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Profile

Timothy Read PhD

  • Department of Medicine
    Professor
  • (404) 727-9706
  • tread@emory.edu
Head shot of Timothy Read

Overview

Dr. Read received a BSc in Biological Sciences from the University of London and then studied Microbial Genetics at the University of Leicester with Professor Brian Wilkins. After completing his PhD completed two doctoral fellowships in bacterial pathogenesis at Emory University. He then moved to the Institute for Genomic Research (TIGR), Rockville, MD, as an Assistant Investigator in 1998 and was Principal Investigator on multiple bacterial genome sequencing and comparison projects, including Bacillus anthracis (anthrax) and three Chlamydia species. He then accepted a position at the Naval Medical Research Center (NMRC) in Rockville, MD where he built the physical and bioinformatics infrastructure for a high-throughput genomics facility concentrating on population genomics of bacterial biothreat agents, and sequenced >100 microbial genomes from 2005 to 2009. His laboratory integrated a variety of approaches for bacterial strain differentiation including microarray resequencing, mult-locus sequence typing (MLST), bead-based pyrosequencing and sequencing by ligation technologies. He has published on microbial genomics and genetics in Science, Nature and PNAS with (by May 2009) 40+ peer-reviewed publications, several book chapters and a book co-authorship. He returned to Emory in February 2009 to start the Emory GRA Genome Center and continue research on Infectious Disease Genomics.

His research interests center around the application of genomics technologies to understanding infectious diseases. In particular, he is interested in trying to frame the questions that only become possible to answer as new and even better instruments for generating DNA sequence information come online.

Genomics for infectious disease detection and clinical diagnosis.

The rapidly decreasing cost of sequencing offers the opportunity in the near future to rapidly acquire large portions of the genome sequence of pathogens, either from DNA extracted from pure cultures or directly from clinical samples (metagenomics). He is interested in applying new technologies to determine their limits of sensitivity and to develop software to extract clinically useful information from the sequence data.

Bacterial Pathogen Genome Evolution.

The availability of multiple high quality genomes of pathogens such as Bacillus anthracis (etiologic agent of anthrax) and its less pathogenic close relatives affords the opportunity to ask questions about the evolution of virulence in these lineages. His particular interest is the extrachromosomal elements such as plasmids and bacteriophage, and intergenic repeat sequences. These extraneous genetic entities often carry vital virulence genes (like the anthrax toxin and plague virulence genes). They are also potent factors for short term genome change, through insertion, expansion and movement in the genomes and through the selection pressure they presumably exert on the genome for resistance. He is interested to find out how (and why) pathogens evolve to infect humans. What are the species that recent ancestors of B. anthracis were infecting before they developed virulence for mammals? What are the danger signs to look for in predicting the source of new emerging diseases? A genome based understanding of pathogen evolution will be vital for interpreting genetic variation in clinical sequence data (see above). The same knowledge can also be applied to vaccine and drug target selection.

Academic Appointment

  • Associate Professor, Division of Infectious Diseases, Emory University School of Medicine
  • Associate Professor, Department of Human Genetics, Emory University School of Medicine
  • Adjunct Assistant Professor, University of Maryland Biotechnology Institute

Education

Degrees

  • Ph.D. from University of Leicester
  • B.Sc. from Royal Holloway College, University of London

Research

Focus

  • Application of Next Generation sequencing technologies to bacterial genomics, focusing on Bacillus anthracis, the Chlamydiaceae, and other biodefense pathogens. Using population genomics to trace evolution of virulence mechanisms. Ecology of bacterial extrachromosomal elements. Functional genomic approaches to vaccine and drug design for bacterial infectious disease agents.

Publications

  • Genomic investigation of MRSA bacteremia relapse reveals diverse genomic profiles but convergence in bacteremia-associated genes.

    03/28/2025 Authors: Talbot BM; Jacko NF; Hofstetter KS; Alahakoon T; Bouiller K; Read TD; David MZ
  • Whole-genome automated assembly pipeline for Chlamydia trachomatis strains from reference, in vitro and clinical samples using the integrated CtGAP pipeline.
    NAR Genom Bioinform Volume: 7 Page(s): lqae187
    03/01/2025 Authors: Olagoke O; Aziz A; Zhu LH; Read TD; Dean D
  • Comparative genomic analysis of emerging non-typeable Haemophilus influenzae (NTHi) causing emerging septic arthritis in Atlanta.
    PeerJ Volume: 13 Page(s): e19081
    01/01/2025 Authors: Bixler BJ; Royer CJ; Petit Iii RA; Moller AG; Sefton S; Thomas S; Tunali A; Collins LF; Farley MM; Satola SW
  • Intraspecific Diversity of Staphylococcus aureus Populations Isolated from Cystic Fibrosis Respiratory Infections.

