Research Topics
Genomes and GenesSpecies | Sudhir KumarSummaryAffiliation: Arizona State University Country: USA Publications
| Collaborators
|
Detail Information
Publications
Pushing back the expansion of introns in animal genomesSudhir Kumar
Center for Evolutionary Functional Genomics, Biodesign Institute, and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
Cell 123:1182-4. 2005..These observations suggest that the common ancestor of most animal phyla had intron-rich genes and reinforce the notion that introns proliferated early in the evolutionary history of eukaryotes...- Mutation rates in mammalian genomesSudhir Kumar
Department of Biology, Arizona State University, Tempe, AZ 85287 1501, USA
Proc Natl Acad Sci U S A 99:803-8. 2002..Our results suggest that the average mammalian genome mutation rate is 2.2 x 10(-9) per base pair per year, which provides further opportunities for estimating species and population divergence times by using molecular clocks... - Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervalsFabia U Battistuzzi
Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, USA
Mol Biol Evol 27:1289-300. 2010..Overall, our results show that simple strategies can be used to enhance our ability to estimate times and their CrIs when using the relaxed-clock methods... - MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequencesSudhir Kumar
Biodesign Institute, A240, Arizona State University, Tempe, AZ 85287 5301, USA
Brief Bioinform 9:299-306. 2008..We also discuss how MEGA might evolve in the future to assist researchers in their growing need to analyze large data set using new computational methods... - MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0Koichiro Tamura
Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, AZ, USA
Mol Biol Evol 24:1596-9. 2007..The current version of MEGA is available free of charge at (http://www.megasoftware.net)... - Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutationsSudhir Kumar
Center for Evolutionary Functional Genomics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287 5301, USA
Genome Res 19:1562-9. 2009..The impending sequencing of thousands of human and many more vertebrate genomes will lead to more accurate classifiers needed in real-world applications... - FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesisSudhir Kumar
Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
Bioinformatics 27:3319-20. 2011..Therefore, FlyExpress is a unique tool for mining spatiotemporal expression patterns in a format readily accessible to the scientific community... - Higher intensity of purifying selection on >90% of the human genes revealed by the intrinsic replacement mutation ratesSankar Subramanian
Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, AZ, USA
Mol Biol Evol 23:2283-7. 2006..These patterns indicate the need for using new approaches for estimating rates of amino acid-altering mutations in order to find positively selected genes and codons in genomes that contain hypermutable CpG's... - Bioinformatics software for biologists in the genomics eraSudhir Kumar
Center for Evolutionary Functional Genomics, The Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, Arizona 85287 5301, USA
Bioinformatics 23:1713-7. 2007..Furthermore, biological intuitiveness and investigator empowerment need to take precedence over the current supposition that biologists should re-tool and become programmers when analyzing genome scale datasets... - MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignmentSudhir Kumar
Life Sciences A 351, The Biodesign Institute, Tempe, AZ 85287 4501, USA
Brief Bioinform 5:150-63. 2004..This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA... - A bag-of-words approach for Drosophila gene expression pattern annotationShuiwang Ji
Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
BMC Bioinformatics 10:119. 2009..Considering that the number of available images is rapidly increasing, it is imperative to design computational methods to automate this task... - Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomesSankar Subramanian
Center for Evolutionary Functional Genomics, Arizona Biodesign Institute, Department of Biology, Arizona State University, Tempe, Arizona 85287-1501, USA
Genome Res 13:838-44. 2003.... - Multiple sequence alignment: in pursuit of homologous DNA positionsSudhir Kumar
Center for Evolutionary Functional Genomics, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, Arizona 85287 5301, USA
Genome Res 17:127-35. 2007.... - Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogasterAntonio Marco
Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287 5301, USA
