Institute for Genome Sciences

On the synthesis and interpretation of consistent but weak gene-disease associations in the era of genome-wide association studies, International journal of epidemiology. 2006 Dec 20

Lange A, Mills RE, Lange CJ, Stewart M, Devine SE, Corbett AH

Classical nuclear localization signals: definition, function, and interaction with importin alpha, The Journal of biological chemistry. 2006 Dec 14

Dunning Hotopp JC, Grifantini R, Kumar N, Tzeng YL, Fouts D, Frigimelica E, Draghi M, Giuliani MM, Rappuoli R, Stephens DS, Grandi G, Tettelin H

Comparative genomics of Neisseria meningitidis: core genome, islands of horizontal transfer and pathogen-specific genes, Microbiology (Reading, England). 2006 Dec 12

Liu Z, Rank R, Kaltenboeck B, Magnino S, Dean D, Burall L, Plaut RD, Read TD, Myers G, Bavoil PM

Genomic plasticity of the rrn-nqrF intergenic segment in the Chlamydiaceae, Journal of bacteriology. 2006 Dec 8

Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, Nelson WC, Richter AR, White O

TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes, Nucleic acids research. 2006 Dec 6

Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E

Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote, PLoS biology. 2006 Nov 13

Wu D, Daugherty SC, Van Aken SE, Pai GH, Watkins KL, Khouri H, Tallon LJ, Zaborsky JM, Dunbar HE, Tran PL, Moran NA, Eisen JA

Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters, PLoS biology. 2006 Nov 13

Cravo AR, Villacreses C, da Silva JC

[Osteopoikilosis: 2 clinical cases], Acta reumatológica portuguesa. 2006 Nov 10

Fonseca JE, Canhão H, Silva C, Miguel C, Mediavilla MJ, Teixeira A, Castelão W, Nero P, Bernardes M, Bernardo A, Mariz E, Godinho F, Santos MJ, Bogas M, Oliveira M, Saavedra MJ, Barcelos A, Cruz M, Santos RA, Maurício L, Rodrigues M, Figueiredo G, Quintal A, Patto JV, Malcata A, da Silva JC, Araújo D, Ventura F, Branco J, Queiroz MV,

[Tuberculosis in rheumatic patients treated with tumour necrosis factor alpha antagonists: the Portuguese experience], Acta reumatológica portuguesa. 2006 Nov 10

Van Ert MN, Easterday WR, Simonson TS, U'Ren JM, Pearson T, Kenefic LJ, Busch JD, Huynh LY, Dukerich M, Trim CB, Beaudry J, Welty-Bernard A, Read T, Fraser CM, Ravel J, Keim P

Strain-specific single-nucleotide polymorphism assays for the Bacillus anthracis Ames strain, Journal of clinical microbiology. 2006 Nov 8

Donia MS, Hathaway BJ, Sudek S, Haygood MG, Rosovitz MJ, Ravel J, Schmidt EW

Natural combinatorial peptide libraries in cyanobacterial symbionts of marine ascidians, Nature chemical biology. 2006 Nov 5

Conners SB, Mongodin EF, Johnson MR, Montero CI, Nelson KE, Kelly RM

Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species, FEMS microbiology reviews. 2006 Oct 26

Savard J, Tautz D, Richards S, Weinstock GM, Gibbs RA, Werren JH, Tettelin H, Lercher MJ

Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects, Genome research. 2006 Oct 25

Vinagre F, Santos MJ, da Silva JC

[Systemic lupus erythematosus and weakness], Acta reumatológica portuguesa. 2006 Oct 23

Cravo AR, da Silva JC

[Paget's disease of the skull and face bones], Acta reumatológica portuguesa. 2006 Oct 23

Cravo AR, Tavares V, Canhão H, da Silva JC

[Back pain and dorsal kyphosis in childhood], Acta reumatológica portuguesa. 2006 Oct 23

Guedes AP, Cardoso VN, De Mattos JC, Dantas FJ, Matos VC, Silva JC, Bezerra RJ, Caldeira-de-Araujo A

Cytotoxic and genotoxic effects induced by stannous chloride associated to nuclear medicine kits, Nuclear medicine and biology. 2006 Oct 18

