2009

Ecological Nitrogen Limitation Shapes the DNA Composition of Plant Genomes

Molecular Biology and Evolution | 26:953–956

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

96

The Timetree of Life

Oxford University Press (New York) | (551 pp)

S.B. Hedges, S. Kumar

95

Discovering the Timetree of Life

The TimeTree of Life (ed. Hedges, Kumar) [Oxford University Press] | 3–18

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 | 276:2605–2610

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 | 312:841–854

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 | 429:59–64

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 | 10:119 (16 pp)

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 | 19:1562–1569

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 Melanogasterc

Bioinformatics | 25:2473–2477

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

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

BioEssays | 31:758–768

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 | 26:2275–2284

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:(21 pp)

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

84

Biological Image Analysis via Matrix Approximation

Encyclopedia of Data Warehousing and Mining (ed. Wang) [Idea Group] | 166–170

J. Ye, R. Janadan, S. Kumar

Automated Annotation of Drosophila Gene Expression Patterns Using a Controlled Vocabulary

Bioinformatics | 24:1881–1888

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 | 9:299–306

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

2007
81

Detecting Molecular Signatures of Adaptive Evolution

Evolutionary Genomics and Proteomics (ed. Pagel, Pomiankowski) [Sinauer] | 241–254

A. Filipski, S. Prohaska, S. Kumar

Nullomers: Really a Matter of Natural Selection?

PLoS One | 2:1022–1025

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

Evolution of Genes and Genomes on the Drosophila Phylogeny

Nature | 450:203–218

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 | 8:140 (8 pp)

C.J. Colbourn, S. Kumar

Bioinformatics Software for Biologists in the Genomics Era

Bioinformatics | 23:1713–1717

S. Kumar, J. Dudley

Multiple Sequence Alignment: In Pursuit of Homologous DNA Positions

Genome Research | 17:127–135

S. Kumar, A. Filipski

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

Molecular Biology and Evolution | 24:1596–1599

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

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

Nature | 450:233–237

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

2006

Classification of Drosophila Embryonic Developmental State Range Based on Gene Expression Pattern Images

Computational Systems Bioinformatics Conference | 2006:293–298

J. Ye, J. Chen, Q. Li, S. Kumar

Codon-based Detection of Positive Selection Can be Biased by Heterogeneous Distribution of Polar Amino Acids along Protein Sequences

Computational Systems Bioinformatics Conference | 2006:335–340

X. Xia, S. Kumar

Signatures of Ecological Resource Availability in the Animal and Plant Proteomes

Molecular Biology and Evolution | 23:1946–1951

J.J. Elser, W.F. Fagan, S. Subramanian, S. Kumar

TimeTree: A Public Knowledge-base of Divergence Times among Organisms

Bioinformatics | 22:2971–2972

S.B. Hedges, J. Dudley, S. Kumar

Constraining Fossil Calibrations for Molecular Clocks

BioEssays | 28:770–771

S.B. Hedges, S. Kumar, M. Van Tuinen

Evolutionary Anatomies of Positions and Types of Disease-associated and Neutral Amino Acid Mutations in the Human Genome

BMC Genomics | 7:306 (9 pp)

S. Subramanian, S. Kumar

Higher Intensity of Purifying Selection on >90% of the Human Genes Revealed by the Intrinsic Replacement Mutation Rates

Molecular Biology and Evolution | 23:2283–2287

S. Subramanian, S. Kumar

2005
66

The Evolution of the Genome: Comparative Genomics in Eukaryotes

The Evolution of the Genome (ed. Gregory) [Elsevier] | 521–583

A. Filipski, S. Kumar

Maximum Likelihood Outperforms Maximum Parsimony Even When Evolutionary Rates are Heterotachous

Molecular Biology and Evolution | 22:2139–2141

S. Gadagkar, S. Kumar

Inferring Species Phylogenies from Multiple Genes: Concatenated Sequence Tree versus Consensus Gene Tree

Journal of Experimental Zoology Part B: Molecular and Developmental Evolution | 304:64–74

