Evolutionary Medicine and Informatics: Publications & Patents
Books
The Timetree of Life by S. Blair Hedges and Sudhir Kumar
Oxford University Press, 2009
The evolutionary history of life includes two primary components: phylogeny and timescale. Phylogeny refers to the branching order (relationships) of species or other taxa within a group and is crucial for understanding the inheritance of traits and for erecting classifications. However, a timescale is equally important because it provides a way to compare phylogeny directly with the evolution of other organisms and with planetary history such as geology, climate, extraterrestrial impacts, and other features.
Molecular Evolution and Phylogenetics by Masatoshi Nei and Sudhir Kumar 
Oxford University Press, 2000
This book presents the statistical methods that are useful in the study of molecular evolution and illustrates how to use them in actual data analysis. It is appropriate for graduate students and researchers (assuming a basic knowledge of evolution, moecular biology, and elementary statistics), allowing many investigators to incorporate refined statistical analysis of large-scale data in their own work.
2011
Li Y-X, Ji S, Kumar S, Ye J & Zhou Z-H (2011) Drosophila gene expression pattern annotation through multi-instance multi-label learning. IEEE/ACM Transactions on Computational Biology and Bioinformatics. In Print
Liang Sun, Shuiwang Ji, Jieping Ye, (2011) Canonical Correlation Analysis for Multilabel Classification: A Least-Squares Formulation, Extensions, and Analysis. IEEE Computer Society January 2011 (vol. 33 no. 1) pp. 194-200
M. Andreína Pacheco, Fabia U. Battistuzzi, Miguel Lentino, Roberto Aguilar, Sudhir Kumar, and Ananias A. Escalante (2011) Evolution of modern birds revealed by Mitogenomics: timing the radiation and origin of major orders. Molecular Biology and Evolution. doi:10.1993/molbev/msr014.
Vanessa E. Gray and Sudhir Kumar (2011) Rampant Purifying Selection Conserves Positions with Post-Translational Modifications in Human Proteins. Molecular Biology and Evolution doi: 10.1093/molbev/msr013.
Dias S, Longacre S, Escalante AA, Udagama-Randeniya PV. (2011) Genetic diversity and recombination at the C-terminal fragment of the merozoite surface protein-1 of Plasmodium vivax (PvMSP-1) in Sri Lanka. Infect Genet Evol. 11:145-156.
Alam MT, Vinayak S, Congpuong K, Wongsrichanalai C, Satimai W, Slutsker L, Escalante AA, Barnwell JW, Udhayakumar V. (2011) Tracking origins and spread of sulfadoxine-resistant Plasmodium falciparum dhps alleles in Thailand. Antimicrob Agents Chemother. 55:155-164.
Elser JJ, Acquisti C, and Kumar S (2011) Stoichiogenomics: the evolutionary ecology of macromolecular elemental composition. Trends in Ecology & Evolution. 26:38-44.
Vinayak S,...Escalante AA, et al (2010) Multiple genetic backgrounds of the amplified Plasmodium falciparum multidrug resistance (pfmdr1) gene and selective sweep of 184F mutation in Cambodia. Journal of Infectious Diseases .201:10, 1551-1560.
2010
Ting Kei Pong, Paul Tseng, Shuiwang Ji, and Jieping Ye. Trace Norm Regularization: Reformulations, Algorithms, and Multi-task Learning. SIAM Journal on Optimization, Vol. 20, No. 6, pp. 3465-3489.
Ji Liu, Peter Wonka, and Jieping Ye. Multi-Stage Dantzig Selector. The Twenty-Fourth Annual Conference on Neural Information Processing Systems (NIPS 2010).
Jun Liu and Jieping Ye. Moreau-Yosida Regularization for Grouped Tree Structure Learning. The Twenty-Fourth Annual Conference on Neural Information Processing Systems (NIPS 2010).
Jinglei Zhang, Berea A. R. Williams, Mikael T. Nilsson and John C. Chaput, The evolvability of lead peptides from small library screens. Chemical Communications 46: 7778-7780.