Rasko DA, Rosovitz MJ, Økstad OA, Fouts DE, Jiang L, Cer RZ, Kolstø AB, Gill SR, Ravel J

Complete sequence analysis of novel plasmids from emetic and periodontal Bacillus cereus isolates reveals a common evolutionary history among the B. cereus-group plasmids, including Bacillus anthracis pXO1, Journal of bacteriology. 2006 Oct 13

Lanie JA, Ng WL, Kazmierczak KM, Andrzejewski TM, Davidsen TM, Wayne KJ, Tettelin H, Glass JI, Winkler ME

Genome sequence of Avery's virulent serotype 2 strain D39 of Streptococcus pneumoniae and comparison with that of unencapsulated laboratory strain R6, Journal of bacteriology. 2006 Oct 13

Genaro G, Moraes W, Silva JC, Adania CH, Franci CR

Plasma hormones in neotropical and domestic cats undergoing routine manipulations, Research in veterinary science. 2006 Oct 2

Neuwald AF

Hypothesis: bacterial clamp loader ATPase activation through DNA-dependent repositioning of the catalytic base and of a trans-acting catalytic threonine, Nucleic acids research. 2006 Sep 29

Klebanoff MA, Andrews WW, Yu KF, Brotman RM, Nansel TR, Zhang J, Cliver SP, Schwebke JR

A pilot study of vaginal flora changes with randomization to cessation of douching, Sexually transmitted diseases. 2006 Sep 27

Khoury MJ, Gwinn M

What role for public health in genetics and vice versa?, Community genetics. 2006 Sep 27

Khoury MJ, Gwinn M

Genomics, epidemiology, and common complex diseases: let's not throw out the baby with the bathwater!, International journal of epidemiology. 2006 Sep 19

Fielding J, Georgiou-Karistianis N, Millist L, Fahey M, White O

Saccadic trajectory in Huntington's disease, Journal of the International Neuropsychological Society : JINS. 2006 Sep 19

Badger JH, Hoover TR, Brun YV, Weiner RM, Laub MT, Alexandre G, Mrázek J, Ren Q, Paulsen IT, Nelson KE, Khouri HM, Radune D, Sosa J, Dodson RJ, Sullivan SA, Rosovitz MJ, Madupu R, Brinkac LM, Durkin AS, Daugherty SC, Kothari SP, Giglio MG, Zhou L, Haft DH, Selengut JD, Davidsen TM, Yang Q, Zafar N, Ward NL

Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus, Journal of bacteriology. 2006 Sep 18

van der Heijde D, Da Silva JC, Dougados M, Geher P, van der Horst-Bruinsma I, Juanola X, Olivieri I, Raeman F, Settas L, Sieper J, Szechinski J, Walker D, Boussuge MP, Wajdula JS, Paolozzi L, Fatenejad S,

Etanercept 50 mg once weekly is as effective as 25 mg twice weekly in patients with ankylosing spondylitis, Annals of the rheumatic diseases. 2006 Sep 12

Fielding J, Georgiou-Karistianis N, White O

The role of the basal ganglia in the control of automatic visuospatial attention, Journal of the International Neuropsychological Society : JINS. 2006 Sep 11

Pohlmann A, Fricke WF, Reinecke F, Kusian B, Liesegang H, Cramm R, Eitinger T, Ewering C, Pötter M, Schwartz E, Strittmatter A, Voss I, Gottschalk G, Steinbüchel A, Friedrich B, Bowien B

Genome sequence of the bioplastic-producing "Knallgas" bacterium Ralstonia eutropha H16, Nature biotechnology. 2006 Sep 10

Janssens AC, Gwinn M, Valdez R, Narayan KM, Khoury MJ

Predictive genetic testing for type 2 diabetes, BMJ (Clinical research ed.). 2006 Sep 8

Romero CM, DeShazer D, Feldblyum T, Ravel J, Woods D, Kim HS, Yu Y, Ronning CM, Nierman WC

Genome sequence alterations detected upon passage of Burkholderia mallei ATCC 23344 in culture and in mammalian hosts, BMC genomics. 2006 Sep 5

Ruhlman T, Lee SB, Jansen RK, Hostetler JB, Tallon LJ, Town CD, Daniell H

Complete plastid genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiosperms, BMC genomics. 2006 Aug 31

