Laboratory of Sudhir Kumar :: Publications 2007-2011

2011

110

Molecular Clock: Testing

eLS 7 pp

F.U. Battistuzzi, A. Filipski, S. Kumar


109

Fast and Slow Implementations of Relaxed-Clock Methods Show Similar Patterns of Accuracy in Estimating Divergence Times

Molecular Biology and Evolution 28(9) 2439-2442

F.U. Battistuzzi, P. Billing-Ross, A. Paliwal, S. Kumar


108

Stoichiogenomics: the Evolutionary Ecology of Macromolecular Elemental Composition

Trends in Ecology & Evolution 26(1) 38-44

J.J. Elser, C. Acquisti, S. Kumar


107

Rampant Purifying Selection Conserves Positions with Posttranslational Modifications in Human Proteins

Molecular Biology and Evolution 28(5) 1565-1568

V.E. Gray, S. Kumar


106

Phylomedicine: An Evolutionary Telescope to Explore and Diagnose the Universe of Disease Mutations

Trends in Genetics 27(9) 377-386

S. Kumar, J.T. Dudley, A. Filipski, L. Liu


105

TimeTree2: Species Divergence Times on the iPhone

Bioinformatics 27(14) 2023-2024

S. Kumar, S.B. Hedges


104

FlyExpress: Visual Mining of Spatiotemporal Patterns for Genes and Publications in Drosophila Embryogenesis

Bioinformatics 27(23) 3319-3320

S. Kumar, C. Konikoff, B. Van Emden, C. Busick, K.T. Davis, S. Ji, L.W. Wu, H. Ramos, T. Brody, S. Panchanathan, J. Ye, T. L. Karr, K. Gerold, M. McCutchan, S. J. Newfeld


103

Evolution of Modern Birds Revealed by Mitogenomics: Timing the Radiation and Origin of Major Orders

Molecular Biology and Evolution 28(6) 1927-1942

M.A. Pacheco, F.U. Battistuzzi, M. Lentino, R.F. Aguilar, S. Kumar, A. Escalante


102

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

Molecular Biology and Evolution 28(10) 2731-2739

K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, S. Kumar


2010

101

Performance of Relaxed-Clock Methods in Estimating Evolutionary Divergence Times and Their Credibility Intervals

Molecular Biology and Evolution 27(6) 1289-1300

F.U. Battistuzzi, A. Filipski, S.B. Hedges, S. Kumar


100

Quantitative Analysis of the Drosophila Segmentation Regulatory Network Using Pattern Generating Potentials

PLOS Biology 8(8) 19 pp

M. Kazemian, C. Blatti, A. Richards, M. McCutchan, N. Wakabayashi-Ito, A.S. Hammonds, S.E. Celniker, S. Kumar, S.A. Wolfe, M.H. Brodsky, S. Sinha


99

More Reliable Estimates of Divergence Times in Pan Using Complete MtDNA Sequences and Accounting for Population Structure

Philosophical Transactions of the Royal Society B-Biological Sciences 365(1556) 3277-3288

A.C. Stone, F.U. Battistuzzi, L.S. Kubatko, G.H. Perry, Jr., E. Trudeau, H. Lin, S. Kumar


2009

98

Ecological Nitrogen Limitation Shapes the DNA Composition of Plant Genomes

Molecular Biology and Evolution 26(5) 953-956

C. Acquisti, J.J. Elser, S. Kumar


97

The Timetree of Life

Oxford University Press 550 pp

S.B. Hedges, S. Kumar


96

Methods for Incorporating the Hypermutability of CpG Dinucleotides in Detecting Natural Selection Operating at the Amino Acid Sequence Level

Genes & Genetic Systems 85(6) 401

Y. Suzuki, T. Gojobori, S. Kumar


95

Signatures of Nitrogen Limitation in the Elemental Composition of the Proteins Involved in the Metabolic Apparatus

Proceedings of the Royal Society B-Biological Sciences 276(1667) 2605-2610

C. Acquisti, S. Kumar, J.J. Elser


94

Association of Orthodenticle with Natural Variation for Early Embryonic Patterning in Drosophila Melanogaster

Journal of Experimental Zoology Part B-Molecular and Developmental Evolution 312(8) 841-854

L.M. Goering, P.K. Hunt, C. Heighington, C. Busick, P.S. Pennings, J. Hermisson, S. Kumar, G. Gibson


93

Phylogenetic Construction of 17 Bacterial Phyla by New Method and Carefully Selected Orthologs

