In Review
173

Adventures in Evolution: The Narrative of Tardigrada, Trundlers in Time

The American Biology Teacher

C. Babaian, S. Kumar

172

Power and pitfalls of computational methods for inferring clone phylogenies and mutation orders from bulk sequencing data

bioRxiv | (https://doi.org/10.1101/697318)

S. Miura, T. Vu, J. Deng, T. Buturla, J. Choi, S. Kumar

Reliable confidence intervals for RelTime estimates of evolutionary divergence times

bioRxiv | (https://doi.org/10.1101/677286)

Q. Tao, K. Tamura, B. Mello, S. Kumar

A new method for inferring timetrees from temporally sampled molecular sequences

bioRxiv | (https://doi.org/10.1101/620187)

S. Miura, K. Tamura, S. Pond, L. A. Huuki, J. Priest, J. Deng, S. Kumar

Molecular dating for phylogenies containing a mix of populations and species

Molecular Ecology Resources (submitted) | (https://doi.org/10.1101/536656)

B. Mello, Q. Tao, S. Kumar

165

Rapid and reliable methods for molecular dating

In The Molecular Evolutionary Clock. Theory and Practice, edited by Simon Ho (submitted)

Q. Tao, K. Tamura, S. Kumar

2019
171

Genome-wide analysis indicates association between heterozygote advantage and healthy aging in humans

BMC Genetics | 20:52 (14 pp)

K. Xu, R. Kosoy, K. Shameer, S. Kumar, L. Liu, B. Readhead, G. M. Belbin, H. C. Lee, R. Chen, J. T. Dudley

167

On estimating evolutionary probabilities of population variants

BMC Evolutionary Biology | 19:133 (14 pp)

R. Patel, S. Kumar

166

A machine learning method for detecting autocorrelation of evolutionary rates in large phylogenies

Molecular Biology and Evolution | 36:811-824

Q. Tao, K. Tamura, F. Battistuzzi, S. Kumar

164

Biological relevance of computationally predicted pathogenicity of noncoding variants

Nature Communications | 10:330 (11 pp)

L. Liu, M. D. Sanderford, R. Patel, P. B. Chandrashekar, G. Gibson, S. Kumar

2018
163

Accurate timetrees require accurate calibrations

Proceedings of the National Academy of Sciences (USA) | 115:E9510-E9511

S. B. Hedges, Q. Tao, M. Walker, S. Kumar

162

Computational enhancement of single-cell sequences for inferring tumor evolution

Bioinformatics | 34:i917-i926

S. Miura, L. A. Huuki, T. Buturla, T. Vu, K. Gomez, S. Kumar

161

Predicting clone genotypes from tumor bulk sequencing of multiple samples

Bioinformatics | 34:4017-4026

S. Miura, K. Gomez, O. Murillo, L. A. Huuki, T. Vu, T. Buturla, S. Kumar

160

Adaptive landscape of protein variation in human exomes

Molecular Biology and Evolution | 35:2015-2025

R. Patel, L. B. Scheinfeldt, M. D. Sanderford, T. R. Lanham, K. Tamura, A. Platt, B. S. Gilksberg, K. Xu, J. T. Dudley, S. Kumar

159

RelTime relaxes the strict molecular clock throughout the phylogeny

Genome Biology and Evolution | 10:1631-1636

F. U. Battistuzzi, Q. Tao, L. Jones, K. Tamura, S. Kumar

158

Theoretical foundation of the RelTime method for estimating divergence times from variable evolutionary rates

Molecular Biology and Evolution | 35:1770-1782

K. Tamura, Q. Tao, S. Kumar

157

MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms

Molecular Biology and Evolution | 35:1547-1549

S. Kumar, G. Stecher, M. Li, C. Knyaz, K. Tamura

156

Neutral theory, disease mutations, and personal exomes

Molecular Biology and Evolution | 35:1297-1303

S. Kumar, R. Patel

155

Somatic evolutionary timings of driver mutations

BMC Cancer | 18:85 (10 pp)

K. Gomez, S. Miura, L. A. Huuki, B.S. Spell, J.P. Townsend, S. Kumar

2017
154

FlyExpress 7: an integrated discovery platform to study coexpressed genes using in situ hybridization images in Drosophila

