Publications

Selected publications supported by sequence data generated and/or analysis performed by the GRC:

G. Yu, N. Hu, L. Wang et al., Gastric microbiota features associated with cancer risk factors and clinical outcomes: A pilot study in gastric cardia cancer patients from Shanxi, China. Int J Cancer,  doi:10.1002/ijc.30700 (2017).

B. Shannon, T. J. Yi, S. Perusini et al., Association of HPV infection and clearance with cervicovaginal immunology and the vaginal microbiota. Mucosal Immunol,  doi:10.1038/mi.2016.129 (2017).

B. Shannon, P. Gajer, T. J. Yi et al., Distinct effects of the cervico-vaginal microbiota and herpes simplex type 2 infection on female genital tract immunology. J Infect Dis,  doi:10.1093/infdis/jix088 (2017).

J. W. Sahl, J. R. Sistrunk, N. I. Baby et al., Insights into enterotoxigenic Escherichia coli diversity in Bangladesh utilizing genomic epidemiology. Sci Rep 7, 3402 doi:10.1038/s41598-017-03631-x (2017).

E. P. Price, M. L. Smith, E. E. Paxinos et al., Whole-Genome Sequences of Burkholderia pseudomallei Isolates Exhibiting Decreased Meropenem Susceptibility. Genome Announc 5,  doi:10.1128/genomeA.00053-17 (2017).

A. Panda, S. Nagaraj, X. Zhao, H. Tettelin, L. J. DeTolla, Complete Genome Sequences of Mycobacterium kansasii Strains Isolated from Rhesus Macaques. Genome Announc 5,  doi:10.1128/genomeA.00187-17 (2017).

R. G. Nowak, S. M. Bentzen, J. Ravel et al., Rectal microbiota among HIV-uninfected, untreated HIV, and treated HIV-infected men who have sex with men (MSM) in Nigeria. Aids,  doi:10.1097/QAD.0000000000001409 (2017).

M. Lin, K. Bachman, Z. Cheng et al., Analysis of complete genome sequence and major surface antigens of Neorickettsia helminthoeca, causative agent of salmon poisoning disease. Microb Biotechnol,  doi:10.1111/1751-7915.12731 (2017).

T. H. Hazen, J. Michalski, Q. Luo et al., Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic E. coli. Sci Rep 7, 3513 doi:10.1038/s41598-017-03489-z (2017).

J. C. Dunning Hotopp, B. E. Slatko, J. M. Foster, Targeted Enrichment and Sequencing of Recent Endosymbiont-Host Lateral Gene Transfers. Sci Rep 7, 857 doi:10.1038/s41598-017-00814-4 (2017).

A. Dara, E. F. Drabek, M. A. Travassos et al., New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali. Genome Med 9, 30 doi:10.1186/s13073-017-0422-4 (2017).

J. Chopyk, S. Chattopadhyay, P. Kulkarni et al., Temporal Variations in Cigarette Tobacco Bacterial Community Composition and Tobacco-Specific Nitrosamine Content Are Influenced by Brand and Storage Conditions. Frontiers in microbiology 8, 358 doi:10.3389/fmicb.2017.00358 (2017).

L. L. Bradford, M. Chibucos, B. Ma, V. Bruno, J. Ravel, Vaginal Candida spp. genomes from women with vulvovaginal candidiasis. Pathog Dis,  doi:10.1093/femspd/ftx061 (2017).

G. Yu, M. H. Gail, D. Consonni et al., Characterizing human lung tissue microbiota and its relationship to epidemiological and clinical features. Genome Biol 17, 163 doi:10.1186/s13059-016-1021-1 (2016).

L. Wallace, S. C. Daugherty, S. Nagaraj et al., Use of Comparative Genomics To Characterize the Diversity of Acinetobacter baumannii Surveillance Isolates in a Health Care Institution. Antimicrob Agents Chemother 60, 5933-5941 doi:10.1128/AAC.00477-16 (2016).

S. Riazuddin, M. Hussain, A. Razzaq et al., Exome sequencing of Pakistani consanguineous families identifies 30 novel candidate genes for recessive intellectual disability. Mol Psychiatry,  doi:10.1038/mp.2016.109 (2016).

M. Oren, M. A. Barela Hudgell, B. D’Allura et al., Short tandem repeats, segmental duplications, gene deletion, and genomic instability in a rapidly diversified immune gene family. BMC genomics 17, 900 doi:10.1186/s12864-016-3241-x (2016).

S. R. Leonard, M. K. Mammel, D. A. Rasko, D. W. Lacher, Hybrid Shiga Toxin-Producing and Enterotoxigenic Escherichia sp. Cryptic Lineage 1 Strain 7v Harbors a Hybrid Plasmid. Applied and environmental microbiology 82, 4309-4319 doi:10.1128/AEM.01129-16 (2016).