Datta S, Prado R, Rodriguez A, Escalante AA (2010) Characterizing molecular adaptation: a hierarchical approach to assess the selective influence of amino acid properties. Bioinformatics 26:2818-2825.
Sajani Dias, Shirley Longacre, Ananias A. Escalante and Preethi V. Udagama-Randeniya (2011) Genetic diversity and recombination at the C-terminal fragment of the merozoite surface protein-1 of Plasmodium vivax (PvMSP-1) in Sri Lanka. Infection, Genetics and Evolution 11: 145-156.
Stone AC, Battistuzzi FU, Kubatko LS, Perry GH, Trudeau E, Lin H & Kumar S (2010) More reliable estimates of divergence times in Pan using complete mtDNA sequences in and accounting for population structure. Philosophical Transactions of Royal Society B 365: 3277-3288.
Elizabeth R. Wasbrough, Steve Dorus, Svenja Hester, Julie Howard-Murkin, Kathryn Lilley, Elaine Wilkina, Ashoka Polpitiyac, Konstantinos Petritisc and Timothy L. Karr (2010) The Drosophila melanogaster sperm proteome-II (DmSP-II). Journal of Proteomics 73: 2171-2185
C. R. Simmons, C. L. Magee, D. A. Smith, L. Lauman, J. C. Chaput, and J. P. Allen (2010) Three-Dimensional Structures Reveal Multiple ADP/ATP Binding Modes for a Synthetic Class of Artificial Proteins. Biochemistry 49: 8689-8699.
Williams, B. A. R. and Chaput, J. C. (2010) Synthesis of Peptide-Oligonucleotide Conjugates using a Heterobifunctional Crosslinker. Curr. Protoc. Nucleic Acid Chem. 4.41.1-4.41.20.
Zhang, S. and Chaput, J. C. (2010) Synthesis of Glycerol Nucleic Acid (GNA) Phosphoramidite Monomers and Oligonucleotide Polymers. Curr. Protoc. Nucleic Acid Chem. 4.40.1-4.40.18.
Maria D. Vibranovski, Domitille S. Chalopin, Hedibert F. Lopes, Manyuan Long and Timothy L. Karr (2010) Direct Evidence for Postmeiotic Transcription During Drosophila melanogaster Spermatogenesis. Genetics 186:431-433.
Anderson CD, Epperson BK, Fortin MJ, Holderegger R, James PM, Rosenberg MS, Scribner KT, and Spear S (2010) Considering spatial and temporal scale in landscape-genetic studies of gene flow. Molecular Ecology 19, 3565–3575.
Daryn A Stover and Brian C Verrelli, (2010)Comparative vertebrate evolutionary analyses of type I collagen: potential of COL1a1 gene structure and intron variation for common bone-related diseases. Molecular Biology and Evolution doi: 10.1093/molbev/msq221.
Kazemian M, Blatti C, Richards A, McCutchan M, Wakabayashi-Ito N, Hammonds AS, Celniker SE, Kumar S, Wolfe SA, Brodsky MH & Sinha S (2010) Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. PLoS Biology doi:10.1371/journal. pbio.1000456.
Jun Liu, Lei Yuan, Jieping Ye (2010) An efficient algorithm for a class of fused lasso problems. The 16th ACM SIGKDD Conference on Knowledge Discovery and Data Mining. (conference)
Pacheco MA, Ryan E, Basco L, Poe A, Udhayakumar V, Collins WE, Escalante AA (2010) Evidence for negative selection on the gene encoding rhoptry -associated protein 1 (RAP-1) in Plasmodium spp. Infection, Genetics and Evolution. 10:655-661.
Tanabe K, Mita T, Jombart T, Eriksson A, Horibe S, Palacpac N, Ranford-Cartwright L, Sawai H, Sakihama N, Ohmae H, Nakamura M, Ferreira MU, Escalante AA, Prugnolle F, Björkman A, Färnert A, Kaneko A, Horii T, Manica A, Kishino H, Balloux F (2010) Plasmodium falciparum accompanied the human expansion out of Africa. Current Biology 20:1283-1289.