Baldo L, Dunning Hotopp JC, Jolley KA, Bordenstein SR, Biber SA, Choudhury RR, Hayashi C, Maiden MC, Tettelin H, Werren JH

Multilocus sequence typing system for the endosymbiont Wolbachia pipientis, Applied and environmental microbiology. 2006 Aug 25

Palenik B, Ren Q, Dupont CL, Myers GS, Heidelberg JF, Badger JH, Madupu R, Nelson WC, Brinkac LM, Dodson RJ, Durkin AS, Daugherty SC, Sullivan SA, Khouri H, Mohamoud Y, Halpin R, Paulsen IT

Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment, Proceedings of the National Academy of Sciences of the United States of America. 2006 Aug 25

Pieper R, Gatlin-Bunai CL, Mongodin EF, Parmar PP, Huang ST, Clark DJ, Fleischmann RD, Gill SR, Peterson SN

Comparative proteomic analysis of Staphylococcus aureus strains with differences in resistance to the cell wall-targeting antibiotic vancomycin, Proteomics. 2006 Aug 25

Chiang LY, Sheppard DC, Bruno VM, Mitchell AP, Edwards JE, Filler SG

Candida albicans protein kinase CK2 governs virulence during oropharyngeal candidiasis, Cellular microbiology. 2006 Aug 24

Modolin M, Mitre AI, da Silva JC, Cintra W, Quagliano AP, Arap S, Ferreira MC

Surgical treatment of lymphedema of the penis and scrotum, Clinics (São Paulo, Brazil). 2006 Aug 22

Neuwald AF

Bayesian shadows of molecular mechanisms cast in the light of evolution, Trends in biochemical sciences. 2006 Aug 22

Cravo AR, Tavares V, Da Silva JC

[Anti-TNF alfa therapy in ankylosing spondylitis], Acta médica portuguesa. 2006 Aug 18

Winograd-Gurvich C, Georgiou-Karistianis N, Fitzgerald PB, Millist L, White OB

Self-paced and reprogrammed saccades: differences between melancholic and non-melancholic depression, Neuroscience research. 2006 Aug 17

Mills RE, Luttig CT, Larkins CE, Beauchamp A, Tsui C, Pittard WS, Devine SE

An initial map of insertion and deletion (INDEL) variation in the human genome, Genome research. 2006 Aug 10

Cantarel BL, Morrison HG, Pearson W

Exploring the relationship between sequence similarity and accurate phylogenetic trees, Molecular biology and evolution. 2006 Aug 4

Dempsey MP, Nietfeldt J, Ravel J, Hinrichs S, Crawford R, Benson AK

Paired-end sequence mapping detects extensive genomic rearrangement and translocation during divergence of Francisella tularensis subsp. tularensis and Francisella tularensis subsp. holarctica populations, Journal of bacteriology. 2006 Aug 3

Nano ME, Nano HD, Mugica JM, Silva JC, Montaña G, Limburg H

Rapid assessment of visual impairment due to cataract and cataract surgical services in urban Argentina, Ophthalmic epidemiology. 2006 Jul 20

Centeno MS, Guerreiro CI, Dias FM, Morland C, Tailford LE, Goyal A, Prates JA, Ferreira LM, Caldeira RM, Mongodin EF, Nelson KE, Gilbert HJ, Fontes CM

Galactomannan hydrolysis and mannose metabolism in Cellvibrio mixtus, FEMS microbiology letters. 2006 Jul 17

Myers GS, Rasko DA, Cheung JK, Ravel J, Seshadri R, DeBoy RT, Ren Q, Varga J, Awad MM, Brinkac LM, Daugherty SC, Haft DH, Dodson RJ, Madupu R, Nelson WC, Rosovitz MJ, Sullivan SA, Khouri H, Dimitrov GI, Watkins KL, Mulligan S, Benton J, Radune D, Fisher DJ, Atkins HS, Hiscox T, Jost BH, Billington SJ, Songer JG, McClane BA, Titball RW, Rood JI, Melville SB, Paulsen IT

Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens, Genome research. 2006 Jul 6

