Publications - Publications 2012

Flores R, Shi J, Fuhrman B, Xu X, Veenstra TD, Gail MH, Gajer P, Ravel J, Goedert JJ

Fecal microbial determinants of fecal and systemic estrogens and estrogen metabolites: a cross-sectional study, Journal of translational medicine. 2012 Dec 21

Ravel J, Gajer P, Fu L, Mauck CK, Koenig SS, Sakamoto J, Motsinger-Reif AA, Doncel GF, Zeichner SL

Twice-daily application of HIV microbicides alter the vaginal microbiota, mBio. 2012 Dec 18

Dong W, Yan B, Johnson BP, Millist L, Davis S, Fielding J, White OB

Ischaemic stroke: the ocular motor system as a sensitive marker for motor and cognitive recovery, Journal of neurology, neurosurgery, and psychiatry. 2012 Dec 06

Erickson AR, Cantarel BL, Lamendella R, Darzi Y, Mongodin EF, Pan C, Shah M, Halfvarson J, Tysk C, Henrissat B, Raes J, Verberkmoes NC, Fraser CM, Hettich RL, Jansson JK

Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease, PloS one. 2012 Nov 28

Bäckhed F, Fraser CM, Ringel Y, Sanders ME, Sartor RB, Sherman PM, Versalovic J, Young V, Finlay BB

Defining a healthy human gut microbiome: current concepts, future directions, and clinical applications, Cell host & microbe. 2012 Nov 19

Steyert SR, Sahl JW, Fraser CM, Teel LD, Scheutz F, Rasko DA

Comparative Genomics and stx Phage Characterization of LEE-Negative Shiga Toxin-Producing Escherichia coli, Frontiers in cellular and infection microbiology. 2012 Nov 07

Johnson BP, Rinehart NJ, Papadopoulos N, Tonge B, Millist L, White O, Fielding J

A closer look at visually guided saccades in autism and Asperger's disorder, Frontiers in integrative neuroscience. 2012 Nov 07

, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA

An integrated map of genetic variation from 1,092 human genomes, Nature. 2012 Nov 06

Kansal R, Rasko DA, Sahl JW, Munson GP, Roy K, Luo Q, Sheikh A, Kuhne KJ, Fleckenstein JM

Transcriptional modulation of enterotoxigenic Escherichia coli virulence genes in response to epithelial cell interactions, Infection and immunity. 2012 Oct 31

Brotman RM, Bradford LL, Conrad M, Gajer P, Ault K, Peralta L, Forney LJ, Carlton JM, Abdo Z, Ravel J

Association between Trichomonas vaginalis and vaginal bacterial community composition among reproductive-age women, Sexually transmitted diseases. 2012 Sep 25

Witzel K, Gwinn-Giglio M, Nadendla S, Shefchek K, Ruppel S

Genome sequence of Enterobacter radicincitans DSM16656(T), a plant growth-promoting endophyte, Journal of bacteriology. 2012 Sep 11

Tettelin H, Sampaio EP, Daugherty SC, Hine E, Riley DR, Sadzewicz L, Sengamalay N, Shefchek K, Su Q, Tallon LJ, Conville P, Olivier KN, Holland SM, Fraser CM, Zelazny AM

Genomic insights into the emerging human pathogen Mycobacterium massiliense, Journal of bacteriology. 2012 Sep 11

White OB, Fielding J

Cognition and eye movements: assessment of cerebral dysfunction, Journal of neuro-ophthalmology : the official journal of the North American Neuro-Ophthalmology Society. 2012 Aug 23

Zupancic ML, Cantarel BL, Liu Z, Drabek EF, Ryan KA, Cirimotich S, Jones C, Knight R, Walters WA, Knights D, Mongodin EF, Horenstein RB, Mitchell BD, Steinle N, Snitker S, Shuldiner AR, Fraser CM

Analysis of the gut microbiota in the old order Amish and its relation to the metabolic syndrome, PloS one. 2012 Aug 15

Gevers D, Knight R, Petrosino JF, Huang K, McGuire AL, Birren BW, Nelson KE, White O, Methé BA, Huttenhower C

The Human Microbiome Project: a community resource for the healthy human microbiome, PLoS biology. 2012 Aug 14

Domingues S, Harms K, Fricke WF, Johnsen PJ, da Silva GJ, Nielsen KM

Natural transformation facilitates transfer of transposons, integrons and gene cassettes between bacterial species, PLoS pathogens. 2012 Aug 02

