Laboratory of Sudhir Kumar :: Publications 2012-2015

2015

148

Deep Model Based Transfer and Multi-Task Learning for Biological Image Analysis

The 21st ACM SIGKDD International Conference on Knowledge Discovery and Data Mining 1475-1484

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


147

Using Disease-Associated Coding Sequence Variation to Investigate Functional Compensation by Human Paralogous Proteins

Evolutionary Bioinformatics 2015(11) 245-251

S. Miura, S. Tate, S. Kumar


146

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(7) 1907-1912

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


145

Conformational Dynamics of Nonsynonymous Variants at Protein Interfaces Reveals Disease Association

Proteins-Structure Function and Bioinformatics 83(3) 428-435

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


144

Phylogenetic Placement of Metagenomic Reads Using the Minimum Evolution Principle

BMC Genomics 2015(16) 9 pp

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


143

Evolutionary Diagnosis of Non-Synonymous Variants Involved in Differential Drug Response

BMC Medical Genomics 2015(8) 6 pp

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


142

Tree of Life Reveals Clock-Like Speciation and Diversification

Molecular Biology and Evolution 32(4) 835-845

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


141

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(7) 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

140

Prospects for Building Large Timetrees Using Molecular Data with Incomplete Gene Coverage Among Species

Molecular Biology and Evolution 31(9) 2542-2550

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


139

Signatures of Natural Selection on Mutations of Residues with Multiple Posttranslational Modifications

Molecular Biology and Evolution 31(7) 1641-1645

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


138

No Positive Selection for G Allele in a P53 Response Element in Europeans

Cell 157(7) 1497-1499

S. Kumar, L. Liu


137

Proper Reporting of Predictor Performance Reply

Nature Methods 11(8) 781-782

S. Kumar, J. Ye, L. Liu


136

MyFX: A Turn-Key Software for Laboratory Desktops to Analyze Spatial Patterns of Gene Expression in Drosophila Embryos

Bioinformatics 30(9) 1319-1321

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


135

MEGA-MD: Molecular Evolutionary Genetics Analysis Software with Mutational Diagnosis of Amino Acid Variation

Bioinformatics 30(9) 1305-1307

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


134

Automated Annotation of Developmental Stages of Drosophila Embryos in Images Containing Spatial Patterns of Expression

Bioinformatics 30(2) 266-273

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


133

Whole-Genome Sequencing of the Snub-Nosed Monkey Provides Insights into Folivory and Evolutionary History

Nature Genetics 46(12) 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

132

The Evolutionary History of Amino Acid Variations Mediating Increased Resistance of S-aureus Identifies Reversion Mutations in Metabolic Regulators

PLOS ONE 8(2) 9 pp

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


131

Structural Dynamics Flexibility Informs Function and Evolution at a Proteome Scale

Biophysical Journal 104(2) 228A

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


130

Structural Dynamics Flexibility Informs Function and Evolution at a Proteome Scale

Evolutionary Applications 6(3) 423-433

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


129

GRASP [Genomic Resource Access for Stoichioproteomics]: Comparative Explorations of the Atomic Content of 12 Drosophila Proteomes

BMC Genomics 14(599) 14 pp

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


128

Evolutionary Balancing Is Critical for Correctly Forecasting Disease-Associated Amino Acid Variants

Molecular Biology and Evolution 30(6) 1252-1257

L. Liu, S. Kumar


127

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


126

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

Molecular Biology and Evolution 30(12) 2725-2729

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


125

Genome-Wide Profiling of Human Cap-Independent Translation-Enhancing Elements

Nature Methods 10(8) 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


124

A Mesh Generation and Machine Learning Framework for Drosophila Gene Expression Pattern Image Analysis

BMC Bioinformatics 2013(14) 372-381

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


2012

123

Exploring Spatial Patterns of Gene Expression from Fruit Fly Embryogenesis on the iPhone

Bioinformatics 28(1) 2847-2848

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


122

Sharing and Re-Use of Phylogenetic Trees (and Associated Data) to Facilitate Synthesis

BMC Research Notes 5(1) 574

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


121

Evolutionary Meta-Analysis of Association Studies Reveals Ancient Constraints Affecting Disease Marker Discovery

Molecular Biology and Evolution 29(9) 2087-2094

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


120

Human Genomic Disease Variants: A Neutral Evolutionary Explanation

Genome Research 22(8) 1383-1394

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


119

Performance of Computational Tools in Evaluating the Functional Impact of Laboratory-Induced Amino Acid Mutations

Bioinformatics 28(16) 2093-2096

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


118

Comparison of Embryonic Expression Within Multigene Families Using the FlyExpress Discovery Platform Reveals More Spatial than Temporal Divergence

Developmental Dynamics 241(1) 150-160

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


117

Statistics and Truth in Phylogenomics

Molecular Biology and Evolution 29(2) 457-472

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


116

Evolutionary Diagnosis Method for Variants in Personal Exomes

Nature Methods 9(9) 855-856

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


115

MEGA-CC: Computing Core of Molecular Evolutionary Genetics Analysis Program for Automated and Iterative Data Analysis

Bioinformatics 28(20) 2685-2686

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


114

Drosophila Gene Expression Pattern Annotation through Multi-Instance Multi-Label Learning

IEEE-ACM Transactions on Computational Biology and Bioinformatics 9(1) 98-112

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


113

Purifying Selection Modulates the Estimates of Population Differentiation and Confounds Genome-Wide Comparisons Across Single-Nucleotide Polymorphisms

Molecular Biology and Evolution 29(12) 3617-3623

T. Maruki, S. Kumar, Y. Kim


112

Estimating Divergence Times in Large Molecular Phylogenies

Proceedings of the National Academy of Sciences of the United States of America 109(47) 19333-19338

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


111

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