Genes, Genomes, Genetics (G3) | 7:2791-2797

S. Kumar, C. Konikoff, M. Sanderford, L. Liu, S. Newfeld, J. Ye, R.J. Kulathinal

153

TimeTree: A resource for timelines, timetrees, and divergence times

Molecular Biology and Evolution | 34:1812-1819

S. Kumar, G. Stecher, M. Suleski, S. B. Hedges

152

The reliability and stability of an inferred phylogenetic tree from empirical data

Molecular Biology and Evolution | 34:718-723

Y. Katsura, C. Stanley, S. Kumar, M. Nei

151

Fast and accurate estimates of divergence times from big data

Molecular Biology and Evolution | 34:45-50

B. Mello, Q. Tao, K. Tamura, S. Kumar

2016
150

e-GRASP: an integrated evolutionary and GRASP resource for exploring disease associations

BMC Genomics | 17:770 (8 pp)

S. Karim, H.F. Nour Eldin, H. Abusamra, N. Salem, E. Alhathli, J. Dudley, M.D. Sanderford, L.B. Scheinfeldt A.G. Chaudhary, M.H. Al-Qahtani, S. Kumar

149

Deep model based transfer and multi-task learning for biological image analysis

Transactions on Big Data | 20 pp

W. Zhang, R. Li, T. Zeng, Q. Sun, S. Kumar, J. Ye, S. Ji

148

MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets

Molecular Biology and Evolution | 33:1870-1874

S. Kumar, G. Stecher, K. Tamura

147

A molecular evolutionary reference for the human variome

Molecular Biology and Evolution | 33:245-254

L. Liu, K. Tamura, M.D. Sanderford, V. Gray, S. Kumar

146

Advances in time estimation methods for molecular data

Molecular Biology and Evolution | 33:863-869

S. Kumar, S.B. Hedges

2015
145

Using disease-associated coding sequence variation to investigate functional compensation by human paralogous proteins

Evolutionary Bioinformatics | 11:245-251

S. Miura, S. Tate, S. Kumar

144

A protocol for diagnosing the effect of calibration priors on posterior time estimates: a case study for the Cambrian explosion of animal phyla

Molecular Biology and Evolution | 32:1907-1912

F.U. Battistuzzi, P. Billing-Ross, O. Murillo, A. Filipski, S. Kumar

143

Conformational dynamics of nonsynonymous variants at protein interfaces reveals disease association

Proteins-Structure Function and Bioinformatics | 83:428-435

B.M. Butler, Z.N. Gerek, S. Kumar, S.B. Ozkan

142

Phylogenetic placement of metagenomic reads using the minimum evolution principle

BMC Genomics | 16:S13 (9 pp)

A. Filipski, K. Tamura, P. Billing-Ross, O. Murillo, S. Kumar

141

Evolutionary Diagnosis of non-synonymous variants involved in differential drug response

BMC Medical Genomics | 8:S6 (6 pp)

N.Z. Gerek, L. Liu, K. Gerold, P. Biparva, E.D. Thomas, S. Kumar

140

Tree of life reveals clock-like speciation and diversification

Molecular Biology and Evolution | 32:835-845

S.B. Hedges, J. Marin, M. Suleski, M. Paymer, S. Kumar

139

Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea): Loss of the ndh gene suite and inverted repeat

American Journal of Botany | 102:1115-1127

M. Sanderson, D. Copetti, A. Burquez, E. Bustamante, J.L.M. Charboneau, L.E. Eguiarte, S. Kumar, H.O. Lee, J. Lee, M. McMahon, K. Steele, R. Wing, T.J. Yang, D. Zwickl, M.F. Wojciechowski

2014
138

Prospects for building large timetrees using molecular data with incomplete gene coverage among species

Molecular Biology and Evolution | 31:2542-2550

A. Filipski, O. Murillo, A. Freydenzon, K. Tamura, S. Kumar

137

Signatures of natural selection on mutations of residues with multiple posttranslational modifications

