Sudhir Kumar

Summary

Affiliation: Arizona State University
Country: USA

Publications

  1. ncbi request reprint Pushing back the expansion of introns in animal genomes
    Sudhir 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
  2. pmc Mutation rates in mammalian genomes
    Sudhir Kumar
    Department of Biology, Arizona State University, Tempe, AZ 85287 1501, USA
    Proc Natl Acad Sci U S A 99:803-8. 2002
  3. pmc Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals
    Fabia U Battistuzzi
    Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, USA
    Mol Biol Evol 27:1289-300. 2010
  4. pmc MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences
    Sudhir Kumar
    Biodesign Institute, A240, Arizona State University, Tempe, AZ 85287 5301, USA
    Brief Bioinform 9:299-306. 2008
  5. ncbi request reprint MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    Koichiro Tamura
    Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, AZ, USA
    Mol Biol Evol 24:1596-9. 2007
  6. pmc Exploring spatial patterns of gene expression from fruit fly embryogenesis on the iPhone
    Sudhir Kumar
    Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University ASU, Tempe, AZ 85287 5301, USA
    Bioinformatics 28:2847-8. 2012
  7. pmc Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations
    Sudhir Kumar
    Center for Evolutionary Functional Genomics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287 5301, USA
    Genome Res 19:1562-9. 2009
  8. pmc Learning sparse representations for fruit-fly gene expression pattern image annotation and retrieval
    Lei Yuan
    Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
    BMC Bioinformatics 13:107. 2012
  9. pmc Statistics and truth in phylogenomics
    Sudhir Kumar
    Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University, Arizona, USA
    Mol Biol Evol 29:457-72. 2012
  10. pmc FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis
    Sudhir Kumar
    Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
    Bioinformatics 27:3319-20. 2011

