pattern Image Annotation and Retrieval. BMC Bioinformatics (2012).
  • Dudley JT, Kim Y, Liu L, Markov GJ, Gerold K, Chen R, Butte AJ, Kumar S. Human Genomic Disease Variants: A Neutral Evolutionary Explanation. (2012).
  • Kumar S, Filipski A, Battistuzzi FU, Kosakovsky Pond SL & Tamura K. Statistics and truth in phylogenomics. (2012).
  • Battistuzzi FU, Filipski A & Kumar S. Molecular clock: testing (version 2.0). Encyclopedia of Life Sciences. John Wiley & Sons, Ltd, Chichester, UK (2011).
  • Battistuzzi FU, Billing-Ross P, Paliwal A & Kumar S. Fast and slow programs implementing relaxed clock methods show similar accuracies in estimating divergence times. Molecular Biology & Evolution (2011).
  • Elser JJ, Acquisti C & Kumar S. Stoichiogenomics: the evolutionary ecology of macromolecular elemental composition. Trends in Ecology & Evolution (2011).
  • Gray VE & Kumar S. Rampant purifying selection conserves positions with post-translational modifications in human proteins. Molecular Biology & Evolution (2011).
  • Kumar S & Hedges SB. TimeTree2: Species divergence times on the iPhone. Bioinformatics (2011).
  • Kumar S, Konikoff C, Van Emden B, Busick C, Davis KT, Ji S, Wu L-W, Ramos H, Brody T, Panchanathan S, Ye J, Karr TL, Gerold K, McCutchan M & Newfeld SJ. FlyExpress: Visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis. Bioinformatics (2011).
  • Pacheco MA, Battistuzzi FU, Lentino M, Aguilar R, Kumar S & Escalante. Evolution of modern birds revealed by Mitogenomics: timing the radiation and origin of major orders. Molecular Biology & Evolution (2011).
  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M & Kumar S. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, evolutionary distance, and Maximum Parsimony methods. Molecular Biology & Evolution (2011).
  • Kumar S, Dudley JT, Filipski A & Liu L. Phylomedicine: An evolutionary telescope to explore and diagnose the universe of disease mutations. (2011).
  • Battistuzzi F, Filipski A, Hedges SB, and Kumar S. Performance of Relaxed-Clock Methods in Estimating Evolutionary Divergence Times and Their Credibility Intervals. Molecular Biology and Evolution (2010).
  • Elser J, Acquisti C, and Kumar S. Stoichiogenomics: the evolutionary ecology of macromolecular elemental composition. Trends in Ecology and Evolution (2010).
  • Kazemian M, Blatti C, Richards A, McCutchan M, Wakabayashi-Ito N, Hammonds AS, Celniker SE, Kumar S, Wolfe SA, Brodsky MH & Sinha S. Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. PLoS Biology (2010).
  • Stone A, Battistuzzi F, Kubatko L, Perry G, Trudeau E, Lin H, and Kumar S. More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure. Philosophical Transactions of Royal Society B (2010).
  • Acquisti CA, Elser JJ & Kumar S. Ecological nitrogen-limitation shapes the DNA composition of plant genomes. Molecular Biology and Evolution (2009).
  • Acquisti CA, Kumar S & Elser JJ. 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 (2009).
  • Goering LM, Hunt PK, Heighington C, Busick C, Pennings P, Hermisson J, Kumar S & Gibson G. Association of orthodenticle with natural variation for early embryonic patterning in Drosophila melanogaster. Journal of Experimental Zoology (Molecular & Developmental Evolution) (2009).
  • Horiike T, Miyata D, Hamada K, Saruhashi S, Shinozawa T, Kumar S, Chakraborty R, Komiyama T & Tateno Y. Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs. Gene (2009).
  • Ji S, Li Y-X, Zhou Z-H, Kumar S & Ye J. A bag-of-words approach for Drosophila gene expression pattern annotation. BMC Bioinformatics (2009).
  • Kumar S, Suleski M, Markov GJ, Lawrence S, Marco A & Filipski AJ. Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations. Genome Research (2009).
  • Li Y-X, Ji S, Kumar S, Ye J & Zhou Z-H. Drosophila Gene Expression Pattern Annotation through Multi-Instance Multi-Label Learning. IEEE/ACM Transactions on Computational Biology and Bioinformatics (2009).
  • Marco A, Konikoff C, Karr TL & Kumar S. Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster. Bioinformatics (2009).
  • Mikhailov KV, Konstantinova AV, Nikitin MA, Troshin PV, Rusin LY, Lyubetsky VA, Panchin YV, Mylnikov AP, Moroz LL, Kumar S & Aleoshin VV. The origin of Metazoa: a transition from temporal to spatial cell differentiation. BioEssays (2009).
  • Suzuki Y, Gojobori T & Kumar S. Methods for incorporating the hypermutability of CpG dinucleotides in detecting natural selection operating at the amino acid sequence level. Molecular Biology and Evolution (2009).
  • S. Blair Hedges, Sudhir Kumar. The Timetree of Life. (2009).
  • Hedges SB & Kumar S. Discovering the timetree of life. The Timetree of Life (2009).
  • Ji S, Yuan L, Li Y-X, Zhou Z-H, Kumar S & Ye J. Drosophila gene expression pattern annotation using sparse features and term-term interaction. ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, (2009).
  • Li Y-X, Ji S, Kumar S, Ye J & Zhou Z-H. Drosophila gene expression pattern annotation by multi-instance multi-label learning. International Joint Conference on Artificial Intelligence (2009).
  • Ji S, Sun L, Jin R, Kumar S & Ye J. Automated annotation of Drosophila gene expression patterns using a controlled vocabulary. Bioinformatics (2008).
  • Kumar S, Dudley J, Nei M & Tamura K. MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics (2008).
  • Ye J, Chen J, Janardan R & Kumar S. Developmental stage annotation of Drosophila gene expression pattern images via an entire solution path for LDA. ACM Transactions on Knowledge Discovery from Data (2008).
  • Andrew Clark, Sudhir Kumar. Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007).
  • C Colbourn, Sudhir Kumar. Lower bounds on multiple sequence alignment using exact 3-way alignment. BMC Bioinformatics (2007).
  • Claudia Acquisti, George Poste, David Curtiss, Sudhir Kumar. Nullomers: really a matter of natural selection?. PLoS ONE (2007).
  • K Tamura, J Dudley, M Nei, Sudhir Kumar. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution (2007).
  • Sudhir Kumar, Alan Filipski. Multiple sequence alignment: In pursuit of homologous DNA positions. Genome Research (2007).
  • Sudhir Kumar, J Dudley. Bioinformatics software for biologists in the genomics era. Bioinformatics (2007).