Molecular Biology and Evolution | 31:1641-1645

V.E. Gray, L. Liu, R. Nirankari, P.V. Hornbeck, S. Kumar

136

No positive selection for G allele in a p53 response element in Europeans

Cell | 157:1497-1499

S. Kumar, L. Liu

135

Reply to: "Proper reporting of predictor performance"

Nature Methods | 11:781-782

S. Kumar, J. Ye, L. Liu

134

myFX: a turn-key software for laboratory desktops to analyze spatial patterns of gene expression in Drosophila embryos

Bioinformatics | 30:1319-1321

I. Montiel, C. Konikoff, B. Braun, M. Packard, S.L. Gramates, Q. Sun, J. Ye, S. Kumar

133

MEGA-MD: molecular evolutionary genetics analysis software with mutational diagnosis of amino acid variation

Bioinformatics | 30:1305-1307

G. Stecher, L. Liu, M.D. Sanderford, D. Peterson, K. Tamura, S. Kumar

132

Automated annotation of developmental stages of Drosophila embryos in images containing spatial patterns of expression

Bioinformatics | 30:266-273

L. Yuan, C. Pan, S. Ji, M. McCutchan, Z.H. Zhou, S. J. Newfeld, S. Kumar, J. Ye

131

Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history

Nature Genetics | 46:1303-1310

X. Zhou, B. Wang, Q. Pan, J. Zhang, S. Kumar, X. Sun, Z. Liu, H. Pan, Y. Lin, G. Liu, W. Zhan, M. Li, B. Ren, X. Ma, H. Ruan, C. Cheng, D. Wang, F. Shi, Y. Hui, Y. Tao, C. Zhang, P. Zhu, Z. Xiang, W. Jiang, J. Chang, H. Wang, Z. Cao, Z. Jiang, B. Li, G. Yang, C. Roos, P.A. Garber, M.W. Bruford, R. Li, M. Li

2013
130

The evolutionary history of amino acid variations mediating increased resistance of S. aureus identifies reversion mutations in metabolic regulators

PLOS ONE | 8:e56466 (9 pp)

M.D. Champion, V. Gray, C. Eberhard, S. Kumar

129

Structural dynamics flexibility informs function and evolution at a proteome scale

Evolutionary Applications | 6:423-433

Z.N. Gerek, S. Kumar, S.B. Ozkan

128

GRASP [Genomic Resource Access for Stoichioproteomics]: comparative explorations of the atomic content of 12 Drosophila proteomes

BMC Genomics | 14:14 pp

J.D.J. Gilbert, C. Acquisti, H.M. Martinson, J.J. Elser, S. Kumar, W.F. Fagan

127

Evolutionary balancing is critical for correctly forecasting disease-associated amino acid variants

Molecular Biology and Evolution | 30:1252-1257

L. Liu, S. Kumar

126

Image-level and group-level models for Drosophila gene expression pattern annotation

BMC Bioinformatics | 14:350 (13 pp)

Q. Sun, S. Muckatira, L. Yuan, S. Ji, S. Newfeld, S. Kumar, J. Ye

125

MEGA6: Molecular Evolutionary Genetics Analysis version 6.0

Molecular Biology and Evolution | 30:2725-2729

K. Tamura, G. Stecher, D. Peterson, A. Filipski, S. Kumar

124

Genome-wide profiling of human cap-independent translation-enhancing elements

Nature Methods | 10:747-750

B.P. Wellensiek, A.C. Larsen, B. Stephens, K. Kukurba, K. Waern, N. Briones, L. Liu, M. Snyder, B. L. Jacobs, S. Kumar, J.C. Chaput

123

A mesh generation and machine learning framework for Drosophila gene expression pattern image analysis

BMC Bioinformatics | 2013:372-381

W. Zhang, D. Feng, R. Li, A. Chernikov, N. Chrisochoides, C. Osgood, C. Konikoff, S. Newfeld, S. Kumar, S. Ji

2012
122

Exploring spatial patterns of gene expression from fruit fly embryogenesis on the iPhone

Bioinformatics | 28:2847-2848

S. Kumar, K. Boccia, M. McCutchan, J. Ye

121

Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis

BMC Research Notes | 5:574 (15 pp)

