Publications - Publications
Yesupriya A, Gwinn M, Khoury MJ
Building a knowledge base on genetic variation and cancer risk through field synopses, Journal of the National Cancer Institute. 2008 Dec 30
Desjardins CA, Gundersen-Rindal DE, Hostetler JB, Tallon LJ, Fadrosh DW, Fuester RW, Pedroni MJ, Haas BJ, Schatz MC, Jones KM, Crabtree J, Forberger H, Nene V
Comparative genomics of mutualistic viruses of Glyptapanteles parasitic wasps, Genome biology. 2008 Dec 30
Vinagre F, Santos A, Santos M, Prata A, Oliveira A, Silva JC
[Salivary gland scintigraphy in the evaluation of patients with sicca complaints], Acta reumatológica portuguesa. 2008 Dec 24
Kevany BM, Rasko DA, Thomas MG
Characterization of the complete zwittermicin A biosynthesis gene cluster from Bacillus cereus, Applied and environmental microbiology. 2008 Dec 19
Tettelin H, Riley D, Cattuto C, Medini D
Comparative genomics: the bacterial pan-genome, Current opinion in microbiology. 2008 Dec 16
Valdés J, Pedroso I, Quatrini R, Dodson RJ, Tettelin H, Blake R, Eisen JA, Holmes DS
Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications, BMC genomics. 2008 Dec 11
Yu W, Wulf A, Liu T, Khoury MJ, Gwinn M
Gene Prospector: an evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases, BMC bioinformatics. 2008 Dec 8
Egan A, Mahurkar A, Crabtree J, Badger JH, Carlton JM, Silva JC
IDEA: Interactive Display for Evolutionary Analyses, BMC bioinformatics. 2008 Dec 8
Guo X, Silva JC
Properties of non-coding DNA and identification of putative cis-regulatory elements in Theileria parva, BMC genomics. 2008 Dec 3
Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI
A core gut microbiome in obese and lean twins, Nature. 2008 Nov 30
Coyne RS, Thiagarajan M, Jones KM, Wortman JR, Tallon LJ, Haas BJ, Cassidy-Hanley DM, Wiley EA, Smith JJ, Collins K, Lee SR, Couvillion MT, Liu Y, Garg J, Pearlman RE, Hamilton EP, Orias E, Eisen JA, Methé BA
Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure, BMC genomics. 2008 Nov 26
Fielding J, Kilpatrick T, Millist L, White O
Multiple sclerosis: Cognition and saccadic eye movements, Journal of the neurological sciences. 2008 Nov 1
Vale AM, Fujiwara RT, da Silva Neto AF, Miret JA, Alvarez DC, da Silva JC, Campos-Neto A, Reed S, Mayrink W, Nascimento E
Identification of highly specific and cross-reactive antigens of Leishmania species by antibodies from Leishmania (Leishmania) chagasi naturally infected dogs, Zoonoses and public health. 2008 Nov 1
de Sousa SM, Rosselli LK, Kiyota E, da Silva JC, Souza GH, Peroni LA, Stach-Machado DR, Eberlin MN, Souza AP, Koch KE, Arruda P, Torriani IL, Yunes JA
Structural and kinetic characterization of a maize aldose reductase, Plant physiology and biochemistry : PPB / Société française de physiologie végétale. 2008 Oct 30
Fricke WF, Kusian B, Bowien B
The genome organization of Ralstonia eutropha strain H16 and related species of the Burkholderiaceae, Journal of molecular microbiology and biotechnology. 2008 Oct 29
Bordenstein SR, Paraskevopoulos C, Dunning Hotopp JC, Sapountzis P, Lo N, Bandi C, Tettelin H, Werren JH, Bourtzis K
Parasitism and mutualism in Wolbachia: what the phylogenomic trees can and cannot say, Molecular biology and evolution. 2008 Oct 28
Ravel J, Jiang L, Stanley ST, Wilson MR, Decker RS, Read TD, Worsham P, Keim PS, Salzberg SL, Fraser-Liggett CM, Rasko DA
The complete genome sequence of Bacillus anthracis Ames "Ancestor", Journal of bacteriology. 2008 Oct 24
