Publications - Publications 2014

Subashchandrabose S, Hazen TH, Brumbaugh AR, Himpsl SD, Smith SN, Ernst RD, Rasko DA, Mobley HL

Host-specific induction of Escherichia coli fitness genes during human urinary tract infection, Proceedings of the National Academy of Sciences of the United States of America. 2014 Dec 08

Chibucos MC, Zweifel AE, Herrera JC, Meza W, Eslamfam S, Uetz P, Siegele DA, Hu JC, Giglio MG

An ontology for microbial phenotypes, BMC microbiology. 2014 Nov 30

O'Connor TD, Fu W, , , Turner E, Mychaleckyj JC, Logsdon B, Auer P, Carlson CS, Leal SM, Smith JD, Rieder MJ, Bamshad MJ, Nickerson DA, Akey JM

Rare variation facilitates inferences of fine-scale population structure in humans, Molecular biology and evolution. 2014 Nov 21

Curtis MM, Russell R, Moreira CG, Adebesin AM, Wang C, Williams NS, Taussig R, Stewart D, Zimmern P, Lu B, Prasad RN, Zhu C, Rasko DA, Huntley JF, Falck JR, Sperandio V

QseC Inhibitors as an Antivirulence Approach for Gram-Negative Pathogens, mBio. 2014 Nov 11

von Mentzer A, Connor TR, Wieler LH, Semmler T, Iguchi A, Thomson NR, Rasko DA, Joffre E, Corander J, Pickard D, Wiklund G, Svennerholm AM, Sjöling A, Dougan G

Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution, Nature genetics. 2014 Nov 10

Eppinger M, Pearson T, Koenig SS, Pearson O, Hicks N, Agrawal S, Sanjar F, Galens K, Daugherty S, Crabtree J, Hendriksen RS, Price LB, Upadhyay BP, Shakya G, Fraser CM, Ravel J, Keim PS

Genomic epidemiology of the haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic, mBio. 2014 Nov 04

Kibbe WA, Arze C, Felix V, Mitraka E, Bolton E, Fu G, Mungall CJ, Binder JX, Malone J, Vasant D, Parkinson H, Schriml LM

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data, Nucleic acids research. 2014 Oct 27

Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J, , White O

Advancing the microbiome research community, Cell. 2014 Oct 11

Sivapalasingam S, McClelland RS, Ravel J, Ahmed A, Cleland CM, Gajer P, Mwamzaka M, Marshed F, Shafi J, Masese L, Fajans M, Anderson ME, Jaoko W, Kurth AE

An Effective Intervention to Reduce Intravaginal Practices Among HIV-1 Uninfected Kenyan Women, AIDS research and human retroviruses. 2014 Sep 29

Ternes AM, Fielding J, Corben LA, White OB, Bradshaw JL, Hocking DR, Georgiou-Karistianis N

Movement planning and online control in multiple sclerosis: assessment using a fitts law reciprocal aiming task, Cognitive and behavioral neurology : official journal of the Society for Behavioral and Cognitive Neurology. 2014 Sep 20

Kembel SW, O'Connor TK, Arnold HK, Hubbell SP, Wright SJ, Green JL

Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest, Proceedings of the National Academy of Sciences of the United States of America. 2014 Sep 15

Tallon LJ, Liu X, Bennuru S, Chibucos MC, Godinez A, Ott S, Zhao X, Sadzewicz L, Fraser CM, Nutman TB, Dunning Hotopp JC

Single molecule sequencing and genome assembly of a clinical specimen of Loa loa, the causative agent of loiasis, BMC genomics. 2014 Sep 12

Fuhrman BJ, Spencer Feigelson H, Flores R, Gail MH, Xu X, Ravel J, Goedert JJ

Associations of the Fecal Microbiome With Urinary Estrogens and Estrogen Metabolites in Postmenopausal Women, The Journal of clinical endocrinology and metabolism. 2014 Sep 11

O'Connor TR, Bailey TL

Creating and validating cis-regulatory maps of tissue-specific gene expression regulation, Nucleic acids research. 2014 Sep 08

Vasicek EM, Berkow EL, Bruno VM, Mitchell AP, Wiederhold NP, Barker KS, Rogers PD

Disruption of the Transcriptional Regulator Cas5 Results in Enhanced Killing of Candida albicans by Fluconazole, Antimicrobial agents and chemotherapy. 2014 Sep 02