Jianhui Chen, Jii Liu, Jieping Ye (2010) Learning incoherent sparse and low-rank patterns from multiple tasks. The 16th ACM SIGKDD Conference on Knowledge Discovery and Data Mining (July 2010) (conference)
Liang Sun, Betul Ceran, Jieping Ye, A scalable two-stage approach for a class of dimensionality reduction techniques The 16th ACM SIGKDD Conference on Knowledge Discovery and Data Mining (July 2010) (conference)
Shuiwang Ji, Lei Tan, Shipeng Yu, Jieping Ye (2010) A shared-subspace learning framework for multi-label classification. ACM Transaction on Knowledge Discovery From Data doi: 10.1145/1754428.1754431.
Michael S Rosenberg, (2010) A Generalized Formula for Converting Chi-Square Tests to Effect Sizes for Meta-Analysis. PLoS One 5(4): e10059. doi:10.1371/journal.pone.0010059.
DAVID L. PEARSON, COREY DEVIN ANDERSON, BRIAN R. MITCHELL, MICHAEL S. ROSENBERG, RONALD NAVARRETE, PAUL COOPMANS5,( 2010) Testing Hypotheses of Bird Extinctions at Rio Palenque, Ecuador, with Informal Species Lists. Conservation Biology 24:500-510.
Amy L Rector and Brian Verrelli, (2010) Glacial cycling, large mammal community composition, and trophic adaptations in the Western Cape, South Africa. Journal of Human Evolution 58: 90-102.
Kristan A Schneider and Yuseob Kim, (2010) An analytical model for genetic hitchhiking in the evolution of antimalarial drug resistance. Theoretical Population Biology September 2010, Volume 78, Issue 2Pages 93-108
Gregory Babbitt, Michael Tolstorukov, Yuseob Kim (2010) The molecular evolution of nucleosome-positioning through sequence-dependent deformation of the DNA polymer. Journal of biomolecular structure &
Elser JJ, Acquisti C, and Kumar S (2011) Stoichiogenomics: the evolutionary ecology of macromolecular elemental composition. Trends in Ecology & Evolution 26:38-44.
Kumar S (2010) Foreword for the book GENES: Conceptual, Molecular, and Developmental by S Mitra. MacMillan Press, India. (In Press)
Charlotte E. Konikoff, Robert G. Wisotzkey, Michael J. Stinchfield and Stuart J. Newfeld (2010) Distinct Molecular Evolutionary Mechanisms Underlie the Functional Diversification of the Wnt and TGFβ Signaling Pathways. Journal of Molecular Evolution 70: 303-312.
Elizabeth O. McCullum, Berea A. R. Williams, Jinglei Zhang and John C. Chaput (2010) Random Mutagenesis by Error-Prone PCR. Methods in Molecular Biology, 634: 103-109.
Griffing S, Syphard L, Sridaran S, McCollum AM, Mixson-Hayden T, Vinayak S, Villegas L, Barnwell JW, Escalante AA, Udhayakumar V (2010) Pfmdr1 amplification and fixation of chloroquine resistant pfcrt alleles in Venezuela. Antimicrobial Agents and Chemotherapy. 54:1572-1579.
Vinayak S, Md Tauqeer A, Mixson-Hayden T, McCollum AM, Sem R, Shah NK, Lim P, Muth S, Rogers WO, Fandeur T, Barnwell JW, Escalante AA, Wongsrichanalai C, Ariey F, Meshnick SR, Udhayakumar V (2010) Origin and Evolution of Sulfadoxine Resistant Plasmodium falciparum. Plos Pathogen. 6:e1000830.
Sutherland CJ, Tanomsing N, Nolder D, Oguike M, Jennison C, Pukrittayakamee S, Dolecek C, Hien TT, do Rosário V, Arez AP, Pinto J, Michon P, Escalante AA, Nosten F, Burke M, Lee R, Blaze M, Otto TD, Barnwell J, Pain A, Williams J, White NJ, Day NPJ, Snounou G, Lockhart PJ, Chiodin PL, Imwong M, Polley SD (2010) The human malaria parasite Plasmodium ovale occurs globally as two non-recombining sympatric species. Journal of Infectious Diseases. 201:1544-1550.
