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) doi: 10.1093/molbev/msv075
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
      Mol Biol Evol (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 (Epub 2014 Nov 2)
          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) (Epub 2014 Apr 16)
                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 (Epub 2014 Jan 9) [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 (Epub 2014 Jan 11) [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 (Epub 2013 Dec 4)
                  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 (Epub 2013 Dec 28)
                    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 (Epub 2013 Oct 16)
                      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 (Epub 2013 Dec 3)
                        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 (Epub 2013 Sept 4)
                          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 (Epub 2013 Jun16)
                            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 (Epub 2013 March 5)
                              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 (Epub 2013 Feb 12)
                                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 (Epub 2013 Feb 13)
                                  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 (Epub 2012 Nov 5) [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) 15 pages (Epub 2012 Oct 22)
                                    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 (Epub 2012 Aug 24) [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. (Epub 2012 Aug 30) [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 (Epub 2012 Aug 24) [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 (Epub 2012 Sep 1)
                                      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 (Epub 2012 Jun 8)
                                        Gray VE, Kukurba KR, Kumar S.
                                          129 Human Genomic Disease Variants: A Neutral Evolutionary Explanation.
                                          Genome Research (2012) 22:1383-1394 (Epub 2012 Jun 4)
                                          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 (Epub 2012 May 23)
                                          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 (Epub 2011 Apr 15)
                                            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 (Epub 2012 Mar 1) [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. (Epub 2011 Sep 26)
                                              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. (Epub 2011 Sep 29) [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. (Epub 2011 Oct 12) [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. (Epub 2011 Jul 20)
                                                Kumar S, Dudley JT, Filipski A, Liu L.
                                                121 TimeTree2: Species Divergence Times on the IPhone.
                                                Bioinformatics (2011) 27:2023-2024. (Epub 2011 May 26) [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. (Epub 2010 Nov 18)
                                                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. (Epub 2011 May 4) [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. (Epub 2011 Apr 15)
                                                  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. (Epub 2011 Jan 27)
                                                  Gray VE, Kumar S.
                                                    116 Molecular Clock: Testing (Version 2.0).
                                                    Encyclopedia of Life Sciences. John Wiley & Sons, Ltd, Chichester, UK (2011) (Epub 15 Jul 2011)
                                                    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. (Epub 2011 Jan 17)
                                                      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. (Epub 2010 Jan 21)
                                                        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 B (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) 8:e1000456.
                                                            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) 8:e1000456.
                                                              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. (Epub 2009 Jun 22)
                                                                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. (Epub 2009 Jul 24)
                                                                  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. (Epub 2009 Jul 6)
                                                                    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, 407-416. (2009) 312B:841-854.
                                                                      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
                                                                        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, 1445-1450. (2009) 10:119
                                                                          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. (Epub 2009 Apr 15)
                                                                              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. (Epub 2009 Mar 2)
                                                                                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. (Epub 2008 Oct 21)
                                                                                  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, 521-583. (2005) 22:2139-2141.
                                                                                                                                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 (4 pp). (2004) 5:202 (13 pp).
                                                                                                                                                  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) 5:202 (13 pp).
                                                                                                                                                    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.
                                                                                                                                                                    Jancovich JK, Mao J, Chinchar VG, Wyatt C, Case ST, Kumar S, Valente G, Subramanian S, Davidson EW, Collins JP, Jacobs BL.
                                                                                                                                                                      52 A Review of the Book Genomes (second Edition) by Brown TA,
                                                                                                                                                                      The Quarterly Review of Biology (2003) 78:225.
                                                                                                                                                                      Jancovich JK, Mao J, Chinchar VG, Wyatt C, Case ST, Kumar S, Valente G, Subramanian S, Davidson EW, Collins JP, Jacobs BL.
                                                                                                                                                                        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.
                                                                                                                                                                                  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). doi: 10.1002/9780470015902.a0001803.pub2
                                                                                                                                                                                                        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.