T. A. Hooven, A. J. Catomeris, L. H. Akabas et al., The essential genome of Streptococcus agalactiae. BMC genomics 17, 406 doi:10.1186/s12864-016-2741-z (2016).

T. H. Hazen, S. R. Leonard, K. A. Lampel et al., Investigating the Relatedness of Enteroinvasive Escherichia coli to Other E. coli and Shigella Isolates by Using Comparative Genomics. Infection and immunity 84, 2362-2371 doi:10.1128/IAI.00350-16 (2016).

F. Del Canto, M. O’Ryan, M. Pardo et al., Chaperone-Usher Pili Loci of Colonization Factor-Negative Human Enterotoxigenic Escherichia coli. Front Cell Infect Microbiol 6, 200 doi:10.3389/fcimb.2016.00200 (2016).

M. C. Chibucos, S. Soliman, T. Gebremariam et al., An integrated genomic and transcriptomic survey of mucormycosis-causing fungi. Nat Commun 7, 12218 doi:10.1038/ncomms12218 (2016).

K. A. Blanchette, A. T. Shenoy, J. Milner, 2nd et al., Neuraminidase A-Exposed Galactose Promotes Streptococcus pneumoniae Biofilm Formation during Colonization. Infection and immunity 84, 2922-2932 doi:10.1128/IAI.00277-16 (2016).

E. P. Szymanski, J. M. Leung, C. J. Fowler et al., Pulmonary Nontuberculous Mycobacterial Infection: A Multisystem Multigenic Disease. Am J Respir Crit Care Med,  doi:10.1164/rccm.201502-0387OC (2015).

H. M. Simpson, R. Z. Khan, C. Song et al., Concurrent Mutations in ATM and Genes Associated with Common gamma Chain Signaling in Peripheral T Cell Lymphoma. PLoS One 10, e0141906 doi:10.1371/journal.pone.0141906 (2015).

F. Sanjar, B. Rusconi, T. H. Hazen et al., Characterization of the pathogenome and phylogenomic classification of enteropathogenic Escherichia coli of the O157:non-H7 serotypes. Pathog Dis,  doi:10.1093/femspd/ftv033 (2015).

J. W. Sahl, J. R. Sistrunk, C. M. Fraser et al., Examination of the Enterotoxigenic Escherichia coli Population Structure during Human Infection. MBio 6,  doi:10.1128/mBio.00501-15 (2015).

J. W. Sahl, C. R. Morris, J. Emberger et al., Defining the phylogenomics of Shigella species: A pathway to diagnostics. J Clin Microbiol,  doi:10.1128/JCM.03527-14 (2015).

R. Rosini, E. Campisi, M. De Chiara et al., Genomic analysis reveals the molecular basis for capsule loss in the group B streptococcus population. PLoS One 10, e0125985 doi:10.1371/journal.pone.0125985 (2015).

J. G. Rodriguez, C. Pino, A. Tauch, M. I. Murcia, Complete Genome Sequence of the Clinical Beijing-Like Strain Mycobacterium tuberculosis 323 Using the PacBio Real-Time Sequencing Platform. Genome Announc 3,  doi:10.1128/genomeA.00371-15 (2015).

I. K. Park, A. P. Hsu, H. Tettelin et al., Clonal diversification, changes in lipid traits and colony morphology in Mycobacterium abscessus clinical isolates. J Clin Microbiol,  doi:10.1128/JCM.02015-15 (2015).

B. M. Nugent, C. L. Wright, A. C. Shetty et al., Brain feminization requires active repression of masculinization via DNA methylation. Nature neuroscience,  doi:10.1038/nn.3988 (2015).

H. Mendes-Soares, V. Krishnan, M. L. Settles et al., Fine-scale analysis of 16S rRNA sequences reveals a high level of taxonomic diversity among vaginal Atopobium spp. Pathog Dis,  doi:10.1093/femspd/ftv020 (2015).

Y. Liu, A. C. Shetty, J. A. Schwartz et al., New signaling pathways govern the host response to C. albicans infection in various niches. Genome research,  doi:10.1101/gr.187427.114 (2015).

M. Jelocnik, N. L. Bachmann, B. Kaltenboeck et al., Genetic diversity in the plasticity zone and the presence of the chlamydial plasmid differentiates Chlamydia pecorum strains from pigs, sheep, cattle, and koalas. BMC genomics 16, 893 doi:10.1186/s12864-015-2053-8 (2015).

T. H. Hazen, P. C. Lafon, N. M. Garrett et al., Insights into the environmental reservoir of pathogenic Vibrio parahaemolyticus using comparative genomics. Frontiers in microbiology 6, 204 doi:10.3389/fmicb.2015.00204 (2015).

T. H. Hazen, S. C. Daugherty, A. Shetty et al., RNA-Seq analysis of isolate- and growth phase-specific differences in the global transcriptomes of enteropathogenic Escherichia coli prototype isolates. Frontiers in microbiology 6, 569 doi:10.3389/fmicb.2015.00569 (2015).