Detail Information

Publications63

  1. ncbi request reprint Pushing back the expansion of introns in animal genomes
    Sudhir 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...
  2. pmc Mutation rates in mammalian genomes
    Sudhir 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...
  3. pmc Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals
    Fabia 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...
  4. pmc MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences
    Sudhir 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...
  5. ncbi request reprint MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    Koichiro 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)...
  6. pmc Exploring spatial patterns of gene expression from fruit fly embryogenesis on the iPhone
    Sudhir Kumar
    Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University ASU, Tempe, AZ 85287 5301, USA
    Bioinformatics 28:2847-8. 2012
    ....
  7. pmc Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations
    Sudhir 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...
  8. pmc Learning sparse representations for fruit-fly gene expression pattern image annotation and retrieval
    Lei Yuan
    Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
    BMC Bioinformatics 13:107. 2012
    ..However, this manual practice does not scale with the continuously expanding collection of images. In addition, existing image retrieval systems based on the expression patterns may be made more accurate using keywords...
  9. pmc Statistics and truth in phylogenomics
    Sudhir 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...
  10. pmc FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis
    Sudhir 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...
  11. pmc Higher intensity of purifying selection on >90% of the human genes revealed by the intrinsic replacement mutation rates
    Sankar 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...
  12. pmc A bag-of-words approach for Drosophila gene expression pattern annotation
    Shuiwang 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...
  13. ncbi request reprint MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
    Sudhir 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...
  14. ncbi request reprint Bioinformatics software for biologists in the genomics era
    Sudhir 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...
  15. doi request reprint Automated annotation of developmental stages of Drosophila embryos in images containing spatial patterns of expression
    Lei Yuan
    School of Computing, Informatics, and Decision Systems Engineering, Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA, National Key Laboratory for Novel Software Technology, Nanjing University, Nanjing 210023, China, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA and Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
    Bioinformatics 30:266-73. 2014
    ..Availability and implementation: The software package is available for download at: http://www.public.asu.edu/∼jye02/Software/Fly-Project/...
  16. pmc 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
    ....
  17. pmc Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes
    Sankar 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
    ....
  18. pmc Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster
    Antonio Marco
    Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287 5301, USA
    Bioinformatics 25:2473-7. 2009
    ..We have also examined the reverse relationship between the expression correlation and the extent of TFBS sharing...
  19. ncbi request reprint Multiple sequence alignment: in pursuit of homologous DNA positions
    Sudhir 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
    ....
  20. ncbi request reprint Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference
    Michael 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...
  21. pmc MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis
    Sudhir Kumar
    Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University ASU, Tempe, AZ 85287 5301, USA
    Bioinformatics 28:2685-6. 2012
    ..Here, we describe MEGA-CC and outline the steps for using MEGA-CC in tandem with MEGA-Proto for iterative and automated data analysis...
  22. pmc Fast and slow implementations of relaxed-clock methods show similar patterns of accuracy in estimating divergence times
    Fabia 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...
  23. pmc Comparison of embryonic expression within multigene families using the FlyExpress discovery platform reveals more spatial than temporal divergence
    Charlotte 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...
  24. pmc Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations
    Rajalakshmi Gurunathan
    Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287 5301, USA
    BMC Bioinformatics 5:202. 2004
    ....
  25. pmc Stoichiogenomics: the evolutionary ecology of macromolecular elemental composition
    James 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...
  26. pmc Signatures of nitrogen limitation in the elemental composition of the proteins involved in the metabolic apparatus
    Claudia Acquisti
    Biodesign Institute, Center for Evolutionary Functional Genomics, Arizona State University, Tempe, AZ 85287 5301, USA
    Proc Biol Sci 276:2605-10. 2009
    ....
  27. pmc Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations
    Vanessa E Gray
    Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
    Bioinformatics 28:2093-6. 2012
    ..Therefore, the comparisons of experimental-profiling results with those from computational predictions need to be sensitive to the evolutionary conservation of the positions harboring the amino acid change...
  28. pmc Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations
    Sudhir 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...
  29. pmc Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders
    M 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...
  30. pmc TimeTree2: species divergence times on the iPhone
    Sudhir Kumar
    Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University, Tempe, AZ 85287 5301, USA
    Bioinformatics 27:2023-4. 2011
    ..Published time estimates are now readily accessible to the scientific community, K-12 and college educators, and the general public, without requiring knowledge of evolutionary nomenclature...
  31. pmc More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure
    Anne 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...
  32. pmc Prospects for inferring very large phylogenies by using the neighbor-joining method
    Koichiro 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...
