Laboratory of Sudhir Kumar :: Publications 2002-2006

2006

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

Computational Systems Bioinformatics Conference 2006(4):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(4):335-340

X. Xia, S. Kumar

Signatures of Ecological Resource Availability in the Animal and Plant Proteomes

Molecular Biology and Evolution 23(10):1946-1951

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

TimeTree: A Public Knowledge-Base of Divergence Times Among Organisms

Bioinformatics 22(23):2971-2972

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

Constraining Fossil Calibrations for Molecular Clocks

BioEssays 28(7):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 2006(7):306-314

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(12):2283-2287

S. Subramanian, S. Kumar

2005

65

The Evolution of the Genome: Comparative Genomics in Eukaryotes

Elsevier Inc. 521-583

A. Filipski, S. Kumar

Maximum Likelihood Outperforms Maximum Parsimony Even When Evolutionary Rates Are Heterotachous

Molecular Biology and Evolution 22(11):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(1):64-74

S. Gadagkar, M. Rosenberg, S. Kumar

62

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, S. Li, F. Pereira, H. Shum, A. Tescher

Molecular Clocks: Four Decades of Evolution

Nature Reviews Genetics 6(8):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(52):18842-18847

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

Pushing Back the Expansion of Introns in Animal Genomes

Cell 123(7):1182-1184

S. Kumar, S.B. Hedges

2004

58

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(332):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(5):202-214

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

Precision of Molecular Time Estimates

Trends in Genetics 20(5):242-247

S.B. Hedges, S. Kumar

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

Genetics 168(1):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(30):11030-11035

K. Tamura, M. Nei, S. Kumar

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

Molecular Biology and Evolution 21(1):36-44

K. Tamura, S. Subramanian, S. Kumar

MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment

Briefings in Bioinformatics 5(2):150-163

S. Kumar, K. Tamura, M. Nei

2003

Genomic Clocks and Evolutionary Timescales

Trends in Genetics 19(4):200-206

S.B. Hedges, S. Kumar

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

Virology 316(1):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(6):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(4):610-621

M. Rosenberg, S. Kumar

Taxon Sampling, Bioinformatics, and Phylogenomics

Systematic Biology 52(1):119-124

M. Rosenberg, S. Kumar

Patterns of Transitional Mutation Biases Within and Among Mammalian Genomes

Molecular Biology and Evolution 20(6):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(5):838-844

S. Subramanian, S. Kumar

2002

Vertebrate Genomes Compared

Science 297(5585):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(4):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(4):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(2):803-808

S. Kumar, S. Subramanian

Evolutionary Distance Estimation Under Heterogeneous Substitution Pattern Among Lineages

Molecular Biology and Evolution 19(10):1727-1736

K. Tamura, S. Kumar