159 Deep Model Based Transfer and Multi-task Learning for Biological Image Analysis
The 21st ACM SIGKDD International Conference on Knowledge Discover and Data Mining(KDD 2015) (2015) 1475-1484
Zhang W, Li R, Zeng T, Sun Q, Kumar S, Ye J, Ji S
    158 Exceptional Reduction of the Plastid Genome of Saguaro Cactus (Carnegia Gigantea): Loss of the Ndh Gene Suite and Inverted Repeat
    American Journal of Botany (2015) 102:1115-1127
    Sanderson MJ, Copetti D, Burquez A, Bustamante E, Charboneau JLM, Eguiarte L, Kumar S, Oh Lee H, Lee J, McMahon M, Steele K, Wing R, Yang TJ, Zwickl D, Wojciechowski MF
      157 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 (2015) 32:1907-1912
      Battistuzzi FU, Billing-Ross P, Murillo O, Filipski A, Kumar S
        156 Conformational Dynamics of Nonsynonymous Variants at Protein Interfaces Reveals Disease Association
        Proteins (2015) 83:428-435
        Butler BM, Gerek ZN, Kumar S, Ozkan SB
          155 Tree of Life Reveals Clock-Like Speciation and Diversification
          Molecular Biology and Evolution (2015) 32:835-845
          S. Blair Hedges, Julie Marin, Michael Suleski, Madeline Paymer, and Sudhir Kumar
          154 Evolutionary Diagnosis of Non-synonymous Variants Involved in Differential Drug Response
          BMC Medical Genomics (2015) Vol. 8, 10.1186
          Gerek ZN, Liu L, Gerold K, Biparva P, Thomas ED, Kumar S
            153 Phylogenetic Placement of Metagenomic Reads Using the Minimum Evolution Principle
            BMC Genomics (2015) Vol. 16, 10.1186
            Filipski A, Tamura K, Billing-Ross P, Murillo O, Kumar S
              152 Whole-genome Sequencing of the Snub-nosed Monkey Provides Insights into Folivory and Evolutionary History
              Nature Genetics (2014) 12:1303-10
              Zhou X, Wang B, Pan Q, Zhang J, Kumar S, Sun X, Liu Z, Pan H, Lin Y, Liu G, Zhan W, Li M, Ren B, Ma X, Ruan H, Cheng C, Wang D, Shi F, Hui Y, Tao Y, Zhang C, Zhu P, Xiang Z, Jiang W, Chang J, Wang H, Cao Z, Jiang Z, Li B, Yang G, Roos C, Garber PA, Bruford MW, Li R, & Li M
              • [Website] Read at Nature Genetics site
              151 Proper Reporting of Predictor Performance (a Reply)
              Nature Methods (2014) 11:781-782
              Kumar S, Ye J & Li Liu
                150 Prospects for Building Large Timetrees Using Molecular Data with Incomplete Gene Coverage Among Species
                Molecular Biology and Evolution (2014) 31:2542-2550
                Filipski A, Murillo O, Freydenzon A, Tamura K & Kumar S
                  149 No Positive Selection for G-allele in a P53 Response Element in Europeans
                  Cell (2014) 157:1497-1499
                  Liu L, Kumar S
                    148 Signatures of Natural Selection on Mutations of Residues with Multiple Posttranslational Modifications
                    Molecular Biology and Evolution (2014) 31:1641-1645
                    Gray VE, Liu L, Nirankari R, Hornbeck PV, Kumar S
                      147 myFX: A Turn-key Software for Laboratory Desktops to Analyze Spatial Patterns of Gene Expression in Drosophila Embryos
                      Bioinformatics (2014) 30:1319-1321 [Software Download]
                      Montiel I, Konikoff C, Braun B, Packard M, Gramates SL, Sun Q, Ye J, Kumar S
                      146 MEGA-MD: Molecular Evolutionary Genetics Analysis Software for Mutational Diagnosis of Amino Acid Variation
                      Bioinformatics (2014) 30:1305-1307 [Software Download]
                      Stecher G, Liu L, Sanderford M, Peterson D, Tamura K, Kumar S
                      • [Website] Software: MEGA-MD Download
                      145 Automated Annotation of Developmental Stages of Drosophila Embryos in Images Containing Spatial Patterns of Expression
                      Bioinformatics (2014) 30:266-273
                      Yuan L, Pan C, Ji S, McCutchan M, Zhou Z, Newfeld SJ, Kumar S, Ye J
                        144 A Mesh Generation and Machine Learning Framework for Drosophila Gene expression Pattern Image Analysis
                        BMC Bioinformatics (2013) 14:372(10pp)
                        Zhang W, Feng D, Li R, Chernikov A, Chrisochoides N, Osgood C, Konikoff C, Newfeld S, Kumar S, Ji S
                          143 MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
                          Molecular Biology and Evolution (2013) 30:2725-2729
                          Tamura K, Stecher G, Peterson D, Filipski A, Kumar S
                            142 Image-level and Group-level Models for Drosophila Gene Expression Pattern Annotation.
                            BMC Bioinformatics (2013) 14:350(13pp)
                            Sun Q, Muckatira S, Yuan L, Ji S, Newfeld S, Kumar S, Ye J
                              141 GRASP [Genomic Resource Access for Stoichioproteomics]: Comparative Explorations of the Atomic Content of 12 Drosophila Proteomes.
                              BMC Genomics (2013) 14:599(14pp)
                              Gilbert JDJ, Acquisti C, Martinson HM, Elser JJ, Kumar S, Fagan F
                                140 Genome-Wide Profiling of Cap-Independent Translation Enhancing Elements in the Human Genome.
                                Nature Methods (2013) 10:747-750
                                Wellensiek BP, Larsen AC, Stephens B, Kukurba K, Waern K, Briones N, Liu L, Snyder M, Jacobs BL, Kumar S, Chaput JC
                                  139 Evolutionary Balancing is Critical for Correctly Forecasting Disease Associated Amino Acid Variants.
                                  Molecular Biology and Evolution (2013) 30:1252-1257
                                  Liu L, Kumar S
                                    138 The Evolutionary History of Amino Acid Variations Mediating Increased Resistance of S. Aureus Identifies Reversion Mutations in Metabolic Regulators.