Ioannidis P, Lu Y, Kumar N, Creasy T, Daugherty S, Chibucos MC, Orvis J, Shetty A, Ott S, Flowers M, Sengamalay N, Tallon LJ, Pick L, Hotopp JC

Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys, BMC genomics. 2014 Aug 29

Brotman RM, He X, Gajer P, Fadrosh D, Sharma E, Mongodin EF, Ravel J, Glover ED, Rath JM

Association between cigarette smoking and the vaginal microbiota: a pilot study, BMC infectious diseases. 2014 Aug 28

Hoffmann DE, Fraser CM, Palumbo F, Ravel J, Rowthorn V, Schwartz J

Probiotics: achieving a better regulatory fit, Food and drug law journal. 2014 Aug 28

Liu L, Zhou W, Cheng CT, Ren X, Somlo G, Fong MY, Chin AR, Li H, Yu Y, Xu Y, O'Connor ST, O'Connor TR, Ann DK, Stark JM, Wang SE

TGFbeta Induces 'BRCAness' and Sensitivity to PARP Inhibition in Breast Cancer by Regulating DNA Repair Genes, Molecular cancer research : MCR. 2014 Aug 07

Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PS, Chun J, Colwell RR, Danchin A, Dawyndt P, Dedeurwaerdere T, DeLong EF, Detter JC, De Vos P, Donohue TJ, Dong XZ, Ehrlich DS, Fraser C, Gibbs R, Gilbert J, Gilna P, Glöckner FO, Jansson JK, Keasling JD, Knight R, Labeda D, Lapidus A, Lee JS, Li WJ, Ma J, Markowitz V, Moore ER, Morrison M, Meyer F, Nelson KE, Ohkuma M, Ouzounis CA, Pace N, Parkhill J, Qin N, Rossello-Mora R, Sikorski J, Smith D, Sogin M, Stevens R, Stingl U, Suzuki K, Taylor D, Tiedje JM, Tindall B, Wagner M, Weinstock G, Weissenbach J, White O, Wang J, Zhang L, Zhou YG, Field D, Whitman WB, Garrity GM, Klenk HP

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains, PLoS biology. 2014 Aug 05

Thompson A, Devine S, Kattan M, Muir A

Prediction of treatment week eight response & sustained virologic response in patients treated with boceprevir plus peginterferon alfa and ribavirin, PloS one. 2014 Aug 01

Crabtree J, Agrawal S, Mahurkar A, Myers GS, Rasko DA, White O

Circleator: Flexible Circular Visualization of Genome-Associated Data with BioPerl and SVG, Bioinformatics (Oxford, England). 2014 Jul 29

Yeruva L, Myers GS, Spencer N, Creasy HH, Adams NE, Maurelli AT, McChesney GR, Cleves MA, Ravel J, Bowlin A, Rank RG

Erratum for Yeruva et al., Early MicroRNA Expression Profile as a Prognostic Biomarker for the Development of Pelvic Inflammatory Disease in a Mouse Model of Chlamydial Genital Infection, mBio. 2014 Jul 29

Doi Y, Hazen TH, Boitano M, Tsai YC, Clark TA, Korlach J, Rasko DA

Whole Genome Assembly of Klebsiella pneumoniae Co-Producing NDM-1 and OXA-232 Carbapenemases Using Single-Molecule, Real-Time Sequencing, Antimicrobial agents and chemotherapy. 2014 Jul 28

Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M

Standardized description of scientific evidence using the Evidence Ontology (ECO), Database : the journal of biological databases and curation. 2014 Jul 22

Khmaladze E, Birdsell DN, Naumann AA, Hochhalter CB, Seymour ML, Nottingham R, Beckstrom-Sternberg SM, Beckstrom-Sternberg J, Nikolich MP, Chanturia G, Zhgenti E, Zakalashvili M, Malania L, Babuadze G, Tsertsvadze N, Abazashvili N, Kekelidze M, Tsanava S, Imnadze P, Ganz HH, Getz WM, Pearson O, Gajer P, Eppinger M, Ravel J, Wagner DM, Okinaka RT, Schupp JM, Keim P, Pearson T

Phylogeography of Bacillus anthracis in the Country of Georgia Shows Evidence of Population Structuring and Is Dissimilar to Other Regional Genotypes, PloS one. 2014 Jul 21

Mirmonsef P, Hotton AL, Gilbert D, Burgad D, Landay A, Weber KM, Cohen M, Ravel J, Spear GT

