Laboratory of Sudhir Kumar :: Publications 2007-2011

2011

107

Molecular Clock: Testing

eLS 7 pp

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

106

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

105

Stoichiogenomics: the Evolutionary Ecology of Macromolecular Elemental Composition

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

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

104

Rampant Purifying Selection Conserves Positions with Posttranslational Modifications in Human Proteins

Molecular Biology and Evolution 28(5):1565-1568

V.E. Gray, S. Kumar

103

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

102

TimeTree2: Species Divergence Times on the iPhone

Bioinformatics 27(14):2023-2024

S. Kumar, S.B. Hedges

101

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

100

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

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

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

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

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

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

94

The Timetree of Life

Oxford University Press 550 pp

S.B. Hedges, S. Kumar

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

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

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

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

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

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

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

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

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

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

83

Biological Image Analysis via Matrix Approximation

Encyclopedia of Data Warehousing and Mining. Idea Group 166-170

J. Ye, R. Janadan, S. Kumar

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

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

80

Detecting Molecular Signatures of Adaptive Evolution

Evolutionary Genomics and Proteomics, Sinauer Associates 241-254

A. Filipski, S. Prohaska, S. Kumar

Nullomers: Really a Matter of Natural Selection?

PLOS ONE 2(10):1022-1025

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

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

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

BMC Bioinformatics 2007(8):140-147

C.J. Colbourn, S. Kumar

Bioinformatics Software for Biologists in the Genomics Era

Bioinformatics 23(14):1713-1717

S. Kumar, J. Dudley

Multiple Sequence Alignment: In Pursuit of Homologous DNA Positions

Genome Research 17(2):127-135

S. Kumar, A. Filipski

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

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