Krief S*, Escalante AA*&, Pacheco MA, Mugisha L, André C, Halbwax M, Fischer A, Krief JM, Kasenene J, Crandfield M, Cornejo OE, Chavatte JM, Lin C, Letourneur F, Charlotte A, Grüner CA, McCutchan T, Rénia L, Snounou G& (2010) The malaria parasite Plasmodium falciparum originated in African Apes and occurs in bonobo. Plos Pathogen 6:e1000765 *=co-first author, &= co-corresponding author.
Oliver Niehuis, Joshua D. Gibson, Michael S. Rosenberg, Bart A. Pannebakker, Tosca Koevoets, Andrea K. Judson, Christopher A. Desjardins, Kathleen Kennedy, David Duggan, Leo W. Beukeboom, Louis van de Zande, David M. Shuker, John H. Werren, Jürgen Gadau (2010) Recombination and Its Impact on the Genome of the Haplodiploid Parasitoid Wasp Nasonia. PLoS One 5(1): e8597. doi:10.1371/journal.pone.0008597.
J D Gibson, O Niehuis, B C Verrelli and J Gadau (2010) Contrasting patterns of selective constraints in nuclear-encoded genes of the oxidative phosphorylation pathway in holometabolous insects and their possible role in hybrid breakdown in Nasonia. Heredity 104:310-317.
Claw KG, Tito RY, Stone AC, Verrelli BC (2010) Haplotype structure and divergence at human and chimpanzee serotonin transporter and receptor genes: implications for behavioral disorder association analyses. Molecular Biology and Evolution (in press).
Ivaylo Ilinkin, Jieping Ye, and Ravi Janardan (2010) Multiple structure alignment and consensus identification for proteins. BMC Bioinformatics. In press.
Shuai Huang, Jing Li, Liang Sun, Jieping Ye, Adam Fleisher, Teresa Wu, Kewei Chen, and Eric Reiman (2010) Learning Brain Connectivity of Alzheimer’s Disease by Sparse Inverse Covariance Estimation. NeuroImage. In press.
S. Zhang, C. Switzer, and J.C. Chaput (2010) The resurgence of acyclic nucleic acids. Chemical Biodiversity 7: 245-258.
Yuseob Kim, Davorka Gulisija (2010) Signature of directional selection in different models of population expansion during colonization into new selective environments. Genetics 184: 571-585.
Yuseob Kim, Jang H Lee, Gregory Babbitt (2010) The enrichment of TATA box and the scarcity of depleted proximal nucleosome in the promoters of duplicated yeast genes. Journal of Molecular Evolution 70: 69-73.
Battistuzzi FU, Filipski A, Hedges SB & Kumar S (2010) Performance of relaxed clock methods in estimating evolutionary divergence times and their credibility intervals. Molecular Biology and Evolution 27: 1289-1300; doi: 10.1093/molbev/msq014
Niehuis, O., J.D. Gibson, M.S. Rosenberg, B. Pannebakker, T. Koevoets, A.K. Judson, C. Desjardins, K. Kennedy, D. Duggan, L.W. Beukeboom, L. van de Zande, D.M. Shuker, J.H. Werren, and J. Gadau (2010) Recombination and its impact on the genome of the haplodiploid parasitoid wasp Nasonia. PLoS ONE 5:e8597
Dorus, S., Parker, R., Busby, J., Busby, S., and Karr, T. L. (2010) Sperm proteomics reveals intensified sexual selection on mouse sperm membrane and acrosome genes. (Molecular Biology and Evolution, in press: Advance Access published on January 15, 2010; doi: doi:10.1093/molbev/msq007).