Silva JC, Almeida JP, Serra S, Faquini I, Quinino S, Magalhães FN, Azevedo-Filho H
Aplasia cutis congenita of the scalp, Arquivos de neuro-psiquiatria. 2008 Oct 24
Emami K, Topakas E, Nagy T, Henshaw J, Jackson KA, Nelson KE, Mongodin EF, Murray JW, Lewis RJ, Gilbert HJ
Regulation of the xylan-degrading apparatus of Cellvibrio japonicus by a novel two-component system, The Journal of biological chemistry. 2008 Oct 15
Carlton JM, Adams JH, Silva JC, Bidwell SL, Lorenzi H, Caler E, Crabtree J, Angiuoli SV, Merino EF, Amedeo P, Cheng Q, Coulson RM, Crabb BS, Del Portillo HA, Essien K, Feldblyum TV, Fernandez-Becerra C, Gilson PR, Gueye AH, Guo X, Kang'a S, Kooij TW, Korsinczky M, Meyer EV, Nene V, Paulsen I, White O, Ralph SA, Ren Q, Sargeant TJ, Salzberg SL, Stoeckert CJ, Sullivan SA, Yamamoto MM, Hoffman SL, Wortman JR, Gardner MJ, Galinski MR, Barnwell JW, Fraser-Liggett CM
Comparative genomics of the neglected human malaria parasite Plasmodium vivax, Nature. 2008 Oct 9
Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics, Nucleic acids research. 2008 Oct 5
Bennett EA, Keller H, Mills RE, Schmidt S, Moran JV, Weichenrieder O, Devine SE
Active Alu retrotransposons in the human genome, Genome research. 2008 Oct 3
Silva JC, Faquini IV, Kitamura MA, Azevedo-Filho HR
Internal carotid artery blood blister-like aneurysm, Arquivos de neuro-psiquiatria. 2008 Sep 24
Lozupone CA, Hamady M, Cantarel BL, Coutinho PM, Henrissat B, Gordon JI, Knight R
The convergence of carbohydrate active gene repertoires in human gut microbes, Proceedings of the National Academy of Sciences of the United States of America. 2008 Sep 19
Leitão JM, Gonçalves H, Mendonça C, da Silva JC
Multiway chemometric decomposition of EEM of fluorescence of CdTe quantum dots obtained as function of pH, Analytica chimica acta. 2008 Sep 16
Vazquez-Juarez RC, Kuriakose JA, Rasko DA, Ritchie JM, Kendall MM, Slater TM, Sinha M, Luxon BA, Popov VL, Waldor MK, Sperandio V, Torres AG
CadA negatively regulates Escherichia coli O157:H7 adherence and intestinal colonization, Infection and immunity. 2008 Sep 15
Bressan GC, Silva JC, Borges JC, Dos Passos DO, Ramos CH, Torriani IL, Kobarg J
Human regulatory protein Ki-1/57 has characteristics of an intrinsically unstructured protein, Journal of proteome research. 2008 Sep 13
van de Werken HJ, Verhaart MR, VanFossen AL, Willquist K, Lewis DL, Nichols JD, Goorissen HP, Mongodin EF, Nelson KE, van Niel EW, Stams AJ, Ward DE, de Vos WM, van der Oost J, Kelly RM, Kengen SW
Hydrogenomics of the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus, Applied and environmental microbiology. 2008 Sep 5
Howe D, Costanzo M, Fey P, Gojobori T, Hannick L, Hide W, Hill DP, Kania R, Schaeffer M, St Pierre S, Twigger S, White O, Rhee SY
Big data: The future of biocuration, Nature. 2008 Sep 4
Lupatini JO, da Silva JC, Pomatti DM, Bettinelli LA
[Metabolic syndrome and life style], Revista gaúcha de enfermagem / EENFUFRGS. 2008 Sep 4
Gurvich CT, Fitzgerald PB, Georgiou-Karistianis N, White OB
Saccadic impairment in schizophrenia with prominent negative symptoms, Neuroreport. 2008 Sep 3
Khoury MJ, Bowen S, Bradley LA, Coates R, Dowling NF, Gwinn M, Kolor K, Moore CA, St Pierre J, Valdez R, Yoon PW
A Decade of Public Health Genomics in the United States: Centers for Disease Control and Prevention 1997-2007, Public health genomics. 2008 Sep 3