B. E. Goldberg, E. F. Mongodin, C. E. Jones et al., The Oral Bacterial Communities of Children with Well-Controlled HIV Infection and without HIV Infection. PLoS One 10, e0131615 doi:10.1371/journal.pone.0131615 (2015).

J. J. Goedert, Y. Gong, X. Hua et al., Fecal Microbiota Characteristics of Patients with Colorectal Adenoma Detected by Screening: A Population-based Study. EBioMedicine 2, 597-603 doi:10.1016/j.ebiom.2015.04.010 (2015).

E. A. Eloe-Fadrosh, A. Brady, J. Crabtree et al., Functional Dynamics of the Gut Microbiome in Elderly People during Probiotic Consumption. MBio 6,  doi:10.1128/mBio.00231-15 (2015).

R. Elkon, B. Milon, L. Morrison et al., RFX transcription factors are essential for hearing in mice. Nat Commun 6, 8549 doi:10.1038/ncomms9549 (2015).

M. S. Donnenberg, T. H. Hazen, T. H. Farag et al., Bacterial Factors Associated with Lethal Outcome of Enteropathogenic Escherichia coli Infection: Genomic Case-Control Studies. PLoS neglected tropical diseases 9, e0003791 doi:10.1371/journal.pntd.0003791 (2015).

E. O. Dareng, B. Ma, A. O. Famooto et al., Prevalent high-risk HPV infection and vaginal microbiota in Nigerian women. Epidemiology and infection, 1-15 doi:10.1017/S0950268815000965 (2015).

M. C. Chibucos, K. A. Etienne, J. Orvis et al., The genome sequence of four isolates from the family Lichtheimiaceae. Pathog Dis,  doi:10.1093/femspd/ftv024 (2015).

S. T. Chancey, X. Bai, N. Kumar et al., Transcriptional Attenuation Controls Macrolide Inducible Efflux and Resistance in Streptococcus pneumoniae and in Other Gram-Positive Bacteria Containing mef/mel(msr(D)) Elements. PLoS One 10, e0116254 doi:10.1371/journal.pone.0116254 (2015).

S. T. Chancey, S. Agrawal, M. R. Schroeder et al., Composite mobile genetic elements disseminating macrolide resistance in Streptococcus pneumoniae. Frontiers in microbiology 6, 26 doi:10.3389/fmicb.2015.00026 (2015).

J. C. Castillo, T. Creasy, P. Kumari et al., Drosophila anti-nematode and antibacterial immune regulators revealed by RNA-Seq. BMC genomics 16, 519 doi:10.1186/s12864-015-1690-2 (2015).

B. L. Cantarel, E. Waubant, C. Chehoud et al., Gut Microbiota in Multiple Sclerosis: Possible Influence of Immunomodulators. Journal of investigative medicine : the official publication of the American Federation for Clinical Research,  doi:10.1097/JIM.0000000000000192 (2015).

V. M. Bruno, A. C. Shetty, J. Yano et al., Transcriptomic Analysis of Vulvovaginal Candidiasis Identifies a Role for the NLRP3 Inflammasome. MBio 6,  doi:10.1128/mBio.00182-15 (2015).

R. A. Brady, V. M. Bruno, D. L. Burns, RNA-Seq Analysis of the Host Response to Staphylococcus aureus Skin and Soft Tissue Infection in a Mouse Model. PLoS One 10, e0124877 doi:10.1371/journal.pone.0124877 (2015).

W. Wang, B. Feng, J. Xiao et al., Cassava genome from a wild ancestor to cultivated varieties. Nat Commun 5, 5110 doi:10.1038/ncomms6110 (2014).

A. Veluchamy, X. Lin, F. Maumus et al., Corrigendum: Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum. Nat Commun 5, 3028 doi:10.1038/ncomms4028 (2014).

H. Tettelin, R. M. Davidson, S. Agrawal et al., High-level Relatedness among Mycobacterium abscessus subsp. massiliense Strains from Widely Separated Outbreaks. Emerging infectious diseases 20, 364-371 doi:10.3201/eid2003.131106 (2014).

L. J. Tallon, X. Liu, S. Bennuru et al., Single molecule sequencing and genome assembly of a clinical specimen of Loa loa, the causative agent of loiasis. BMC genomics 15, 788 doi:10.1186/1471-2164-15-788 (2014).

F. Sanjar, T. H. Hazen, S. M. Shah et al., Genome Sequence of Escherichia coli O157:H7 Strain 2886-75, Associated with the First Reported Case of Human Infection in the United States. Genome Announc 2,  doi:10.1128/genomeA.01120-13 (2014).