S. Gadagkar, M. Rosenberg, S. Kumar

Automatic Annotation Techniques for Gene Expression Images of the Fruit Fly Embryo

Visual Communications and Image Processing 2005, Pts 1-4 | 5960:576–583

M. Gargesha, J. Yang, B. Van Emden, S. Panchanathan, S. Kumar

Molecular Clocks: Four Decades of Evolution

Nature Reviews Genetics | 6:654–662

S. Kumar

Placing Confidence Limits on the Molecular Age of the Human-Chimpanzee Divergence

Proceedings of the National Academy of Sciences (USA) | 102:18842–18847

S. Kumar, A. Filipski, V. Swarna, A. Walker, S.B. Hedges

Pushing Back the Expansion of Introns in Animal Genomes

Cell | 123:1182–1184

S. Kumar, S.B. Hedges

2004
59

Image Registration and Similarity Computation for Chicken Gene Expression Patterns

Genomic Signal Processing and Statistics | (4 pp)

M. Gargesha, P. Antin, B. Van Emden, S. Panchanathan, S. Kumar

The Spectrum of Human Rhodopsin Disease Mutations through the Lens of Interspecific Variation

Gene | 12:107–118

A. Briscoe, C. Gaur, S. Kumar

Identifying Spatially Similar Gene Expression Patterns in Early Stage Fruit Fly Embryo Images: Binary Feature versus Invariant Moment Digital Representations

BMC Bioinformatics | 16:202–214

R. Gurunathan, B. Van Emden, S. Panchanathan, S. Kumar

Precision of Molecular Time Estimates

Trends in Genetics | 20:242–247

S.B. Hedges, S. Kumar

Gene Expression Intensity Shapes Evolutionary Rates of the Proteins Encoded by the Vertebrate Genome

Genetics | 168:373–381

S. Subramanian, S. Kumar

Prospects for Inferring Very Large Phylogenies by Using the Neighbor-joining Method

Proceedings of the National Academy of Sciences (USA) | 101:11030–11035

K. Tamura, M. Nei, S. Kumar

Temporal Patterns of Fruit Fly (Drosophila) Evolution Revealed by Mutation Clocks

Molecular Biology and Evolution | 21:36–44

K. Tamura, S. Subramanian, S. Kumar

MEGA3: Integrated Software for Molecular Evolutionary Genetics Analysis and Sequence Alignment

Briefings in Bioinformatics | 5:150–163

S. Kumar, K. Tamura, M. Nei

2003

Genomic Clocks and Evolutionary Timescales

Trends in Genetics | 19:200–206

S.B. Hedges, S. Kumar

Genomic Sequence of a Ranavirus (family Iridoviridae) Associated with Salamander Mortalities in North America

Virology | 316:90–103

J. Jancovich, J. Mao, V. Chinchar, C. Wyatt, S. Case, S. Kumar, G. Valente, S. Subramanian, E. Davidson, J. Collins, B. Jacobs

Quantifying the Intragenic Distribution of Human Disease Mutations

Annals of Human Genetics | 67:567–579

M. Miller, J. Parker, S. Rissing, S. Kumar

Heterogeneity of Nucleotide Frequencies among Evolutionary Lineages and Phylogenetic Inference

Molecular Biology and Evolution | 20:610–621

M. Rosenberg, S. Kumar

Taxon Sampling, Bioinformatics, and Phylogenomics

Systematic Biology | 52:119–124

M. Rosenberg, S. Kumar

Patterns of Transitional Mutation Biases within and among Mammalian Genomes

Molecular Biology and Evolution | 20:988–993

M. Rosenberg, S. Subramanian, S. Kumar

Neutral Substitutions Occur at a Faster Rate in Exons than in Noncoding DNA in Primate Genomes

Genome Research | 13:838–844

S. Subramanian, S. Kumar

2002

Vertebrate Genomes Compared

Science | 297:1283–1285

S.B. Hedges, S. Kumar

Measuring Conservation of Contiguous Sets of Autosomal Markers on Bovine and Porcine Genomes in relation to the Map of the Human Genome