A. Stoltzfus, B. O'Meara, J. Whitacre, R. Mounce, E. L. Gillespie, S. Kumar, D.F. Rosauer, R.A. Vos

120

Evolutionary meta-analysis of association studies reveals ancient constraints affecting disease marker discovery

Molecular Biology and Evolution | 29:2087-2094

J.T. Dudley, R. Chen, M.D. Sanderford, A.J. Butte, S. Kumar

119

Human genomic disease variants: a neutral evolutionary explanation

Genome Research | 22:1383-1394

J.T. Dudley, Y. Kim, L. Liu, G. J. Markov, K. Gerold, R. Chen, A.J. Butte, S. Kumar

118

Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations

Bioinformatics | 28:2093-2096

V.E. Gray, K.R. Kukurba, S. Kumar

117

Comparison of embryonic expression within multigene families using the FlyExpress discovery platform reveals more spatial than temporal divergence

Developmental Dynamics | 241:150-160

C. Konikoff, T.L. Karr, M. McCutchan, S.J. Newfeld, S. Kumar

116

Statistics and truth in phylogenomics

Molecular Biology and Evolution | 29:457-472

S. Kumar, A.J. Filipski, F.U. Battistuzzi, S. Pond, K. Tamura

115

Evolutionary diagnosis method for variants in personal exomes

Nature Methods | 9:855-856

S. Kumar, M.D. Sanderford, V.E. Gray, J. Ye, L. Liu

114

MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis

Bioinformatics | 28:2685-2686

S. Kumar, G. Stecher, D. Peterson, K. Tamura

113

Drosophila gene expression pattern annotation through multi-instance multi-label learning

IEEE-ACM Transactions on Computational Biology and Bioinformatics | 9:98-112

Y.X. Li, S. Ji, S. Kumar, J. Ye, Z.H. Zhou

112

Purifying selection modulates the estimates of population differentiation and confounds genome-wide comparisons across single-nucleotide polymorphisms

Molecular Biology and Evolution | 29:3617-3623

T. Maruki, S. Kumar, Y. Kim

111

Estimating divergence times in large molecular phylogenies

Proceedings of the National Academy of Sciences (USA) | 109:19333-19338

K. Tamura, F.U. Battistuzzi, P. Billing-Ross, O. Murillo, A. Filipski, S. Kumar

110

Learning sparse representations for fruit-fly gene expression pattern image annotation and retrieval

BMC Bioinformatics | 13:107 (15 pp)

L. Yuan, A. Woodard, S. Ji, Y. Jiang, Z.H. Zhou, S. Kumar, J. Ye

2011
109

Molecular clock: testing

eLS | 7 pp

F.U. Battistuzzi, A. Filipski, S. Kumar

108

Fast and slow implementations of relaxed-clock methods show similar patterns of accuracy in estimating divergence times

Molecular Biology and Evolution | 28:2439-2442

F.U. Battistuzzi, P. Billing-Ross, A. Paliwal, S. Kumar

107

Stoichiogenomics: the evolutionary ecology of macromolecular elemental composition

Trends in Ecology & Evolution | 26:38-44

J.J. Elser, C. Acquisti, S. Kumar

106

Rampant purifying selection conserves positions with posttranslational modifications in human proteins

Molecular Biology and Evolution | 28:1565-1568

V.E. Gray, S. Kumar

105

Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations

Trends in Genetics | 27:377-386

S. Kumar, J.T. Dudley, A. Filipski, L. Liu

103

FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis

Bioinformatics | 27:3319-3320

S. Kumar, C. Konikoff, B. Van Emden, C. Busick, K.T. Davis, S. Ji, L.W. Wu, H. Ramos, T. Brody, S. Panchanathan, J. Ye, T. L. Karr, K. Gerold, M. McCutchan, S. J. Newfeld