M. Sait, M. Livingstone, E. M. Clark et al., Genome sequencing and comparative analysis of three Chlamydia pecorum strains associated with different pathogenic outcomes. BMC genomics 15, 23 doi:10.1186/1471-2164-15-23 (2014).

Q. Luo, P. Kumar, T. J. Vickers et al., Enterotoxigenic Escherichia coli Secretes a Highly Conserved Mucin-Degrading Metalloprotease To Effectively Engage Intestinal Epithelial Cells. Infection and immunity 82, 509-521 doi:10.1128/IAI.01106-13 (2014).

S. B. Liggett, Y. A. Bochkov, T. Pappas et al., Genome sequences of rhinovirus a isolates from wisconsin pediatric respiratory studies. Genome Announc 2,  doi:10.1128/genomeA.00200-14 (2014).

S. B. Liggett, Y. A. Bochkov, T. Pappas et al., Genome sequences of rhinovirus B isolates from wisconsin pediatric respiratory studies. Genome Announc 2,  doi:10.1128/genomeA.00202-14 (2014).

S. B. Liggett, Y. A. Bochkov, T. Pappas et al., Genome sequences of rhinovirus C isolates from wisconsin pediatric respiratory studies. Genome Announc 2,  doi:10.1128/genomeA.00203-14 (2014).

L. Klasson, N. Kumar, R. Bromley et al., Extensive duplication of the Wolbachia DNA in chromosome four of Drosophila ananassae. BMC genomics 15, 1097 doi:10.1186/1471-2164-15-1097 (2014).

A. C. Jacobs, M. G. Thompson, C. C. Black et al., AB5075, a Highly Virulent Isolate of Acinetobacter baumannii, as a Model Strain for the Evaluation of Pathogenesis and Antimicrobial Treatments. MBio 5,  doi:10.1128/mBio.01076-14 (2014).

P. Ioannidis, Y. Lu, N. Kumar et al., Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys. BMC genomics 15, 738 doi:10.1186/1471-2164-15-738 (2014).

H. D. Hosgood, 3rd, A. R. Sapkota, N. Rothman et al., The potential role of lung microbiota in lung cancer attributed to household coal burning exposures. Environmental and molecular mutagenesis,  doi:10.1002/em.21878 (2014).

T. H. Hazen, L. Zhao, J. W. Sahl et al., 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. Antimicrob Agents Chemother,  doi:10.1128/AAC.01605-13 (2014).

T. H. Hazen, L. Zhao, M. A. Boutin et al., Comparative genomics of an IncA/C multidrug resistance plasmid from Escherichia coli and Klebsiella species isolated from ICU patients: the utility of whole genome sequencing in healthcare settings. Antimicrob Agents Chemother,  doi:10.1128/AAC.02573-14 (2014).

T. H. Hazen, M. S. Humphrys, J. B. Ochieng et al., Draft Genome Sequences of Nine Enteropathogenic Escherichia coli Strains from Kenya. Genome Announc 2,  doi:10.1128/genomeA.00582-14 (2014).

D. W. Fadrosh, B. Ma, P. Gajer et al., An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. Microbiome 2, 6 doi:10.1186/2049-2618-2-6 (2014).

K. A. Etienne, M. C. Chibucos, Q. Su et al., Draft Genome Sequence of Mortierella alpina Isolate CDC-B6842. Genome Announc 2,  doi:10.1128/genomeA.01180-13 (2014).

M. Eppinger, T. Pearson, S. S. Koenig et al., Genomic epidemiology of the haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic. MBio 5,  doi:10.1128/mBio.01721-14 (2014).

V. G. Dugan, S. J. Emrich, G. I. Giraldo-Calderon et al., Standardized metadata for human pathogen/vector genomic sequences. PLoS One 9, e99979 doi:10.1371/journal.pone.0099979 (2014).

M. Donati, H. Huot-Creasy, M. Humphrys et al., Genome Sequence of Chlamydia suis MD56, Isolated from the Conjunctiva of a Weaned Piglet. Genome Announc 2,  doi:10.1128/genomeA.00425-14 (2014).

S. Zubair, E. P. de Villiers, M. Younan et al., Genome Sequences of Two Pathogenic Streptococcus agalactiae Isolates from the One-Humped Camel Camelus dromedarius. Genome Announc 1,  doi:10.1128/genomeA.00515-13 (2013).

J. C. Zapata, M. Goicochea, Y. Nadai et al., Genetic variation in vitro and in vivo of an attenuated Lassa vaccine candidate. J Virol,  doi:10.1128/JVI.03035-13 (2013).

G. Yu, D. Fadrosh, B. Ma, J. Ravel, J. J. Goedert, Anal microbiota profiles in HIV-positive and HIV-negative MSM. Aids,  doi:10.1097/QAD.0000000000000154 (2013).

A. Veluchamy, X. Lin, F. Maumus et al., Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum. Nat Commun 4, 2091 doi:10.1038/ncomms3091 (2013).