                                    PLoS ONE (2013) 8:e56466(9pp)
                                    Champion MD, Gray V, Eberhard C, Kumar S
                                      137 Structural Dynamics Flexibility Informs Function and Evolution at a Proteome Scale.
                                      Evolutionary Applications (2013) 6:423-433
                                      Gerek ZN, Kumar S, Ozkan SB
                                        136 Estimating Divergence Times in Large Molecular Phylogenies.
                                        Proceedings of the National Academy of Sciences (2012) 109:19333-19338 [Software Download]
                                        Tamura K, Battistuzzi FU, Billing-Ross P, Murillo O, Filipski A, Kumar S.
                                        • [Website] Software: RelTime-CC (RelTime Computational Core) Beta Download
                                        • [Website] ASU News - A new computational method for timing the tree of life
                                        • [Website] F1000Prime - Article Recommendation
                                        135 Sharing and Re-use of Phylogenetic Trees (and Associated Data) to Facilitate Synthesis.
                                        BMC Research Notes (2012) 5:574(15pp)
                                        Stoltzfus SA, O'Meara B, Whitacre J, Mounce R, Gillespie EL, Kumar S, Rosauer DF, Vos RA.
                                          134 MEGA-CC: Computing Core of Molecular Evolutionary Genetics Analysis Program for Automated and Iterative Data Analysis.
                                          Bioinformatics (2012) 28:2685-2686 [Software Download]
                                          Kumar S, Stecher G, Peterson D, Tamura K.
                                          133 Evolutionary Diagnosis Methods for Variants in Personal Exomes.
                                          Nature Methods (2012) 9:855-856 [Web Service]
                                          Kumar S, Sanderford M, Gray VE, Ye J, Liu L.
                                          • [Website] ASU News: Cutting through the genomic thicket in search of disease variants
                                          • [Web Service] [Image Archive] [Image Archive] A new evolutionary diagnosis (EvoD) approach to predict functional impact of nonsynonymous single nucleotide variants (nSNVs)
                                          132 Exploring Spatial Patterns of Gene Expression from Fruit Fly Embryogenesis on the IPhone.
                                          Bioinformatics (2012) 28:2847-2848 [iTunes Download]
                                          Kumar S, Boccia K, McCutchan M, Ye J.
                                          • [iTunes Download] [Image Archive] Explore gene expression patterns from Fruit Fly embryogenesis using the FlyExpress resource on the iPhone
                                          131 Purifying Selection Modulates the Estimates of Population Differentiation and Confounds Genome-Wide Comparisons Across Single Nucleotide Polymorphisms.
                                          Molecular Biology and Evolution (2012) 29:3617-3623
                                          Maruki T, Kumar S, Kim Y.
                                            130 Performance of Computational Tools in Evaluating the Functional Impact of Laboratory-Induced Amino Acid Mutations.
                                            Bioinformatics (2012) 28:2093-2096
                                            Gray VE, Kukurba KR, Kumar S.
                                              129 Human Genomic Disease Variants: A Neutral Evolutionary Explanation.
                                              Genome Research (2012) 22:1383-1394
                                              Dudley JT, Kim Y, Liu L, Markov GJ, Gerold K, Chen R, Butte AJ, Kumar S.
                                              128 Learning Sparse Representations for Fruit-Fly Gene Expression Pattern Image Annotation and Retrieval.
                                              BMC Bioinformatics (2012) 13:107(15pp)
                                              Yuan L, Woodard A, Ji S, Jiang Y, Zhou ZH, Kumar S, Ye J.
                                                127 Drosophila Gene Expression Pattern Annotation Through Multi-instance Multi-label Learning.
                                                ACM/IEEE Transactions on Computational Biology and Bioinformatics (2012) 2012:98-112
                                                Li YX, Ji S, Kumar S, Ye J, Zhou ZH.
                                                  126 Evolutionary Meta-analysis of Association Studies Reveals Ancient Constraints Affecting Disease Marker Discovery.
                                                  Molecular Biology and Evolution (2012) 29:2087-2094 [Web Service]
                                                  Dudley JT, Chen R, Sanderford M, Butte AJ, Kumar S.
                                                  • [Web Service] [Image Archive] [Image Archive] A new measure for ranking SNPs that integrates evolutionary conservation scores and the Pvalue (Erank).
                                                  • [Website] [Archive] Science Daily: Evolutionary Information Improves Discovery of Mutations Associated With Diseases
                                                  • [Website] [Archive] ASU News: Evolutionary information improves genomic medicine
                                                  125 Statistics and Truth in Phylogenomics.
                                                  Molecular Biology and Evolution (2012) 29:457-472
                                                  Kumar S, Filipski AJ, Battistuzzi FU, Kosakovsky Pond SL, Tamura K.
                                                    124 Comparison of Embryonic Expression Within Multigene Families Employing the FlyExpress Discovery Platform Reveals Significantly More Spatial Than Temporal Divergence.
                                                    Developmental Dynamics (2012) 241:150-160 [Web Service]
                                                    Konikoff CE, Karr TL, McCutchan M, Newfeld SJ, Kumar S.
                                                    • [Web Site] [Image Archive] FlyExpress is a platform to explore expression patterns of developmentally relevant genes in Drosophila embryogenesis.
                                                    123 FlyExpress: Visual Mining of Spatiotemporal Patterns for Genes and Publications in Drosophila Embryogenesis.
                                                    Bioinformatics (2011) 27:3319-3320 [Web Service]
                                                    Kumar S, Konikoff C, Van Emden B, Busick C, Davis KT, Ji S, Wu LW, Ramos H, Brody T, Panchanathan S, Ye J, Karr TL, Gerold K, McCutchan M, Newfeld SJ.
                                                    • [Web Site] [Image Archive] FlyExpress is a platform to explore expression patterns of developmentally relevant genes in Drosophila embryogenesis.
                                                    122 Phylomedicine: An Evolutionary Telescope to Explore and Diagnose the Universe of Disease Mutations.
                                                    Trends in Genetics (2011) 27:377-386
                                                    Kumar S, Dudley JT, Filipski A, Liu L.