Meinicke P, Brodag T, Fricke WF, Waack S

P-value based visualization of codon usage data, Algorithms for molecular biology : AMB. 2006 Jun 29

Parker D, Kennan RM, Myers GS, Paulsen IT, Songer JG, Rood JI

Regulation of type IV fimbrial biogenesis in Dichelobacter nodosus, Journal of bacteriology. 2006 Jun 21

Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE

Metagenomic analysis of the human distal gut microbiome, Science (New York, N.Y.). 2006 Jun 2

Klein SL, Gerhard DS, Wagner L, Richardson P, Schriml LM, Sater AK, Warren WC, McPherson JD

Resources for genetic and genomic studies of Xenopus, Methods in molecular biology (Clifton, N.J.). 2006 Jun 2

Lin H, Zhu W, Silva JC, Gu X, Buell CR

Intron gain and loss in segmentally duplicated genes in rice, Genome biology. 2006 May 23

Ramaswamy SV, Ferrieri P, Madoff LC, Flores AE, Kumar N, Tettelin H, Paoletti LC

Identification of novel cps locus polymorphisms in nontypable group B Streptococcus, Journal of medical microbiology. 2006 May 11

Cotrim C, Cordeiro A, Loureiro MJ, Santos MJ, Simões O, Cordeiro P, da Silva JC, Carrageta M

Exercise stress echocardiography for detection of pulmonary arterial hypertension in a patient with systemic sclerosis, Revista portuguesa de cardiologia : orgão oficial da Sociedade Portuguesa de Cardiologia = Portuguese journal of cardiology : an official journal of the Portuguese Society of Cardiology. 2006 May 5

Chibucos MC, Morris PF

Levels of polyamines and kinetic characterization of their uptake in the soybean pathogen Phytophthora sojae, Applied and environmental microbiology. 2006 May 4

Pereira RM, Baptista MC, Vasques MI, Horta AE, Portugal PV, Bessa RJ, Silva JC, Pereira MS, Marques CC

Cryosurvival of bovine blastocysts is enhanced by culture with trans-10 cis-12 conjugated linoleic acid (10t,12c CLA), Animal reproduction science. 2006 Apr 27

Lin BK, Clyne M, Walsh M, Gomez O, Yu W, Gwinn M, Khoury MJ

Tracking the epidemiology of human genes in the literature: the HuGE Published Literature database, American journal of epidemiology. 2006 Apr 26

Town CD, Cheung F, Maiti R, Crabtree J, Haas BJ, Wortman JR, Hine EE, Althoff R, Arbogast TS, Tallon LJ, Vigouroux M, Trick M, Bancroft I

Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy, The Plant cell. 2006 Apr 21

Fouts DE, Rasko DA, Cer RZ, Jiang L, Fedorova NB, Shvartsbeyn A, Vamathevan JJ, Tallon L, Althoff R, Arbogast TS, Fadrosh DW, Read TD, Gill SR

Sequencing Bacillus anthracis typing phages gamma and cherry reveals a common ancestry, Journal of bacteriology. 2006 Apr 19

Smith GD, Gwinn M, Ebrahim S, Palmer LJ, Khoury MJ

Make it HuGE: human genome epidemiology reviews, population health, and the IJE, International journal of epidemiology. 2006 Apr 17

Lee SB, Kaittanis C, Jansen RK, Hostetler JB, Tallon LJ, Town CD, Daniell H

The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms, BMC genomics. 2006 Mar 23

DeBoy RT, Mongodin EF, Emerson JB, Nelson KE

Chromosome evolution in the Thermotogales: large-scale inversions and strain diversification of CRISPR sequences, Journal of bacteriology. 2006 Mar 20

Bruno VM, Kalachikov S, Subaran R, Nobile CJ, Kyratsous C, Mitchell AP

Control of the C. albicans cell wall damage response by transcriptional regulator Cas5, PLoS pathogens. 2006 Mar 17

Waack S, Keller O, Asper R, Brodag T, Damm C, Fricke WF, Surovcik K, Meinicke P, Merkl R

Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models, BMC bioinformatics. 2006 Mar 16

Gatlin CL, Pieper R, Huang ST, Mongodin E, Gebregeorgis E, Parmar PP, Clark DJ, Alami H, Papazisi L, Fleischmann RD, Gill SR, Peterson SN