    11/16/2024 Authors: Alexander AM; Loo HQ; Askew L; Raghuram V; Read TD; Goldberg JB
  • Defense Heterogeneity in Host Populations Gives Rise to Pathogen Diversity.
    Am Nat Volume: 204 Page(s): 370 - 380
    10/01/2024 Authors: Hoang KL; Read TD; King KC
  • Erratum for Balthazar et al., "A laboratory-based predictive pathway for the development of Neisseria gonorrhoeae high-level resistance to corallopyronin A, an inhibitor of bacterial RNA polymerase".
    Microbiol Spectr Volume: 12 Page(s): e0140624
    08/06/2024 Authors: Balthazar JT; Golparian D; Unemo M; Read TD; Grosse M; Stadler M; Pfarr K; Schiefer A; Hoerauf A; Edwards JL
  • Chlamydia suis undergoes interclade recombination promoting Tet-island exchange.
    BMC Genomics Volume: 25 Page(s): 724
    07/26/2024 Authors: Seth-Smith H; Bommana S; Dean D; Read TD; Marti H
  • Genomic insights into the evolution of secondary metabolism of Escovopsis and its allies, specialized fungal symbionts of fungus-farming ants.
    mSystems Volume: 9 Page(s): e0057624
    07/23/2024 Authors: Berasategui A; Salem H; Moller AG; Christopher Y; Vidaurre Montoya Q; Conn C; Read TD; Rodrigues A; Ziemert N; Gerardo N
  • Average nucleotide identity-based Staphylococcus aureus strain grouping allows identification of strain-specific genes in the pangenome.
    mSystems Volume: 9 Page(s): e0014324
    07/23/2024 Authors: Raghuram V; Petit RA; Karol Z; Mehta R; Weissman DB; Read TD
  • A laboratory-based predictive pathway for the development of Neisseria gonorrhoeae high-level resistance to corallopyronin A, an inhibitor of bacterial RNA polymerase.
    Microbiol Spectr Volume: 12 Page(s): e0056024
    06/04/2024 Authors: Balthazar JT; Golparian D; Unemo M; Read TD; Grosse M; Stadler M; Pfarr K; Schiefer A; Hoerauf A; Edwards JL
  • Strain Differences in Bloodstream and Skin Infection: Methicillin-Resistant Staphylococcus aureus Isolated in 2018-2021 in a Single Health System.
    Open Forum Infect Dis Volume: 11 Page(s): ofae261
    06/01/2024 Authors: Hofstetter KS; Jacko NF; Shumaker MJ; Talbot BM; Petit RA; Read TD; David MZ
  • Incomplete immunity in a natural animal-microbiota interaction selects for higher pathogen virulence.
    Curr Biol Volume: 34 Page(s): 1357 - 1363.e3
    03/25/2024 Authors: Hoang KL; Read TD; King KC
  • The Burden and Impact of Early Post-transplant Multidrug-Resistant Organism Detection Among Renal Transplant Recipients, 2005-2021.
    Open Forum Infect Dis Volume: 11 Page(s): ofae060
    03/01/2024 Authors: Babiker A; Karadkhele G; Bombin A; Watkins R; Robichaux C; Smith G; Beechar VB; Steed DB; Jacob JT; Read TD
  • Experimentally evolved Staphylococcus aureus shows increased survival in the presence of Pseudomonas aeruginosa by acquiring mutations in the amino acid transporter, GltT.
    Microbiology (Reading) Volume: 170
    03/01/2024 Authors: Alexander AM; Luu JM; Raghuram V; Bottacin G; van Vliet S; Read TD; Goldberg JB
  • The role of hypermutation and collateral sensitivity in antimicrobial resistance diversity of Pseudomonas aeruginosa populations in cystic fibrosis lung infection.
    mBio Volume: 15 Page(s): e0310923
    02/14/2024 Authors: Vanderwoude J; Azimi S; Read TD; Diggle SP
  • Average Nucleotide Identity based Staphylococcus aureus strain grouping allows identification of strain-specific genes in the pangenome.