Free Glycogen in Vaginal Fluids Is Associated with Lactobacillus Colonization and Low Vaginal pH, PloS one. 2014 Jul 17

Franz E, Delaquis P, Morabito S, Beutin L, Gobius K, Rasko DA, Bono J, French N, Osek J, Lindstedt BA, Muniesa M, Manning S, LeJeune J, Callaway T, Beatson S, Eppinger M, Dallman T, Forbes KJ, Aarts H, Pearl DL, Gannon VP, Laing CR, Strachan NJ

Exploiting the explosion of information associated with whole genome sequencing to tackle Shiga toxin-producing Escherichia coli (STEC) in global food production systems, International journal of food microbiology. 2014 Jul 11

Di L, Pagan PE, Packer D, Martin CL, Akther S, Ramrattan G, Mongodin EF, Fraser CM, Schutzer SE, Luft BJ, Casjens SR, Qiu WG

BorreliaBase: a phylogeny-centered browser of Borrelia genomes, BMC bioinformatics. 2014 Jul 03

Neuwald AF

Protein domain hierarchy Gibbs sampling strategies, Statistical applications in genetics and molecular biology. 2014 Jul 02

Ternes AM, Fielding J, Addamo PK, White O, Georgiou-Karistianis N

Concurrent motor and cognitive function in multiple sclerosis: a motor overflow and motor stability study, Cognitive and behavioral neurology : official journal of the Society for Behavioral and Cognitive Neurology. 2014 Jun 27

Yeruva L, Myers GS, Spencer N, Creasy HH, Adams NE, Maurelli AT, McChesney GR, Cleves MA, Ravel J, Bowlin A, Rank RG

Early microRNA expression profile as a prognostic biomarker for the development of pelvic inflammatory disease in a mouse model of chlamydial genital infection, mBio. 2014 Jun 24

Lo Re V, Wang L, Devine S, Baser O, Olufade T

Hepatic Decompensation in Patients With HIV/Hepatitis B Virus (HBV)/Hepatitis C Virus (HCV) Triple Infection Versus HIV/HCV Coinfection and the Effect of Anti-HBV Nucleos(t)ide Therapy, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2014 Jun 18

Brotman RM, Shardell MD, Gajer P, Tracy JK, Zenilman JM, Ravel J, Gravitt PE

Interplay Between the Temporal Dynamics of the Vaginal Microbiota and Human Papillomavirus Detection, The Journal of infectious diseases. 2014 Jun 18

Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH

Standardized metadata for human pathogen/vector genomic sequences, PloS one. 2014 Jun 17

Hazen TH, Humphrys MS, Ochieng JB, Parsons M, Bopp CA, O'Reilly CE, Mintz E, Rasko DA

Draft Genome Sequences of Nine Enteropathogenic Escherichia coli Strains from Kenya, Genome announcements. 2014 Jun 12

Hazen TH, Zhao L, Boutin MA, Stancil A, Robinson G, Harris AD, Rasko DA, Johnson JK

Comparative Genomics of an IncA/C Multidrug Resistance Plasmid from Escherichia coli and Klebsiella Isolates from Intensive Care Unit Patients and the Utility of Whole-Genome Sequencing in Health Care Settings, Antimicrobial agents and chemotherapy. 2014 Jun 09

Hosgood HD, Sapkota AR, Rothman N, Rohan T, Hu W, Xu J, Vermeulen R, He X, White JR, Wu G, Wei F, Mongodin EF, Lan Q

The potential role of lung microbiota in lung cancer attributed to household coal burning exposures, Environmental and molecular mutagenesis. 2014 Jun 03

Jacobs AC, Thompson MG, Black CC, Kessler JL, Clark LP, McQueary CN, Gancz HY, Corey BW, Moon JK, Si Y, Owen MT, Hallock JD, Kwak YI, Summers A, Li CZ, Rasko DA, Penwell WF, Honnold CL, Wise MC, Waterman PE, Lesho EP, Stewart RL, Actis LA, Palys TJ, Craft DW, Zurawski DV

AB5075, a Highly Virulent Isolate of Acinetobacter baumannii, as a Model Strain for the Evaluation of Pathogenesis and Antimicrobial Treatments, mBio. 2014 May 27

Romero R, Hassan SS, Gajer P, Tarca AL, Fadrosh DW, Bieda J, Chaemsaithong P, Miranda J, Chaiworapongsa T, Ravel J

