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Creative Data Solutions (CDS) is a Vanderbilt Shared Resource and has extensive experience in providing effective and robust solutions to challenges pertaining to research data using modern informatics and bioinformatics approaches.
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Publications
- Human metapneumovirus and lower respiratory tract disease in otherwise healthy infants and children.
Williams JV, Harris PA, Tollefson SJ, Halburnt-Rush LL, Pingsterhaus JM, Edwards KM, Wright PF, Crowe JE
(2004) N Engl J Med 350: 443-50 - Inferring ancient divergences requires genes with strong phylogenetic signals.
Salichos L, Rokas A
(2013) Nature 497: 327-31 - Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.
Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Harvard FlyBase curators, Berkeley Drosophila Genome Project, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M
(2007) Nature 450: 219-32 - Evolutionary flux of canonical microRNAs and mirtrons in Drosophila.
Berezikov E, Liu N, Flynt AS, Hodges E, Rooks M, Hannon GJ, Lai EC
(2010) Nat Genet 42: 6-9; author reply 9-10 - Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis.
Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL, Chapman J, Damasceno CM, Dorrance AE, Dou D, Dickerman AW, Dubchak IL, Garbelotto M, Gijzen M, Gordon SG, Govers F, Grunwald NJ, Huang W, Ivors KL, Jones RW, Kamoun S, Krampis K, Lamour KH, Lee MK, McDonald WH, Medina M, Meijer HJ, Nordberg EK, Maclean DJ, Ospina-Giraldo MD, Morris PF, Phuntumart V, Putnam NH, Rash S, Rose JK, Sakihama Y, Salamov AA, Savidor A, Scheuring CF, Smith BM, Sobral BW, Terry A, Torto-Alalibo TA, Win J, Xu Z, Zhang H, Grigoriev IV, Rokhsar DS, Boore JL
(2006) Science 313: 1261-6 - A sperm cytoskeletal protein that signals oocyte meiotic maturation and ovulation.
Miller MA, Nguyen VQ, Lee MH, Kosinski M, Schedl T, Caprioli RM, Greenstein D
(2001) Science 291: 2144-7 - The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia.
Brucker RM, Bordenstein SR
(2013) Science 341: 667-9 - Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.
Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, Allen JE, Amon J, Arcà B, Arensburger P, Artemov G, Assour LA, Basseri H, Berlin A, Birren BW, Blandin SA, Brockman AI, Burkot TR, Burt A, Chan CS, Chauve C, Chiu JC, Christensen M, Costantini C, Davidson VL, Deligianni E, Dottorini T, Dritsou V, Gabriel SB, Guelbeogo WM, Hall AB, Han MV, Hlaing T, Hughes DS, Jenkins AM, Jiang X, Jungreis I, Kakani EG, Kamali M, Kemppainen P, Kennedy RC, Kirmitzoglou IK, Koekemoer LL, Laban N, Langridge N, Lawniczak MK, Lirakis M, Lobo NF, Lowy E, MacCallum RM, Mao C, Maslen G, Mbogo C, McCarthy J, Michel K, Mitchell SN, Moore W, Murphy KA, Naumenko AN, Nolan T, Novoa EM, O'Loughlin S, Oringanje C, Oshaghi MA, Pakpour N, Papathanos PA, Peery AN, Povelones M, Prakash A, Price DP, Rajaraman A, Reimer LJ, Rinker DC, Rokas A, Russell TL, Sagnon N, Sharakhova MV, Shea T, Simão FA, Simard F, Slotman MA, Somboon P, Stegniy V, Struchiner CJ, Thomas GW, Tojo M, Topalis P, Tubio JM, Unger MF, Vontas J, Walton C, Wilding CS, Willis JH, Wu YC, Yan G, Zdobnov EM, Zhou X, Catteruccia F, Christophides GK, Collins FH, Cornman RS, Crisanti A, Donnelly MJ, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Hansen IA, Howell PI, Kafatos FC, Kellis M, Lawson D, Louis C, Luckhart S, Muskavitch MA, Ribeiro JM, Riehle MA, Sharakhov IV, Tu Z, Zwiebel LJ, Besansky NJ
(2015) Science 347: 1258522 - G protein-coupled receptors in Anopheles gambiae.