Vinayak S, Alam T, Sem R, Shah NK, Susanti AI, Lim P, Muth S, Maguire JD, Rogers WO, Fandeur T, Barnwell JW, Escalante AA, Wongsrichanalai C, Ariey F, Meshnick SR, Udhayakumar V (2010) Multiple genetic backgrounds of the amplified Plasmodium falciparum multidrug resistance (pfmdr1) gene and selective sweep of 184F mutation in Cambodia Journal of Infectious Diseases
2009
J.M. Stomel, J.W. Wilson, M.A. Leon, P. Stafford, and J.C. Chaput (2009) A Man-made ATP-Binding Protein Evolved Independent of Nature Causes Abnormal Growth in Bacterial Cells. PLoS ONE 4 e7385.
B.A.R. Williams, C.W. Diehnelt, P. Belcher, M. Greving, N.W. Woodbury, S.A. Johnston, and J.C. Chaput (2009) Creating Protein Affinity Reagents by Combining Peptide Ligands on Synthetic DNA Scaffolds. Journal of the American Chemical Society 131: 17233-17241.
B.A.R. Williams, L. Lin, S.M. Lindsay, and J.C. Chaput (2009) Evolution of a Histone H4-K16 Acetyl-Specific DNA Aptamer. Journal of the American Chemical Society 131: 6330-6331.
C.R. Simmons, J.M. Stomel, M.D. McConnell, D.A. Smith, J.L. Watkins, J.P. Allen, and J.C. Chaput (2009) A Synthetic Protein Selected for Ligand Binding Affinity Mediates ATP Hydrolysis. ACS Chemical Biology 4: 649-658.
Yuseob Kim, Thomas Wiehe (2009) Simulation of DNA sequence evolution under models of recurrent directional selection. Briefings in Bioinformatics 10: 84-96.
Suzuki Y, Gojobori T & Kumar S (2009) Methods for incorporating the hypermutability of CpG dinucleotides in detecting natural selection operating at the amino acid sequence level. Molecular Biology and Evolution 26:2275-2284.
Kumar S, Suleski M, Markov GJ, Lawrence S, Marco A & Filipski AJ (2009) Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations. Genome Research 19:1562-1569.
Hedges SB & Kumar S (2009) Discovering the timetree of life. The Timetree of Life edited by Hedges SB & Kumar S. Oxford University Press, New York, 3-18.
Hedges SB & Kumar S (2009) The Timetree of Life. Oxford University Press, New York, (551 pp).
Joganic JL, Lynch JM, Littlefield TR, Verrelli BC (2009) Risk factors associated with deformational plagiocephaly. Pediatrics 24:e1126-e1133.
Mingrui Wu and Jieping Ye (2009) A Small Sphere and Large Margin Approach for Novelty Detec- tion Using Training Data with Outliers. IEEE Transactions on Pattern Analysis and Machine Intelligence Vol. 31, No. 11, pp. 2088-2092.
Antonio, M, Konikoff, C., Karr, T.L., Kumar, S. (2009) Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster. Bioinformatics 25: 2473-2477.
Vibranovski MD, Lopes HF, Karr TL, Long M (2009) Stage-Specific Expression Profiling of Drosophila Spermatogenesis Suggests that Meiotic Sex Chromosome Inactivation Drives Genomic Relocation of Testis-Expressed Genes. PLoS Genet 5: e1000731.
Bacon DJ, McCollum AM, Griffing SM, Salas C, Soberon V, Santolalla M, Haley R, Tsukayama P, Lucas C, Escalante AA, Udhayakumar V (2009) Dynamics of malaria drug resistance patterns in the Amazon basin region following changes in Peruvian national treatment policy for uncomplicated malaria. Antimicrobial Agents Chemotherapy 53: 2042-2051.
Chowell G., Munayco C., Escalante A., McKenzie F.E. (2009) The spatial and temporal patterns of falciparum and vivax malaria in Perú: 1994–2006. Malaria Journal 8: 142.
2008
J.L. Watkins and J.C. Chaput (2008) Searching Combinatorial Libraries for Native Proteins with Novel Folds. ChemBioChem 9: 1361-1363.
J.C. Chaput, N.W. Woodbury, L.A. Stearns, B.A.R. Williams (2008) Creating Protein Biocatalysts as Tools for Future Industrial Applications. Expert Opinion on Biological Therapy 8: 1087-1098.