Genome | 45:769–776

Z. Jiang, J. Melville, H. Cao, S. Kumar, A. Filipski, A. Gibbins

BEST: A Novel Computational Approach for Comparing Gene Expression Patterns from Early Stages of Drosophila melanogaster Development

Genetics | 162:2037–2047

S. Kumar, K. Jayaraman, S. Panchanathan, R. Gurunathan, A. Marti-Subirana, S. Newfeld

Mutation Rates in Mammalian Genomes

Proceedings of the National Academy of Sciences (USA) | 99:803–808

S. Kumar, S. Subramanian

Evolutionary Distance Estimation under Heterogeneous Substitution Pattern among Lineages

Molecular Biology and Evolution | 19:1727–1736

K. Tamura, S. Kumar

2001
39

Elucidating Gene Interaction Networks Based on Gene Expression Pattern Image Analysis

Proceedings of the International Conference on Biomedical Engineering | 5:232–234

S. Kumar, S. Panchanathan

Does Nonneutral Evolution Shape Observed Patterns of DNA Variation in Animal Mitochondrial Genomes?

Annual Review of Genetics | 35:539–566

A. Gerber, R. Loggins, S. Kumar, T. Dowling

A Genomic Timescale for the Origin of Eukaryotes

BMC Evolutionary Biology | 1:4 (10 pp)

S.B. Hedges, H. Chen, S. Kumar, D.Y.C. Wang, A.S. Thompson, H. Watanabe

Mutation and Linkage Disequilibrium in Human mtDNA

European Journal of Human Genetics | 9:969–972

P. Hedrick, S. Kumar

Classification and Indexing of Gene Expression Images

Applications of Digital Image Processing XXIV | 4472:471–481

K. Jayaraman, S. Panchanathan, S. Kumar, A. Tescher

Disparity Index: A Simple Statistic to Measure and Test the Homogeneity of Substitution Patterns between Molecular Sequences

Genetics | 158:1321–1327

S. Kumar, S. Gadagkar

Determination of the Number of Conserved Chromosomal Segments between Species

Genetics | 157:1387–1395

S. Kumar, S. Gadagkar, A. Filipski, X. Gu

MEGA2: Molecular Evolutionary Genetics Analysis Software

Bioinformatics | 17:1244–1245

S. Kumar, K. Tamura, I. Jakobsen, M. Nei

Understanding Human Disease Mutations through the Use of Interspecific Genetic Variation

Human Molecular Genetics | 10:2319–2328

M. Miller, S. Kumar

Incomplete Taxon Sampling is Not a Problem for Phylogenetic Inference

Proceedings of the National Academy of Sciences (USA) | 98:10751–10756

M. Rosenberg, S. Kumar

Traditional Phylogenetic Reconstruction Methods Reconstruct Shallow and Deep Evolutionary Relationships Equally Well

Molecular Biology and Evolution | 18:1823–1827

M. Rosenberg, S. Kumar

2000

Efficiency of the Neighbor-joining Method in Reconstructing Deep and Shallow Evolutionary Relationships in Large Phylogenies

Journal of Molecular Evolution | 51:544–553

S. Kumar, S. Gadagkar

Questioning Evidence for Recombination in Human Mitochondrial DNA

Science | 288:1931a (2 pp)

S. Kumar, P. Hendric, T. Dowling, M. Stoneking

Expansion and Molecular Evolution of the Interferon-induced 2 '-5 ' Oligoadenylate Synthetase Gene Family

Molecular Biology and Evolution | 17:738–750

S. Kumar, C. Mitnik, G. Valente, G. Floyd-Smith

25

Molecular Evolution and Phylogenetics

Oxford University Press [New York] | (333 pp)

M. Nei, S. Kumar

Single Column Discrepancy and Dynamic Max-Mini Optimizations for Quickly Finding the Most Parsimonious Evolutionary Trees

Bioinformatics | 16:140–151

P. Purdom, P. Bradford, K. Tamura, S. Kumar