Hill CA, Fox AN, Pitts RJ, Kent LB, Tan PL, Chrystal MA, Cravchik A, Collins FH, Robertson HM, Zwiebel LJ
(2002) Science 298: 176-8 - Virus-like Particles Identify an HIV V1V2 Apex-Binding Neutralizing Antibody that Lacks a Protruding Loop.
Cale EM, Gorman J, Radakovich NA, Crooks ET, Osawa K, Tong T, Li J, Nagarajan R, Ozorowski G, Ambrozak DR, Asokan M, Bailer RT, Bennici AK, Chen X, Doria-Rose NA, Druz A, Feng Y, Joyce MG, Louder MK, O'Dell S, Oliver C, Pancera M, Connors M, Hope TJ, Kepler TB, Wyatt RT, Ward AB, Georgiev IS, Kwong PD, Mascola JR, Binley JM
(2017) Immunity 46: 777-791.e10 - Microtubule-depolymerizing kinesins.
Walczak CE, Gayek S, Ohi R
(2013) Annu Rev Cell Dev Biol 29: 417-41 - SIRT4 Is a Lysine Deacylase that Controls Leucine Metabolism and Insulin Secretion.
Anderson KA, Huynh FK, Fisher-Wellman K, Stuart JD, Peterson BS, Douros JD, Wagner GR, Thompson JW, Madsen AS, Green MF, Sivley RM, Ilkayeva OR, Stevens RD, Backos DS, Capra JA, Olsen CA, Campbell JE, Muoio DM, Grimsrud PA, Hirschey MD
(2017) Cell Metab 25: 838-855.e15 - Conservation of small RNA pathways in platypus.
Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z, Kellis M, Grützner F, Stark A, Hannon GJ
(2008) Genome Res 18: 995-1004 - De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements.
Schlesinger F, Smith AD, Gingeras TR, Hannon GJ, Hodges E
(2013) Genome Res 23: 1601-14 - Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases.
O'Maille PE, Malone A, Dellas N, Andes Hess B, Smentek L, Sheehan I, Greenhagen BT, Chappell J, Manning G, Noel JP
(2008) Nat Chem Biol 4: 617-23 - Drosophila matrix metalloproteinases are required for tissue remodeling, but not embryonic development.
Page-McCaw A, Serano J, Santé JM, Rubin GM
(2003) Dev Cell 4: 95-106 - Cloning of the Schizosaccharomyces pombe TFIID gene reveals a strong conservation of functional domains present in Saccharomyces cerevisiae TFIID.
Hoffmann A, Horikoshi M, Wang CK, Schroeder S, Weil PA, Roeder RG
(1990) Genes Dev 4: 1141-8 - Mental retardation and abnormal skeletal development (Dyggve-Melchior-Clausen dysplasia) due to mutations in a novel, evolutionarily conserved gene.
Cohn DH, Ehtesham N, Krakow D, Unger S, Shanske A, Reinker K, Powell BR, Rimoin DL
(2003) Am J Hum Genet 72: 419-28 - Comparing phylogeny and the predicted pathogenicity of protein variations reveals equal purifying selection across the global human mtDNA diversity.
Pereira L, Soares P, Radivojac P, Li B, Samuels DC
(2011) Am J Hum Genet 88: 433-9 - Extracellular chloride signals collagen IV network assembly during basement membrane formation.
Cummings CF, Pedchenko V, Brown KL, Colon S, Rafi M, Jones-Paris C, Pokydeshava E, Liu M, Pastor-Pareja JC, Stothers C, Ero-Tolliver IA, McCall AS, Vanacore R, Bhave G, Santoro S, Blackwell TS, Zent R, Pozzi A, Hudson BG
(2016) J Cell Biol 213: 479-94 - Drosophila roadblock and Chlamydomonas LC7: a conserved family of dynein-associated proteins involved in axonal transport, flagellar motility, and mitosis.
Bowman AB, Patel-King RS, Benashski SE, McCaffery JM, Goldstein LS, King SM
(1999) J Cell Biol 146: 165-80 - miR-8 microRNAs regulate the response to osmotic stress in zebrafish embryos.
Flynt AS, Thatcher EJ, Burkewitz K, Li N, Liu Y, Patton JG
(2009) J Cell Biol 185: 115-27 - Variations of oral microbiota are associated with pancreatic diseases including pancreatic cancer.