                                                    121 TimeTree2: Species Divergence Times on the IPhone.
                                                    Bioinformatics (2011) 27:2023-2024 [iTunes Download]
                                                    Kumar S, Hedges SB.
                                                    • [Web Site] [Image Archive] TIMETREE is a public resource for knowledge on the timescale and evolutionary history of life
                                                    • [Website] [Archive] The Telegraph (UK): TimeTree: evolutionary iPhone app shows when you shared an ancestor with chimps
                                                    • [Website] [Archive] The Hindu: iPhone app shows your common ancestors
                                                    • [Website] [Archive] The Register: Steve Jobs in iPhone bitchslap to creationists, Tea Party
                                                    • [Website] [Archive] ASU News: Grasping the tree of life: There's an app for that, too
                                                    • [Google News Results] More Results: Google News
                                                    120 Stoichiogenomics: the Evolutionary Ecology of Macromolecular Elemental Composition.
                                                    Trends in Ecology & Evolution (2011) 26:38-44
                                                    Elser JJ, Acquisti C, Kumar S.
                                                      119 MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods.
                                                      Molecular Biology and Evolution (2011) 28:2731-2739 [Software Download]
                                                      Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S.
                                                      118 Fast and Slow Implementations of Relaxed-Clock Methods Show Similar Patterns of Accuracy in Estimating Divergence Times.
                                                      Molecular Biology and Evolution (2011) 28:2439-2442
                                                      Battistuzzi FU, Billing-Ross P, Paliwal A, Kumar S.
                                                      117 Rampant Purifying Selection Conserves Positions with Posttranslational Modifications in Human Proteins.
                                                      Molecular Biology and Evolution (2011) 28:1565-1568
                                                      Gray VE, Kumar S.
                                                        116 Molecular Clock: Testing (Version 2.0).
                                                        Encyclopedia of Life Sciences. John Wiley & Sons, Ltd, Chichester, UK (2011) (7pp)
                                                        Battistuzzi FU, Filipski A, Kumar S.
                                                          115 Evolution of Modern Birds Revealed by Mitogenomics: Timing the Radiation and Origin of Major Orders.
                                                          Molecular Biology and Evolution (2011) 28:1927-1942
                                                          Pacheco MA, Battistuzzi FU, Lentino M, Aguilar RF, Kumar S, Escalante AA.
                                                            114 Performance of Relaxed-Clock Methods in Estimating Evolutionary Divergence Times and Their Credibility Intervals.
                                                            Molecular Biology and Evolution (2010) 27:1289-1300
                                                            Battistuzzi FU, Filipski A, Hedges SB, Kumar S.
                                                              113 More Reliable Estimates of Divergence Times in Pan Using Complete MtDNA Sequences and Accounting for Population Structure.
                                                              Philosophical Transactions of Royal Society (2010) 365:3277-3288
                                                              Stone AC, Battistuzzi FU, Kubatko LS, Perry GH Jr, Trudeau E, Lin H, Kumar S.
                                                                112 Quantitative Analysis of the Drosophila Segmentation Regulatory Network Using Pattern Generating Potentials.
                                                                PLoS Biology (2010) 17:8(8pp)
                                                                Kazemian M, Blatti C, Richards A, McCutchan M, Wakabayashi-Ito N, Hammonds AS, Celniker SE, Kumar S, Wolfe SA, Brodsky MH, Sinha S.
                                                                  111 Foreword for the Book GENES: Conceptual, Molecular, and Developmental by S Mitra.
                                                                  MacMillan Press, India. (2010) 17:8(8pp)
                                                                  Kumar S.
                                                                    110 Positional Conservation and Amino Acids Shape the Correct Diagnosis and Population Frequencies of Benign and Damaging Personal Amino Acid Mutations.
                                                                    Genome Research (2009) 19:1562-1569
                                                                    Kumar S, Suleski MP, Markov GJ, Lawrence S, Marco A, Filipski AJ.
                                                                      109 Relationship Between Gene Co-Expression and Sharing of Transcription Factor Binding Sites in Drosophila Melanogaster.
                                                                      Bioinformatics (2009) 25:2473-2477
                                                                      Marco A, Konikoff C, Karr TL, Kumar S.
                                                                        108 Methods for Incorporating the Hypermutability of CpG Dinucleotides in Detecting Natural Selection Operating at the Amino Acid Sequence Level.
                                                                        Molecular Biology and Evolution (2009) 26:2275-2284
                                                                        Suzuki Y, Gojobori T, Kumar S.
                                                                          107 Association of Orthodenticle with Natural Variation for Early Embryonic Patterning in Drosophila Melanogaster.
                                                                          Journal of Experimental Zoology (Molecular & Developmental Evolution) (2009) 312B:841-854
                                                                          Goering LM, Hunt PK, Heighington C, Busick C, Pennings PS, Hermisson J, Kumar S, Gibson G.
                                                                          106 Drosophila Gene Expression Pattern Annotation Using Sparse Features and Term-Term Interactions.
                                                                          ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (2009) 407-416
                                                                          Ji S, Yuan L, Li YX, Zhou ZH, Kumar S, Ye J.
                                                                            105 A Bag-of-Words Approach for Drosophila Gene Expression Pattern Annotation.
                                                                            BMC Bioinformatics (2009) 10:119(16pp)
                                                                            Ji S, Li YX, Zhou ZH, Kumar S, Ye J.
                                                                              104 Drosophila Gene Expression Pattern Annotation Through Multi-Instance Multi-Label Learning.
                                                                              International Joint Conference on Artificial Intelligence (2009) 1445-1450
                                                                              Li YX, Ji S, Kumar S, Ye J, Zhou ZH.
                                                                                103 The Origin of Metazoa: a Transition from Temporal to Spatial Cell Differentiation.
                                                                                BioEssays (2009) 31:758-68
                                                                                Mikhailov KV, Konstantinova AV, Nikitin MA, Troshin PV, Rusin LY, Lyubetsky VA, Panchin YV, Mylnikov AP, Moroz LL, Kumar S, Aleoshin VV.