  • Y. Zhang, Sudhir Kumar, D. Sturgill, M. Parisi, B. Oliver. Constraint and turnover in sex-biased gene expression in the genus Drosophila. Nature (2007).
  • Filipski A, Prohaska S, Kumar S. Detecting Molecular Signatures of Adaptive Evolution. Evolutionary Genomics and Proteomics (2007).
  • James Elser, W Fagan, S Subramanian, Sudhir Kumar. Signatures of ecological resource availability in the animal and plant proteomes. Molecular Biology and Evolution (2006).
  • S Hedges, J Dudley, Sudhir Kumar. TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics (2006).
  • S Hedges, Sudhir Kumar, M van Tuinen. Constraining fossil calibrations for molecular clocks. BioEssays (2006).
  • S Subramanian, Sudhir Kumar. Evolutionary anatomies of positions and types of disease-associated and neutral amino acid mutations in the human genome. BMC Genomics (2006).
  • S Subramanian, Sudhir Kumar. Higher intensity of natural selection on >90% of the human genes revealed by the intrinsic replacement mutation rates. Molecular Biology and Evolution (2006).
  • Sudhir Kumar, A Filiski. Multiple sequence alignment: in pursuit of homologous DNA positions. Genome Research (in press) (2006).
  • Xia, X, Kumar, Sudhir. Codon-based detection of positive selection can be biased by heterogeneous distribution of polar amino acids along protein sequences. World Scientific Publishing Co. Pte. Ltd (2006).
  • Ye, J, Chen, J, Li, Q, Kumar, Sudhir. Classification of Drosophila embryonic developmental stage range based on gene expression pattern images. World Scientific Publishing Co. Pte. Ltd (2006).
  • Filipski, A, Kumar, Sudhir. Comparative Genomics in Eukaryotes. The Evolution of the Genome (2005).
  • Kumar, Sudhir, Filipski, A. Reconstructing Vertebrate Phylogeny. Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics (2005).
  • M Gargesha, J Yang, B Van Emden, S Panchanathan, Sudhir Kumar. Automatic Annotation Techniques for Gene Expression Images of the Fruit Fly Embryo. Proceedings of SPIE (Visual Communications and Image Processing 2005) (2005).
  • S Gadagkar, M Rosenberg, Sudhir Kumar. Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree. Journal of Experimental Zoology (Molecular & Developmental Evolution) (2005).
  • S Gadagkar, Sudhir Kumar. Maximum Likelihood Outperforms Maximum Parsimony even when Evolutionary Rates are Heterotachous. Molecular Biology and Evolution (2005).
  • Sudhir Kumar. Molecular Clocks: four decades of evolution. Nature Reviews Genetics (2005).
  • Sudhir Kumar, A Filipski, V Swarna, A Walker, S Hedges. Placing confidence limits on the molecular age of the human-chimpanzee divergence. Proceedings of the National Academy of Sciences (USA) (2005).
  • Sudhir Kumar, S Hedges. Pushing back the expansion of introns in animal genomes. Cell (2005).
  • Filipski, A (Author) ,Kumar, Sudhir (Author) . Comparative Genomics in Eukaryotes. The Evolution of the Genome (2005).
  • Gargesha, M, Yang, J, Emden, B, Panchanathan, S, Kumar, Sudhir. Automatic annotation techniques for gene expression images of the fruit fly embryo. (2005).
  • Kumar, Sudhir, Hedges, S. Pushing Back the expansion of Introns in Animal Genomes. (2005).
  • Kumar, Sudhir, Filipski, A. Phylogenetic Analysis. Dictionary of Bioinformatics (2004).
  • Kumar, Sudhir, Filipski, A. Phylogenetic Analysis. Dictionary of Bioinformatics and Computational Biology (2004).
  • A Briscoe, C Gaur, Sudhir Kumar. The spectrum of human rhodopsin disease mutations through the lens of interspecific variation. Gene (2004).
  • K Tamura, M Nei, Sudhir Kumar. Prospects for Inferring Very Large Phylogenies by Using the Neighbor-Joining Method. Proceedings of the National Academy of Sciences (USA) (2004).
  • K Tamura, S Subramanian, Sudhir Kumar. Temporal Patterns of Fruit Fly Evolution Revealed by Mutation Clocks. Molecular Biology and Evolution (2004).
  • R Gurunathan, B Van Emden, S Panchanathan, Sudhir Kumar. Identifying Spatially Similar Gene Expression Patterns in Early Stage Fruit Fly Embryo Images: Binary Feature Versus Invariant Moment Digital Representations. BMC Bioinformatics (2004).
  • S Hedges, Sudhir Kumar. Precision of Molecular Time Estimates. Trends in Genetics (2004).
  • S Subramanian, Sudhir Kumar. Gene Expression Intensity Shapes Evolutionary Rates of the Proteins Encoded by the Vertebrate Genome. Genetics (2004).
  • Sudhir Kumar, K Tamura, M Nei. MEGA3: Integrated Software for Molecular Evolutionary Genetics Analysis and Sequence Alignment. Briefings in Bioinformatics (2004).
  • Gargesha, M, Antin, P, Van Emden, B, Panchanathan, S, Kumar, Sudhir. Image Registration and Similarity Computation for Chicken Gene Expression Patterns. (2004).
  • J Jancovich, J Collind, Bertram Jacobs, J Mao, V Chinchar, C Wyatt, S Case, Sudhir Kumar, G Valente, S Subramanian, E Davidson. Genomic Sequence of a Ranavirus (Family Iridoviridae) Associated with Salamander Mortalities in North America. Virology (2003).
  • M Miller, J Parker, S Rissing, Sudhir Kumar. Quantifying the Inragenic Distribution of Disease Mutations. Annals of Human Genetics (2003).
  • M Rosenberg, S Subramanian, Sudhir Kumar. Patterns of Mutational Biases Within and Among Mammalian Genomes. Molecular Biology and Evolution (2003).
  • M Rosenberg, Sudhir Kumar. Herogeneity of Nucleotide Frequencies Among Evolutionary Lineages and Phylogenetic Inference. Molecular Biology and Evolution (2003).
  • Michael Rosenberg, Sudhir Kumar. Taxon sampling, bioinformatics, and phylogenomics. Systematic Biology (2003).
  • S Hedges, Sudhir Kumar. Genomic Clocks and Evolutionary Timescales. Trends in Genetics (2003).
  • S Subramanian, Sudhir Kumar. Neutral Substitutions Occur at a Faster Rate in Exons Than in Noncoding DNA in Primate Genomes. Genome Research (2003).
  • . . Review of: A Review of Genomes (Second Edition) by Brown TA (2003).
  • . . Review of: MacTrees Made Easy (2003).
  • K Tamura, Sudhir Kumar. Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Molecular Biology Evolution (2002).