S. Subashchandrabose, T. H. Hazen, D. A. Rasko, H. L. Mobley, Draft genome sequences of five recent human uropathogenic Escherichia coli isolates. Pathog Dis,  doi:10.1111/2049-632X.12059 (2013).

N. Sambuughin, X. Liu, S. Bijarnia et al., Exome sequencing reveals SCO2 mutations in a family presented with fatal infantile hyperthermia. J Hum Genet,  doi:http://www.nature.com/jhg/journal/vaop/ncurrent/suppinfo/jhg2012156s1.html (2013).

C. K. Robinson, J. Wierzchos, C. Black et al., Microbial diversity and the presence of algae in halite endolithic communities are correlated to atmospheric moisture in the hyper-arid zone of the Atacama Desert. Environ Microbiol,  doi:10.1111/1462-2920.12364 (2013).

B. R. Ravel J, Gajer P, Ma B, Nandy M, Fadrosh D, Sakamoto J, Koenig S, Fu L, Zhou X, Hickey RJ, Schwebke JR, Forney LJ, Daily temporal dynamics of vaginal microbiota before, during and after episodes of bacterial vaginosis. Microbiome 1,  (2013).

M. F. Poelchau, J. A. Reynolds, C. G. Elsik, D. L. Denlinger, P. A. Armbruster, Deep sequencing reveals complex mechanisms of diapause preparation in the invasive mosquito, Aedes albopictus. Proc Biol Sci 280, 20130143 doi:10.1098/rspb.2013.0143 (2013).

R. J. A. Poelchau M.F., Elsik C.G., Denlinger D.L., Armbruster P, Deep sequencing reveals complex mechanisms of diapuase preparation in the invasive mosquito, Aedes albopictus. Proceedings of the Royal Society of London 280,  (2013).

P. J. Planet, R. Rampersaud, S. R. Hymes et al., Genome Sequence of the Human Abscess Isolate Streptococcus intermedius BA1. Genome Announc 1,  doi:10.1128/genomeA.00117-12 (2013).

E. F. Mongodin, S. R. Casjens, J. F. Bruno et al., Inter- and intra-specific pan-genomes of Borrelia burgdorferi sensu lato: genome stability and adaptive radiation. BMC genomics 14, 693 doi:10.1186/1471-2164-14-693 (2013).

T. Magoc, S. Pabinger, S. Canzar et al., GAGE-B: An Evaluation of Genome Assemblers for Bacterial Organisms. Bioinformatics,  doi:10.1093/bioinformatics/btt273 (2013).

X. Liu, Q. Hu, S. Liu et al., Serum Antibody Repertoire Profiling Using In Silico Antigen Screen. PLoS ONE 8, e67181 doi:10.1371/journal.pone.0067181 (2013).

S. Z. Kimaro Mlacha, S. Romero-Steiner, J. C. Dunning Hotopp et al., Phenotypic, genomic, and transcriptional characterization of Streptococcus pneumoniae interacting with human pharyngeal cells. BMC genomics 14, 383 doi:10.1186/1471-2164-14-383 (2013).

E. Khurana, Y. Fu, V. Colonna et al., Integrative annotation of variants from 1092 humans: application to cancer genomics. Science 342, 1235587 doi:10.1126/science.1235587 (2013).

P. Ioannidis, K. L. Johnston, D. R. Riley et al., Extensively duplicated and transcriptionally active recent lateral gene transfer from a bacterial Wolbachia endosymbiont to its host filarial nematode Brugia malayi. BMC genomics 14, 639 doi:10.1186/1471-2164-14-639 (2013).

M. S. Humphrys, T. Creasy, Y. Sun et al., Simultaneous transcriptional profiling of bacteria and their host cells. PLoS ONE 8, e80597 doi:10.1371/journal.pone.0080597 (2013).

T. H. Hazen, J. W. Sahl, C. M. Fraser et al., Draft Genome Sequences of Three O157 Enteropathogenic Escherichia coli Isolates. Genome Announc 1,  doi:10.1128/genomeA.00516-13 (2013).

J. M. Harro, S. Daugherty, V. M. Bruno et al., Draft Genome Sequence of the Methicillin-Resistant Staphylococcus aureus Isolate MRSA-M2. Genome Announc 1,  doi:10.1128/genomeA.00037-12 (2013).

T. A. Gray, J. A. Krywy, J. Harold, M. J. Palumbo, K. M. Derbyshire, Distributive conjugal transfer in mycobacteria generates progeny with meiotic-like genome-wide mosaicism, allowing mapping of a mating identity locus. PLoS Biol 11, e1001602 doi:10.1371/journal.pbio.1001602 (2013).

W. F. Fricke, C. Maddox, Y. Song, J. S. Bromberg, Human Microbiota Characterization in the Course of Renal Transplantation. Am J Transplant,  doi:10.1111/ajt.12588 (2013).