Gene 429(2) 59-64

T. Horiike, D. Miyata, K. Hamada, S. Saruhashi, T. Shinozawa, S. Kumar, R. Chakraborty, T. Komiyama, Y. Tateno


92

A Bag-of-Words Approach for Drosophila Gene Expression Pattern Annotation

BMC Bioinformatics 2009(10) 119-135

S. Ji, Y.X. Li, Z.H. Zhou, S. Kumar, J. Ye


91

Drosophila Gene Expression Pattern Annotation Using Sparse Features and Term-Term Interactions

Kdd-09: 15th ACM Sigkdd Conference on Knowledge Discovery and Data Mining 407-415

S. Ji, L. Yuan, Y.X. Li, Z.H. Zhou, S. Kumar, J. Ye


90

Positional Conservation and Amino Acids Shape the Correct Diagnosis and Population Frequencies of Benign and Damaging Personal Amino Acid Mutations

Genome Research 19(9) 1562-1569

S. Kumar, M.P. Suleski, G.J. Markov, S. Lawrence, A. Marco, A.J. Filipski


89

Relationship Between Gene Co-Expression and Sharing of Transcription Factor Binding Sites in Drosophila Melanogaster

Bioinformatics 25(19) 2473-2477

A. Marco, C. Konikoff, T.L. Karr, S. Kumar


88

The Origin of Metazoa: A Transition from Temporal to Spatial Cell Differentiation

Bioessays 31(7) 758-768

K.V. Mikhailov, A.V. Konstantinova, M.A. Nikitin, P.V. Troshin, L.Y. Rusin, V.A. Lyubetsky, Y.V. Panchin, A.P. Mylnikov, L.L. Moroz, S. Kumar, V.V. Aleoshin


87

Methods for Incorporating the Hypermutability of CpG Dinucleotides in Detecting Natural Selection Operating at the Amino Acid Sequence Level

Molecular Biology and Evolution 26(10) 2275-2284

Y. Suzuki, T. Gojobori, S. Kumar


2008

86

Developmental Stage Annotation of Drosophila Gene Expression Pattern images via an entire solution path for LDA

ACM Transactions on Knowledge Discovery from Data 2(1) 21 pp

J. Ye, J. Chen, R. Janardan, S. Kumar


85

Encyclopedia of Data Warehousing and Mining: Biological Image Analysis via Matrix Approximation

Idea Group 166-170

J. Ye, R. Janadan, S. Kumar


84

Automated Annotation of Drosophila Gene Expression Patterns Using a Controlled Vocabulary

Bioinformatics 24(17) 1881-1888

S. Ji, L. Sun, R. Jin, S. Kumar, J. Ye


83

MEGA: A Biologist-Centric Software for Evolutionary Analysis of DNA and Protein Sequences

Briefings in Bioinformatics 9(4) 299-306

S. Kumar, M. Nei, J. Dudley, K. Tamura


2007

82

Evolutionary Genomics and Proteomics: Detecting Molecular Signatures of Adaptive Evolution

Sinauer Associates 241-254

A. Filipski, S. Prohaska, S. Kumar


81

Nullomers: Really a Matter of Natural Selection?

PLOS ONE 2(10) 1022-1025

C. Acquisti, G. Poste, D. Curtiss, S. Kumar


80

Evolution of Genes and Genomes on the Drosophila Phylogeny

Nature 450(7167) 203-218

A.G. Clark, M.B. Eisen, D.R. Smith, C.M. Bergman, B. Oliver, T.A. Markow, T.C. Kaufman, M. Kellis, W. Gelbart, V.N. Iyer, D.A. Pollard, T.B. Sackton, S. Kumar, et al


79

Lower Bounds on Multiple Sequence Alignment Using Exact 3-Way Alignment

BMC Bioinformatics 2007(8) 140-147

C.J. Colbourn, S. Kumar


78

Bioinformatics Software for Biologists in the Genomics Era

Bioinformatics 23(14) 1713-1717

S. Kumar, J. Dudley


77

Multiple Sequence Alignment: In Pursuit of Homologous DNA Positions

Genome Research 17(2) 127-135

S. Kumar, A. Filipski


76

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0

Molecular Biology and Evolution 24(8) 1596-1599

K. Tamura, J. Dudley, M. Nei, S. Kumar


75

Constraint and Turnover in Sex-Biased Gene Expression in the Genus Drosophila

Nature 450(7167) 233-U2

Y. Zhang, D. Sturgill, M. Parisi, S. Kumar, B. Oliver