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


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 (6 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


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 | 16:140–151

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


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

Genetics | 152:783–795

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 | 266:163–171

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


Divergence times of eutherian mammals

Science | 285:2031a (7 pp)

S.B. Hedges, S. Kumar


Genome maps 10. Comparative genomics. Mammalian radiations. Wall chart.

Science | 286:463–478

S.J. O'Brien, J.F. Eisenberg, M. Miyamoto, S.B. Hedges, S. Kumar, D.E. Wilson, M. Menotti-Raymond, W.J. Murphy, W.G. Nash, L.A. Lyons, J.C. Menninger, R. Stanyon, J. Wienberg, N.G. Copeland, N.A. Jenkins, J. Gellin, M. Yerle, L. Andersson, J. Womack, T. Broad, J. Postlethwait, et al.


A molecular timescale for vertebrate evolution

Nature | 392:917–920

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) | 95:12390–12397

M. Nei, S. Kumar, K. Takahashi


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

Molecular Biology and Evolution | 14:829–842

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 | 71:4761–4770

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 | 14:1035–1041

M. Yeager, S. Kumar, A. Hughes

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

Molecular Biology and Evolution | 14:527–536

J. Zhang, S. Kumar

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

Molecular Biology and Evolution | 14:1335–1338

J. Zhang, S. Kumar, M. Nei