Proteomic profiling of cell envelope-associated proteins from Staphylococcus aureus, Proteomics. 2006 Mar 8

Diep BA, Gill SR, Chang RF, Phan TH, Chen JH, Davidson MG, Lin F, Lin J, Carleton HA, Mongodin EF, Sensabaugh GF, Perdreau-Remington F

Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus, Lancet. 2006 Mar 6

Ferdinands M, Seneviratne J, O'Brien T, White O

Ophthalmoplegia in tiger snake envenomation, Journal of clinical neuroscience : official journal of the Neurosurgical Society of Australasia. 2006 Mar 2

Janssens AC, Gwinn M, Khoury MJ, Subramonia-Iyer S

Does genetic testing really improve the prediction of future type 2 diabetes?, PLoS medicine. 2006 Feb 28

Gwinn M, Khoury MJ

Genomics and public health in the United States: signposts on the translation highway, Community genetics. 2006 Feb 21

Dunning Hotopp JC, Lin M, Madupu R, Crabtree J, Angiuoli SV, Eisen JA, Eisen J, Seshadri R, Ren Q, Wu M, Utterback TR, Smith S, Lewis M, Khouri H, Zhang C, Niu H, Lin Q, Ohashi N, Zhi N, Nelson W, Brinkac LM, Dodson RJ, Rosovitz MJ, Sundaram J, Daugherty SC, Davidsen T, Durkin AS, Gwinn M, Haft DH, Selengut JD, Sullivan SA, Zafar N, Zhou L, Benahmed F, Forberger H, Halpin R, Mulligan S, Robinson J, White O, Rikihisa Y, Tettelin H

Comparative genomics of emerging human ehrlichiosis agents, PLoS genetics. 2006 Feb 17

Dalio MB, Haikel Júnior LF, Dalio RB, Pinto AP, Silva JC, Vespúcio MV, Guimarães MA, Garcia SB

A study of the effects of pinealectomy on intestinal cell proliferation in infant newborn rats, Acta cirúrgica brasileira / Sociedade Brasileira para Desenvolvimento Pesquisa em Cirurgia. 2006 Feb 13

Unfer TC, Conterato GM, da Silva JC, Duarte MM, Emanuelli T

Influence of hormone replacement therapy on blood antioxidant enzymes in menopausal women, Clinica chimica acta; international journal of clinical chemistry. 2006 Feb 10

Ioannidis JP, Gwinn M, Little J, Higgins JP, Bernstein JL, Boffetta P, Bondy M, Bray MS, Brenchley PE, Buffler PA, Casas JP, Chokkalingam A, Danesh J, Smith GD, Dolan S, Duncan R, Gruis NA, Hartge P, Hashibe M, Hunter DJ, Jarvelin MR, Malmer B, Maraganore DM, Newton-Bishop JA, O'Brien TR, Petersen G, Riboli E, Salanti G, Seminara D, Smeeth L, Taioli E, Timpson N, Uitterlinden AG, Vineis P, Wareham N, Winn DM, Zimmern R, Khoury MJ,

A road map for efficient and reliable human genome epidemiology, Nature genetics. 2006 Feb 8

Mills RE, Bennett EA, Iskow RC, Luttig CT, Tsui C, Pittard WS, Devine SE

Recently mobilized transposons in the human and chimpanzee genomes, American journal of human genetics. 2006 Feb 2

Gwinn M, Khoury MJ

Expanded publishing model for genetic association studies, Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology. 2006 Jan 25

Hughes MA, Silva JC, Geromanos SJ, Townsend CA

Quantitative proteomic analysis of drug-induced changes in mycobacteria, Journal of proteome research. 2006 Jan 6

Silva JC, Denny R, Dorschel C, Gorenstein MV, Li GZ, Richardson K, Wall D, Geromanos SJ

Simultaneous qualitative and quantitative analysis of the Escherichia coli proteome: a sweet tale, Molecular & cellular proteomics : MCP. 2006 Jan 5

Gwinn MR, Vallyathan V

Respiratory burst: role in signal transduction in alveolar macrophages, Journal of toxicology and environmental health. Part B, Critical reviews. 2006 Jan 5