                                                                                  102 Signatures of Nitrogen Limitation in the Elemental Composition of the Proteins Involved in the Metabolic Apparatus.
                                                                                  Proceedings of the Royal Society of London Series B-Biological Sciences (2009) 276:2605-2610
                                                                                  Acquisti C, Kumar S, Elser JJ.
                                                                                    101 Ecological Nitrogen Limitation Shapes the DNA Composition of Plant Genomes.
                                                                                    Molecular Biology and Evolution (2009) 26:953-956
                                                                                    Acquisti C, Elser JJ, Kumar S.
                                                                                      100 Phylogenetic Construction of 17 Bacterial Phyla by New Method and Carefully Selected Orthologs.
                                                                                      Gene (2009) 429:59-64
                                                                                      Horiike T, Miyata D, Hamada K, Saruhashi S, Shinozawa T, Kumar S, Chakraborty R, Komiyama T, Tateno Y.
                                                                                        99 Discovering the Timetree of Life. The Timetree of Life Edited by Hedges SB & Kumar S.
                                                                                        Oxford University Press, New York, 3-18. (2009) [Download PDF]
                                                                                        Hedges SB, Kumar S.
                                                                                          98 The Timetree of Life.
                                                                                          Oxford University Press, New York, (551 pp). (2009) [Download Book Chapter]
                                                                                          Hedges SB, Kumar S.
                                                                                            97 Automated Annotation of Drosophila Gene Expression Patterns Using a Controlled Vocabulary.
                                                                                            Bioinformatics (2008) 24:1881-1888
                                                                                            Ji S, Sun L, Jin R, Kumar S, Ye J.
                                                                                              96 MEGA: A Biologist-Centric Software for Evolutionary Analysis of DNA and Protein Sequences.
                                                                                              Briefings in Bioinformatics (2008) 9:299-306
                                                                                              Kumar S, Nei M, Dudley J, Tamura K.
                                                                                              • [Website] [Archive] New Hot Papers: Current Classics Scientist Sudhir Kumar on MEGA Integrated Software
                                                                                              95 Molecular Phylogeny Reconstruction.
                                                                                              Encyclopedia of Life Sciences. (2008) Macmillan Reference Ltd, Oxford, Nature Publishing Group, UK.
                                                                                              Kumar S, Filipski A.
                                                                                                94 Developmental Stage Annotation of Drosophila Gene Expression Pattern Images via an Entire Solution Path for LDA.
                                                                                                ACM Transactions on Knowledge Discovery from Data (2008) 2:1-21
                                                                                                Ye J, Chen J, Janardan R, Kumar S.
                                                                                                  93 Biological Image Analysis via Matrix Approximation.
                                                                                                  Encyclopedia of Data Warehousing and Mining (2nd Ed.) edited by John Wang, Idea Group, Inc., Pennsylvania, 166-170. (2008) 2:1-21
                                                                                                  Ye J, Janardan R, Kumar S.
                                                                                                    92 Molecular Signatures of Adaptive Evolution.
                                                                                                    Evolutionary Genomics and Proteomics (2007) edited by Pagel M & Pomiankowski A. Sinauer Associates, Inc., Massachusetts, 241-254.
                                                                                                    Filipski A, Prohaska S, Kumar S.
                                                                                                      91 Evolution of Genes and Genomes on the Drosophila Phylogeny.
                                                                                                      Nature (2007) 450:203-218
                                                                                                      Drosophila 12 Genomes Consortium.
                                                                                                        90 Constraint and Turnover in Sex-Biased Gene Expression in the Genus Drosophila.
                                                                                                        Nature (2007) 450:233-237
                                                                                                        Zhang Y, Sturgill D, Parisi M, Kumar S, Oliver B.
                                                                                                        • [Website] [Archive] ASU News: ASU’s fruit fly study advances genetics
                                                                                                        89 Nullomers: Really a Matter of Natural Selection?
                                                                                                        PLoS ONE 2 (2007) (3 pp)
                                                                                                        Acquisti C, Poste G, Curtiss D, Kumar S.
                                                                                                          88 Bioinformatics Software for Biologists in the Genomics Era.
                                                                                                          Bioinformatics (2007) 23:1713-1717
                                                                                                          Kumar S, Dudley J.
                                                                                                            87 MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0.
                                                                                                            Molecular Biology and Evolution (2007) 24:1596-1599 [www.megasoftware.net]
                                                                                                            Tamura K, Dudley J, Nei M, Kumar S.
                                                                                                            • [Website] [Archive] Thomson Reuters Sciencewatch: Two publications given Current Classics designation
                                                                                                            86 Multiple Sequence Alignment: In Pursuit of Homologous DNA Positions.
                                                                                                            Genome Research (2007) 17:127-135
                                                                                                            Kumar S, Filipski A.
                                                                                                              85 Lower Bounds on Multiple Sequence Alignment Using Exact 3-Way Alignment.
                                                                                                              BMC Bioinformatics (2007) 8:140 (8 pp)
                                                                                                              Colbourn CJ, Kumar S.
                                                                                                                84 Evolutionary Anatomies of Positions and Types of Disease-associated and Neutral Amino Acid Mutations in the Human Genome.
                                                                                                                BMC Genomics (2006) 7:306 (9 pp)
                                                                                                                Subramanian S, Kumar S.
                                                                                                                  83 TimeTree: A Public Knowledge-base of Divergence Times Among Organisms.
                                                                                                                  Bioinformatics (2006) 22:2971-2972.
                                                                                                                  Hedges SB, Dudley J, Kumar S.
                                                                                                                    82 Higher Intensity of Purifying Selection on >90% of the Human Genes Revealed by the Intrinsic Replacement Mutation Rates.
                                                                                                                    Molecular Biology and Evolution (2006) 23:2283-2287
                                                                                                                    Subramanian S, Kumar S.
                                                                                                                      81 Signatures of Ecological Resource Availability in the Animal and Plant Proteomes.
                                                                                                                      Molecular Biology and Evolution (2006) 23:1946-1951
                                                                                                                      Elser JJ, Fagan WF, Subramanian S, Kumar S.