The vaginal microbiota of pregnant women who subsequently have spontaneous preterm labor and delivery and those with a normal delivery at term, Microbiome. 2014 May 27

Jackson HT, Mongodin EF, Davenport KP, Fraser CM, Sandler AD, Zeichner SL

Culture-independent evaluation of the appendix and rectum microbiomes in children with and without appendicitis, PloS one. 2014 Apr 23

Hocking DR, Corben LA, Fielding J, Cremer PD, Millist L, White OB, Delatycki MB

Saccade reprogramming in Friedreich ataxia reveals impairments in the cognitive control of saccadic eye movement, Brain and cognition. 2014 Apr 19

Romero R, Hassan SS, Gajer P, Tarca AL, Fadrosh DW, Nikita L, Galuppi M, Lamont RF, Chaemsaithong P, Miranda J, Chaiworapongsa T, Ravel J

Correction: The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women, Microbiome. 2014 Apr 15

Feigelson HS, Bischoff K, Ardini MA, Ravel J, Gail MH, Flores R, Goedert JJ

Feasibility of self-collection of fecal specimens by randomly sampled women for health-related studies of the gut microbiome, BMC research notes. 2014 Apr 01

Sahl JW, Caporaso JG, Rasko DA, Keim P

The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes, PeerJ. 2014 Apr 01

O'Connor TE, Carpenter HE, Bidari S, Waters MF, Hedna VS

Role of inflammatory markers in Takayasu arteritis disease monitoring, BMC neurology. 2014 Mar 28

Liggett SB, Bochkov YA, Pappas T, Lemanske RF, Gern JE, Sengamalay N, Zhao X, Su Q, Fraser CM, Palmenberg AC

Genome sequences of rhinovirus C isolates from wisconsin pediatric respiratory studies, Genome announcements. 2014 Mar 27

Liggett SB, Bochkov YA, Pappas T, Lemanske RF, Gern JE, Sengamalay N, Zhao X, Su Q, Fraser CM, Palmenberg AC

Genome sequences of rhinovirus B isolates from wisconsin pediatric respiratory studies, Genome announcements. 2014 Mar 27

Liggett SB, Bochkov YA, Pappas T, Lemanske RF, Gern JE, Sengamalay N, Zhao X, Su Q, Fraser CM, Palmenberg AC

Genome sequences of rhinovirus a isolates from wisconsin pediatric respiratory studies, Genome announcements. 2014 Mar 27

Hye RJ, Peden EK, O'Connor TP, Browne BJ, Dixon BS, Schanzer AS, Jensik SC, Dember LM, Jaff MR, Burke SK

Human type I pancreatic elastase treatment of arteriovenous fistulas in patients with chronic kidney disease, Journal of vascular surgery. 2014 Mar 27

Lacoste S, Bhatia R, Bhatia S, O'Connor TR

Granulocytes affect double-strand break repair assays in primary human lymphocytes, PloS one. 2014 Mar 25

Montalvo NF, Davis J, Vicente J, Pittiglio R, Ravel J, Hill RT

Integration of culture-based and molecular analysis of a complex sponge-associated bacterial community, PloS one. 2014 Mar 11

Ravel J, Wommack KE

All hail reproducibility in microbiome research, Microbiome. 2014 Mar 07

Meadow JF, Altrichter AE, Kembel SW, Moriyama M, O'Connor TK, Womack AM, Brown GZ, Green JL, Bohannan BJ

Bacterial communities on classroom surfaces vary with human contact, Microbiome. 2014 Mar 07

Tettelin H, Davidson RM, Agrawal S, Aitken ML, Shallom S, Hasan NA, Strong M, Nogueira de Moura VC, De Groote MA, Duarte RS, Hine E, Parankush S, Su Q, Daugherty SC, Fraser CM, Brown-Elliott BA, Wallace RJ, Holland SM, Sampaio EP, Olivier KN, Jackson M, Zelazny AM

High-level Relatedness among Mycobacterium abscessus subsp. massiliense Strains from Widely Separated Outbreaks, Emerging infectious diseases. 2014 Feb 25

Fadrosh DW, Ma B, Gajer P, Sengamalay N, Ott S, Brotman RM, Ravel J

An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform, Microbiome. 2014 Feb 24

Neuwald AF

Evaluating, Comparing, and Interpreting Protein Domain Hierarchies, Journal of computational biology : a journal of computational molecular cell biology. 2014 Feb 21