Babbitt, G. A. & Kim, Y. (2008) Inferring natural selection on fine-scale chromatin organization in yeast. Molecular Biology and Evolution 25:1714-1727.
Innan, H. & Kim, Y. (2008) Detecting local adaptation using the joint sampling of polymorphism in ancestral and derived populations. Genetics 179: 1713-1720.
Ji S, Sun L, Jin R, Kumar S & Ye J (2008) Automated annotation of Drosophila gene expression patterns using a controlled vocabulary. Bioinformatics 24:1881-1888.
Kumar S, Dudley J, Nei M & Tamura K (2008) MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics 9:299-306.
Verrelli BC, Lewis CM, Stone AC, Perry GH (2008) Different selective pressures shape the molecular evolution of color vision in chimpanzee and human populations. Molecular Biology and Evolution 25:2735-2743.
Verrelli BC (2008) The Genetics of Malarial Resistance and Susceptibility. In: Handbook of Human Molecular Evolution, (ed: D.N. Cooper, H. Kehrer-Sawatzki),Wiley & Sons, UK.
Shuiwang Ji and Jieping Ye (2008) Generalized Linear Discriminant Analysis: A Unified Framework and Efficient Model Selection. IEEE Transactions on Neural Networks Vol. 19, No. 10, pp. 1768-1782.
Shuiwang Ji and Jieping Ye (2008) Kernel Uncorrelated and Regularized Discriminant Analysis: A Theoretical and Computational Study. IEEE Transactions on Knowledge and Data Engineering Vol. 20, No. 10, pp. 1311-1321.
Shuiwang Ji, Liang Sun, Rong Jin, Sudhir Kumar, and Jieping Ye (2008) Automated annotation of Drosophila gene expression patterns using a controlled vocabulary. Bioinformatics 24(17):1881-1888.
Liang Sun, Shuiwang Ji, and Jieping Ye (2008) Adaptive Diffusion Kernel Learning from Biological Networks for Protein Function Prediction. BMC Bioinformatics 9:162.
Qi Li, Chandra Kambhamettu and Jieping Ye (2008) Identity Representability of Facial Expressions: An Evaluation Using Feature Pixel Distributions. Neurocomputing Vol. 71, No. 10-12, pp. 1902-1912.
Karr, T. L. (2008) Application of proteomics to ecology and population biology Heredity 100: 200-206.
Dorus, S., Freeman, Z.N., Parker, E.R., Heath, B.D., and Karr, T.L. (2008) Recent origins of sperm genes in Drosophila. Molecular Biology and Evolution 25: 2157-166.
Jane M. Carlton, Ananias A. Escalante, Daniel Neafsey and Sarah K. Volkman (2008) Comparative evolutionary genomics of human malaria parasites. Trends in Parasitology 24: 545-550.
Yuriko Nishimoto, Nobuko Arisue, Satoru Kawai, Ananias A. Escalante, Toshihiro Horii, Kazuyuki Tanabe and Tetsuo Hashimoto (2008) Evolution and phylogeny of the heterogeneous cytosolic SSU rRNA genes in the genus Plasmodium. Molecular Phylogenetics and Evolution 7: 45-53.
2007
L. Lin, D. Hom, S.M. Lindsay, J.C. Chaput (2007) In Vitro Selection of Histone H4 Aptamers for Recognition Imaging Microscopy. Journal of the American Chemical Society 129: 14568-14569.
Y-W. Yang, R.S. Zhang, E.O. McCullum, and J.C. Chaput (2007) Experimental Evidence that GNA and TNA were not Sequential Polymers in the Prebiotic Evolution of RNA. Journal of Molecular Evolution 65: 289-295.
M.D. Smith, M.A. Rosenow, M. Wang, J.P. Allen, J.W. Szostak, and J.C. Chaput (2007) Structural Insights into the Evolution of a Non-Biological Protein: Importance of Surface Residues in Protein Fold Optimization PLos One 2 e467.
S.S. Mansy, J. Zhang, R. Kummerle, M. Nilsson, J.J. Chou, J.W. Szostak and J.C. Chaput (2007) Structure and Evolutionary Analysis of a Non-biological ATP-binding Protein. Journal of Molecular Biology 371: 501-513.