A. Fischer, I. Santana-Cruz, M. Giglio et al., Genome Sequence of Mycoplasma feriruminatoris sp. nov., a Fast-Growing Mycoplasma Species. Genome Announc 1,  doi:10.1128/genomeA.00216-12 (2013).

M. Eppinger, S. Daugherty, S. Agrawal et al., Whole-Genome Draft Sequences of 26 Enterohemorrhagic Escherichia coli O157:H7 Strains. Genome Announc 1, e0013412 doi:10.1128/genomeA.00134-12 (2013).

E. A. Eloe-Fadrosh, D. A. Rasko, The human microbiome: from symbiosis to pathogenesis. Annual review of medicine 64, 145-163 doi:10.1146/annurev-med-010312-133513 (2013).

E. A. Eloe-Fadrosh, M. A. McArthur, A. M. Seekatz et al., Impact of oral typhoid vaccination on the human gut microbiota and correlations with s. Typhi-specific immunological responses. PLoS ONE 8, e62026 doi:10.1371/journal.pone.0062026 (2013).

A. Crits-Christoph, C. K. Robinson, T. Barnum et al., Colonization patterns of soil microbial communities in the Atacama Desert. Microbiome 1, 28 doi:10.1186/2049-2618-1-28 (2013).

M. C. Chibucos, J. Crabtree, S. Nagaraj, S. Chaturvedi, V. Chaturvedi, Draft Genome Sequences of Human Pathogenic Fungus Geomyces pannorum Sensu Lato and Bat White Nose Syndrome Pathogen Geomyces (Pseudogymnoascus) destructans. Genome Announc 1,  doi:10.1128/genomeA.01045-13 (2013).

Y. P. Chen, J. S. Pettis, Y. Zhao et al., Genome sequencing and comparative genomics of honey bee microsporidia, Nosema Apis reveal novel insights into host-parasite interactions. BMC genomics 14, 451 doi:10.1186/1471-2164-14-451 (2013).

T. G. Blanchard, S. J. Czinn, P. Correa et al., Genome sequences of 65 Helicobacter pylori strains isolated from asymptomatic individuals and patients with gastric cancer, peptic ulcer disease, or gastritis. Pathog Dis,  doi:10.1111/2049-632X.12045 (2013).

D. V. Zurawski, M. G. Thompson, C. N. McQueary et al., Genome sequences of four divergent multidrug-resistant Acinetobacter baumannii strains isolated from patients with sepsis or osteomyelitis. J Bacteriol 194, 1619-1620 doi:10.1128/JB.06749-11 (2012).

H. Tettelin, E. P. Sampaio, S. C. Daugherty et al., Genomic Insights into the Emerging Human Pathogen Mycobacterium massiliense. Journal of Bacteriology 194, 5450 doi:10.1128/jb.01200-12 (2012).

S. R. Steyert, J. W. Sahl, C. M. Fraser et al., Comparative genomics and stx phage characterization of LEE-negative Shiga toxin-producing Escherichia coli. Frontiers in Cellular and Infection Microbiology 2,  doi:10.3389/fcimb.2012.00133 (2012).

M. Sellitto, G. Bai, G. Serena et al., Proof of concept of microbiome-metabolome analysis and delayed gluten exposure on celiac disease autoimmunity in genetically at-risk infants. PLoS One 7, e33387 doi:10.1371/journal.pone.0033387 (2012).

J. W. Sahl, D. A. Rasko, Analysis of global transcriptional profiles of enterotoxigenic Escherichia coli isolate E24377A. Infection and immunity 80, 1232-1242 doi:10.1128/IAI.06138-11 (2012).

J. W. Sahl, M. N. Matalka, D. A. Rasko, Phylomark, a tool to identify conserved phylogenetic markers from whole-genome alignments. Applied and environmental microbiology 78, 4884-4892 doi:10.1128/AEM.00929-12 (2012).

J. Ravel, P. Gajer, F. Li et al., Twice-Daily Application of HIV Microbicides Alter the Vaginal Microbio. MBio 3,  doi:10.1128/mBio.00370-12 (2012).

D. A. Rasko, Clostridium difficile healthcare-associated epidemics. Nat Genet 45, 6-7 doi:10.1038/ng.2499 (2012).

E. A. Ozer, J. P. Allen, A. R. Hauser, Draft Genome Sequence of the Pseudomonas aeruginosa Bloodstream Isolate PABL056. Journal of Bacteriology 194, 5999 doi:10.1128/jb.01421-12 (2012).

N. Kumar, T. Creasy, Y. Sun et al., Efficient subtraction of insect rRNA prior to transcriptome analysis of Wolbachia-Drosophila lateral gene transfer. BMC Research Notes 5, 230 (2012).