White JR, Escobar-Paramo P, Mongodin EF, Nelson KE, DiRuggiero J
Extensive genome rearrangements and multiple horizontal gene transfers in a population of pyrococcus isolates from Vulcano Island, Italy, Applied and environmental microbiology. 2008 Aug 22
Rasko DA, Moreira CG, Li de R, Reading NC, Ritchie JM, Waldor MK, Williams N, Taussig R, Wei S, Roth M, Hughes DT, Huntley JF, Fina MW, Falck JR, Sperandio V
Targeting QseC signaling and virulence for antibiotic development, Science (New York, N.Y.). 2008 Aug 22
Popoutchi P, dos Reis Lemos CR, Silva JC, Nogueira AA, Feres O, Ribeiro da Rocha JJ
Postmenopausal intestinal obstructive endometriosis: case report and review of the literature, São Paulo medical journal = Revista paulista de medicina. 2008 Aug 19
Yesupriya A, Yu W, Clyne M, Gwinn M, Khoury MJ
The continued need to synthesize the results of genetic associations across multiple studies, Genetics in medicine : official journal of the American College of Medical Genetics. 2008 Aug 18
Fricke WF, Wright MS, Lindell AH, Harkins DM, Baker-Austin C, Ravel J, Stepanauskas R
Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate Escherichia coli SMS-3-5, Journal of bacteriology. 2008 Aug 15
Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sebaihia M, Thomson NR, Chaudhuri R, Henderson IR, Sperandio V, Ravel J
The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates, Journal of bacteriology. 2008 Aug 1
Yousef Mohamad K, Roche SM, Myers G, Bavoil PM, Laroucau K, Magnino S, Laurent S, Rasschaert D, Rodolakis A
Preliminary phylogenetic identification of virulent Chlamydophila pecorum strains, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases. 2008 Jul 29
Hirschman L, Clark C, Cohen KB, Mardis S, Luciano J, Kottmann R, Cole J, Markowitz V, Kyrpides N, Morrison N, Schriml LM, Field D,
Habitat-Lite: a GSC case study based on free text terms for environmental metadata, Omics : a journal of integrative biology. 2008 Jul 28
Yousef Mohamad K, Rekiki A, Myers G, Bavoil PM, Rodolakis A
Identification and characterisation of coding tandem repeat variants in incA gene of Chlamydophila pecorum, Veterinary research. 2008 Jul 25
Passos MR, Ferreira DC, Arze WN, Silva JC, Passos FD, Curvelo JA
Penile myiasis as a differential diagnosis for genital ulcer: a case report, The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases. 2008 Jul 21
Kilian M, Poulsen K, Blomqvist T, Håvarstein LS, Bek-Thomsen M, Tettelin H, Sørensen UB
Evolution of Streptococcus pneumoniae and its close commensal relatives, PloS one. 2008 Jul 16
McLane LM, Pulliam KF, Devine SE, Corbett AH
The Ty1 integrase protein can exploit the classical nuclear protein import machinery for entry into the nucleus, Nucleic acids research. 2008 Jun 27
Coates RJ, Khoury MJ, Gwinn M
Five genetic variants associated with prostate cancer, The New England journal of medicine. 2008 Jun 20
Garrity GM, Field D, Kyrpides N, Hirschman L, Sansone SA, Angiuoli S, Cole JR, Glöckner FO, Kolker E, Kowalchuk G, Moran MA, Ussery D, White O
Toward a standards-compliant genomic and metagenomic publication record, Omics : a journal of integrative biology. 2008 Jun 20
Field D, Garrity GM, Sansone SA, Sterk P, Gray T, Kyrpides N, Hirschman L, Glöckner FO, Kottmann R, Angiuoli S, White O, Dawyndt P, Thomson N, Gil IS, Morrison N, Tatusova T, Mizrachi I, Vaughan R, Cochrane G, Kagan L, Murphy S, Schriml L,
