Publications - Publications 2013

Gebremariam T, Liu M, Luo G, Bruno V, Phan QT, Waring AJ, Edwards JE, Filler SG, Yeaman MR, Ibrahim AS

CotH3 mediates fungal invasion of host cells during mucormycosis, The Journal of clinical investigation. 2013 Dec 20

Chibucos MC, Crabtree J, Nagaraj S, Chaturvedi S, Chaturvedi V

Draft Genome Sequences of Human Pathogenic Fungus Geomyces pannorum Sensu Lato and Bat White Nose Syndrome Pathogen Geomyces (Pseudogymnoascus) destructans, Genome announcements. 2013 Dec 19

Yu G, Fadrosh D, Ma B, Ravel J, Goedert JJ

Anal microbiota profiles in HIV-positive and HIV-negative MSM, AIDS (London, England). 2013 Dec 11

Zapata JC, Goicochea M, Nadai Y, Eyzaguirre LM, Carr JK, Tallon LJ, Sadzewicz L, Myers G, Fraser CM, Su Q, Djavani M, Lukashevich IS, Salvato MS

Genetic variation in vitro and in vivo of an attenuated Lassa vaccine candidate, Journal of virology. 2013 Dec 11

Humphrys MS, Creasy T, Sun Y, Shetty AC, Chibucos MC, Drabek EF, Fraser CM, Farooq U, Sengamalay N, Ott S, Shou H, Bavoil PM, Mahurkar A, Myers GS

Simultaneous transcriptional profiling of bacteria and their host cells, PloS one. 2013 Dec 04

Song Y, Garg S, Girotra M, Maddox C, von Rosenvinge EC, Dutta A, Dutta S, Fricke WF

Microbiota Dynamics in Patients Treated with Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection, PloS one. 2013 Nov 26

Fu W, O'Connor TD, Akey JM

Genetic architecture of quantitative traits and complex diseases, Current opinion in genetics & development. 2013 Nov 26

Fricke WF, Rasko DA

Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions, Nature reviews. Genetics. 2013 Nov 26

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

Enterotoxigenic Escherichia coli secrete a highly conserved mucin-degrading metalloprotease to effectively engage intestinal epithelial cells, Infection and immunity. 2013 Nov 18

Huang K, Brady A, Mahurkar A, White O, Gevers D, Huttenhower C, Segata N

MetaRef: a pan-genomic database for comparative and community microbial genomics, Nucleic acids research. 2013 Nov 06

Thaipisuttikul I, Hittle LE, Chandra R, Zangari D, Dixon CL, Garrett TA, Rasko DA, Dasgupta N, Moskowitz SM, Malmström L, Goodlett DR, Miller SI, Bishop RE, Ernst RK

A divergent Pseudomonas aeruginosa palmitoyltransferase essential for cystic fibrosis-specific lipid A, Molecular microbiology. 2013 Nov 06

Glass EM, Dribinsky Y, Yilmaz P, Levin H, Van Pelt R, Wendel D, Wilke A, Eisen JA, Huse S, Shipanova A, Sogin M, Stajich J, Knight R, Meyer F, Schriml LM

MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment, The ISME journal. 2013 Oct 24

Brotman RM, Shardell MD, Gajer P, Fadrosh D, Chang K, Silver MI, Viscidi RP, Burke AE, Ravel J, Gravitt PE

Association between the vaginal microbiota, menopause status, and signs of vulvovaginal atrophy, Menopause (New York, N.Y.). 2013 Oct 21

Liu SH, Cummings DA, Zenilman JM, Gravitt PE, Brotman RM

Characterizing the Temporal Dynamics of Human Papillomavirus DNA Detectability Using Short-Interval Sampling, Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology. 2013 Oct 15

Brotman RM, Ravel J, Bavoil PM, Gravitt PE, Ghanem KG

Microbiome, sex hormones, and immune responses in the reproductive tract: Challenges for vaccine development against sexually transmitted infections, Vaccine. 2013 Oct 14

