Publications

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

Brady, R. A., Bruno, V. M. & Burns, D. L. 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).

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

Castillo, J. C., Creasy, T., Kumari, P. 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).

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

Chancey, S. T., Bai, X., Kumar, N. 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).

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

Goldberg, B. E., Mongodin, E. F., Jones, C. E. 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).

Hazen, T. H., Daugherty, S. C., Shetty, A. 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).

Hazen, T. H., Lafon, P. C., Garrett, N. M. 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).

Jelocnik, M., Bachmann, N. L., Kaltenboeck, B. 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).

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

Rosini, R., Campisi, E., De Chiara, M. 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).

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

Simpson, H. M., Khan, R. Z., Song, C. 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).

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

Liu, Y., Shetty, A. C., Schwartz, J. A. 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).

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

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

Goedert, J. J., Gong, Y., Hua, X. 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).

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

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

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

Donnenberg, M. S., Hazen, T. H., Farag, T. H. 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).

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

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

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

Eppinger, M., Pearson, T., Koenig, S. S. 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).

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

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

Jacobs, A. C., Thompson, M. G., Black, C. C. 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).

Sanjar, F., Hazen, T. H., Shah, S. M. 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 announcements 2, doi:10.1128/genomeA.01120-13 (2014).

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

Ioannidis, P., Lu, Y., Kumar, N. 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).

Klasson, L., Kumar, N., Bromley, R. 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).

Luo, Q., Kumar, P., Vickers, T. J. 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).

Fadrosh, D. W., Ma, B., Gajer, P. 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).

Hazen, T. H., Zhao, L., Sahl, J. W. 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. Antimicrobial agents and chemotherapy, doi:10.1128/AAC.01605-13 (2014).

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

Sait, M., Livingstone, M., Clark, E. M. 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).

Hosgood, H. D., 3rd, Sapkota, A. R., Rothman, N. 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).

Hazen, T. H., Zhao, L., Boutin, M. A. 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. Antimicrobial agents and chemotherapy, doi:10.1128/AAC.02573-14 (2014).

Tettelin, H., Davidson, R. M., Agrawal, S. 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).

Tallon, L. J., Liu, X., Bennuru, S. 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).

Chibucos, M. C., 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 1, doi:10.1128/genomeA.01045-13 (2013).

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

Eloe-Fadrosh, E. A., McArthur, M. A., Seekatz, A. M. 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).

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

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

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

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

Poelchau M.F., R. J. A., 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).

Ravel J, B. R., 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).

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

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

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

Robinson, C. K., Wierzchos, J., Black, C. 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. Environmental microbiology, doi:10.1111/1462-2920.12364 (2013).

Fricke, W. F., Maddox, C., Song, Y. & Bromberg, J. S. Human Microbiota Characterization in the Course of Renal Transplantation. American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons, doi:10.1111/ajt.12588 (2013).

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

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

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

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

Sambuughin, N., Liu, X., Bijarnia, S. et al. Exome sequencing reveals SCO2 mutations in a family presented with fatal infantile hyperthermia. Journal of human genetics, doi:10.1038/jhg.2012.156 (2013).

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

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

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

Chen, Y. P., Pettis, J. S., Zhao, Y. 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).

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

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

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

Mongodin, E. F., Casjens, S. R., Bruno, J. F. 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).

Ioannidis, P., Johnston, K. L., Riley, D. R. 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).

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

Bruggemann, H., Lomholt, H. B., 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 7, e34171, doi:10.1371/journal.pone.0034171 (2012).

Cole, J. W., Stine, O. C., Liu, X. et al. Rare variants in ischemic stroke: an exome pilot study. PloS one 7, e35591, doi:10.1371/journal.pone.0035591 (2012).

Kumar, N., Creasy, T., Sun, Y. et al. Efficient subtraction of insect rRNA prior to transcriptome analysis of Wolbachia-Drosophila lateral gene transfer. BMC research notes 5, 230, doi:10.1186/1756-0500-5-230 (2012).

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

Sellitto, M., Bai, G., Serena, G. 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).

Steyert, S. R., Sahl, J. W., Fraser, C. M. et al. Comparative Genomics and stx Phage Characterization of LEE-Negative Shiga Toxin-Producing Escherichia coli. Frontiers in cellular and infection microbiology 2, 133, doi:10.3389/fcimb.2012.00133 (2012).

Flores, R., Shi, J., Gail, M. H. 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).

Georgi, L., Johnson-Cicalese, J., Honig, J. 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).

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

Flores, R., Shi, J., Fuhrman, B. 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).

Dorsey, S. G., Lovering, R. M., Renn, C. L. et al. Genetic deletion of trkB.T1 increases neuromuscular function. American journal of physiology. Cell physiology 302, C141-153, doi:10.1152/ajpcell.00469.2010 (2012).

Sahl, J. W., Matalka, M. N. & Rasko, D. A. 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).

Hasan, N. A., Choi, S. Y., Eppinger, M. et al. Genomic diversity of 2010 Haitian cholera outbreak strains. Proceedings of the National Academy of Sciences of the United States of America 109, E2010-2017, doi:10.1073/pnas.1207359109 (2012).

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

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

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

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

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

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

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

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

Tettelin, H., Sampaio, E. P., Daugherty, S. C. et al. Genomic insights into the emerging human pathogen Mycobacterium massiliense. Journal of bacteriology 194, 5450, doi:10.1128/JB.01200-12 (2012).

Angiuoli, S. V., White, J. R., Matalka, M., White, O. & Fricke, W. F. 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).

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

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

Poelchau, M. F., Reynolds, J. A., Denlinger, D. L., Elsik, C. G. & Armbruster, P. A. 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).

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

Sahl, J. W., Johnson, J. K., Harris, A. D. 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).

Grinblat-Huse, V., Drabek, E. F., Creasy, H. H. et al. Genome sequences of the zoonotic pathogens Chlamydia psittaci 6BC and Cal10. Journal of bacteriology 193, 4039-4040, doi:10.1128/JB.05277-11 (2011).

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

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

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

Eppinger, M., Mammel, M. K., Leclerc, J. E., Ravel, J. & Cebula, T. A. 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).

Donia, M. S., Fricke, W. F., Partensky, F. 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).

Sahl, J. W., Steinsland, H., Redman, J. C. 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).

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

Eppinger, M., Mammel, M. K., Leclerc, J. E., Ravel, J. & Cebula, T. A. 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).

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

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

Han, A., Zenilman, J. M., Melendez, J. H. 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).

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