Mohawk KL, Poly F, Sahl JW, Rasko DA, Guerry P

High Frequency, Spontaneous motA Mutations in Campylobacter jejuni Strain 81-176, PloS one. 2014 Feb 18

Field D, Sterk P, Kottmann R, De Smet JW, Amaral-Zettler L, Cochrane G, Cole JR, Davies N, Dawyndt P, Garrity GM, Gilbert JA, Glöckner FO, Hirschman L, Klenk HP, Knight R, Kyrpides N, Meyer F, Karsch-Mizrachi I, Morrison N, Robbins R, San Gil I, Sansone S, Schriml L, Tatusova T, Ussery D, Yilmaz P, White O, Wooley J, Caporaso G

Genomic standards consortium projects, Standards in genomic sciences. 2014 Feb 15

Neuwald AF

A Bayesian Sampler for Optimization of Protein Domain Hierarchies, Journal of computational biology : a journal of computational molecular cell biology. 2014 Feb 04

Romero R, Hassan SS, Gajer P, Tarca AL, Fadrosh DW, Nikita L, Galuppi M, Lamont RF, Chaemsaithong P, Miranda J, Chaiworapongsa T, Ravel J

The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women, Microbiome. 2014 Feb 03

Luo Q, Kumar P, Vickers TJ, Sheikh A, Lewis WG, Rasko DA, Sistrunk J, Fleckenstein JM

Enterotoxigenic Escherichia coli Secretes a Highly Conserved Mucin-Degrading Metalloprotease To Effectively Engage Intestinal Epithelial Cells, Infection and immunity. 2014 Jan 30

Kembel SW, Meadow JF, O'Connor TK, Mhuireach G, Northcutt D, Kline J, Moriyama M, Brown GZ, Bohannan BJ, Green JL

Architectural design drives the biogeography of indoor bacterial communities, PloS one. 2014 Jan 29

Etienne KA, Chibucos MC, Su Q, Orvis J, Daugherty S, Ott S, Sengamalay NA, Fraser CM, Lockhart SR, Bruno VM

Draft Genome Sequence of Mortierella alpina Isolate CDC-B6842, Genome announcements. 2014 Jan 23

Levine JA, Hansen AM, Michalski JM, Hazen TH, Rasko DA, Kaper JB

H-NST Induces LEE Expression and the Formation of Attaching and Effacing Lesions in Enterohemorrhagic Escherichia coli, PloS one. 2014 Jan 21

Ravel J, Wommack KE

Thank you to Microbiome's peer reviewers in 2013, Microbiome. 2014 Jan 20

Devine S, Markewitz D, Hendrix P, Coleman D

Soil Aggregates and Associated Organic Matter under Conventional Tillage, No-Tillage, and Forest Succession after Three Decades, PloS one. 2014 Jan 20

Dutta SK, Girotra M, Garg S, Dutta A, von Rosenvinge EC, Maddox C, Song Y, Bartlett JG, Vinayek R, Fricke WF

Efficacy of Combined Jejunal and Colonic Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection, Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association. 2014 Jan 16

Sait M, Livingstone M, Clark EM, Wheelhouse N, Spalding L, Markey B, Magnino S, Lainson FA, Myers GS, Longbottom D

Genome sequencing and comparative analysis of three Chlamydia pecorum strains associated with different pathogenic outcomes, BMC genomics. 2014 Jan 14

Sanjar F, Hazen TH, Shah SM, Koenig SS, Agrawal S, Daugherty S, Sadzewicz L, Tallon LJ, Mammel MK, Feng P, Soderlund R, Tarr PI, Debroy C, Dudley EG, Cebula TA, Ravel J, Fraser CM, Rasko DA, Eppinger M

Genome Sequence of Escherichia coli O157:H7 Strain 2886-75, Associated with the First Reported Case of Human Infection in the United States, Genome announcements. 2014 Jan 09

Marsan D, Wommack KE, Ravel J, Chen F

Draft Genome Sequence of Synechococcus sp. Strain CB0101, Isolated From the Chesapeake Bay Estuary, Genome announcements. 2014 Jan 09

Hazen TH, Zhao L, Sahl JW, Robinson G, Harris AD, Rasko DA, Johnson JK

Characterization of Klebsiella sp. 10982, a colonizer of humans that contains novel antibiotic resistance alleles and exhibits genetic similarities to plant and clinical Klebsiella isolates, Antimicrobial agents and chemotherapy. 2014 Jan 06