Mongodin EF, Casjens SR, Bruno JF, Xu Y, Drabek EF, Riley DR, Cantarel BL, Pagan PE, Hernandez YA, Vargas LC, Dunn JJ, Schutzer SE, Fraser CM, Qiu WG, Luft BJ

Inter- and intra-specific pan-genomes of Borrelia burgdorferi sensu lato: genome stability and adaptive radiation, BMC genomics. 2013 Oct 10

Davis J, Fricke WF, Hamann MT, Esquenazi E, Dorrestein PC, Hill RT

Characterization of the Bacterial Community of the Chemically Defended Hawaiian Sacoglossan Elysia rufescens, Applied and environmental microbiology. 2013 Sep 06

Kolbe SC, Kilpatrick TJ, Mitchell PJ, White O, Egan GF, Fielding J

Inhibitory saccadic dysfunction is associated with cerebellar injury in multiple sclerosis, Human brain mapping. 2013 Sep 03

Enatsu R, Matsumoto R, Piao Z, O'Connor T, Horning K, Burgess RC, Bulacio J, Bingaman W, Nair DR

Cortical negative motor network in comparison with sensorimotor network: a cortico-cortical evoked potential study, Cortex; a journal devoted to the study of the nervous system and behavior. 2013 Aug 26

Nisa S, Hazen TH, Assatourian L, Nougayrède JP, Rasko DA, Donnenberg MS

In vitro evolution of an archetypal enteropathogenic Escherichia coli strain, Journal of bacteriology. 2013 Aug 02

O'Connor TD, Mundy NI

Evolutionary Modeling of Genotype-Phenotype Associations, and Application to Primate Coding and Non-coding mtDNA Rate Variation, Evolutionary bioinformatics online. 2013 Jul 28

Liu SH, Brotman RM, Zenilman JM, Gravitt PE, Cummings DA

Menstrual Cycle and Detectable Human Papillomavirus in Reproductive-age Women: A Time Series Study, The Journal of infectious diseases. 2013 Jul 24

Hovis KM, Mojica S, McDermott JE, Pedersen L, Simhi C, Rank RG, Myers GS, Ravel J, Hsia RC, Bavoil PM

Genus-optimized strategy for the identification of chlamydial type III secretion substrates, Pathogens and disease. 2013 Jul 19

Hazen TH, Sahl JW, Fraser CM, Donnenberg MS, Scheutz F, Rasko DA

Draft Genome Sequences of Three O157 Enteropathogenic Escherichia coli Isolates, Genome announcements. 2013 Jul 18

Hazen TH, Sahl JW, Fraser CM, Donnenberg MS, Scheutz F, Rasko DA

Refining the pathovar paradigm via phylogenomics of the attaching and effacing Escherichia coli, Proceedings of the National Academy of Sciences of the United States of America. 2013 Jul 15

Qian F, Chung L, Zheng W, Bruno V, Alexander RP, Wang Z, Wang X, Kurscheid S, Zhao H, Fikrig E, Gerstein M, Snyder M, Montgomery RR

Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis, Viruses. 2013 Jul 08

O'Connor TD, Kiezun A, Bamshad M, Rich SS, Smith JD, Turner E, , , Leal SM, Akey JM

Fine-scale patterns of population stratification confound rare variant association tests, PloS one. 2013 Jul 04

Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, Malig M, Hernandez-Rodriguez J, Hernando-Herraez I, Prüfer K, Pybus M, Johnstone L, Lachmann M, Alkan C, Twigg D, Petit N, Baker C, Hormozdiari F, Fernandez-Callejo M, Dabad M, Wilson ML, Stevison L, Camprubí C, Carvalho T, Ruiz-Herrera A, Vives L, Mele M, Abello T, Kondova I, Bontrop RE, Pusey A, Lankester F, Kiyang JA, Bergl RA, Lonsdorf E, Myers S, Ventura M, Gagneux P, Comas D, Siegismund H, Blanc J, Agueda-Calpena L, Gut M, Fulton L, Tishkoff SA, Mullikin JC, Wilson RK, Gut IG, Gonder MK, Ryder OA, Hahn BH, Navarro A, Akey JM, Bertranpetit J, Reich D, Mailund T, Schierup MH, Hvilsom C, Andrés AM, Wall JD, Bustamante CD, Hammer MF, Eichler EE, Marques-Bonet T