  • S Hedges, H Chen, Sudhir Kumar, DY-C Wang, A Thompson, H Watanabe. A genomic timescale for the origin of eukaryotes. BMC Evolutionary Biology (2002).
  • S Hedges, Sudhir Kumar. Vertebrate genomes compared. Science (2002).
  • Z Jiang, J Melville, H Cao, Sudhir Kumar, A Filipski, AM Gibbins. Measuring conservation of contiguous sets of autosomal markers on bovine and porcine genomes in relation to the map of the human genome. Genome (2002).
  • . . Review of: Genomic Regulatory Systems: Development and Evolution (2002).
  • . . Review of: Modern Genetic Analysis: Integrating Genes and Genomes (2002).
  • Kumar, Sudhir, Subramanian, S. Mutation rates in mammalian genomes. (2002).
  • Kumar, Sudhir, Filipski, A. Molecular Clock Testing. Encyclopedia of Life Sciences (2001).
  • Kumar, Sudhir, Filipski, A. Molecular Phylogeny Reconstruction. Encyclopedia of Life Sciences (2001).
  • A Gerber, R Loggins, Sudhir Kumar, T Dowling. Does nonneutral evolution shape observed patterns of DNA variation in animal mitochondrial genomes?. Annual Review of Genetics (2001).
  • M Miller, Sudhir Kumar. Understanding human disease mutations through the use of interspecific genetic variation. Human Molecular Genetics (2001).
  • M Rosenberg, Sudhir Kumar. Traditional phylogenetic reconstruction methods reconstruct shallow and deep evolutionary relationships equally well. Molecular Biology & Evolution (2001).
  • P Hedrick, Sudhir Kumar. Mutation and linkage disequilibrium in human mtDNA. European Journal of Human Genetics (2001).
  • Sudhir Kumar, K Tamura, I Jakobsen, M Nei. MEGA2: Molecular Evolutionary Genetics Analysis software. Bioinformatics (2001).
  • Sudhir Kumar, S Gadagkar. Disparity Index: A simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences. Genetics (2001).
  • Sudhir Kumar, S Gadagkar, A Filipski, X Gu. Determination of the number of conserved chromosomal segments between species. Genetics (2001).
  • Jayaraman, K, Panchanathan, S, Kumar, Sudhir. Classification and indexing of gene expression images. (2001).
  • Kumar, Sudhir, Panchanathan, S. Elucidating gene interaction networks based on gene expression pattern image analysis. (2001).
  • Rosenberg, M, Kumar, Sudhir. Incomplete taxon sampling is not a problem for phylogenetic inference. (2001).
  • P Purdom, P Bradford, K Tamura, Sudhir Kumar. Single column discrepancy and dynamic max-mini optimizations for quickly finding the most parsimonious evolutionary trees. Bioinformatics (2000).
  • Sudhir Kumar, C Mitnik, G Valente, G Floyd-Smith. Expansion and molecular evolution of the interferon-induced 2'-5' oligoadenylate synthetase gene family. Molecular Biology & Evolution (2000).
  • Sudhir Kumar, P Hedrick, T Dowling, M Stoneking. Questioning evidence for recombination in human mitochondrial DNA. Science (2000).
  • Sudhir Kumar, S Gadagkar. Efficiency of the neighbor-joining method in reconstructing deep and shallow evolutionary relationships in large phylogenies. Journal of Molecular Evolution (2000).
  • Masatoshi Nei, Sudhir Kumar. Molecular Evolution and Phylogenetics. (2000).
  • . . Review of: Genomes (2000).
Research Activity
Fall 2017
Course NumberCourse Title
BDE 792Research
BDE 799Dissertation
Summer 2017
Course NumberCourse Title
BDE 792Research
Spring 2017
Course NumberCourse Title
BDE 799Dissertation
Fall 2016
Course NumberCourse Title
BDE 792Research
BDE 799Dissertation
Summer 2016
Course NumberCourse Title
BDE 792Research
Spring 2016
Course NumberCourse Title
BDE 799Dissertation
Fall 2015
Course NumberCourse Title
BDE 792Research
BDE 799Dissertation
Summer 2015
Course NumberCourse Title
BDE 792Research
Spring 2015
Course NumberCourse Title
BDE 792Research
BDE 799Dissertation
Fall 2014
Course NumberCourse Title
BDE 792Research
BDE 799Dissertation
Summer 2014
Course NumberCourse Title
BDE 792Research
Spring 2014
Course NumberCourse Title
MBB 495Undergraduate Research
BDE 792Research
BDE 799Dissertation
Fall 2013
Course NumberCourse Title
BIO 189Life Sciences Career Paths
MBB 495Undergraduate Research
MIC 495Undergraduate Research
BIO 591Seminar
BDE 791Seminar
BDE 792Research
BDE 799Dissertation
Spring 2013
Course NumberCourse Title
BIO 493Honors Thesis
MBB 495Undergraduate Research
Presentations
  • Sudhir Kumar. Phylomedicine: Evolutionary lessons and solutions for genomic medicine. VWR Distinguished Speaker-Georgia Tech School of Biology (Oct 2013).
  • Sudhir Kumar. Phylomedicine: Evolutionary lessons and solutions for genomic medicine. Molecular Medicine: Next-Gen Sequencing for the Clinic 2013, Frankfurt, Germany (Sep 2013).
  • Koichiro Tamura, Fabia U Battistuzzi, Paul Billing-Ross, Oscar Murillo, Alan Filipski, Sudhir Kumar. Estimating divergence times in large molecular phylogenies. Society for Molecular Biology and Evolution Annual Conference, Chicago, IL (Jul 2013).
  • Sudhir Kumar. Phylomedicine: Evolutionary Lessons and Solutions for Genomic Medicine [Nei Lecture]. Annual Conference of the Society for Molecular Biology and Evolution, Chicago, Il (Jul 2013).
  • Oscar Murillo, Alan Filipski, Anna Freydenzon, Sudhir Kumar. Estimating very large species timetrees using multigene alignments with species-sparsity. Society for Molecular Biology and Evolution Annual conference July 7 – 11, 2013, Chicago , IL (Jul 2013).
  • Stephanie Tate, Sayaka Miura, Sudhir Kumar. Using Mendelian disease-associated variation data to test functional compensation of gene duplicates in humans. Society for Molecular Biology and Evolution Annual Conference (Jul 2013).
  • Z. Nevin Gerek, Sudhir Kumar, S. Banu Ozkan. Structural dynamics flexibility informs function and evolution at a proteome scale. Society for Molecular Biology and Evolution Annual Conference in Chicago, IL (Jul 2013).
  • Sudhir Kumar. Phylomedicine: Evolutionary lessons and solutions for genomic medicine. Evolutionary Biology Conference, Nanjing Normal University, China (Jun 2013).