    01/31/2024 Authors: Raghuram V; Petit RA; Karol Z; Mehta R; Weissman DB; Read TD
  • Unique microbial diversity, community composition, and networks among Pacific Islander endocervical and vaginal microbiomes with and without Chlamydia trachomatis infection in Fiji.
    mBio Volume: 15 Page(s): e0306323
    01/16/2024 Authors: Bommana S; Hu Y-J; Kama M; Wang R; Kodimerla R; Jijakli K; Read TD; Dean D
  • Metagenome-wide characterization of shared antimicrobial resistance genes in sympatric people and lemurs in rural Madagascar.
    PeerJ Volume: 12 Page(s): e17805
    01/01/2024 Authors: Talbot BM; Clennon JA; Rakotoarison MFN; Rautman L; Durry S; Ragazzo LJ; Wright PC; Gillespie TR; Read TD
  • Corrigendum: Patterns of within-host spread of Chlamydia trachomatis between vagina, endocervix and rectum revealed by comparative genomic analysis.
    Front Microbiol Volume: 15 Page(s): 1441327
    01/01/2024 Authors: Joseph SJ; Bommana S; Ziklo N; Kama M; Dean D; Read TD
  • Factors associated with foreign body infection in methicillin-resistant Staphylococcus aureus bacteremia.
    Front Immunol Volume: 15 Page(s): 1335867
    01/01/2024 Authors: Bouiller K; Jacko NF; Shumaker MJ; Talbot BM; Read TD; David MZ
  • The Role of Hypermutation and Collateral Sensitivity in Antimicrobial Resistance Diversity of Pseudomonas aeruginosa Populations in Cystic Fibrosis Lung Infection.
    bioRxiv
    11/22/2023 Authors: Vanderwoude J; Azimi S; Read TD; Diggle SP
  • Comparison of genomic diversity between single and pooled Staphylococcus aureus colonies isolated from human colonization cultures.
    Microb Genom Volume: 9
    11/01/2023 Authors: Raghuram V; Gunoskey JJ; Hofstetter KS; Jacko NF; Shumaker MJ; Hu Y-J; Read TD; David MZ
  • Integrative analysis of microbial 16S gene and shotgun metagenomic sequencing data improves statistical efficiency.
    Res Sq
    10/03/2023 Authors: Yue Y; Read TD; Fedirko V; Satten GA; Hu Y-J
  • Transcriptional activation of ompA in Neisseria gonorrhoeae mediated by the XRE family member protein NceR.
    mBio Volume: 14 Page(s): e0124423
    08/31/2023 Authors: Holley CL; Dhulipala V; Maurakis SA; Greenawalt AN; Read TD; Cornelissen CN; Shafer WM
  • Experimentally Evolved Staphylococcus aureus Survives in the Presence of Pseudomonas aeruginosa by Acquiring Mutations in the Amino Acid Transporter, GltT.
    bioRxiv
    07/24/2023 Authors: Alexander AM; Luu JM; Raghuram V; Bottacin G; van Vliet S; Read TD; Goldberg JB
  • Integrative analysis of microbial 16S gene and shotgun metagenomic sequencing data improves statistical efficiency.
    bioRxiv
    06/30/2023 Authors: Yue Y; Read TD; Fedirko V; Satten GA; Hu Y-J
  • Comparison of genomic diversity between single and pooled Staphylococcus aureus colonies isolated from human colonisation cultures.
    bioRxiv
    06/14/2023 Authors: Raghuram V; Gunoskey JJ; Hofstetter KS; Jacko NF; Shumaker MJ; Hu Y-J; Read TD; David MZ
  • Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes.
    BMC Bioinformatics Volume: 24 Page(s): 243
    06/09/2023 Authors: Mehta RS; Petit RA; Read TD; Weissman DB
  • Development of an Amplicon Nanopore Sequencing Strategy for Detection of Mutations Conferring Intermediate Resistance to Vancomycin in Staphylococcus aureus Strains.
    Microbiol Spectr Volume: 11 Page(s): e0272822