Robbins RJ, Amaral-Zettler L, Bik H, Blum S, Edwards J, Field D, Garrity G, Gilbert JA, Kottmann R, Krishtalka L, Lapp H, Lawrence C, Morrison N, Tuama EÓ, Parr C, San Gil I, Schindel D, Schriml L, Vieglas D, Wooley J

RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics, March 2011, Standards in genomic sciences. 2012 Jul 28

Hsiao WW, Li KL, Liu Z, Jones C, Fraser-Liggett CM, Fouad AF

Microbial transformation from normal oral microbiota to acute endodontic infections, BMC genomics. 2012 Jul 28

Kaye KS, Devine ST, Ford KD, Anderson DJ

Surgical site infection prophylaxis strategies for cardiothoracic surgery: a decision-analytic model, Scandinavian journal of infectious diseases. 2012 Jul 25

Liolios K, Schriml L, Hirschman L, Pagani I, Nosrat B, Sterk P, White O, Rocca-Serra P, Sansone SA, Taylor C, Kyrpides NC, Field D

The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness, Standards in genomic sciences. 2012 Jul 20

Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, Adam M Phillippy

Hybrid error correction and de novo assembly of single-molecule sequencing reads, Nature biotechnology. 2012 Jul 01

Ma B, Forney LJ, Ravel J

Vaginal microbiome: rethinking health and disease, Annual review of microbiology. 2012 Jun 28

Flores R, Shi J, Gail MH, Gajer P, Ravel J, Goedert JJ

Association of fecal microbial diversity and taxonomy with selected enzymatic functions, PloS one. 2012 Jun 28

Neuwald AF, Lanczycki CJ, Marchler-Bauer A

Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures, BMC bioinformatics. 2012 Jun 22

Mulangi V, Chibucos MC, Phuntumart V, Morris PF

Kinetic and phylogenetic analysis of plant polyamine uptake transporters, Planta. 2012 Jun 19

Hasan NA, Choi SY, Eppinger M, Clark PW, Chen A, Alam M, Haley BJ, Taviani E, Hine E, Su Q, Tallon LJ, Prosper JB, Furth K, Hoq MM, Li H, Fraser-Liggett CM, Cravioto A, Huq A, Ravel J, Cebula TA, Colwell RR

Genomic diversity of 2010 Haitian cholera outbreak strains, Proceedings of the National Academy of Sciences of the United States of America. 2012 Jun 18

A framework for human microbiome research, Nature. 2012 Jun 13

Structure, function and diversity of the healthy human microbiome, Nature. 2012 Jun 13

Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL, Rodriguez-Mueller B, Zucker J, Thiagarajan M, Henrissat B, White O, Kelley ST, Methé B, Schloss PD, Gevers D, Mitreva M, Huttenhower C

Metabolic reconstruction for metagenomic data and its application to the human microbiome, PLoS computational biology. 2012 Jun 13

Cantarel BL, Lombard V, Henrissat B

Complex carbohydrate utilization by the healthy human microbiome, PloS one. 2012 Jun 13

Bai G, Gajer P, Nandy M, Ma B, Yang H, Sakamoto J, Blanchard MH, Ravel J, Brotman RM

Comparison of storage conditions for human vaginal microbiome studies, PloS one. 2012 May 24

Faherty CS, Redman JC, Rasko DA, Barry EM, Nataro JP

Shigella flexneri effectors OspE1 and OspE2 mediate induced adherence to the colonic epithelium following bile salts exposure, Molecular microbiology. 2012 May 23

Kos VN, Desjardins CA, Griggs A, Cerqueira G, Van Tonder A, Holden MT, Godfrey P, Palmer KL, Bodi K, Mongodin EF, Wortman J, Feldgarden M, Lawley T, Gill SR, Haas BJ, Birren B, Gilmore MS

Comparative genomics of vancomycin-resistant Staphylococcus aureus strains and their positions within the clade most commonly associated with Methicillin-resistant S. aureus hospital-acquired infection in the United States, mBio. 2012 May 22

Macklaim JM, Cohen CR, Donders G, Gloor GB, Hill JE, Parham GP, Ravel J, Spear G, van de Wijgert J, Reid G

Exploring a road map to counter misconceptions about the cervicovaginal microbiome and disease, Reproductive sciences (Thousand Oaks, Calif.). 2012 May 21