                                                                                                                      • [Website] [Archive] ASU News: Ecological differences help unlock genomic mysteries
                                                                                                                      • [Website] [Archive] ASU News: Researchers study interplay between environment, evolution
                                                                                                                      80 Classification of Drosophila Embryonic Developmental Stage Range Based on Gene Expression Pattern Images.
                                                                                                                      Computational Systems Bioinformatics Conference (2006) 4:293-298
                                                                                                                      Ye J, Chen J, Li Q, Kumar S.
                                                                                                                        79 Codon-based Detection of Positive Selection Can Be Biased by Heterogeneous Distribution of Polar Amino Acids Along Protein Sequences.
                                                                                                                        Computational Systems Bioinformatics Conference (2006) 4:335-340
                                                                                                                        Xia X, Kumar S.
                                                                                                                          78 Constraining Fossil Calibrations for Molecular Clocks.
                                                                                                                          BioEssays (2006) 28:770-771
                                                                                                                          Hedges SB, Kumar S, van Tuinen M.
                                                                                                                            77 Pushing Back the Expansion of Introns in Animal Genomes.
                                                                                                                            Cell (2005) 123:1182-1184
                                                                                                                            Kumar S, Hedges SB.
                                                                                                                              76 Placing Confidence Limits on the Molecular Age of the Human-chimpanzee Divergence.
                                                                                                                              Proceedings of the National Academy of Sciences (USA) (2005) 102:18842-18847
                                                                                                                              Kumar S, Filipski A, Swarna V, Walker A, Hedges SB.
                                                                                                                              75 Molecular Clocks: Four Decades of Evolution.
                                                                                                                              Nature Reviews Genetics (2005) 6:654-662
                                                                                                                              Kumar S.
                                                                                                                                74 Inferring Species Phylogenies from Multiple Genes: Concatenated Sequence Tree Versus Consensus Gene Tree.
                                                                                                                                Journal of Experimental Zoology (Molecular & Developmental Evolution) (2005) 304B:64-74
                                                                                                                                Gadagkar SR, Rosenberg MS, Kumar S.
                                                                                                                                  73 Maximum Likelihood Outperforms Maximum Parsimony Even when Evolutionary Rates Are Heterotachous.
                                                                                                                                  Molecular Biology and Evolution (2005) 22:2139-2141
                                                                                                                                  Gadagkar SR, Kumar S.
                                                                                                                                    72 Comparative Genomics in Eukaryotes.
                                                                                                                                    The Evolution of the Genome edited by Ryan TG. Elsevier, San Diego. (2005) 521-583
                                                                                                                                    Filipski A, Kumar S.
                                                                                                                                      71 Automatic Annotation Techniques for Gene Expression Images of the Fruit Fly Embryo.
                                                                                                                                      Proceedings of SPIE (Visual Communications and Image Processing 2005) (2005) 5960:576-583.
                                                                                                                                      Gargesha M, Yang J, Van Emden B, Panchanathan S, Kumar S
                                                                                                                                        70 Reconstructing Vertebrate Phylogeny.
                                                                                                                                        Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics edited by Subramaniam S. John Wiley & Sons, New York. (2005) 5960:576-583.
                                                                                                                                        Kumar S, Filipski A
                                                                                                                                          69 MEGA3: Integrated Software for Molecular Evolutionary Genetics Analysis and Sequence Alignment.
                                                                                                                                          Briefings in Bioinformatics (2004) 5:150-163 [www.megasoftware.net]
                                                                                                                                          Kumar S, Tamura K, Nei M.
                                                                                                                                          • [Website] [Archive] Silicon India: Indian researcher among America's top scholars
                                                                                                                                          68 Gene Expression Intensity Shapes Evolutionary Rates of the Proteins Encoded by the Vertebrate Genome.
                                                                                                                                          Genetics (2004) 168:373-381
                                                                                                                                          Subramanian S, Kumar S.
                                                                                                                                            67 Precision of Molecular Time Estimates.
                                                                                                                                            Trends in Genetics (2004) 20:242-247
                                                                                                                                            Hedges SB, Kumar S.
                                                                                                                                              66 Prospects for Inferring Very Large Phylogenies by Using the Neighbor-joining Method.
                                                                                                                                              Proceedings of the National Academy of Sciences (USA) (2004) 101:11030-11035
                                                                                                                                              Tamura K, Nei M, Kumar S.
                                                                                                                                                65 Temporal Patterns of Fruit Fly (Drosophila) Evolution Revealed by Mutation Clocks.
                                                                                                                                                Molecular Biology and Evolution (2004) 21:36-44
                                                                                                                                                Tamura K, Subramanian S, Kumar S.
                                                                                                                                                  64 The Spectrum of Human Rhodopsin Disease Mutations Through the Lens of Interspecific Variation.
                                                                                                                                                  Gene (2004) 332:107-118
                                                                                                                                                  Briscoe AD, Gaur C, Kumar S.
                                                                                                                                                    63 Identifying Spatially Similar Gene Expression Patterns in Early Stage Fruit Fly Embryo Images: Binary Feature Versus Invariant Moment Digital Representations.
                                                                                                                                                    BMC Bioinformatics (2004) 5:202(13 pp)
                                                                                                                                                    Gurunathan R, Van Emden B, Panchanathan S, Kumar S.
                                                                                                                                                      62 Image Registration and Similarity Computation for Chicken Gene Expression Patterns.
                                                                                                                                                      Genomic Signal Processing and Statistics (GENSIPS), IEEE Signal Processing Society (2004) (4pp)
                                                                                                                                                      Gargesha M, Antin P, Van Emden B, Panchanathan S, Kumar S.
                                                                                                                                                        61 Bayesian Phylogenetic Analysis.
                                                                                                                                                        Dictionary of Bioinformatics and Computational Biology edited by Hancock J & Zvelebil M, Wiley-Liss, New York. (2004) (4pp)
                                                                                                                                                        Kumar S, Filipski A.
                                                                                                                                                          60 Neutral Substitutions Occur at a Faster Rate in Exons Than in Noncoding DNA in Primate Genomes.
                                                                                                                                                          Genome Research (2003) 13:838-844
                                                                                                                                                          Subramanian S, Kumar S.