Bioinformatics 25:2473-7. 2009..We discuss these results in light of reverse engineering approaches to computationally predict regulatory sequences by using comparative genomics... - Nullomers: really a matter of natural selection?Claudia Acquisti
Center for Evolutionary Functional Genomics, Arizona State University, Tempe, Arizona, United States of America
PLoS ONE 2:e1022. 2007.... - Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inferenceMichael S Rosenberg
Department of Biology and Center for Evolutionary Functional Genomics, Arizona State University, USA
Mol Biol Evol 20:610-21. 2003..In these specific simulation conditions, we did not find a significant interaction between phylogenetic accuracy and substitution pattern heterogeneity among lineages, even when the taxon sampling is increased... - Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representationsRajalakshmi Gurunathan
Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287 5301, USA
BMC Bioinformatics 5:202. 2004.... - Stoichiogenomics: the evolutionary ecology of macromolecular elemental compositionJames J Elser
School of Life Sciences, Arizona State University, Tempe, AZ 85287 4501, USA
Trends Ecol Evol 26:38-44. 2011..In this review, we show that with these findings, new directions for future investigations are emerging, particularly via the increasing availability of diverse metagenomic and metatranscriptomic data sets... - Signatures of nitrogen limitation in the elemental composition of the proteins involved in the metabolic apparatusClaudia Acquisti
Biodesign Institute, Center for Evolutionary Functional Genomics, Arizona State University, Tempe, AZ 85287 5301, USA
Proc Biol Sci 276:2605-10. 2009.... - Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutationsSudhir Kumar
School of Life Sciences, Arizona State University, Tempe, AZ 85287 4501, USA
Trends Genet 27:377-86. 2011..We conclude that the patterns of long-term evolutionary conservation and permissible sequence divergence are essential and instructive modalities for functional assessment of human genetic variations... - Prospects for inferring very large phylogenies by using the neighbor-joining methodKoichiro Tamura
Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe, 85287-4501, USA
Proc Natl Acad Sci U S A 101:11030-5. 2004..Our results encourage the use of complex models of nucleotide substitution for estimating evolutionary distances and hint at bright prospects for the application of the NJ and related methods in inferring large phylogenies... - Lower bounds on multiple sequence alignment using exact 3-way alignmentCharles J Colbourn
Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287 5301, USA
BMC Bioinformatics 8:140. 2007..Although numerous cost metrics can be used to determine the quality of an alignment, many are based on sum-of-pairs (SP) measures and their generalizations... - Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major ordersM Andreina Pacheco
Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University, AZ, USA
Mol Biol Evol 28:1927-42. 2011..Such findings support the choice of COX 1 among mt genes as target for developing DNA barcoding approaches in birds... - More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structureAnne C Stone
School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
Philos Trans R Soc Lond B Biol Sci 365:3277-88. 2010..1-1.5, 1.1-0.76 and 0.25-0.18 Ma for the chimpanzee/bonobo, western/(eastern + central) and eastern/central chimpanzee divergences, respectively... - TimeTree: a public knowledge-base of divergence times among organismsS Blair Hedges
Department of Biology, Pennsylvania State University, University Park, PA 16802 5301, USA
Bioinformatics 22:2971-2. 2006..AVAILABILITY: TimeTree is available at http://www.timetree.net.. - TimeTree2: species divergence times on the iPhoneSudhir Kumar
Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University, Tempe, AZ 85287 5301, USA
Bioinformatics 27:2023-4. 2011..timetree.org, with an iPhone app available from iTunes (http://itunes.apple.com/us/app/timetree/id372842500?mt=8) and a YouTube tutorial (http://www.youtube.com/watch?v=CxmshZQciwo)... - Evolutionary anatomies of positions and types of disease-associated and neutral amino acid mutations in the human genomeSankar Subramanian
Center for Evolutionary Functional Genomics, The Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, Arizona 85287 5301, USA
BMC Genomics 7:306. 2006..We compare these patterns with 5,308 non-synonymous Single Nucleotide Polymorphisms (nSNPs) in 2,592 genes from primary SNP resources... - Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene treeSudhindra R Gadagkar
Department of Biology, University of Dayton, Dayton, Ohio 46469 2320, USA