  • Sudhir Kumar. Phylomedicine: Evolutionary lessons and solutions for genomic medicine. Biology Conference, Chinese Academy of Sciences (CAS), Beijing, China (May 2013).
  • Sudhir Kumar. Phylomedicine: Evolutionary lessons and solutions for genomic medicine. Quantitative Biology Colloquium, University of Arizona, Tucson, Arizona (Apr 2013).
  • Sudhir Kumar. Phylomedicine: Evolutionary lessons and solutions for genomic medicine. Mount Sinai School of Medicine CME Seminar Series, New York, New York (Apr 2013).
  • Sudhir Kumar. Phylomedicine: Evolutionary lessons and solutions for genomic medicine In Scottsdale, AZ. National Cancer Institute Annual Conference of Physical Sciences-Oncology (Apr 2013).
  • Sudhir Kumar. Phylomedicine: Evolutionary lessons and solutions for genomic medicine. Temple University Evolution Meeting (Apr 2013).
  • Sudhir Kumar. Phylomedicine: Evolutionary lessons and solutions for genomic medicine. Sigma Xi Meeting, Oakland University, Rochester, MI (Apr 2013).
  • Michael E McCutchan, Sudhir Kumar. Advances in the FlyExpress platform facilitate the integration of gene expression spatial patterns with associated regulatory sequence. Annual Srosophila conference in Washington DC (Apr 2013).
  • Sudhir Kumar, Ivan Montiel, Qian Sun, Michael McCutchan, Bremen Braun, Adam Orr, Stuart Newfeld, Jieping Ye. myFX: Turn-key software for laboratory desktops that analyzes spatial patterns of gene expression in Drosophila embryos. Annual Drosophila conference in Washginton D.C (Apr 2013).
  • Jieping Ye, Lei Yuan, Qian Sun, Cheng Pan, Michael McCutchan, Stuart Newfeld, Sudhir Kumar. Automated annotation of developmental stages of Drosophila embryos by image analysis. Annual Drosophila conference in Washington D.C (Apr 2013).
  • Wenlu Zhang, Daming Feng, Andrey Chernikov, Nikos Chrisochoides, Sudhir Kumar, Shuiwang Ji. An integrated image-to-mesh conversion and machine learning framework for gene express pattern image analysis. Annual Drosophila conference in Washington D.C (Apr 2013).
  • Stephanie Tate, Sayaka Miura, Sudhir Kumar. Using Mendelian disease-associated variation data to test functional compensation of gene duplicates in humans. Undergraduate Research Poster Symposium, Arizona State University (Mar 2013).
  • Oscar Murillo, Alan Filipski, Anna Freydenzon, Sudhir Kumar. Estimating very large species timetrees using multigene alignments with species-sparsity. Undergraduate Research Poster Symposium Arizona State University (Mar 2013).
  • Z. Nevin Gerek, Sudhir Kumar, S. Banu Ozkan. Structural dynamics flexibility informs function and evolution at a proteome scale. 57th Annual Biophysical Society Meeting, Philadelphia, PA (Feb 2013).
  • Brandon Butler, Nevin Gerek, Sudhir Kumar, Sefika (Banu) Ozkan. Position specific structural flexibility for protein function and evolutionary studies. ASU/Mayo Research Summit (Dec 2012).
  • Sudhir Kumar. New Methods and tools for the next generation of pohylogenetics. Society for Evolutionary Studies Annual Meeting @ Tokyo Metropolitan University (Aug 2012).
  • Sudhir Kumar. Bioinformatics Resources for Enabling Discoveries from Genomes to Phenotypes. Society for Molecular Biology and Evolution Annual Meeting @ Dublin, Ireland (Jun 2012).
  • Sudhir Kumar. Genomics and spatio-temporal expression. ASU Complex Adative Systems Initiative and USC Physical Sciences Oncology Center (Jun 2012).
  • Sudhir Kumar, David Pisani, Mark Wilkinson, Karen Meusemann, Emma Teeling. The animal tree of life and its applications. SMBE Annual Meeting in Dublin, IReland (Jun 2012).
  • Sudhir Kumar. Making Sense of Molecular Data. Biomedicine: Big Data and New Paths to Personalized Medicine at ASU (May 2012).
  • Sudhir Kumar, Michael McCutchan, Stuart J Newfeld. Fly Express: A platform for discovering co-expressed genes via comparative image analysis of spatial patterns in Drosophila embryogenesis. Fly Express Conference in Chicago, Illinois, USA (Apr 2012).
  • Fabia Battistuzzi, Sudhir Kumar. Early evolution of life. AbSciCon Meeting in Atlanta, Georgia (Mar 2012).
  • Sudhir Kumar. Phylomedicine. International Conference on Bioinformatics & Computational Biology at Bangkok, Thailand (Mar 2012).
  • Sudhir Kumar. Introduction to Phylomedicine. SMBE Satellite Meeting on Phylomedicine at ASU (Mar 2012).
  • Sudhir Kumar Liz Garcia-Peterson. Molecular Evolutionary Analysis of Genetic Variation in Skeletal Muscle Sodium-channel Gene (scn4a). Annual Biomedical Research Conference for Minority Students (ABRCMS (Nov 2011).
  • Sudhir Kumar. Phylomedicine: An evolutionary telescope to explore and diagnose the universe of disease mutations. ORSP Research Seminar Series @ Midwestern University (Nov 2011).
  • Sudhir Kumar. Phylomedicine: An evolutionary telescope to explore and diagnose the universe of disease mutations. Molecular Biosciences Seminar at Montana State, Bozeman, MT (Oct 2011).
  • Sudhir Kumar. Global Organizing Committee (GOC). Annual meeting of the Society for Moleculary Biology and Evolution in Kyoto, Japan (Jul 2011).
  • Sudhir Kumar. Workshop: Methods for multiple alignment and phylogenetic tree making for large sequence data set Title: Maximum ikelihood methods in MEGA 5. SMBE Annual Meeting @ Kyoto, Japan (Jul 2011).
  • Sudhir Kumar. TimeTree2: A knowledgebase of species divergence times from molecular data. SMBE Annual Meeting @ Kyoto, Japan (Jul 2011).
  • Sudhir Kumar. MEGA (Molecular Evolutionary Genetics Analysis) version 5.0. SMBE Annual Meeting @ Kyoto, Japan (Jul 2011).
  • Sudhir Kumar. TimeTree2: Species divergence times from molecular data. ISMB/ECCB in Vienna, Austria (Jul 2011).
  • Sudhir Kumar. Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. ISMB/ECCB in Vienna, Austria (Jul 2011).