T. H. Hazen, J. W. Sahl, J. C. Redman et al., Draft genome sequences of the diarrheagenic Escherichia coli collection. J Bacteriol 194, 3026-3027 doi:10.1128/JB.00426-12 (2012).

T. H. Hazen, G. L. Robinson, A. D. Harris, D. A. Rasko, J. K. Johnson, Genome sequence of Klebsiella oxytoca 11492-1, a nosocomial isolate possessing a FOX-5 AmpC beta-lactamase. J Bacteriol 194, 3028-3029 doi:10.1128/JB.00391-12 (2012).

N. A. Hasan, S. Y. Choi, M. Eppinger et al., Genomic diversity of 2010 Haitian cholera outbreak strains. Proceedings of the National Academy of Sciences,  doi:10.1073/pnas.1207359109 (2012).

L. Georgi, J. Johnson-Cicalese, J. Honig et al., The first genetic map of the American cranberry: exploration of synteny conservation and quantitative trait loci. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik,  doi:10.1007/s00122-012-2010-8 (2012).

C. Genomes Project, G. R. Abecasis, A. Auton et al., An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56-65 doi:10.1038/nature11632 (2012).

P. Gajer, R. M. Brotman, G. Bai et al., Temporal dynamics of the human vaginal microbiota. Science translational medicine 4, 132ra152 doi:10.1126/scitranslmed.3003605 (2012).

R. Flores, J. Shi, M. H. Gail et al., Assessment of the human faecal microbiota: II. Reproducibility and associations of 16S rRNA pyrosequences. European journal of clinical investigation 42, 855-863 doi:10.1111/j.1365-2362.2012.02659.x (2012).

R. Flores, J. Shi, B. Fuhrman et al., Fecal microbial determinants of fecal and systemic estrogens and estrogen metabolites: a cross-sectional study. Journal of translational medicine 10, 253 doi:10.1186/1479-5876-10-253 (2012).

A. M. Earl, M. Eppinger, W. F. Fricke et al., Whole-genome sequences of Bacillus subtilis and close relatives. J Bacteriol 194, 2378-2379 doi:10.1128/JB.05675-11 (2012).

S. G. Dorsey, R. M. Lovering, C. L. Renn et al., Genetic deletion of trkB.T1 increases neuromuscular function. American Journal of Physiology – Cell Physiology 302, C141-C153 doi:10.1152/ajpcell.00469.2010 (2012).

J. W. Cole, O. C. Stine, X. Liu et al., Rare Variants in Ischemic Stroke: An Exome Pilot Study. PLoS ONE 7, e35591 doi:10.1371/journal.pone.0035591 (2012).

H. Bruggemann, H. B. Lomholt, H. Tettelin, M. Kilian, CRISPR/cas loci of type II Propionibacterium acnes confer immunity against acquisition of mobile elements present in type I P. acnes. PLoS One 7, e34171 doi:10.1371/journal.pone.0034171 (2012).

G. Bai, P. Gajer, M. Nandy et al., Comparison of storage conditions for human vaginal microbiome studies. PLoS One 7, e36934 doi:10.1371/journal.pone.0036934 (2012).

J. Zan, W. F. Fricke, C. Fuqua, J. Ravel, R. T. Hill, Genome sequence of Ruegeria sp. strain KLH11, an N-acylhomoserine lactone-producing bacterium isolated from the marine sponge Mycale laxissima. J Bacteriol 193, 5011-5012 doi:10.1128/JB.05556-11 (2011).

A. J. Vogler, F. Chan, D. M. Wagner et al., Phylogeography and molecular epidemiology of Yersinia pestis in Madagascar. PLoS neglected tropical diseases 5, e1319 doi:10.1371/journal.pntd.0001319 (2011).

J. W. Sahl, H. Steinsland, J. C. Redman et al., A Comparative Genomic Analysis of Diverse Clonal Types of Enterotoxigenic Escherichia coli Reveals Pathovar-Specific Conservation. Infection and immunity 79, 950-960 doi:10.1128/iai.00932-10 (2011).

J. W. Sahl, J. K. Johnson, A. D. Harris et al., Genomic comparison of multi-drug resistant invasive and colonizing Acinetobacter baumannii isolated from diverse human body sites reveals genomic plasticity. BMC genomics 12, 291 doi:10.1186/1471-2164-12-291 (2011).

M. Rivarola, J. T. Foster, A. P. Chan et al., Castor bean organelle genome sequencing and worldwide genetic diversity analysis. PLoS One 6, e21743 doi:10.1371/journal.pone.0021743 (2011).

M. F. Poelchau, J. A. Reynolds, D. L. Denlinger, C. G. Elsik, P. A. Armbruster, A de novo transcriptome of the Asian tiger mosquito, Aedes albopictus, to identify candidate transcripts for diapause preparation. BMC genomics 12, 619 doi:10.1186/1471-2164-12-619 (2011).