                                                                                                                                                            59 Genomic Clocks and Evolutionary Timescales.
                                                                                                                                                            Trends in Genetics (2003) 19:200-206
                                                                                                                                                            Blair Hedges S, Kumar S.
                                                                                                                                                              58 Heterogeneity of Nucleotide Frequencies Among Evolutionary Lineages and Phylogenetic Inference.
                                                                                                                                                              Molecular Biology and Evolution (2003) 20:610-621
                                                                                                                                                              Rosenberg MS, Kumar S.
                                                                                                                                                                57 Taxon Sampling, Bioinformatics, and Phylogenomics.
                                                                                                                                                                Systematic Biology (2003) 52:119-124
                                                                                                                                                                Rosenberg MS, Kumar S.
                                                                                                                                                                  56 Patterns of Transitional Mutation Biases Within and Among Mammalian Genomes.
                                                                                                                                                                  Molecular Biology and Evolution (2003) 20:988-993
                                                                                                                                                                  Rosenberg MS, Subramanian S, Kumar S.
                                                                                                                                                                    55 Quantifying the Intragenic Distribution of Human Disease Mutations.
                                                                                                                                                                    Annals of Human Genetics (2003) 67:567-579
                                                                                                                                                                    Miller MP, Parker JD, Rissing SW, Kumar S.
                                                                                                                                                                      54 Genomic Sequence of a Ranavirus (family Iridoviridae) Associated with Salamander Mortalities in North America.
                                                                                                                                                                      Virology (2003) 316:90-103
                                                                                                                                                                      Jancovich JK, Mao J, Chinchar VG, Wyatt C, Case ST, Kumar S, Valente G, Subramanian S, Davidson EW, Collins JP, Jacobs BL.
                                                                                                                                                                        53 MacTrees Made Easy, a Review of the Book Phylogenetic Trees Made Easy: a How-to-manual for Molecular Biologists by Hall BG.
                                                                                                                                                                        Molecular Phylogenetics and Evolution (2003) 27:165-167
                                                                                                                                                                        Kumar S
                                                                                                                                                                          52 A Review of the Book Genomes (second Edition) by Brown TA,
                                                                                                                                                                          The Quarterly Review of Biology (2003) 78:225
                                                                                                                                                                          Kumar S
                                                                                                                                                                            51 Mutation Rates in Mammalian Genomes.
                                                                                                                                                                            Proceedings of the National Academy of Sciences (USA) (2002) 99:803-808
                                                                                                                                                                            Kumar S, Subramanian S.
                                                                                                                                                                              50 BEST: A Novel Computational Approach for Comparing Gene Expression Patterns from Early Stages of Drosophila Melanogaster Development. [Web Service]
                                                                                                                                                                              Genetics (2002) 162:2037-2047
                                                                                                                                                                              Kumar S, Jayaraman K, Panchanathan S, Gurunathan R, Marti-Subirana A, Newfeld SJ.
                                                                                                                                                                              • [Web Site] [Image Archive] FlyExpress is a platform to explore expression patterns of developmentally relevant genes in Drosophila embryogenesis.
                                                                                                                                                                              49 Vertebrate Genomes Compared.
                                                                                                                                                                              Science (2002) 297:1283-1285
                                                                                                                                                                              Hedges SB, Kumar S.
                                                                                                                                                                                48 Evolutionary Distance Estimation Under Heterogeneous Substitution Pattern Among Lineages.
                                                                                                                                                                                Molecular Biology and Evolution (2002) 19:1727-1736
                                                                                                                                                                                Tamura K, Kumar S.
                                                                                                                                                                                  47 Measuring Conservation of Contiguous Sets of Autosomal Markers on Bovine and Porcine Genomes in Relation to the Map of the Human Genome.
                                                                                                                                                                                  Genome (2002) 45:769-776
                                                                                                                                                                                  Jiang Z, Melville JS, Cao H, Kumar S, Filipski A, Gibbins AM.
                                                                                                                                                                                    46 A Review of the Book Modern Genetic Analysis: Integrating Genes and Genomes (second Edition) by Griffiths AJF, Gelbart WM, Lewontin RC & Miller JH.
                                                                                                                                                                                    The Quarterly Review of Biology (2002) 77:456-457
                                                                                                                                                                                    Kumar S, Newfeld SJ.
                                                                                                                                                                                      45 A Review of the Book Genomic Regulatory Systems: Development and Evolution by Davidson EH.
                                                                                                                                                                                      The Quarterly Review of Biology (2002) 77:456-457
                                                                                                                                                                                      Rawls A, Kumar S.
                                                                                                                                                                                        44 MEGA2: Molecular Evolutionary Genetics Analysis Software.
                                                                                                                                                                                        Bioinformatics (2001) 17:1244-1245 [www.megasoftware.net]
                                                                                                                                                                                        Kumar S, Tamura K, Jakobsen IB, Nei M.
                                                                                                                                                                                          43 Determination of the Number of Conserved Chromosomal Segments Between Species.
                                                                                                                                                                                          Genetics (2001) 157:1387-1395
                                                                                                                                                                                          Kumar S, Gadagkar SR, Filipski A, Gu X.
                                                                                                                                                                                            42 Disparity Index: A Simple Statistic to Measure and Test the Homogeneity of Substitution Patterns Between Molecular Sequences.
                                                                                                                                                                                            Genetics (2001) 158:1321-1327 (See expanded proof in Genetics KumarCorrection.pdf)
                                                                                                                                                                                            Kumar S, Gadagkar SR.
                                                                                                                                                                                              41 Incomplete Taxon Sampling is Not a Problem for Phylogenetic Inference.
                                                                                                                                                                                              Proceedings of the National Academy of Sciences (USA) (2001) 98:10751-10756
                                                                                                                                                                                              Rosenberg MS, Kumar S.
                                                                                                                                                                                                40 Traditional Phylogenetic Reconstruction Methods Reconstruct Shallow and Deep Evolutionary Relationships Equally Well.
                                                                                                                                                                                                Molecular Biology and Evolution (2001) 18:1823-1827
                                                                                                                                                                                                Rosenberg MS, Kumar S.