  33. pmc Lower bounds on multiple sequence alignment using exact 3-way alignment
    Charles 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...
  34. ncbi request reprint Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree
    Sudhindra 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...
  35. ncbi request reprint TimeTree: a public knowledge-base of divergence times among organisms
    S Blair Hedges
    Department of Biology, Pennsylvania State University, University Park, PA 16802 5301, USA
    Bioinformatics 22:2971-2. 2006
    ..Results are presented and summarized, allowing users to quickly determine the range and robustness of time estimates and the degree of consensus from the published literature...
  36. pmc Placing confidence limits on the molecular age of the human-chimpanzee divergence
    Sudhir 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...
  37. pmc Evolutionary anatomies of positions and types of disease-associated and neutral amino acid mutations in the human genome
    Sankar 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...
  38. pmc Taxon sampling, bioinformatics, and phylogenomics
    Michael S Rosenberg
    Department of Biology, Arizona State University, Tempe, Arizona 85287 1501, USA
    Syst Biol 52:119-24. 2003
  39. pmc BEST: a novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development
    Sudhir 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...
  40. doi request reprint Image-level and group-level models for Drosophila gene expression pattern annotation
    Qian Sun
    Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
    BMC Bioinformatics 14:350. 2013
    ..It is thus imperative to design an automated system for efficient image annotation and comparison...
  41. pmc Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome
    Sankar 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...
  42. ncbi request reprint Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks
    Koichiro 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...
  43. ncbi request reprint Signatures of ecological resource availability in the animal and plant proteomes
    James 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...
  44. pmc Automated annotation of Drosophila gene expression patterns using a controlled vocabulary
    Shuiwang 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
    ..However, the number of patterns generated by high-throughput in situ hybridization is rapidly increasing. It is, therefore, tempting to approach this problem by employing computational methods...
  45. pmc Genome-wide profiling of human cap-independent translation-enhancing elements
    Brian P Wellensiek
    Center for Evolutionary Medicine and Informatics in the Biodesign Institute, Arizona State University, Tempe, Arizona, USA
    Nat Methods 10:747-50. 2013
    ..We identified >12,000 translation-enhancing elements (TEEs) in the human genome, generated a high-resolution map of human TEE-bearing regions (TBRs), and validated the function of a subset of sequences in vitro and in cultured cells. ..
  46. ncbi request reprint Molecular clocks: four decades of evolution
    Sudhir 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...
  47. pmc Evolutionary balancing is critical for correctly forecasting disease-associated amino acid variants
    Li Liu
    Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University, USA
    Mol Biol Evol 30:1252-7. 2013
    ..These advances are implemented in a web resource for use in practical applications (www.mypeg.info, last accessed March 13, 2013)...
  48. ncbi request reprint Genomic sequence of a ranavirus (family Iridoviridae) associated with salamander mortalities in North America
    James K Jancovich
    School of Life Sciences, Arizona State University, Tempe, AZ 85287 4601, USA
    Virology 316:90-103. 2003
    ....
  49. ncbi request reprint Patterns of transitional mutation biases within and among mammalian genomes
    Michael 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...
  50. ncbi request reprint Constraining fossil calibrations for molecular clocks
    S Blair Hedges
    Bioessays 28:770-1; author reply 772-3. 2006
  51. ncbi request reprint Evolution of genes and genomes on the Drosophila phylogeny
    Andrew 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...
  52. ncbi request reprint Evolutionary distance estimation under heterogeneous substitution pattern among lineages
    Koichiro 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...
  53. pmc Characterization of Smoc-1 uncovers two transcript variants showing differential tissue and age specific expression in Bubalus bubalis
    Jyoti 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...
  54. ncbi request reprint Precision of molecular time estimates
    S Blair Hedges
    NASA Astrobiology Institute and Department of Biology, Pennsylvania State University, University Park, PA 16802 5301, USA
    Trends Genet 20:242-7. 2004
  55. ncbi request reprint The spectrum of human rhodopsin disease mutations through the lens of interspecific variation
    Adriana 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
    ....
  56. pmc Organization and differential expression of the GACA/GATA tagged somatic and spermatozoal transcriptomes in Buffalo Bubalus bubalis
    Jyoti 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...
  57. ncbi request reprint Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous
    Sudhindra R Gadagkar
    Mol Biol Evol 22:2139-41. 2005
    ....
  58. ncbi request reprint Genomics. Vertebrate genomes compared
    S 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
  59. ncbi request reprint Multiple Sclerosis in Keralite siblings after migration to the Middle East: a report of familial Multiple Sclerosis from India
    Sunil K Narayan
    Jawaharlal Institute of Postgraduate Medical Education and Research, Pondicherry 6, India
    J Neurol Sci 260:244-8. 2007
    ..To report Multiple Sclerosis (MS) in two migrant Indian siblings in the Middle East...
  60. pmc Constraint and turnover in sex-biased gene expression in the genus Drosophila
    Yu 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...
  61. ncbi request reprint Chromosomal localization, copy number assessment, and transcriptional status of BamHI repeat fractions in water buffalo Bubalus bubalis
    Deepali 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...
  62. ncbi request reprint Genomic clocks and evolutionary timescales
    S 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...
  63. ncbi request reprint Measuring conservation of contiguous sets of autosomal markers on bovine and porcine genomes in relation to the map of the human genome
    Zhihua 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...