102

Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders

Molecular Biology and Evolution | 28:1927-1942

M.A. Pacheco, F.U. Battistuzzi, M. Lentino, R.F. Aguilar, S. Kumar, A. Escalante

101

MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods

Molecular Biology and Evolution | 28:2731-2739

K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, S. Kumar

2010
100

Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals

Molecular Biology and Evolution | 27:1289-1300

F.U. Battistuzzi, A. Filipski, S.B. Hedges, S. Kumar

Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials

PLOS Biology | 8:19 pp

M. Kazemian, C. Blatti, A. Richards, M. McCutchan, N. Wakabayashi-Ito, A.S. Hammonds, S.E. Celniker, S. Kumar, S.A. Wolfe, M.H. Brodsky, S. Sinha

More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure

Philosophical Transactions of the Royal Society B-Biological Sciences | 365:3277-3288

A.C. Stone, F.U. Battistuzzi, L.S. Kubatko, G.H. Perry, Jr., E. Trudeau, H. Lin, S. Kumar

2009

Ecological nitrogen limitation shapes the DNA composition of plant genomes

Molecular Biology and Evolution | 26:953-956

C. Acquisti, J.J. Elser, S. Kumar

96

The Timetree of Life

Oxford University Press

S.B. Hedges, S. Kumar

95

Discovering the Timetree of Life

Oxford University Press | 17 pp

S.B. Hedges, S. Kumar

Signatures of nitrogen limitation in the elemental composition of the proteins involved in the metabolic apparatus

Proceedings of the Royal Society B-Biological Sciences | 276:2605-2610

C. Acquisti, S. Kumar, J.J. Elser

Association of orthodenticle with natural variation for early embryonic patterning in Drosophila melanogaster

Journal of Experimental Zoology Part B-Molecular and Developmental Evolution | 312:841-854

L.M. Goering, P.K. Hunt, C. Heighington, C. Busick, P.S. Pennings, J. Hermisson, S. Kumar, G. Gibson

Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs

Gene | 429:59-64

T. Horiike, D. Miyata, K. Hamada, S. Saruhashi, T. Shinozawa, S. Kumar, R. Chakraborty, T. Komiyama, Y. Tateno

A bag-of-words approach for Drosophila gene expression pattern annotation

BMC Bioinformatics | 10:119 (16 pp)

S. Ji, Y.X. Li, Z.H. Zhou, S. Kumar, J. Ye

Drosophila gene expression pattern annotation using sparse features and term-term interactions

KDD-09: 15th ACM Sigkdd Conference on Knowledge Discovery and Data Mining | 407-415

S. Ji, L. Yuan, Y.X. Li, Z.H. Zhou, S. Kumar, J. Ye

Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations

Genome Research | 19:1562-1569

S. Kumar, M.P. Suleski, G.J. Markov, S. Lawrence, A. Marco, A.J. Filipski

Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster

Bioinformatics | 25:2473-2477

A. Marco, C. Konikoff, T.L. Karr, S. Kumar

The origin of Metazoa: a transition from temporal to spatial cell differentiation

BioEssays | 31:758-768

K.V. Mikhailov, A.V. Konstantinova, M.A. Nikitin, P.V. Troshin, L.Y. Rusin, V.A. Lyubetsky, Y.V. Panchin, A.P. Mylnikov, L.L. Moroz, S. Kumar, V.V. Aleoshin

Methods for incorporating the hypermutability of CpG dinucleotides in detecting natural selection operating at the amino acid sequence level

Molecular Biology and Evolution | 26:2275-2284

Y. Suzuki, T. Gojobori, S. Kumar

2008

Developmental stage annotation of Drosophila gene expression pattern images via an entire solution path for LDA

ACM Transactions on Knowledge Discovery from Data | 2:21 pp

J. Ye, J. Chen, R. Janardan, S. Kumar

84

Biological image analysis via matrix approximation

Encyclopedia of Data Warehousing and Mining. Idea Group | 166-170

J. Ye, R. Janadan, S. Kumar

Automated annotation of Drosophila gene expression patterns using a controlled vocabulary

Bioinformatics | 24:1881-1888

S. Ji, L. Sun, R. Jin, S. Kumar, J. Ye

MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences

Briefings in Bioinformatics | 9:299-306

S. Kumar, M. Nei, J. Dudley, K. Tamura

2007
81

Detecting molecular signatures of adaptive evolution

Evolutionary Genomics and Proteomics, Sinauer Associates | 241-254

A. Filipski, S. Prohaska, S. Kumar

Nullomers: really a matter of natural selection?