    02/14/2023 Authors: Moller AG; Petit RA; Davis MH; Read TD
  • Patterns of within-host spread of Chlamydia trachomatis between vagina, endocervix and rectum revealed by comparative genomic analysis.
    bioRxiv
    01/26/2023 Authors: Joseph SJ; Bommana S; Ziklo N; Kama M; Dean D; Read TD
  • Patterns of within-host spread of Chlamydia trachomatis between vagina, endocervix and rectum revealed by comparative genomic analysis.
    Front Microbiol Volume: 14 Page(s): 1154664
    01/01/2023 Authors: Joseph SJ; Bommana S; Ziklo N; Kama M; Dean D; Read TD
  • Pre-epidemic evolution of the MRSA USA300 clade and a molecular key for classification.
    Front Cell Infect Microbiol Volume: 13 Page(s): 1081070
    01/01/2023 Authors: Bianco CM; Moustafa AM; O'Brien K; Martin MA; Read TD; Kreiswirth BN; Planet PJ
  • Unsuspected Clonal Spread of Methicillin-Resistant Staphylococcus aureus Causing Bloodstream Infections in Hospitalized Adults Detected Using Whole Genome Sequencing.
    Clin Infect Dis Volume: 75 Page(s): 2104 - 2112
    12/19/2022 Authors: Talbot BM; Jacko NF; Petit RA; Pegues DA; Shumaker MJ; Read TD; David MZ
  • Potent In Vitro and Ex Vivo Anti-Gonococcal Activity of the RpoB Inhibitor Corallopyronin A.
    mSphere Volume: 7 Page(s): e0036222
    10/26/2022 Authors: Edwards JL; Balthazar JT; Esposito DLA; Ayala JC; Schiefer A; Pfarr K; Hoerauf A; Alt S; Hesterkamp T; Grosse M
  • Metagenomic Shotgun Sequencing of Endocervical, Vaginal, and Rectal Samples among Fijian Women with and without Chlamydia trachomatis Reveals Disparate Microbial Populations and Function across Anatomic Sites: a Pilot Study.
    Microbiol Spectr Volume: 10 Page(s): e0010522
    06/29/2022 Authors: Bommana S; Richards G; Kama M; Kodimerla R; Jijakli K; Read TD; Dean D
  • A Single Amino Acid Substitution in Elongation Factor G Can Confer Low-Level Gentamicin Resistance in Neisseria gonorrhoeae.
    Antimicrob Agents Chemother Volume: 66 Page(s): e0025122
    05/17/2022 Authors: Holley CL; Dhulipala V; Balthazar JT; Le Van A; Begum AA; Chen S-C; Read TD; Matoga M; Hoffman IF; Golparian D
  • Association of Secretor Status and Recent Norovirus Infection With Gut Microbiome Diversity Metrics in a Veterans Affairs Population.
    Open Forum Infect Dis Volume: 9 Page(s): ofac125
    05/01/2022 Authors: Johnson JA; Read TD; Petit RA; Marconi VC; Meagley KL; Rodriguez-Barradas MC; Beenhouwer DO; Brown ST; Holodniy M; Lucero-Obusan CA
  • Suppression of p53 response by targeting p53-Mediator binding with a stapled peptide.
    Cell Rep Volume: 39 Page(s): 110630
    04/05/2022 Authors: Allen BL; Quach K; Jones T; Levandowski CB; Ebmeier CC; Rubin JD; Read T; Dowell RD; Schepartz A; Taatjes DJ
  • Species-Wide Phylogenomics of the Staphylococcus aureus Agr Operon Revealed Convergent Evolution of Frameshift Mutations.
    Microbiol Spectr Volume: 10 Page(s): e0133421
    02/23/2022 Authors: Raghuram V; Alexander AM; Loo HQ; Petit RA; Goldberg JB; Read TD
  • Species-Scale Genomic Analysis of Staphylococcus aureus Genes Influencing Phage Host Range and Their Relationships to Virulence and Antibiotic Resistance Genes.
    mSystems Volume: 7 Page(s): e0108321
    02/22/2022 Authors: Moller AG; Petit RA; Read TD
  • Unrecognized introductions of SARS-CoV-2 into the US state of Georgia shaped the early epidemic.
    Virus Evol Volume: 8 Page(s): veac011