B. Williams, K. Lund, Y. Liu, H. Yan, and J.C. Chaput (2007) Self-Assembled Peptide Nanoarrays: An Approach to studying Protein-Protein Interactions. Angewandte Chemical International Edition 46: 3051-3054.
Kim, Y. (2007) Rate of adaptive peak shifts with partial genetic robustness. Evolution 61:1847-56.
Filipski A, Prohaska S & Kumar S (2007) Molecular signatures of adaptive evolution. Evolutionary Genomics and Proteomics edited by Pagel M & Pomiankowski A. Sinauer Associates, Inc., Massachussets, 241-254.
Drosophila 12 Genomes Consortium (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218.
Zhang Y, Sturgill D, Parisi M, Kumar S & Oliver B (2007) Constraint and turnover in sex-biased gene expression in the genus Drosophila. Nature 450:233-237.
Kumar S & Dudley J (2007) Bioinformatics software for biologists in the genomics era. Bioinformatics 23:1713-1717.
Tamura K, Dudley J, Nei M & Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24:1596-1599. [www.megasoftware.net]
Kumar S & Filipski A (2007) Multiple sequence alignment: In pursuit of homologous DNA positions. Genome Research 17:127-135.
Colbourn CJ & Kumar S (2007) Lower bounds on multiple sequence alignment using exact 3-way alignment. BMC Bioinformatics 8:140 (8 pp).
Ogden, T.H.†, and M.S. Rosenberg (2007) Alignment and topological accuracy of the direct optimization approach via POY and traditional phylogenetics via ClustalW + PAUP*. Systematic Biology 56:182–193.
Ogden, T.H.†, and M.S. Rosenberg (2007) How should gaps be treated in parsimony? A comparison of approaches using simulation. Molecular Phylogenetics and Evolution 42:817–826.
Perry GH, Martin RD, Verrelli BC (2007) Signatures of functional constraint at aye-aye opsin genes: the potential of adaptive color vision in a nocturnal primate. Molecular Biology and Evolution 24:1963-1970.
Perry GH, Tito RY, Verrelli BC (2007) The evolutionary history of human and chimpanzee Y-chromosome gene loss. Molecular Biology and Evolution 24:853-859.
Karr, T. L. (2007) Flies and the sperm proteome Human Molecular Genetics 16 Spec No 2:R124-R133.
A McCollum, K Mueller, L Villegas, V Udhayakumar, Ananias Escalante (2007) Common origin and fixation of Plasmodium falciparum dhfr and dhps mutations associated with sulphadoxine-pyrimethamine resistance in a low transmission area in South America. Antimicrobial Agents and Chemotherapy 51: 2085-2091.
2006
Kim, Y. (2006) Allele frequency distribution under recurrent selective sweeps. Genetics 172: 1967-1978.
Xue, Y., Daly, A., Yngvadottir, B., Liu, M., Coop, G., Kim, Y., Sabeti, P., Chen, Y., Stalker, J., Huckle, E., Burton, J., Leonard, S., Rogers, J. & Tyler-Smith, C. (2006) Spread of an inactive form of caspase-12 in humans is due to recent positive selection. American Journal of Human Genetics 78:659-70.
Subramanian S & Kumar S (2006) Evolutionary anatomies of positions and types of disease-associated and neutral amino acid mutations in the human genome. BMC Genomics 7:306 (9 pp).
Hedges SB, Dudley J & Kumar S (2006) TimeTree: A public knowledge-base of divergence times among organisms. Bioinformatics 22:2971-2972.
Subramanian S & Kumar S (2006) Higher intensity of natural selection on >90% of the human genes revealed by the intrinsic replacement mutation rates. Molecular Biology and Evolution 23:2283-2287.
Elser JJ, Fagan WF, Subramanian S & Kumar S (2006) Signatures of ecological resource availability in the animal and plant proteomes. Molecular Biology and Evolution 23:1946-1951.