Hazen TH, Robinson GL, Harris AD, Rasko DA, Johnson JK

Genome sequence of Klebsiella oxytoca 11492-1, a nosocomial isolate possessing a FOX-5 AmpC β-lactamase, Journal of bacteriology. 2012 May 14

Hazen TH, Sahl JW, Redman JC, Morris CR, Daugherty SC, Chibucos MC, Sengamalay NA, Fraser-Liggett CM, Steinsland H, Whittam TS, Whittam B, Manning SD, Rasko DA

Draft genome sequences of the diarrheagenic Escherichia coli collection, Journal of bacteriology. 2012 May 14

Li Y, Powell DA, Shaffer SA, Rasko DA, Pelletier MR, Leszyk JD, Scott AJ, Masoudi A, Goodlett DR, Wang X, Raetz CR, Ernst RK

LPS remodeling is an evolved survival strategy for bacteria, Proceedings of the National Academy of Sciences of the United States of America. 2012 May 14

Kumar N, Creasy T, Sun Y, Flowers M, Tallon LJ, Dunning Hotopp JC

Efficient subtraction of insect rRNA prior to transcriptome analysis of Wolbachia-Drosophila lateral gene transfer, BMC research notes. 2012 May 14

Sahl JW, Matalka MN, Rasko DA

Phylomark, a tool to identify conserved phylogenetic markers from whole-genome alignments, Applied and environmental microbiology. 2012 May 11

Gilbert JA, Bao Y, Wang H, Sansone SA, Edmunds SC, Morrison N, Meyer F, Schriml LM, Davies N, Sterk P, Wilkening J, Garrity GM, Field D, Robbins R, Smith DP, Mizrachi I, Moreau C

Report of the 13(th) Genomic Standards Consortium Meeting, Shenzhen, China, March 4-7, 2012, Standards in genomic sciences. 2012 May 04

Gajer P, Brotman RM, Bai G, Sakamoto J, Schütte UM, Zhong X, Koenig SS, Fu L, Ma ZS, Zhou X, Abdo Z, Forney LJ, Ravel J

Temporal dynamics of the human vaginal microbiota, Science translational medicine. 2012 May 03

Earl AM, Eppinger M, Fricke WF, Rosovitz MJ, Rasko DA, Daugherty S, Losick R, Kolter R, Ravel J

Whole-genome sequences of Bacillus subtilis and close relatives, Journal of bacteriology. 2012 Apr 11

Brüggemann H, Lomholt HB, Tettelin H, Kilian M

CRISPR/cas loci of type II Propionibacterium acnes confer immunity against acquisition of mobile elements present in type I P. acnes, PloS one. 2012 Mar 30

Eppinger M, Radnedge L, Andersen G, Vietri N, Severson G, Mou S, Ravel J, Worsham PL

Novel plasmids and resistance phenotypes in Yersinia pestis: unique plasmid inventory of strain Java 9 mediates high levels of arsenic resistance, PloS one. 2012 Mar 30

Yuan S, Cohen DB, Ravel J, Abdo Z, Forney LJ

Evaluation of methods for the extraction and purification of DNA from the human microbiome, PloS one. 2012 Mar 23

Sellitto M, Bai G, Serena G, Fricke WF, Sturgeon C, Gajer P, White JR, Koenig SS, Sakamoto J, Boothe D, Gicquelais R, Kryszak D, Puppa E, Catassi C, Ravel J, Fasano A

Proof of concept of microbiome-metabolome analysis and delayed gluten exposure on celiac disease autoimmunity in genetically at-risk infants, PloS one. 2012 Mar 14

Casjens SR, Mongodin EF, Qiu WG, Luft BJ, Schutzer SE, Gilcrease EB, Huang WM, Vujadinovic M, Aron JK, Vargas LC, Freeman S, Radune D, Weidman JF, Dimitrov GI, Khouri HM, Sosa JE, Halpin RA, Dunn JJ, Fraser CM

Genome stability of Lyme disease spirochetes: comparative genomics of Borrelia burgdorferi plasmids, PloS one. 2012 Mar 14

de Filippis I, de Lemos AP, Hostetler JB, Wollenberg K, Sacchi CT, Dunning Hotopp JC, Harrison LH, Bash MC, Prevots DR

Molecular epidemiology of Neisseria meningitidis serogroup B in Brazil, PloS one. 2012 Mar 14

Flores R, Shi J, Gail MH, Ravel J, Goedert JJ

Assessment of the human faecal microbiota: I. Measurement and reproducibility of selected enzymatic activities, European journal of clinical investigation. 2012 Mar 13