    01/01/2022 Authors: Babiker A; Martin MA; Marvil C; Bellman S; Petit Iii RA; Bradley HL; Stittleburg VD; Ingersoll J; Kraft CS; Li Y
  • Dynamic PET-facilitated modeling and high-dose rifampin regimens for Staphylococcus aureus orthopedic implant-associated infections.
    Sci Transl Med Volume: 13 Page(s): eabl6851
    12/01/2021 Authors: Gordon O; Lee DE; Liu B; Langevin B; Ordonez AA; Dikeman DA; Shafiq B; Thompson JM; Sponseller PD; Flavahan K
  • Comparing whole-genome shotgun sequencing and DNA metabarcoding approaches for species identification and quantification of pollen species mixtures.
    Ecol Evol Volume: 11 Page(s): 16082 - 16098
    11/01/2021 Authors: Bell KL; Petit RA; Cutler A; Dobbs EK; Macpherson JM; Read TD; Burgess KS; Brosi BJ
  • The whale shark genome reveals patterns of vertebrate gene family evolution.
    Elife Volume: 10
    08/19/2021 Authors: Tan M; Redmond AK; Dooley H; Nozu R; Sato K; Kuraku S; Koren S; Phillippy AM; Dove AD; Read T
  • A global metagenomic map of urban microbiomes and antimicrobial resistance.
    Cell Volume: 184 Page(s): 3376 - 3393.e17
    06/24/2021 Authors: Danko D; Bezdan D; Afshin EE; Ahsanuddin S; Bhattacharya C; Butler DJ; Chng KR; Donnellan D; Hecht J; Jackson K
  • Symbiont Genomic Features and Localization in the Bean Beetle Callosobruchus maculatus.
    Appl Environ Microbiol Volume: 87 Page(s): e0021221
    05/26/2021 Authors: Berasategui A; Moller AG; Weiss B; Beck CW; Bauchiero C; Read TD; Gerardo NM; Salem H
  • SHIFTWORK, FUNCTIONAL BOWEL SYMPTOMS AND THE MICROBIOME
    Volume: 44 Page(s): A6 - A6
    05/01/2021 Authors: Rogers A; Hu Y; Yue Y; Wessel E; Christie J; Read T
  • Structures of Neisseria gonorrhoeae MtrR-operator complexes reveal molecular mechanisms of DNA recognition and antibiotic resistance-conferring clinical mutations.
    Nucleic Acids Res Volume: 49 Page(s): 4155 - 4170
    04/19/2021 Authors: Beggs GA; Ayala JC; Kavanaugh LG; Read TD; Hooks GM; Schumacher MA; Shafer WM; Brennan RG
  • Whole-Genome Enrichment and Sequencing of Chlamydia trachomatis Directly from Patient Clinical Vaginal and Rectal Swabs.
    mSphere Volume: 6
    03/03/2021 Authors: Bowden KE; Joseph SJ; Cartee JC; Ziklo N; Danavall D; Raphael BH; Read TD; Dean D
  • Genes Influencing Phage Host Range in Staphylococcus aureus on a Species-Wide Scale.
    mSphere Volume: 6
    01/13/2021 Authors: Moller AG; Winston K; Ji S; Wang J; Hargita Davis MN; Sols-Lemus CR; Read TD
  • Generation of Tetracycline and Rifamycin Resistant Chlamydia Suis Recombinants.
    Front Microbiol Volume: 12 Page(s): 630293
    01/01/2021 Authors: Marti H; Bommana S; Read TD; Pesch T; Prhauser B; Dean D; Borel N
  • Shiftwork, functional bowel symptoms, and the microbiome.
    PeerJ Volume: 9 Page(s): e11406
    01/01/2021 Authors: Rogers AE; Hu Y-J; Yue Y; Wissel EF; Petit Iii RA; Jarrett S; Christie J; Read TD
  • Vaginal Microbiome Composition in Early Pregnancy and Risk of Spontaneous Preterm and Early Term Birth Among African American Women.
    Front Cell Infect Microbiol Volume: 11 Page(s): 641005
    01/01/2021 Authors: Dunlop AL; Satten GA; Hu Y-J; Knight AK; Hill CC; Wright ML; Smith AK; Read TD; Pearce BD; Corwin EJ
  • Genome-wide binding analysis of 195 DNA binding proteins reveals "reservoir" promoters and human specific SVA-repeat family regulation.
