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