                                                                                                                                                                                                  39 Understanding Human Disease Mutations Through the Use of Interspecific Genetic Variation.
                                                                                                                                                                                                  Human Molecular Genetics (2001) 21:2319-2328
                                                                                                                                                                                                  Miller MP, Kumar S.
                                                                                                                                                                                                  38 Mutation and Linkage Disequilibrium in Human MtDNA.
                                                                                                                                                                                                  European Journal of Human Genetics (2001) 9:969-972
                                                                                                                                                                                                  Hedrick P, Kumar S.
                                                                                                                                                                                                    37 A Genomic Timescale for the Origin of Eukaryotes.
                                                                                                                                                                                                    BMC Evolutionary Biology (2001) 1:4(10 pp)
                                                                                                                                                                                                    Hedges SB, Chen H, Kumar S, Wang DY, Thompson AS, Watanabe H.
                                                                                                                                                                                                      36 Elucidating Gene Interaction Networks Based on Gene Expression Pattern Image Analysis.
                                                                                                                                                                                                      Proceedings of the International Conference on Biomedical Engineering (2001) 5A:232-234
                                                                                                                                                                                                      Kumar S, Panchanathan S.
                                                                                                                                                                                                        35 Does Nonneutral Evolution Shape Observed Patterns of DNA Variation in Animal Mitochondrial Genomes?
                                                                                                                                                                                                        Annual Review of Genetics (2001) 35:539-566
                                                                                                                                                                                                        Gerber AS, Loggins R, Kumar S, Dowling TE.
                                                                                                                                                                                                          34 Classification and Indexing of gene Expression Images.
                                                                                                                                                                                                          Proceedings of SPIE (Applications of Digital Image Processing XXIV) (2001) 4472:471-481
                                                                                                                                                                                                          Jayaraman K, Panchanathan S, Kumar S.
                                                                                                                                                                                                          • [Website] SPIE Digital Library: Abstract
                                                                                                                                                                                                          33 Molecular phylogeny Reconstruction.
                                                                                                                                                                                                          Encyclopedia of Life Sciences. Macmillan Reference Ltd, Oxford, Nature Publishing Group, UK (2001) (4 pp)
                                                                                                                                                                                                          Kumar S, Filipski A.
                                                                                                                                                                                                            32 Molecular Clock: Testing.
                                                                                                                                                                                                            Encyclopedia of Life Sciences. Macmillan Reference Ltd, Oxford, Nature Publishing Group, UK (2001) (5 pp)
                                                                                                                                                                                                            Kumar S, Filipski A.
                                                                                                                                                                                                              31 Efficiency of the Neighbor-joining Method in Reconstructing Deep and Shallow Evolutionary Relationships in Large Phylogenies.
                                                                                                                                                                                                              Journal of Molecular Evolution (2000) 51:544-553
                                                                                                                                                                                                              Kumar S, Gadagkar SR.
                                                                                                                                                                                                                30 Questioning Evidence for Recombination in Human Mitochondrial DNA.
                                                                                                                                                                                                                Science (2000) 288:1931a
                                                                                                                                                                                                                Kumar S, Hedrick P, Dowling T, Stoneking M.
                                                                                                                                                                                                                  29 Expansion and Molecular Evolution of the Interferon-induced 2’-5’ Oligoadenylate Synthetase Gene Family.
                                                                                                                                                                                                                  Molecular Biology and Evolution (2000) 17:738-750
                                                                                                                                                                                                                  Kumar S, Mitnik C, Valente G, Floyd-Smith G.
                                                                                                                                                                                                                    28 Molecular Evolution and Phylogenetics.
                                                                                                                                                                                                                    Oxford University Press, New York (333 pp) (2000) [Translated in Russian, Chinese & Japanese]
                                                                                                                                                                                                                    Nei M, Kumar S.
                                                                                                                                                                                                                      27 Single Column Discrepancy and Dynamic Max-mini Optimizations for Quickly Finding the Most Parsimonious Evolutionary Trees.
                                                                                                                                                                                                                      Bioinformatics (2000) 16:140-151
                                                                                                                                                                                                                      Purdom PW Jr, Bradford PG, Tamura K, Kumar S.
                                                                                                                                                                                                                        26 A Review of the Book Genomes by Brown TA.
                                                                                                                                                                                                                        [The Quarterly Review of Biology (2000) 75:316-317
                                                                                                                                                                                                                          25 LDA: Linkage Disequilibrium Analysis of Bi-Allelic Sites in Molecular Sequence Data.
                                                                                                                                                                                                                          Version 1.0. Arizona State University, Tempe, Arizona. (2000) [Download LDA]
                                                                                                                                                                                                                            24 Molecular Evolution of a development Pathway: Phylogenetic Analyses of Transforming Growth Factor-ß Familyligands, Receptors, and Smad Signal Transducers.
                                                                                                                                                                                                                            Genetics (1999) 152:783-795
                                                                                                                                                                                                                            Newfeld SJ, Wisotzkey RG, Kumar S.
                                                                                                                                                                                                                              23 Divergence times of Eutherian Mammals.
                                                                                                                                                                                                                              Science (1999) 285:2031a (6 pp)
                                                                                                                                                                                                                              Hedges SB, Kumar S.
                                                                                                                                                                                                                                22 Divergence Time Estimates for the Early History of Animal Phyla and the Origin of Plants, Animals, and Fungi.
                                                                                                                                                                                                                                Proceedings of the Royal Society, London (1999) B266:163-171
                                                                                                                                                                                                                                Wang DY, Kumar S, Hedges SB.
                                                                                                                                                                                                                                  21 Genome Maps 10. Comparative Genomics. Mammalian Radiations. Wall Chart.
                                                                                                                                                                                                                                  Science (1999) 286:463-478
                                                                                                                                                                                                                                  O'Brien SJ, Eisenberg JF, Miyamoto M, Hedges SB, Kumar S, Wilson DE, Menotti-Raymond M, Murphy WJ, Nash WG, Lyons LA, Menninger JC, Stanyon R, Wienberg J, Copeland NG, Jenkins NA, Gellin J, Yerle M, Andersson L, Womack J, Broad T, Postlethwait J, et al.