    PLoS One Volume: 16 Page(s): e0237055
    01/01/2021 Authors: Smallegan MJ; Shehata S; Spradlin SF; Swearingen A; Wheeler G; Das A; Corbet G; Nebenfuehr B; Ahrens D; Tauber D
  • Effect of genetic background on the evolution of Vancomycin-Intermediate Staphylococcus aureus (VISA).
    PeerJ Volume: 9 Page(s): e11764
    01/01/2021 Authors: Su M; Davis MH; Peterson J; Solis-Lemus C; Satola SW; Read TD
  • A Comparison of the Bacterial Nasal Microbiome in Allergic Rhinitis Patients Before and After Immunotherapy.
    Laryngoscope Volume: 130 Page(s): E882 - E888
    12/01/2020 Authors: Bender ME; Read TD; Edwards TS; Hargita M; Cutler AJ; Wissel EF; Wise SK
  • Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes.
    mSystems Volume: 5
    08/04/2020 Authors: Petit RA; Read TD
  • Glucocorticoid receptor sensitivity in early pregnancy in an African American cohort.
    Am J Reprod Immunol Volume: 84 Page(s): e13252
    07/01/2020 Authors: Clarke LS; Corwin EJ; Dunlop AL; Hankus A; Bradner JM; Paul S; Jiao Y; Smith AK; Patrushev N; Mulle JG
  • Genotypic and Phenotypic Diversity of Staphylococcus aureus Isolates from Cystic Fibrosis Patient Lung Infections and Their Interactions with Pseudomonas aeruginosa.
    mBio Volume: 11
    06/23/2020 Authors: Bernardy EE; Petit RA; Raghuram V; Alexander AM; Read TD; Goldberg JB
  • Genomic analysis of variability in Delta-toxin levels between Staphylococcus aureus strains.
    PeerJ Volume: 8 Page(s): e8717
    01/01/2020 Authors: Su M; Lyles JT; Petit Iii RA; Peterson J; Hargita M; Tang H; Solis-Lemus C; Quave CL; Read TD
  • Invasive Nontypeable Haemophilus influenzae Infection Among Adults With HIV in Metropolitan Atlanta, Georgia, 2008-2018.
    JAMA Volume: 322 Page(s): 2399 - 2410
    12/24/2019 Authors: Collins LF; Havers FP; Tunali A; Thomas S; Clennon JA; Wiley Z; Tobin-D'Angelo M; Parrott T; Read TD; Satola SW
  • Transformation of Australian Community Pharmacies Into Good Clinical Practice Compliant Trial Pharmacies for HIV Pre-Exposure Prophylaxis
    FRONTIERS IN PHARMACOLOGY Volume: 10
    11/07/2019 Authors: Lal L; Ryan K; Liu IY; Price B; Lockwood T; Aguirre I; Slobodian P; Lam A; Vassan M; Lim K
  • Interaction between Streptococcus pneumoniae and Staphylococcus aureus Generates OH Radicals That Rapidly Kill Staphylococcus aureus Strains.
    J Bacteriol Volume: 201
    11/01/2019 Authors: Wu X; Gordon O; Jiang W; Antezana BS; Angulo-Zamudio UA; Del Rio C; Moller A; Brissac T; Tierney ARP; Warncke K
  • Determinants of Phage Host Range in Staphylococcus Species.
    Appl Environ Microbiol Volume: 85
    06/01/2019 Authors: Moller AG; Lindsay JA; Read TD
  • Association of HIV Preexposure Prophylaxis With Incidence of Sexually Transmitted Infections Among Individuals at High Risk of HIV Infection.
    JAMA Volume: 321 Page(s): 1380 - 1390
    04/09/2019 Authors: Traeger MW; Cornelisse VJ; Asselin J; Price B; Roth NJ; Willcox J; Tee BK; Fairley CK; Chang CC; Armishaw J
  • Human mAbs to Staphylococcus aureus IsdA Provide Protection Through Both Heme-Blocking and Fc-Mediated Mechanisms.
    J Infect Dis Volume: 219 Page(s): 1264 - 1273
    04/08/2019 Authors: Bennett MR; Bombardi RG; Kose N; Parrish EH; Nagel MB; Petit RA; Read TD; Schey KL; Thomsen IP; Skaar EP
  • Genome-Based Prediction of Bacterial Antibiotic Resistance.
    J Clin Microbiol Volume: 57