S. Mojica, H. Huot Creasy, S. Daugherty et al., Genome sequence of the obligate intracellular animal pathogen Chlamydia pecorum E58. J Bacteriol 193, 3690 doi:10.1128/JB.00454-11 (2011).

Z. Liu, W. Hsiao, B. L. Cantarel, E. F. Drabek, C. Fraser-Liggett, Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data. Bioinformatics 27, 3242-3249 doi:10.1093/bioinformatics/btr547 (2011).

A. Han, J. M. Zenilman, J. H. Melendez et al., The importance of a multifaceted approach to characterizing the microbial flora of chronic wounds. Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society 19, 532-541 doi:10.1111/j.1524-475X.2011.00720.x (2011).

V. Grinblat-Huse, E. F. Drabek, H. H. Creasy et al., Genome sequences of the zoonotic pathogens Chlamydia psittaci 6BC and Cal10. J Bacteriol 193, 4039-4040 doi:JB.05277-11 [pii]

10.1128/JB.05277-11 (2011).

M. Eppinger, M. K. Mammel, J. E. Leclerc, J. Ravel, T. A. Cebula, Genomic anatomy of Escherichia coli O157:H7 outbreaks. Proceedings of the National Academy of Sciences of the United States of America 108, 20142-20147 doi:10.1073/pnas.1107176108 (2011).

M. Eppinger, M. K. Mammel, J. E. Leclerc, J. Ravel, T. A. Cebula, Genome signatures of Escherichia coli O157:H7 isolates from the bovine host reservoir. Applied and environmental microbiology 77, 2916-2925 doi:10.1128/AEM.02554-10 (2011).

M. D. Dumas, S. W. Polson, D. Ritter et al., Impacts of poultry house environment on poultry litter bacterial community composition. PLoS One 6, e24785 doi:10.1371/journal.pone.0024785 (2011).

M. S. Donia, W. F. Fricke, F. Partensky et al., Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis. Proceedings of the National Academy of Sciences of the United States of America 108, E1423-1432 doi:10.1073/pnas.1111712108 (2011).

A. Collingro, P. Tischler, T. Weinmaier et al., Unity in variety–the pan-genome of the Chlamydiae. Molecular biology and evolution 28, 3253-3270 doi:10.1093/molbev/msr161 (2011).

B. L. Cantarel, A. R. Erickson, N. C. VerBerkmoes et al., Strategies for metagenomic-guided whole-community proteomics of complex microbial environments. PLoS One 6, e27173 doi:10.1371/journal.pone.0027173 (2011).

D. E. Bessen, N. Kumar, G. S. Hall et al., Whole-genome association study on tissue tropism phenotypes in group A Streptococcus. J Bacteriol 193, 6651-6663 doi:10.1128/JB.05263-11 (2011).

S. V. Angiuoli, J. R. White, M. Matalka, O. White, W. F. Fricke, Resources and costs for microbial sequence analysis evaluated using virtual machines and cloud computing. PLoS One 6, e26624 doi:10.1371/journal.pone.0026624 (2011).

K. A. Thom, W. W. Hsiao, A. D. Harris et al., Patients with Acinetobacter baumannii bloodstream infections are colonized in the gastrointestinal tract with identical strains. American journal of infection control 38, 751-753 doi:10.1016/j.ajic.2010.03.005 (2010).

J. A. Rathe, X. Liu, L. J. Tallon, J. E. Gern, S. B. Liggett, Full-genome sequence and analysis of a novel human rhinovirus strain within a divergent HRV-A clade. Arch Virol 155, 83-87 doi:10.1007/s00705-009-0549-8 (2010).

T. A. Peterson, A. Adadey, I. Santana-Cruz et al., DMDM: domain mapping of disease mutations. Bioinformatics 26, 2458-2459 doi:10.1093/bioinformatics/btq447 (2010).

D. G. Moriel, I. Bertoldi, A. Spagnuolo et al., Identification of protective and broadly conserved vaccine antigens from the genome of extraintestinal pathogenic Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America 107, 9072-9077 doi:0915077107 [pii]

10.1073/pnas.0915077107 (2010).

M. Eppinger, P. L. Worsham, M. P. Nikolich et al., Genome sequence of the deep-rooted Yersinia pestis strain Angola reveals new insights into the evolution and pangenome of the plague bacterium. J Bacteriol 192, 1685-1699 doi:10.1128/JB.01518-09 (2010).

P. J. Turnbaugh, M. Hamady, T. Yatsunenko et al., A core gut microbiome in obese and lean twins. Nature 457, 480-484 doi:10.1038/nature07540 (2009).

M. Eppinger, Z. Guo, Y. Sebastian et al., Draft genome sequences of Yersinia pestis isolates from natural foci of endemic plague in China. J Bacteriol 191, 7628-7629 doi:10.1128/JB.01227-09 (2009).