PLOS ONE | 2:1022-1025

C. Acquisti, G. Poste, D. Curtiss, S. Kumar

Evolution of genes and genomes on the Drosophila phylogeny

Nature | 450:203-218

A.G. Clark, M.B. Eisen, D.R. Smith, C.M. Bergman, B. Oliver, T.A. Markow, T.C. Kaufman, M. Kellis, W. Gelbart, V.N. Iyer, D.A. Pollard, T.B. Sackton, S. Kumar, et al

Lower bounds on multiple sequence alignment using exact 3-way alignment

BMC Bioinformatics | 8:140 (8 pp)

C.J. Colbourn, S. Kumar

Bioinformatics software for biologists in the genomics era

Bioinformatics | 23:1713-1717

S. Kumar, J. Dudley

Multiple sequence alignment: in pursuit of homologous DNA positions

Genome Research | 17:127-135

S. Kumar, A. Filipski

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0

Molecular Biology and Evolution | 24:1596-1599

K. Tamura, J. Dudley, M. Nei, S. Kumar

Constraint and turnover in sex-biased gene expression in the genus Drosophila

Nature | 450:233-U2

Y. Zhang, D. Sturgill, M. Parisi, S. Kumar, B. Oliver

2006

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

Computational Systems Bioinformatics Conference | 2006:293-298

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 | 2006:335-340

X. Xia, S. Kumar

Signatures of ecological resource availability in the animal and plant proteomes

Molecular Biology and Evolution | 23:1946-1951

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

TimeTree: a public knowledge-base of divergence times among organisms

Bioinformatics | 22:2971-2972

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

Constraining fossil calibrations for molecular clocks

BioEssays | 28:770-771

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 | 7:306 (9 pp)

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 | 23:2283-2287

S. Subramanian, S. Kumar

2005
66

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 | 22:2139-2141

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

63

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

35

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 (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

25

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

1999

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

21

Divergence times of eutherian mammals

Science | 285:2031a (7 pp)

S.B. Hedges, S. Kumar

20

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.

1998

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

1997

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

1996

Continental breakup and the ordinal diversification of birds and mammals

Nature | 381:226-229

S.B. Hedges, P. Parker, C. Sibley, S. Kumar

Patterns of nucleotide substitution in mitochondrial protein coding genes of vertebrates

Genetics | 143:537-548

S. Kumar

Stepwise algorithm for finding minimum evolution trees

Molecular Biology and Evolution | 13:584-593

S. Kumar

Evolution of the hedgehog gene family

Genetics | 142:965-972

S. Kumar, K. Balczarek, Z. Lai

Evolutionary relationships of eukaryotic kingdoms

Journal of Molecular Evolution | 42:183-193

S. Kumar, A. Rzhetsky

Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites

Molecular Biology and Evolution | 13:650-659

Z. Yang, S. Kumar

1995

Four-cluster analysis: a simple method to test phylogenetic hypotheses

Molecular Biology and Evolution | 12:163-167

A. Rzhetsky, S. Kumar, M. Nei

18S Ribosomal-RNA data indicate that aschelminthes are polyphyletic in origin and consist of at least 3 distinct clades

Molecular Biology and Evolution | 12:1132-1137

B. Winnepenninckx, T. Backeljau, L. Mackey, J. Brooks, R. De Watcher, S. Kumar, J. Garey

A new method of inference of ancestral nucleotide and amino-acid-sequences

Genetics | 141:1641-1650

Z. Yang, S. Kumar, M. Nei

1994

MEGA - Molecular Evolutionary Genetics Analysis software for microcomputers

Computer Applications in the Biosciences | 10:189-191

S. Kumar, K. Tamura, M. Nei

1993
2

A guide to Molecular Evolutionary Genetics Analysis program for microcomputers.

Pennsylvania State University, University Park, Pennsylvania | 135 pp

S. Kumar, K. Tamura, M. Nei

1992

Human origins and analysis of mitochondrial DNA sequences

Science | 255:737-739

S.B. Hedges, S. Kumar, K. Tamura, M. Stoneking