Ogden, T.H.†, and M.S. Rosenberg (2006) Multiple sequence alignment accuracy and phylogenetic inference. Systematic Biology 55:314–328.
Stone AC, Verrelli BC (2006) Focusing on comparative ape population genetics in the post-genomic age. Current Opinion in Genetics and Development 16:586-591.
Verrelli BC, Tishkoff SA, Stone AC, Touchman JW (2006) Contrasting histories of G6PD molecular evolution and malarial resistance in humans and chimpanzees. Molecular Biology and Evolution 23:1592-1601.
Hedrick PW, Verrelli BC (2006) "Ground truth" for selection on CCR5. Trends in Genetics 22:293-296.
Perry GH, Verrelli BC, Stone AC (2006) Molecular evolution of the primate developmental genes MSX1 and PAX9. Molecular Biology and Evolution 23:644-654.
Jieping Ye (2006) Comments on the Complete Characterization of a Family of Solutions to a Gener- alized Fisher Criterion. Journal of Machine Learning Research. 9: 517–519.
Qi Li, Jieping Ye, and Chandra Kambhamettu (2006) Spatial Interest Pixels (SIPs): Useful low-level features of visual media data. Journal of Multimedia Tools and Applications. 30: 89–108.
Jieping Ye, Ravi Janardan, Qi Li, and Haesun Park (2006) Feature Reduction via Generalized Uncor- related Linear Discriminant Analysis. IEEE Transactions on Knowledge and Data Engineering. 18: 1312–1322.
Jieping Ye and Tao Xiong (2006) Computational and theoretical analysis of null space and orthogonal linear discriminant analysis. Journal of Machine Learning Research. 7: 1183–1204.
Clark, M., Heath, B. D., Anderson, C and Karr, T. L. (2006). Induced paternal effects mimic cytoplasmic incompatibility in Drosophila Genetics 173: 727-734.
Dorus, S., Busby, S. A., Shabanowitz, J., Hunt, D. and Karr, T. L. (2006) Genomic and functional evolution of the sperm proteome. Nature Genetics 38: 1440-5.
A McCollum, L Slutsker, J Barnwell, V Udhayakumar, Ananias Escalante, A Poe, M Hamel, C Huber, Z Zhou, Y Shi, P Ouma, J Vulule, P Bloland (2006) Antifolate resistance in Plasmodium falciparum: multiple origins and identification of novel dhfr alleles. Journal of Infectious Diseases 194(2): 189-97.
Z Zhou, A Poe, J Limor, K Grady, I Goldman, A McCollum, Ananias Escalante, J Barnwell, V Udhayakumar (2006) Pyrosequencing-a high-throughput method for detecting single nucleotide polymorphisms (SNPs) in the dihydrofolate reductase and dihydropteroate synthetase genes of Plasmodium falciparum. Journal of Clinical Microbiology 44: 3900-3910.
2005
Kim, Y. & Orr, H. A. (2005) Adaptation in sexuals vs. asexuals: clonal interference and the Fisher-Muller model. Genetics 171:1377-1386
Nielsen, R., Williamson, S., Kim, Y., Hubisz, M. J., Clark, A. G., and Bustamante, C. D. (2005) Genomic scans for selective sweeps using SNP data. Genome Research 15: 1566-1575
Jensen, J. D., Kim, Y., Bauer DuMont, V., Aquadro, C. F. & Bustamante, C. D. (2005) Distinguishing between selective sweeps and demography using DNA polymorphism data. Genetics 170:1401-1410
Kumar S & Hedges SB (2005) Pushing back the expansion of introns in animal genomes. Cell 123:1182-1184.
Kumar S, Filipski A, Swarna V, Walker A & Hedges SB (2005) Placing confidence limits on the molecular age of the human-chimpanzee divergence. Proceedings of the National Academy of Sciences (USA) 102:18842-18847.
Kumar S (2005) Molecular clocks: Four decades of evolution. Nature Reviews Genetics 6:654-662.
Rosenberg, M.S. (2005) Multiple sequence alignment accuracy and evolutionary distance estimation. BMC Bioinformatics 6:278. [10 pages]
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