Laboratory of Sudhir Kumar :: Publications 2002-2006



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



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


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 of the United States of America 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



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


MEGA3: An Integrated Software for Molecular Evolutionary Genetic Analysis and Sequence Alignment

Integrative and Comparative Biology 43(6) 947

S. Kumar, K. Tamura, M. Nei


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 of the United States of America 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



Genomic Clocks and Evolutionary Timescales

Trends in Genetics 19(4) 200-206

S.B. Hedges, S. Kumar


Prediction of Human Epileptic Seizures Based on Optimization and Phase Changes of Brain Electrical Activity

Optimization Methods & Software 18(1) 81-104

L. Iasemidis, P. Pardalos, D. Shiau, W. Chaovalitwongse, K. Narayanan, S. Kumar, P. Carney, J. Sackellares


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



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 of the United States of America 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