2016
151

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

150

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

149

MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets

Molecular Biology and Evolution | 33:1870-1874

S. Kumar, G. Stecher, K. Tamura

148

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

147

Advances in time estimation methods for molecular data

Molecular Biology and Evolution | 33:863-869

S. Kumar, S.B. Hedges

2015
146

Integration of structural dynamics and molecular evolution via protein interaction networks: a new era in genomic medicine

Current Opinion in Structural Biology | 35:135-142

A. Kumar, B.M Butler, S. Kumar, S.B. Ozkan

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