Great ape genetic diversity and population history, Nature. 2013 Jul 03

Subashchandrabose S, Hazen TH, Rasko DA, Mobley HL

Draft genome sequences of five recent human uropathogenic Escherichia coli isolates, Pathogens and disease. 2013 Jul 02

Hoffmann DE, Fortenberry JD, Ravel J

Are changes to the common rule necessary to address evolving areas of research? A case study focusing on the human microbiome project, The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics. 2013 Jun 27

Morris CR, Grassel CL, Redman JC, Sahl JW, Barry EM, Rasko DA

Utilizing transcriptomics to identify mediators of pathogenesis in Shigella flexneri: characterization of intracellular growth regulator, icgR, Infection and immunity. 2013 Jun 10

Thandapani P, O'Connor TR, Bailey TL, Richard S

Defining the RGG/RG Motif, Molecular cell. 2013 Jun 10

Kimaro Mlacha SZ, Romero-Steiner S, Hotopp JC, Kumar N, Ishmael N, Riley DR, Farooq U, Creasy TH, Tallon LJ, Liu X, Goldsmith CS, Sampson J, Carlone GM, Hollingshead SK, Scott JA, Tettelin H

Phenotypic, genomic, and transcriptional characterization of Streptococcus pneumoniae interacting with human pharyngeal cells, BMC genomics. 2013 Jun 09

Seekatz AM, Panda A, Rasko DA, Toapanta FR, Eloe-Fadrosh EA, Khan AQ, Liu Z, Shipley ST, Detolla LJ, Sztein MB, Fraser CM

Differential response of the cynomolgus macaque gut microbiota to Shigella infection, PloS one. 2013 Jun 05

Blanchard TG, Czinn SJ, Correa P, Nakazawa T, Keelan M, Morningstar L, Santana-Cruz I, Maroo A, McCracken C, Shefchek K, Daugherty S, Song Y, Fraser CM, Fricke WF

Genome sequences of 65 Helicobacter pylori strains isolated from asymptomatic individuals and patients with gastric cancer, peptic ulcer disease, or gastritis, Pathogens and disease. 2013 May 23

Deng X, Salazar JK, Frezet S, Maccannell D, Ribot EM, Fields PI, Fricke WF, Zhang W

Genome Sequence of Salmonella enterica Serotype Tennessee Strain CDC07-0191, Implicated in the 2006-2007 Multistate Food-Borne Outbreak Linked to Peanut Butter in the United States, Genome announcements. 2013 May 23

Eloe-Fadrosh EA, McArthur MA, Seekatz AM, Drabek EF, Rasko DA, Sztein MB, Fraser CM

Impact of oral typhoid vaccination on the human gut microbiota and correlations with s. Typhi-specific immunological responses, PloS one. 2013 Apr 24

Liu CM, Hungate BA, Tobian AA, Serwadda D, Ravel J, Lester R, Kigozi G, Aziz M, Galiwango RM, Nalugoda F, Contente-Cuomo TL, Wawer MJ, Keim P, Gray RH, Price LB

Male circumcision significantly reduces prevalence and load of genital anaerobic bacteria, mBio. 2013 Apr 16

Alaish SM, Smith AD, Timmons J, Greenspon J, Eyvazzadeh D, Murphy E, Shea-Donahue T, Cirimotich S, Mongodin E, Zhao A, Fasano A, Nataro JP, Cross A

Gut microbiota, tight junction protein expression, intestinal resistance, bacterial translocation and mortality following cholestasis depend on the genetic background of the host, Gut microbes. 2013 Apr 15

Schwartz JA, Olarte KT, Michalek JL, Jandu GS, Michel SL, Bruno VM

Regulation of copper toxicity by Candida albicans GPA2, Eukaryotic cell. 2013 Apr 12