Hickey RJ, Zhou X, Pierson JD, Ravel J, Forney LJ

Understanding vaginal microbiome complexity from an ecological perspective, Translational research : the journal of laboratory and clinical medicine. 2012 Mar 06

Gilbert JA, Catlett C, Desai N, Knight R, White O, Robbins R, Sankaran R, Sansone SA, Field D, Meyer F

Conceptualizing a Genomics Software Institute (GSI), Standards in genomic sciences. 2012 Mar 05

Flores R, Shi J, Gail MH, Gajer P, Ravel J, Goedert JJ

Assessment of the human faecal microbiota: II. Reproducibility and associations of 16S rRNA pyrosequences, European journal of clinical investigation. 2012 Mar 03

Gyllborg MC, Sahl JW, Cronin DC, Rasko DA, Mandel MJ

Draft genome sequence of Vibrio fischeri SR5, a strain isolated from the light organ of the Mediterranean squid Sepiola robusta, Journal of bacteriology. 2012 Feb 29

Zurawski DV, Thompson MG, McQueary CN, Matalka MN, Sahl JW, Craft DW, Rasko DA

Genome sequences of four divergent multidrug-resistant Acinetobacter baumannii strains isolated from patients with sepsis or osteomyelitis, Journal of bacteriology. 2012 Feb 29

De Paula AJ, Silva JC, Paschoarelli LC, Fujii JB

Backpacks and school children's obesity: challenges for public health and ergonomics, Work (Reading, Mass.). 2012 Feb 09

Fielding J, Kilpatrick T, Millist L, Clough M, White O

Longitudinal assessment of antisaccades in patients with multiple sclerosis, PloS one. 2012 Feb 02

Berns KI, Casadevall A, Cohen ML, Ehrlich SA, Enquist LW, Fitch JP, Franz DR, Fraser-Liggett CM, Grant CM, Imperiale MJ, Kanabrocki J, Keim PS, Lemon SM, Levy SB, Lumpkin JR, Miller JF, Murch R, Nance ME, Osterholm MT, Relman DA, Roth JA, Vidaver AK

Policy: Adaptations of avian flu virus are a cause for concern, Nature. 2012 Jan 31

Berns KI, Casadevall A, Cohen ML, Ehrlich SA, Enquist LW, Fitch JP, Franz DR, Fraser-Liggett CM, Grant CM, Imperiale MJ, Kanabrocki J, Keim PS, Lemon SM, Levy SB, Lumpkin JR, Miller JF, Murch R, Nance ME, Osterholm MT, Relman DA, Roth JA, Vidaver AK

Adaptations of Avian Flu Virus Are a Cause for Concern, Science (New York, N.Y.). 2012 Jan 31

Moreira AI, Silva JC, Ferreira MS, Lanhoso A

Bilateral dysgerminoma in a patient with a previous diagnosis of Swyer syndrome, The journal of obstetrics and gynaecology research. 2012 Jan 25

Riley DR, Angiuoli SV, Crabtree J, Dunning Hotopp JC, Tettelin H

Using Sybil for interactive comparative genomics of microbes on the web, Bioinformatics (Oxford, England). 2012 Jan 18

Boisen N, Scheutz F, Rasko DA, Redman JC, Persson S, Simon J, Kotloff KL, Levine MM, Sow S, Tamboura B, Toure A, Malle D, Panchalingam S, Krogfelt KA, Nataro JP

Genomic Characterization of Enteroaggregative Escherichia coli From Children in Mali, The Journal of infectious diseases. 2012 Jan 13

Schmidt EW, Donia MS, McIntosh JA, Fricke WF, Ravel J

Origin and Variation of Tunicate Secondary Metabolites, Journal of natural products. 2012 Jan 10

Faria NR, Hodges-Mameletzis I, Silva JC, Rodés B, Erasmus S, Paolucci S, Ruelle J, Pieniazek D, Taveira N, Treviño A, Gonçalves MF, Jallow S, Xu L, Camacho RJ, Soriano V, Goubau P, Sousa JD, Vandamme AM, Suchard MA, Lemey P

The phylogeographic footprint of colonial history in the global dispersal of HIV-2 group A, The Journal of general virology. 2012 Jan 04

Sahl JW, Rasko DA

Analysis of the global transcriptional profiles of enterotoxigenic Escherichia coli (ETEC) isolate E24377A, Infection and immunity. 2012 Jan 03