Meeting report: the fifth Genomic Standards Consortium (GSC) workshop, Omics : a journal of integrative biology. 2008 Jun 20
Van Brabant B, Gray T, Verslyppe B, Kyrpides N, Dietrich K, Glöckner FO, Cole J, Farris R, Schriml LM, De Vos P, De Baets B, Field D, Dawyndt P,
Laying the foundation for a Genomic Rosetta Stone: creating information hubs through the use of consensus identifiers, Omics : a journal of integrative biology. 2008 Jun 20
Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity G, Kodira CD, Kyrpides N, Madupu R, Markowitz V, Tatusova T, Thomson N, White O
Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation, Omics : a journal of integrative biology. 2008 Jun 20
DeBoy RT, Mongodin EF, Fouts DE, Tailford LE, Khouri H, Emerson JB, Mohamoud Y, Watkins K, Henrissat B, Gilbert HJ, Nelson KE
Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus, Journal of bacteriology. 2008 Jun 13
Brotman RM, Ravel J
Ready or not: the molecular diagnosis of bacterial vaginosis, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2008 Jun 4
Huntley JF, Conley PG, Rasko DA, Hagman KE, Apicella MA, Norgard MV
Native outer membrane proteins protect mice against pulmonary challenge with virulent type A Francisella tularensis, Infection and immunity. 2008 May 27
Brotman RM, Klebanoff MA, Nansel TR, Andrews WW, Schwebke JR, Zhang J, Yu KF, Zenilman JM, Scharfstein DO
A longitudinal study of vaginal douching and bacterial vaginosis--a marginal structural modeling analysis, American journal of epidemiology. 2008 May 23
Raberg M, Reinecke F, Reichelt R, Malkus U, König S, Pötter M, Fricke WF, Pohlmann A, Voigt B, Hecker M, Friedrich B, Bowien B, Steinbüchel A
Ralstonia eutropha H16 flagellation changes according to nutrient supply and state of poly(3-hydroxybutyrate) accumulation, Applied and environmental microbiology. 2008 May 23
Yesupriya A, Evangelou E, Kavvoura FK, Patsopoulos NA, Clyne M, Walsh MC, Lin BK, Yu W, Gwinn M, Ioannidis JP, Khoury MJ
Reporting of human genome epidemiology (HuGE) association studies: an empirical assessment, BMC medical research methodology. 2008 May 20
Yu W, Wulf A, Yesupriya A, Clyne M, Khoury MJ, Gwinn M
HuGE Watch: tracking trends and patterns of published studies of genetic association and human genome epidemiology in near-real time, European journal of human genetics : EJHG. 2008 May 14
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A
The minimum information about a genome sequence (MIGS) specification, Nature biotechnology. 2008 May 9
Schutzer SE, Schlater LR, Ronning CM, DeShazer D, Luft BJ, Dunn JJ, Ravel J, Fraser-Liggett CM, Nierman WC
Characterization of clinically-attenuated Burkholderia mallei by whole genome sequencing: candidate strain for exclusion from Select Agent lists, PloS one. 2008 Apr 30
Marques SM, da Silva JC
An optimized luciferase bioluminescent assay for coenzyme A, Analytical and bioanalytical chemistry. 2008 Apr 25
Yu W, Clyne M, Dolan SM, Yesupriya A, Wulf A, Liu T, Khoury MJ, Gwinn M
GAPscreener: an automatic tool for screening human genetic association literature in PubMed using the support vector machine technique, BMC bioinformatics. 2008 Apr 22
Donia MS, Ravel J, Schmidt EW
A global assembly line for cyanobactins, Nature chemical biology. 2008 Apr 20