J Exp Zool B Mol Dev Evol 304:64-74. 2005..Therefore, it will be prudent to report the number of individual genes supporting an inferred clade in the concatenated sequence tree, in addition to the bootstrap support... - Placing confidence limits on the molecular age of the human-chimpanzee divergenceSudhir Kumar
Center for Evolutionary Functional Genomics, Biodesign Institute, and School of Life Sciences, Arizona State University, Tempe, AZ 85287 5301, USA
Proc Natl Acad Sci U S A 102:18842-7. 2005..We conclude that tests of hypotheses about the timing of human-chimpanzee divergence demand more precise fossil-based calibrations... - Taxon sampling, bioinformatics, and phylogenomicsMichael S Rosenberg
Department of Biology, Arizona State University, Tempe, Arizona 85287-1501, USA
Syst Biol 52:119-24. 2003 - BEST: a novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster developmentSudhir Kumar
Center for Evolutionary Functional Genomics, Arizona State University, Tempe, Arizona 85287, USA
Genetics 162:2037-47. 2002..These computational developmental biology methodologies are likely to make the great wealth of embryonic gene expression pattern data easily accessible and to accelerate the discovery of developmental networks... - Statistics and truth in phylogenomicsSudhir Kumar
Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University, Arizona, USA
Mol Biol Evol 29:457-72. 2012..Here, we present a theoretical overview and discuss practical aspects of the interplay between effect sizes, bias, and P values as it relates to the statistical inference of evolutionary truth in phylogenomics... - Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genomeSankar Subramanian
Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe 85287-4501, USA
Genetics 168:373-81. 2004..These results provide insights into the differential relationship and effect of the increasing complexity of animal body form on evolutionary rates of proteins... - Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocksKoichiro Tamura
Center for Evolutionary Functional Genomics, Arizona Biodesign Institute, and School of Life Sciences, Arizona State University, USA
Mol Biol Evol 21:36-44. 2004..The inferred temporal pattern of fruit fly evolution shows correspondence with the cooling patterns of paleoclimate changes and habitat fragmentation in the Cenozoic... - Signatures of ecological resource availability in the animal and plant proteomesJames J Elser
School of Life Sciences, Arizona State University, USA
Mol Biol Evol 23:1946-51. 2006..This constitutes the first evidence for an influence of environmental resource availability on proteomes of multicellular organisms... - Automated annotation of Drosophila gene expression patterns using a controlled vocabularyShuiwang Ji
Department of Computer Science and Engineering, Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
Bioinformatics 24:1881-8. 2008..The proposed framework is evaluated by comparing its annotation with that of human curators, and promising performance in terms of F1 score has been reported... - Molecular clocks: four decades of evolutionSudhir Kumar
Center for Evolutionary Functional Genomics, The Biodesign Institute and School of Life Sciences, Arizona State University, Tempe 85287 5301, USA
Nat Rev Genet 6:654-62. 2005..As DNA-sequencing technologies have progressed, the use of molecular clocks has increased, with a profound effect on our understanding of the temporal diversification of species and genomes... - Patterns of transitional mutation biases within and among mammalian genomesMichael S Rosenberg
Center for Evolutionary Functional Genomics and Department of Biology, Arizona State University, USA
Mol Biol Evol 20:988-93. 2003..The estimates show no relationship to potential intrachromosomal or interchromosomal effects. This uniformity points to similarity in point mutation processes in genomic regions with substantially different GC-content biases... - Fast and slow implementations of relaxed-clock methods show similar patterns of accuracy in estimating divergence timesFabia U Battistuzzi
Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University, USA
Mol Biol Evol 28:2439-42. 2011..These results will encourage the analysis of larger data sets as well as the evaluation of the robustness of estimated times to changes in the model of evolutionary rates and clock calibrations... - Genomic sequence of a ranavirus (family Iridoviridae) associated with salamander mortalities in North AmericaJames K Jancovich
School of Life Sciences, Arizona State University, Tempe, AZ 85287-4601, USA
Virology 316:90-103. 2003.... - Comparison of embryonic expression within multigene families using the FlyExpress discovery platform reveals more spatial than temporal divergenceCharlotte E Konikoff
