Laboratory of Sudhir Kumar :: Publications 1997-2001

2001

38

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(12):969-972

P. Hedrick, S. Kumar

34

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(3):1321-1327

S. Kumar, S. Gadagkar

Determination of the number of conserved chromosomal segments between species

Genetics 157(3):1387-1395

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

MEGA2: Molecular Evolutionary Genetics Analysis software

Bioinformatics 17(12):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(21):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(19):10751-10756

M. Rosenberg, S. Kumar

Traditional phylogenetic reconstruction methods reconstruct shallow and deep evolutionary relationships equally well

Molecular Biology and Evolution 18(9):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(6):544-553

S. Kumar, S. Gadagkar

Questioning evidence for recombination in human mitochondrial DNA

Science 288(5473):1931a

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(5):738-750

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

24

Molecular evolution and phylogenetics

Oxford University Press 333 pp

M. Nei, S. Kumar

Single column discrepancy and dynamic max-mini optimizations for quickly finding the most parsimonious evolutionary trees

Bioinformatics 16(2):140-151

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

1999

Molecular evolution of a developmental pathway: phylogenetic analyses of transforming growth factor-beta family ligands, receptors and smad signal Transducers

Genetics 152(2):783-795

S. Newfeld, R. Wisotzkey, S. Kumar

Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi

Proceedings of the Royal Society B-Biological Sciences 266(1415):163-171

D. Wang, S. Kumar, S.B. Hedges

Divergence times of eutherian mammals

Science 285(5436):2031a

S.B. Hedges, S. Kumar

1998

A molecular timescale for vertebrate evolution

Nature 392(6679):917-920

S. Kumar, S.B. Hedges

The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small

Proceedings of the National Academy of Sciences (USA) 95(21):12390-12397

M. Nei, S. Kumar, K. Takahashi

1997

Evolution and functional diversification of the paired box (Pax) DNA-binding domains

Molecular Biology and Evolution 14(8):829-842

K. Balczarek, Z. Lai, S. Kumar

Tempo and mode of nucleotide substitutions in GAG and ENV gene fragments in human immunodeficiency virus type 1 populations with a known transmission History

Journal of Virology 71(6):4761-4770

T. Leitner, S. Kumar, J. Albert

Sequence convergence in the peptide-binding region of primate and rodent MBC class Ib molecules

Molecular Biology and Evolution 14(10):1035-1041

M. Yeager, S. Kumar, A. Hughes

Detection of convergent and parallel evolution at the amino acid sequence level

Molecular Biology and Evolution 14(5):527-536

J. Zhang, S. Kumar

Small-sample tests of episodic adaptive evolution: a case study of primate lysozymes

Molecular Biology and Evolution 14(12):1335-1338

J. Zhang, S. Kumar, M. Nei