Desai JV, Bruno VM, Ganguly S, Stamper RJ, Mitchell KF, Solis N, Hill EM, Xu W, Filler SG, Andes DR, Fanning S, Lanni F, Mitchell AP

Regulatory Role of Glycerol in Candida albicans Biofilm Formation, mBio. 2013 Apr 09

Chung LM, Ferguson JP, Zheng W, Qian F, Bruno V, Montgomery RR, Zhao H

Differential expression analysis for paired RNA-seq data, BMC bioinformatics. 2013 Mar 27

Lindsay B, Ochieng B, Ikumapayi U, Aliou T, Ahmed D, Li S, Panchalingam S, Levine MM, Kotloff K, Rasko DA, Morris CR, Juma J, Fields BS, Dione M, Malle D, Becker SM, Houpt ER, Nataro JP, Sommerfelt H, Pop M, Oundo J, Antonio M, Hossain A, Tamboura B, Stine OC

Quantitative Polymerase Chain Reaction for Detection of Shigella Improves Ascertainment of Shigella Burden in Children with Moderate to Severe Diarrhea in Low Income Countries, Journal of clinical microbiology. 2013 Mar 27

Desjardins CA, Cerqueira GC, Goldberg JM, Hotopp JC, Haas BJ, Zucker J, Ribeiro JM, Saif S, Levin JZ, Fan L, Zeng Q, Russ C, Wortman JR, Fink DL, Birren BW, Nutman TB

Genomics of Loa loa, a Wolbachia-free filarial parasite of humans, Nature genetics. 2013 Mar 24

Meadow JF, Bateman AC, Herkert KM, O'Connor TK, Green JL

Significant changes in the skin microbiome mediated by the sport of roller derby, PeerJ. 2013 Mar 12

von Rosenvinge EC, Song Y, White JR, Maddox C, Blanchard T, Fricke WF

Immune status, antibiotic medication and pH are associated with changes in the stomach fluid microbiota, The ISME journal. 2013 Mar 07

Eppinger M, Daugherty S, Agrawal S, Galens K, Sengamalay N, Sadzewicz L, Tallon L, Cebula TA, Mammel MK, Feng P, Soderlund R, Tarr PI, Debroy C, Dudley EG, Fraser CM, Ravel J

Whole-Genome Draft Sequences of 26 Enterohemorrhagic Escherichia coli O157:H7 Strains, Genome announcements. 2013 Feb 28

White JR, Maddox C, White O, Angiuoli SV, Fricke WF

CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota, Microbiome. 2013 Feb 04

Harro JM, Daugherty S, Bruno VM, Jabra-Rizk MA, Rasko DA, Shirtliff ME

Draft Genome Sequence of the Methicillin-Resistant Staphylococcus aureus Isolate MRSA-M2, Genome announcements. 2013 Jan 31

Planet PJ, Rampersaud R, Hymes SR, Whittier S, Della-Latta PA, Narechania A, Daugherty SC, Santana-Cruz I, Desalle R, Ravel J, Ratner AJ

Genome Sequence of the Human Abscess Isolate Streptococcus intermedius BA1, Genome announcements. 2013 Jan 31

Eloe-Fadrosh EA, Rasko DA

The human microbiome: from symbiosis to pathogenesis, Annual review of medicine. 2013 Jan 18

Enatsu R, Kubota Y, Kakisaka Y, Bulacio J, Piao Z, O'Connor T, Horning K, Mosher J, Burgess RC, Bingaman W, Nair DR

Reorganization of posterior language area in temporal lobe epilepsy: a cortico-cortical evoked potential study, Epilepsy research. 2013 Jan 11

Fu W, O'Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Rieder MJ, Altshuler D, Shendure J, Nickerson DA, Bamshad MJ, , Akey JM

Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants, Nature. 2013 Jan 10

Wommack KE, Ravel J

Microbiome, demystifying the role of microbial communities in the biosphere, Microbiome. 2013 Jan 09