  • Presenting author: Saurabh Sinha, University of Illinois Urbana-Champaign, United States ASU Author Sudhir Kumar. Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. ISMB/ECCB in Vienna, Austria (Jul 2011).
  • Sudhir Kumar. Comparative Genomics as an Evolutionary Telescope for Genomic Medicine to Peer into the Universe of Human Mutations. ISMB/ECCB in Vienna, Austria (Jul 2011).
  • Sudhir Kumar. Phylomedicine. Barrett's Honors College (Jun 2011).
  • Sudhir Kumar. Data Mining for Biomedical Informatics. SIAM International Conference on Data Mining, Mesa, Arizona (May 2011).
  • Sudhir Kumar. Phylomedicine. Pennsylvania State University Symposium (Mar 2011).
  • Sudhir Kumar. MEGA software: Philosophy and Future. Workshop on Bioinformatic Software for Comparative Genomics and Metagenomics (Mar 2011).
  • Sudhir Kumar. Molecular Evolution in Personal Medicine. Interdisciplinary Graduate Student's Symposium on Evolution Across Fields @ Institute for Evolution (Feb 2011).
  • Sudhir Kumar. Species Delimitation using nuclear sequence Markers. SMBE Meeting in Berlin (Feb 2011).
  • J. Dudley, A. Butte, S. Kumar. Evolutionary biology in health and medicine. SMBE 2010 (Annual Meeting of the Society for Molecular Biology and Evolution) (Jul 2010).
  • Kumar S, Peterson D. MEGA 5: Molecular Evolutionary Genetics Analysis. Evolution 2010 (Jun 2010).
  • Kumar S, Luo Y. A genome-wide analysis of decay of overlapping genes in the bacterium E. coli. Evolution 2010 (Jun 2010).
  • Gray V, Kumar S. The evolutionary anatomies of post-translational modifications in human proteins. Evolution 2010 (Jun 2010).
  • Battistuzzi F, Kumar S. Performance of relaxed clock methods in estimating evolutionary divergence times and their credibility intervals. Evolution 2010 (Jun 2010).
  • Sudhir Kumar. Statistics and truth in phylogenomics. Molecular Phylogenetics 2010 (May 2010).
  • Konikoff C, Kumar S. 2010 FlyExpress: A platform for discovering co-expressed genes via comparative image analysis of spatial patterns in Drosophila embryogenesis. MCB Colloquium (Dec 2009).
  • Shuiwang Ji, Sudhir Kumar. Computational Biology of Spatiotemporal Expressions in Fruit Fly Embyogenesis. Computer Science and Artificial Intelligence Laboratory (Dec 2009).
  • Kumar. Bioinformatics tools and software. Invited talk at Stanford University (Nov 2009).
  • Kumar. Times and time ratios of great ape evolutionary branchings from molecular data. The first 4 million years of human evolution Meeting. Royal Society, London (Oct 2009).
  • Kumar. Course in Molecular Evolution and Phylogenetics (2 day). Centers for Diseases Control course (Jul 2009).
  • Ying-xin, Li. Drosophila Gene Expression Pattern Annotation through Multi-instance Multi-label Learning. 21st International Joint Conference on Artificial Intelligence (Jul 2009).
  • Jieping Ye. Drosophila Gene Expression Pattern Annotation Using Sparse Features and Term-term Interaction. ACM SIGKDD International Conference on Knowledge Discovery and data Mining (Jul 2009).
  • Kumar. Positional conservation and amino acids dictate the correct diagnosis of benign and damaging personal amino acid mutations. Society for Molecular Biology and Evolution Annual Conference (Jun 2009).
  • Fabia Battistuzzi, Sudhir Kumar. Effects of rate evolution models on molecular clocks times and credibility intervals estimates. Society for Molecular Biology and Evolution Annual meeting (Jun 2009).
  • Konikoff C, Kumar S. Drosophila multi-gene family expression and evolution. SMBE 2009 (Jun 2009).
  • Konikoff C, Kumar S. Drosophila paralogous gene expression. 50th Annual Drosophila Research Conference (Jun 2009).
  • Konikoff C (with Kumar S, , Marco A, Karr T). Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster. SMBE 2009 (Jun 2009).
  • Kumar. Evolutionary bioinformatics of human disease mutations. Chalk Talk (Apr 2009).
  • Kumar. Spirit of the Senses talk. talk (Apr 2009).
  • Kumar. FlyExpress Database. Drosophila Conference (Mar 2009).
  • Kumar. AAAS Annual Meeting. AAAS (Feb 2009).
  • Kumar. Annual Biocomputing Seminar. Biocomputing seminar (Jan 2009).
  • Kumar, Sudhir. Software tools and knowledge-bases for discoveries from genomes (species) to phenotypes. University of North Carolina, invited speaker (Oct 2008).
  • Kumar, Sudhir. Software tools and Knowledge-bases for discoveries from genomes to phenotypes. Symposium on Evolutionary Bioinformatics (Oct 2008).
  • Kumar, Sudhir. Evolutionary anatomies of disease mutation. McDonald Department of Genetics Fall Seminar Series (Oct 2008).
  • Kumar, Sudhir. Presentation to Summer Interns and High School teachers regarding EFG activities and research. Summer Brown Bag Lunch Seminar, Biodesign (Jul 2008).
  • Kumar, Sudhir. Molecular Evolutionary Analysis Meets Epigenomics. New Insight of Genome Evolution into Fundamental Activities of Life (Mar 2008).
  • Kumar, Sudhir. Discussion Leader. Gordon Conference in Molecular Evolution (Feb 2008).
  • Kumar, Sudhir. Software tools and Knowledge-bases for discoveries from genomes (species) to phenotypes. Global Center for Excellence (Jan 2008).
  • Kumar, Sudhir. FlyExpress: The Next Steps (Sep 2007).
  • Kumar, Sudhir. Evolutionary anatomies of disease mutations in proteins. BioOhio2007 (Jul 2007).
  • Van Emden, B, Kumar, Sudhir. 2007 Drosophila Research Conference (Mar 2007).
  • Kumar, Sudhir. Evolutionary anatomies of disease mutations. Microbiology Dept Seminar Series (Nov 2006).
  • Kumar, Sudhir. Evolutionary anatomies of disease mutations. Seminar Series (Sep 2006).
  • Van Emden, B, Ramos, H, Panchanathan, S, Newfeld, S, Kumar, Sudhir. FlyExpress: An Image-Matching Web-Tool for Finding Genes with Overlapping Patterns of Expression in Drosophila Embryos. 47th Annual Drosophila Research Conference (Mar 2006).
  • Gargesha, M, Van Emden, B, Panchanathan, S, Kumar, Sudhir. Comparison of Computational Techniques for Identifying Spatially Similar Embryonic Gene Expression Patterns. 47th Annual Drosophila Research Conference (Mar 2006).