                                                                                                                                                                                                                                    20 A molecular Timescalefor Vertebrate Evolution.
                                                                                                                                                                                                                                    Nature (1998) 392:917-920
                                                                                                                                                                                                                                    Kumar S, Hedges SB.
                                                                                                                                                                                                                                    19 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) (1998) 95:12390-12397
                                                                                                                                                                                                                                    Nei M, Kumar S, Takahashi K.
                                                                                                                                                                                                                                      18 Detection of Convergent and Parallel Evolution at the Amino Acid Sequence Level.
                                                                                                                                                                                                                                      Molecular Biology and Evolution (1997) 14:527-536
                                                                                                                                                                                                                                      Zhang J, Kumar S.
                                                                                                                                                                                                                                        17 Evolution and Functional Diversification of the Paired Box ( Pax) DNA-binding Domains.
                                                                                                                                                                                                                                        Molecular Biology and Evolution (1997) 14:829-842
                                                                                                                                                                                                                                        Balczarek KA, Lai ZC, Kumar S.
                                                                                                                                                                                                                                          16 Small-sample Tests of episodic Adaptive Evolution: A Case Study of Primate Lysozymes.
                                                                                                                                                                                                                                          Molecular Biology and Evolution (1997) 14:1335-1338
                                                                                                                                                                                                                                          Zhang J, Kumar S, Nei M.
                                                                                                                                                                                                                                            15 Sequence convergence in the Peptide-binding Region of Primate and Rodent MHC Class Ib Molecules.
                                                                                                                                                                                                                                            Molecular Biology and Evolution (1997) 14:1035-1041
                                                                                                                                                                                                                                            Yeager M, Kumar S, Hughes AL.
                                                                                                                                                                                                                                              14 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 (1997) 71:4761-4770
                                                                                                                                                                                                                                              Leitner T, Kumar S, Albert J.
                                                                                                                                                                                                                                                13 Patterns of nucleotide Substitution in Mitochondrial Protein Coding Genes of Vertebrates.
                                                                                                                                                                                                                                                Genetics (1996) 143:537-548
                                                                                                                                                                                                                                                Kumar S.
                                                                                                                                                                                                                                                  12 A Stepwise Algorithm for Finding minimum Evolution Trees.
                                                                                                                                                                                                                                                  Molecular Biology and Evolution (1996) 13:584-593
                                                                                                                                                                                                                                                  Kumar S.
                                                                                                                                                                                                                                                    11 Evolutionary Relationships of eukaryotic Kingdoms.
                                                                                                                                                                                                                                                    Journal of Molecular Evolution (1996) 42:183-193
                                                                                                                                                                                                                                                    Kumar S, Rzhetsky A.
                                                                                                                                                                                                                                                      10 Evolution of the hedgehog Gene Family.
                                                                                                                                                                                                                                                      Genetics (1996) 142:965-972
                                                                                                                                                                                                                                                      Kumar S, Balczarek KA, Lai ZC.
                                                                                                                                                                                                                                                      9 Approximate Methods for Estimating the Pattern of Nucleotide Substitution and the Variation of Substitution Rates Among Sites.
                                                                                                                                                                                                                                                      Molecular Biology and Evolution (1996) 13:650-659
                                                                                                                                                                                                                                                      Yang Z, Kumar S.
                                                                                                                                                                                                                                                        8 Continental Breakup and the Ordinal Diversification of Birds and Mammals.
                                                                                                                                                                                                                                                        Nature (1996) 381:226-229
                                                                                                                                                                                                                                                        Hedges SB, Parker PH, Sibley CG, Kumar S.
                                                                                                                                                                                                                                                          7 PHYLTEST: Phylogenetic Hypothesis Testing Software. Version 2.0.
                                                                                                                                                                                                                                                          Pennsylvania State University, University Park, Pennsylvania. (1996) [Download PHYLTEST]
                                                                                                                                                                                                                                                          Kumar S.
                                                                                                                                                                                                                                                            6 A New Method of Inference of Ancestral Nucleotide and Amino Acid Sequences.
                                                                                                                                                                                                                                                            Genetics (1995) 141:1641-1650
                                                                                                                                                                                                                                                            Yang Z, Kumar S, Nei M.
                                                                                                                                                                                                                                                              5 Four-cluster Analysis: A Simple Method to Test Phylogenetic Hypotheses.
                                                                                                                                                                                                                                                              Molecular Biology and Evolution (1995) 12:163-167
                                                                                                                                                                                                                                                              Rzhetsky A, Kumar S, Nei M.
                                                                                                                                                                                                                                                                4 18S RRNA Data Indicate That Aschelminthes Are Polyphyletic in Origin and Consist of at Least Three Distinct Clades.
                                                                                                                                                                                                                                                                Molecular Biology and Evolution (1995) 12:1132-1137
                                                                                                                                                                                                                                                                Winnepenninckx B, Backeljau T, Mackey LY, Brooks JM, De Wachter R, Kumar S, Garey JR.
                                                                                                                                                                                                                                                                  3 MEGA: Molecular Evolutionary Genetics Analysis Software for Microcomputers.
                                                                                                                                                                                                                                                                  Computer Applications in Biosciences (1994) 10:189-191 [Download MEGA for DOS]
                                                                                                                                                                                                                                                                  Kumar S, Tamura K, Nei M.
                                                                                                                                                                                                                                                                    2 A Guide to Molecular Evolutionary Genetics Analysis Program for Microcomputers.
                                                                                                                                                                                                                                                                    Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, Pennsylvania (1993) (140 pp)
                                                                                                                                                                                                                                                                    Kumar S, Tamura K, Nei M.
                                                                                                                                                                                                                                                                      1 Human Origins and Analysis of Mitochondrial DNA Sequences.
                                                                                                                                                                                                                                                                      Science (1992) 255:737-739
                                                                                                                                                                                                                                                                      Hedges SB, Kumar S, Tamura K, Stoneking M.