Farrell JJ, Zhang L, Zhou H, Chia D, Elashoff D, Akin D, Paster BJ, Joshipura K, Wong DT
(2012) Gut 61: 582-8 - Phylogeographic origin of Helicobacter pylori is a determinant of gastric cancer risk.
de Sablet T, Piazuelo MB, Shaffer CL, Schneider BG, Asim M, Chaturvedi R, Bravo LE, Sicinschi LA, Delgado AG, Mera RM, Israel DA, Romero-Gallo J, Peek RM, Cover TL, Correa P, Wilson KT
(2011) Gut 60: 1189-95 - Lateral phage transfer in obligate intracellular bacteria (wolbachia): verification from natural populations.
Chafee ME, Funk DJ, Harrison RG, Bordenstein SR
(2010) Mol Biol Evol 27: 501-5 - Parasitism and mutualism in Wolbachia: what the phylogenomic trees can and cannot say.
Bordenstein SR, Paraskevopoulos C, Dunning Hotopp JC, Sapountzis P, Lo N, Bandi C, Tettelin H, Werren JH, Bourtzis K
(2009) Mol Biol Evol 26: 231-41 - Functional divergence for every paralog.
Soria PS, McGary KL, Rokas A
(2014) Mol Biol Evol 31: 984-92 - Frequent and widespread parallel evolution of protein sequences.
Rokas A, Carroll SB
(2008) Mol Biol Evol 25: 1943-53 - Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets.
Zhou X, Shen XX, Hittinger CT, Rokas A
(2018) Mol Biol Evol 35: 486-503 - Dynamic Evolution of Nitric Oxide Detoxifying Flavohemoglobins, a Family of Single-Protein Metabolic Modules in Bacteria and Eukaryotes.
Wisecaver JH, Alexander WG, King SB, Hittinger CT, Rokas A
(2016) Mol Biol Evol 33: 1979-87 - Internal diversification of mitochondrial haplogroup R0a reveals post-last glacial maximum demographic expansions in South Arabia.
Cerný V, Mulligan CJ, Fernandes V, Silva NM, Alshamali F, Non A, Harich N, Cherni L, El Gaaied AB, Al-Meeri A, Pereira L
(2011) Mol Biol Evol 28: 71-8 - CTDGFinder: A Novel Homology-Based Algorithm for Identifying Closely Spaced Clusters of Tandemly Duplicated Genes.
Ortiz JF, Rokas A
(2017) Mol Biol Evol 34: 215-229 - Novel information theory-based measures for quantifying incongruence among phylogenetic trees.
Salichos L, Stamatakis A, Rokas A
(2014) Mol Biol Evol 31: 1261-71 - Bacteriophage flux in endosymbionts (Wolbachia): infection frequency, lateral transfer, and recombination rates.
Bordenstein SR, Wernegreen JJ
(2004) Mol Biol Evol 21: 1981-91 - Computing the Internode Certainty and Related Measures from Partial Gene Trees.
Kobert K, Salichos L, Rokas A, Stamatakis A
(2016) Mol Biol Evol 33: 1606-17 - The embryonic muscle transcriptome of Caenorhabditis elegans.
Fox RM, Watson JD, Von Stetina SE, McDermott J, Brodigan TM, Fukushige T, Krause M, Miller DM
(2007) Genome Biol 8: R188 - Novel genes exhibit distinct patterns of function acquisition and network integration.
Capra JA, Pollard KS, Singh M
(2010) Genome Biol 11: R127 - How old is my gene?
Capra JA, Stolzer M, Durand D, Pollard KS
(2013) Trends Genet 29: 659-68 - Helicobacter pylori genetic diversity within the gastric niche of a single human host.
Israel DA, Salama N, Krishna U, Rieger UM, Atherton JC, Falkow S, Peek RM
(2001) Proc Natl Acad Sci U S A 98: 14625-30 - Receptor-type guanylate cyclase is required for carbon dioxide sensation by Caenorhabditis elegans.
Hallem EA, Spencer WC, McWhirter RD, Zeller G, Henz SR, Rätsch G, Miller DM, Horvitz HR, Sternberg PW, Ringstad N
(2011) Proc Natl Acad Sci U S A 108: 254-9
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