  • Kumar, Sudhir. Evolutionary Functional Genomics in the Biodesign Institute: Taking a computational approach to understanding and harnessing the biological design. ASU Emeritus Faculty Association Luncheon (Nov 2005).
  • Kumar, Sudhir, Tamura, K, Nei, M. MEGA3: An Integrated Software for Molecular Evolutionary Genetics Analysis and Sequence Alignment. Annual Meeting of The Society for Molecular Biology & Evolution (Jun 2005).
  • Hedges, B, Dudley, J, Pisani, D, Swarna, V, Valente, G, Kumar, Sudhir. Time Tree: A Database of Species Divergence Times. Annual Meeting of The Society for Molecular Biology & Evolution (Jun 2005).
  • Kumar, Sudhir. In silico Analysis and Management of Fruit Fly Gene Expression Pattern Images. Special Presentation to the NAS Panel on Chemical Imaging (Apr 2005).
  • Gargesha, Madhusudhana, Yang, Jian, Van Emden, Bernard, Panchanathan, Sethuraman, Kumar, Sudhir. Computational Annotation of View, Orientation and Stage of Fruit Fly Gene Expression Pattern Images from Early Developmental Stages. 46th Annual Drosophila Research Conference (Mar 2005).
  • Kumar, Sudhir. Evolutionary and Population Genomics in the Future of Statistics Conference. Indian School of Business, Hyderabad, India (Dec 2004).
  • Kumar, Sudhir. Evolutionary Functional Genomics. Bio Basics class in Fulton School of Engineering (Nov 2004).
  • Jancovich, J, Bremont, M, Touchman, J, Kumar, Sudhir, Valente, G, Collins, J, Jacobs, B. Genomic Sequence of Epizoodic Haematopoetic Necrosis Virus (EHNV): An Evolutionary Link Between Frog and Salamander Ranaviruses?. International Poxvirus and Iridovirus Symposium (Sep 2004).
  • Kumar, Sudhir. Genomic Timescales: Precision and Robustness. International Conference of Zoology Conference (Aug 2004).
  • Subramanian, S, Kumar, Sudhir. Gene Expression Intensity Shapes Evolutionary Rates of the Proteins Encoded by the Vertebrate Genome. Annual Meetings of The Society for Molecular Biology & Evolution (Jun 2004).
  • Urrutia, A, Kalyanamaran, V, Kumar, Sudhir. Codon Bias in Human: Beyond GC Content and Context Mutations. Annual Meeting of The Society for Molecular Biology & Evolution (Jun 2004).
  • Kumar, Sudhir, Van Emden, B, Gurunathan, R, Panchanathan, S, Newfeld, S. FlyExpress: The Drosophila Gene Expression Pattern Search and Analysis Tool. Drosophila Research Conference (Mar 2004).
  • Kumar, Sudhir. An Overview of the Embryonic Gene Expression Database (FlyExpress) and a timescale of Fruit Fly (Drosophila) Evolution. Center for Insect Science Hexapodium (Feb 2004).
  • Kumar, Sudhir. Distance and Parsimony Methods. Molecular Evolution and Systematics, Chinese Academy of Sciences, Beijing, China
  • Kumar, Sudhir. Genomic Bounds on the Timing of Human-Chimpanzee Divergence. International Conference on the Future of Statistical Theory, Practice, and Education
  • Kumar, Sudhir. Bioinformatics Research Center, North Carolina State University, Raleigh, NC
  • Kumar, Sudhir. Department of Biology, Duke University, Durham, NC
  • Kumar, Sudhir. Society for Molecular Biology & Evolution, Newport Beach, CA
  • Kumar, Sudhir. MEGA3: An integrate platform for molecular evolutionary genetics analysis and sequence alignment. Evolutionary Genomics Conference
  • Kumar, Sudhir. Neutral Substitutions occur at a faster rate in exons than in non-coding DNA in primates. Comparative and Functional Genomics Workshop
  • Kumar, Sudhir. Molecular Evolutionary Genetics Analysis Software. International Meeting on Evolutionary Genomics
  • Kumar, Sudhir, Tamura, K, Nei, M. MEGA3: An integrate platform for molecular evolutionary genetics analysis and sequence alignment. Annual meetings of The Society for Integrative and Comparative Biology
  • Kumar, Sudhir. Evolutionary anatomies of the locations and types of disease-associated nonsynonymous mutations in the human genome. EMBO workshop on "Human Evolution and Disease, Center for Cellular and Molecular Biology, Hyderabad, India
  • Kumar, Sudhir, Van Emden, B, Parkhurst, W, Newfeld, S. FlyExpress: The Drosophila in situ Gene Expression Pattern Database and Search Tool. 1st International Biocurator Meeting
  • Kumar, Sudhir. Department of Biological Sciences, University of Idaho, Moscow, ID
  • Kumar, Sudhir. Birla Institute of Technology & Sciences, Pilani, India
  • Kumar, Sudhir. Department of Biology, Tokyo Metropolitan University, Tokyo, Japan
  • Kumar, Sudhir. Genetics Program, University of Arizona, Tucson, Arizona
  • Kumar, Sudhir. Graduate University for Advanced Studies, Hayama, Japan
  • Kumar, Sudhir. University of South Carolina, Columbia, South Carolina
  • Kumar, Sudhir. Grantsmanship. SOLUR Undergraduate Seminar
  • Kumar, Sudhir. Software tools and Knowledge-bases for discoveries from genomes (species) to phenotypes. Japan Biological Information Research Center (JBIRC)
  • Kumar, Sudhir. ASU President's Community Enrichment Program, Phoenix, Arizona
  • Kumar, Sudhir. Biomedical Engineering, Indian Institute of Science, Bangalore, India
  • Kumar, Sudhir. Department of Biology, Grand Canyon University, Phoenix, Arizona
  • Kumar, Sudhir. Department of Biology, Hong Kong University, Hong Kong, China
  • Kumar, Sudhir. Department of Biology, Ohio State University, Columbus, Ohio
  • Kumar, Sudhir. Department of Biology, Syracuse University, Syracuse, New York
  • Kumar, Sudhir. Department of Biology, Tokyo Metropolitan University, Tokyo, Japan
  • Kumar, Sudhir. Ecology & Evolutionary Biology Program/IGERT, Indiana University, Bloomington, Indiana
  • Kumar, Sudhir. Program in Ecology and Evolutionary Biology, University of Illinois, Urbana Champaign, Illinois
  • Kumar, Sudhir, Kumar, Sudhir. Estimating Neutral Evolutionary Rates in Mammals. International Workshop on Population Genetics @ University of Montreal, Montreal, Canada
  • Kumar, Sudhir. Department of Biology, Indiana University, Bloomington, Indiana
  • Kumar, Sudhir. Department of Biology, University of Michigan, Ann Arbor, MI