School of Life Sciences and Center for Evolutionary Medicine and Informatics in the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
Dev Dyn 241:150-60. 2012..The FlyExpress discovery platform was developed to facilitate data-driven comparative analysis of expression pattern images from Drosophila embryos... - Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachousSudhindra R Gadagkar
Mol Biol Evol 22:2139-41. 2005.... - Precision of molecular time estimatesS Blair Hedges
NASA Astrobiology Institute and Department of Biology, Pennsylvania State University, University Park, PA 16802-5301, USA
Trends Genet 20:242-7. 2004 - Genomics. Vertebrate genomes comparedS Blair Hedges
NASA Astrobiology Institute and Department of Biology, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802-5301, USA
Science 297:1283-5. 2002 - Evolutionary distance estimation under heterogeneous substitution pattern among lineagesKoichiro Tamura
Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
Mol Biol Evol 19:1727-36. 2002..We also discuss the relationship of the substitution and mutation rate estimates when the substitution pattern is not the same in the lineages leading to the two sequences compared... - The spectrum of human rhodopsin disease mutations through the lens of interspecific variationAdriana D Briscoe
Comparative and Evolutionary Physiology Group, University of California, Irvine, Department of Ecology and Evolutionary Biology, 321 Steinhaus Hall, Irvine, CA 92697, USA
Gene 332:107-18. 2004.... - Evolution of genes and genomes on the Drosophila phylogenyAndrew G Clark
Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
Nature 450:203-18. 2007..These may prove to underlie differences in the ecology and behaviour of these diverse species... - Organization and differential expression of the GACA/GATA tagged somatic and spermatozoal transcriptomes in Buffalo Bubalus bubalisJyoti Srivastava
Molecular Genetics Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
BMC Genomics 9:132. 2008..Moreover, the distribution of GACA and GATA repeats in the prokaryotic and eukaryotic genomes was studied to highlight their significance in genome evolution... - Characterization of Smoc-1 uncovers two transcript variants showing differential tissue and age specific expression in Bubalus bubalisJyoti Srivastava
Molecular Genetics Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
BMC Genomics 8:436. 2007..The main objective of this study was to gain an insight into its structural and functional organization, and expressional status of Smoc-1 in water buffalo, Bubalus bubalis... - Constraining fossil calibrations for molecular clocksS Blair Hedges
Bioessays 28:770-1; author reply 772-3. 2006 - Multiple Sclerosis in Keralite siblings after migration to the Middle East: a report of familial Multiple Sclerosis from IndiaSunil K Narayan
Jawaharlal Institute of Postgraduate Medical Education and Research, Pondicherry 6, India
J Neurol Sci 260:244-8. 2007..Onset of MS in South Indian siblings after several years of stay in the Middle East may support aetiological postulations of gene-environment interactions... - Genomic clocks and evolutionary timescalesS Blair Hedges
NASA Astrobiology Institute and Department of Biology, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802 5301, USA
Trends Genet 19:200-6. 2003..Fortunately, time estimates inferred using many genes or proteins have greater precision and appear to be robust to different approaches... - Constraint and turnover in sex-biased gene expression in the genus DrosophilaYu Zhang
Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, USA
Nature 450:233-7. 2007..This higher divergence and turnover of genes with male-biased expression may be due to high transcription rates in the male germline, greater functional pleiotropy of genes expressed in females, and/or sexual competition... - Measuring conservation of contiguous sets of autosomal markers on bovine and porcine genomes in relation to the map of the human genomeZhihua Jiang
Department of Animal and Poultry Science, University of Guelph, ON, Canada
Genome 45:769-76. 2002..These results provide basic guidelines for further gene and QTL mapping of the bovine and porcine genomes, as well as insight into the evolution of mammalian genomes... - Chromosomal localization, copy number assessment, and transcriptional status of BamHI repeat fractions in water buffalo Bubalus bubalisDeepali Pathak
Molecular Genetics Laboratory, National Institute of Immunology, New Delhi, India
DNA Cell Biol 25:206-14. 2006..Phylogenetic analysis of these sequences showed a close relationship between buffalo and cattle. The prospect of this approach in comparative genomics is highlighted...