Fedorova ND, Khaldi N, Joardar VS, Maiti R, Amedeo P, Anderson MJ, Crabtree J, Silva JC, Badger JH, Albarraq A, Angiuoli S, Bussey H, Bowyer P, Cotty PJ, Dyer PS, Egan A, Galens K, Fraser-Liggett CM, Haas BJ, Inman JM, Kent R, Lemieux S, Malavazi I, Orvis J, Roemer T, Ronning CM, Sundaram JP, Sutton G, Turner G, Venter JC, White OR, Whitty BR, Youngman P, Wolfe KH, Goldman GH, Wortman JR, Jiang B, Denning DW, Nierman WC
Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus, PLoS genetics. 2008 Apr 11
Gwinn M, Guessous I, Khoury M
Intention to analyze in pharmacogenomics studies, Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology. 2008 Mar 19
Lange A, Mills RE, Devine SE, Corbett AH
A PY-NLS nuclear targeting signal is required for nuclear localization and function of the Saccharomyces cerevisiae mRNA-binding protein Hrp1, The Journal of biological chemistry. 2008 Mar 14
da Cruz AC, Pochapski MT, Tramonti R, da Silva JC, Antunes AC, Pilatti GL, Santos FA
Evaluation of physical-chemical properties and biocompatibility of a microrough and smooth bioactive glass particles, Journal of materials science. Materials in medicine. 2008 Mar 6
Janssens AC, Gwinn M, Bradley LA, Oostra BA, van Duijn CM, Khoury MJ
A critical appraisal of the scientific basis of commercial genomic profiles used to assess health risks and personalize health interventions, American journal of human genetics. 2008 Mar 5
Brotman RM, Ghanem KG, Klebanoff MA, Taha TE, Scharfstein DO, Zenilman JM
The effect of vaginal douching cessation on bacterial vaginosis: a pilot study, American journal of obstetrics and gynecology. 2008 Mar 4
Bek-Thomsen M, Tettelin H, Hance I, Nelson KE, Kilian M
Population diversity and dynamics of Streptococcus mitis, Streptococcus oralis, and Streptococcus infantis in the upper respiratory tracts of adults, determined by a nonculture strategy, Infection and immunity. 2008 Mar 3
Lin H, Ouyang S, Egan A, Nobuta K, Haas BJ, Zhu W, Gu X, Silva JC, Meyers BC, Buell CR
Characterization of paralogous protein families in rice, BMC plant biology. 2008 Feb 19
Fahey MC, Cremer PD, Aw ST, Millist L, Todd MJ, White OB, Halmagyi M, Corben LA, Collins V, Churchyard AJ, Tan K, Kowal L, Delatycki MB
Vestibular, saccadic and fixation abnormalities in genetically confirmed Friedreich ataxia, Brain : a journal of neurology. 2008 Jan 30
Yu W, Gwinn M, Clyne M, Yesupriya A, Khoury MJ
A navigator for human genome epidemiology, Nature genetics. 2008 Jan 29
Seedorf H, Fricke WF, Veith B, Brüggemann H, Liesegang H, Strittmatter A, Miethke M, Buckel W, Hinderberger J, Li F, Hagemeier C, Thauer RK, Gottschalk G
The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features, Proceedings of the National Academy of Sciences of the United States of America. 2008 Jan 24
Gwinn MR, Weston A
Application of oligonucleotide microarray technology to toxic occupational exposures, Journal of toxicology and environmental health. Part A. 2008 Jan 24
Limburg H, Barria von-Bischhoffshausen F, Gomez P, Silva JC, Foster A
Review of recent surveys on blindness and visual impairment in Latin America, The British journal of ophthalmology. 2008 Jan 22
Jiang SM, Ishmael N, Dunning Hotopp J, Puliti M, Tissi L, Kumar N, Cieslewicz MJ, Tettelin H, Wessels MR
Variation in the group B Streptococcus CsrRS regulon and effects on pathogenicity, Journal of bacteriology. 2008 Jan 18
Wommack KE, Bhavsar J, Ravel J
Metagenomics: read length matters, Applied and environmental microbiology. 2008 Jan 11
Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments, Genome biology. 2008 Jan 11