  • Kumar, Sudhir. Department of Computer Science, Arizona State University, Tempe, AZ
  • Kumar, Sudhir. Building Fruit Fly Developmental Networks: in silico Approaches for analyzing in situ Gene Expression Patterns. The 12th International Workshop on Beyond the Identification of Transcribed Sequences: Functional, Evolutionary, and Expression Analysis sponsored by Department of Energy, Washington DC
  • Kumar, Sudhir. Building Fruit Fly Developmental Networks: in silico approaches for Analyzing in situ Gene Expression Patterns. The 18th International Symposium in Conjunction with Award of the International Prize for Biology, Tokyo, Japan
  • Kumar, Sudhir. Rates of Point Mutation in Mammals. Evolutionary Genetics. American Genetic Association, Arizona State University, Tempe, Arizona
  • Kumar, Sudhir. Phylogenetics: Evolutionary Patterns, Challenges, and Bioinformatics Solutions. Genomics, Genetics and Bioinformatics
Service
  • Academic Exchange and Collaboration - Tokyo Metropolitan University, Japan and Arizona State Univ, Coordinator (2012 - Present)
  • Biological Design Graduate Program, Co-director (2012 - Present)
  • Molecular Biology & Evolution, Editor-in-Chief (2012 - Present)
  • Molecular Biology & Evolution, Editor-in-Chief (2012 - Present)
  • Big Data Faculty Search Committee, Computer Science, Member (2012 - Present)
  • Genomics Faculty Search Committee, Member (2012 - Present)
  • NSF CAREER Mentor, Mentor (2012 - Present)
  • SoLS Complexity Committee, Member (2011 - Present)
  • SoLS Complexity Committee, Member (2011 - Present)
  • A2C2 Arizona Advanced Computing Center, Internal Advisory Board for HPC (2011 - Present)
  • A2C2 Arizona Advanced Computing Center, Internal Advisory Board for HPC (2011 - Present)
  • A2C2 Arizona Advanced Computing Center, Internal Advisory Board for HPC (2011 - Present)
  • Israel Science Foundation, Reviewer (2011 - Present)
  • Israel Science Foundation, Reviewer (2011 - Present)
  • Münster Graduate School of Evolution (MGSE), Advisory Board Member (2011 - Present)
  • Münster Graduate School of Evolution (MGSE), Advisory Board Member (2011 - Present)
  • Münster Graduate School of Evolution (MGSE), Advisory Board Member (2011 - Present)
  • NIH Peer Review, Review Grant Proposals (2011 - Present)
  • NIH Peer Review, Review Grant Proposals (2011 - Present)
  • NIH/Genome Variation and Evolution (GVE), Standing Member of GVE (2011 - Present)
  • Genomics Search Committee, Member (2011 - Present)
  • Biomolecules, Editorial Board (2010 - Present)
  • Biomolecules, Honorary Editor (2010 - Present)
  • Biomolecules, Honorary Editor (2010 - Present)
  • Biomolecules, invited/honorary editorial member (2010 - Present)
  • University-wide meta planning in Engineering & Informatics, Member (2010 - Present)
  • University-wide meta planning in Engineering & Informatics, Member (2010 - Present)
  • Biodesign Data Club, co-organizer with Joshua LaBaer (2010 - Present)
  • Genome at ASU, co-organizer (2010 - Present)
  • EARS, nominated member (2010 - Present)
  • National Science Foundation Review Panel, reviewing member (2010 - Present)
  • Quarterly Review of Biol, Invited Editor (2010 - Present)
  • Quarterly Review of Biology, Invited Editor (2010 - Present)
  • Quarterly Review of Biology, Invited Editor (2010 - Present)
  • Biodesign Personnel Committee (Academic Affairs), Chair (2009 - Present)
  • Bioinformatics and Biology Insights, Editorial Board (2009 - Present)
  • Biodesign Research Faculty Promotion Committee, Chair (2005 - Present)
  • Molecular Biology & Evolution, Associate Editor (2004 - Present)
  • Molecular Biology & Evolution, Associate Editor (2004 - Present)
  • Biodesign Executive Committee, member (2004 - Present)
  • Biodesign Executive Committee, member (2004 - Present)
  • Biodesign Executive Committee, member (2004 - Present)
  • Biodesign Executive Committee, member (2004 - Present)
  • Biodesign Executive Committee, Member (2004 - Present)
  • Evolutionary Bioinformatics Online, Associate Editor (2004 - Present)
  • Evolutionary Bioinformatics Online, Associate Editor (2004 - Present)
  • Evolutionary Bioinformatics Online, Associate Editor (2004 - Present)
  • Molecular and Developmental Evolution, Editorial Board Member (2004 - Present)
  • Molecular and Developmental Evolution, Editorial Board Member (2004 - Present)
  • Center for Evolutionary Medicine & Informatics, Director (2003 - Present)
  • Center for Evolutionary Medicine & Informatics, Director (2003 - Present)
  • Center for Evolutionary Medicine & Informatics, Director (2003 - Present)
  • Executive Committee, Computational Biosciences Program, Member (2000 - Present)
  • Executive Committee, Computational Biosciences Program, Member (2000 - Present)
  • Biological Design Graduate Program, Co-director (2012 - 2013)
  • Quarterly Review of Biology, Invited Editor (2010 - 2013)
  • Molecular and Developmental Evolution, Editorial Board Member (2004 - 2013)
  • NC State University Genomics Graduate Program, Program Reviewer (2013 - 2013)
  • Society for Molecular Biology and Evolution Annual Meeting, Poster Judge (2012 - 2012)
  • Molecular Biology & Evolution, Associate Editor (2004 - 2012)
  • Personnel Committee for GEB, Chair (2011 - 2011)
  • Biodesign CS Team, Chair (2011 - 2011)
  • Biodesign Data Club, co-organizer with Joshua LaBaer (2010 - 2011)
  • Biodesign Personnel Committee, Chair (2008 - 2010)
  • NIH Biodata Management and Analysis (BDMA) standing review panel, panel member (2006 - 2010)
  • Science Foundation Ireland, reviewing member (2008 - 2009)
  • Genome Research, Editorial Board Member (2005 - 2009)
  • Wellcome Trust, Ad hoc reviewer (2005 - 2009)
  • Evolutionary Bioinformatics Online, Associate Editor (2004 - 2009)
  • Molecular and Developmental Evolution, Editorial Board Member (2004 - 2009)
  • Evolutionary Genomic Focus Group, NASA Astrobiology Focus Group, Member (2000 - 2009)
  • Penn State Astrobiology Research Center, Associate Member (1998 - 2009)
  • Strategic Planning Committee (SoLS), Member (2008 - 2009)
  • FlyBase Advisory Committee, Member (2007 - 2008)
  • National Evolutionary Synthesis Center (NEScent), Member of Advisory Committee (2006 - 2008)
  • Evolutionary Informatics: Supporting Interoperability in Evolutionary Analysis, Member, Working Group (2006 - 2008)
  • Molecular Biology & Evolution, Associate Editor (2004 - 2008)
  • Web Advisory Committee, Member (2007 - 2008)
  • University Curricular and Planning Committee, advisory committee to develop PhD and Masters program in Informatics (2007 - 2008)
  • Biodesign Graduate program, Evaluator and participant (2006 - 2007)
  • Canada Foundation for Innovation (CFI), Ad hoc reviewer (2005 - 2007)
  • Gene: Functional Genomics, Board of Editors (2005 - 2007)
  • American Genetic Association, Webmaster (2004 - 2007)
  • Society for Molecular Biology and Evolution, Webmaster (2004 - 2007)
  • Society for Molecular Biology and Evolution, Secretary (2003 - 2007)
  • Journal of Heredity, Associate Editor (1999 - 2007)
  • Program Committee, Member (2007 - 2007)
  • Personnel Committee (BMI), Member (2005 - 2007)
  • Faculty Recruitment Committee, Member (2005 - 2007)
  • Executive Committee (Computational Bioscience Program), Member (2000 - 2007)
  • Center for Evolutionary Functional Genomics (Biodesign Institute), Director (2002 - 2007)
  • Danish National Research Foundation (2006), Ad Hoc Reviewer (2006 - 2006)
  • External Advisory Board, INBRE, University of South Carolina, Member (2006 - 2006)
  • Gene (Functional Genomics), Associate Editor (2005 - 2006)
  • Society for Molecular Biology & Evolution, Secretary (2004 - 2006)
  • 2006 SMBE Meetings at Arizona State University: Genetics, Evolution, and Biology, Host and Chair of the Organizing Committee (2006 - 2006)
  • University of South Dakota, Consultant Minisymposium--advising on a strategy needed to set up a planned Center for Evolutionary Genetics and Informatics at USD (2006 - 2006)
  • Nanyang University, External Examiner for Doctoral Candidate (2006 - 2006)
  • CSR/NIH, Panelist (2005 - 2005)
  • National Institutes of Health--BDMA: Biodata Management and Analysis, Ad Hoc Reviewer (2005)
  • Search committee for Integrative Neuroscience, SoLS, Member (2005 - 2005)
  • 5-Year Review of IGB at UC Irvine, Panel Member (2005 - 2005)
  • Biomedical Taskforce Search Committee for Leader of BMI Department, Member (2005 - 2005)
  • Genome Database Workshop at National Evolutionary Synthesis Center, Organizer (2005 - 2005)
  • Steering Committee, NIH-funded Post-Baccalaureate Research Education Program in Biomedical Sciences, Member (2005 - 2005)
  • Integrative Neuroscience Search Committee, Member (2004 - 2005)
  • Taskforce on Biomedical Informatics, Member (2004 - 2005)
  • National Science Foundation Information Technology Research Grant Panel, Panel member (2002 - 2004)
  • Bioinformatics/ BMC Bioinformatics, Ad Hoc Reviewer (2004)
  • Bioinformatics/Bioengineering Search Committee, Member (2004)
  • Development Genes & Evolution; Nucleic Acids Research, Ad Hoc Reviewer (2004)
  • Evolution, Molecular Biology & Evolution, Journal of Molecular Evolution, Ad Hoc Reviewer (2004)
  • Evolutionary Bioinformatics Faculty Search Committee, Member (2004)
  • Genetics; Gene; Genome Research, Ad Hoc Reviewer (2004)
  • National Institutes of Health--Population Genetic Analysis Program: Immunity to Vaccines/Infections, Panel Member (2004)
  • National Institutes of Health--Software Development and Maintenence, Panel Member (2004)
  • National Institutes of Health: Development (DEV-1), Ad Hoc Panel Member (2004)
  • National Science Foundation--Systematic Biology, Ad Hoc Reviewer (2004)
  • Proceedings of the National Academy of Sciences (USA)/ Nature, Ad Hoc Reviewer (2004)
  • Symposium on Evolutionary and Population Genomics, Symposium Organizer (2004)
  • Workshop on Molecular Evolution and Systematics, Workshop Teacher (2004)
  • Faculty in Genomics, Evolution, & Bioinformatics, Leader (2003 - 2004)
  • SoLS Executive Committee, Member (2003 - 2004)
  • Arizona Research Laboratories, Research Scientist (2003)
  • AzBio Executive Committee, Member (2003)
  • Bioinformatics, Ad Hoc Reviewer (2003)
  • Bioinformatics Faculty Search Committee, Mamber (2003)
  • Center for Evolutionary Functional Genomics, Director (2003)
  • Committee on Membership Enhancement in the Society for Molecular Biology and Evolution, Member (2003)
  • Development Genes and Evolution, Ad Hoc Reviewer (2003)
  • EARS Faculty, Member (2003)
  • Evolution, Ad Hoc Reviewer (2003)
  • Gene, Ad Hoc Reviewer (2003)
  • Genetics, Ad Hoc Reviewer (2003)
  • Genome Research, Ad Hoc Reviewer (2003)
  • Journal of Experimental Zoology, part B: Molecular and Developmental Evolution, Editorial Board Member (2003)
  • Journal of Molecular Evolution, Ad Hoc Reviewer (2003)
  • Junior Faculty Search Committee, Member (2003)
  • Molecular Biology and Evolution, Ad Hoc Reviewer (2003)
  • Nature, Ad Hoc Reviewer (2003)
  • Nucleic Acid Research, Ad Hoc Reviewer (2003)
  • Proceedings of the National Academy of Sciences (USA), Ad Hoc Reviewer (2003)
  • Proceedings of the Royal Society (UK), Ad Hoc Reviewer (2003)
  • Science, Ad Hoc Reviewer (2003)
  • Search Committee for Evolutionary Bioinformatics/Computational Biology Junior Faculty, Chair (2003)
  • Search Committee for SoLS Director, Member (2003)
  • Target Hire (Brian Verrelli) Search Committee, Chair (2003)
  • Target Hire (S. Blair Hedges) Search Committee, Chair (2003)
  • Trends in Ecology and Evolution, Ad Hoc Reviewer (2003)
  • Tucson Drosophila Committee for generating a White Paper for Fruit Fly genome sequencing project, Member (2003)
  • International Genomics Consortium, Representative from ASU (2001 - 2001)
  • Information Technology Hot Team, Prop 301, Member (2000 - 2001)
  • Planning Committee, Academic degree program in Comp. Biosci, Member (2000 - 2000)