    03/01/2019 Authors: Su M; Satola SW; Read TD
  • Stability of the vaginal, oral, and gut microbiota across pregnancy among African American women: the effect of socioeconomic status and antibiotic exposure.
    PeerJ Volume: 7 Page(s): e8004
    01/01/2019 Authors: Dunlop AL; Knight AK; Satten GA; Cutler AJ; Wright ML; Mitchell RM; Read TD; Mulle J; Hertzberg VS; Hill CC
  • Whole-Genome Sequences of Staphylococcus aureus Isolates from Cystic Fibrosis Lung Infections.
    Microbiol Resour Announc Volume: 8
    01/01/2019 Authors: Bernardy EE; Petit RA; Moller AG; Blumenthal JA; McAdam AJ; Priebe GP; Chande AT; Rishishwar L; Jordan IK; Read TD
  • Quantitative and qualitative assessment of pollen DNA metabarcoding using constructed species mixtures.
    Mol Ecol Volume: 28 Page(s): 431 - 455
    01/01/2019 Authors: Bell KL; Burgess KS; Botsch JC; Dobbs EK; Read TD; Brosi BJ
  • USA300 Staphylococcus aureus persists on multiple body sites following an infection.
    BMC Microbiol Volume: 18 Page(s): 206
    12/05/2018 Authors: Read TD; Petit RA; Yin Z; Montgomery T; McNulty MC; David MZ
  • Whole genome sequencing for investigations of meningococcal outbreaks in the United States: a retrospective analysis.
    Sci Rep Volume: 8 Page(s): 15803
    10/25/2018 Authors: Whaley MJ; Joseph SJ; Retchless AC; Kretz CB; Blain A; Hu F; Chang H-Y; Mbaeyi SA; MacNeil JR; Read TD
  • Fine-scale differentiation between Bacillus anthracis and Bacillus cereus group signatures in metagenome shotgun data.
    PeerJ Volume: 6 Page(s): e5515
    01/01/2018 Authors: Petit Iii RA; Hogan JM; Ezewudo MN; Joseph SJ; Read TD
  • Staphylococcus aureus viewed from the perspective of 40,000+ genomes.
    PeerJ Volume: 6 Page(s): e5261
    01/01/2018 Authors: Petit RA; Read TD
  • Invasive Methicillin-Resistant Staphylococcus aureus USA500 Strains from the U.S. Emerging Infections Program Constitute Three Geographically Distinct Lineages.
    mSphere Volume: 3
    01/01/2018 Authors: Frisch MB; Castillo-Ramrez S; Petit RA; Farley MM; Ray SM; Albrecht VS; Limbago BM; Hernandez J; See I; Satola SW
  • The Female Genital Tract Microbiome Is Associated With Vaginal Antiretroviral Drug Concentrations in Human Immunodeficiency Virus-Infected Women on Antiretroviral Therapy.
    J Infect Dis Volume: 216 Page(s): 990 - 999
    11/15/2017 Authors: Donahue Carlson R; Sheth AN; Read TD; Frisch MB; Mehta CC; Martin A; Haaland RE; Patel AS; Pau C-P; Kraft CS
  • Erratum to: draft sequencing and assembly of the genome of the world's largest fish, the whale shark: Rhincodon typus smith 1828.
    BMC Genomics Volume: 18 Page(s): 755
    09/25/2017 Authors: Read TD; Petit RA; Joseph SJ; Alam T; Weil MR; Ahmad M; Bhimani R; Vuong JS; Haase CP; Webb DH
  • Draft sequencing and assembly of the genome of the world's largest fish, the whale shark: Rhincodon typus Smith 1828.
    BMC Genomics Volume: 18 Page(s): 532
    07/14/2017 Authors: Read TD; Petit RA; Joseph SJ; Alam MT; Weil MR; Ahmad M; Bhimani R; Vuong JS; Haase CP; Webb DH
  • Lung Tissue Concentrations of Pyrazinamide among Patients with Drug-Resistant Pulmonary Tuberculosis.
    Antimicrob Agents Chemother Volume: 61
    06/01/2017 Authors: Kempker RR; Heinrichs MT; Nikolaishvili K; Sabulua I; Bablishvili N; Gogishvili S; Avaliani Z; Tukvadze N; Little B; Bernheim A
  • Protocol for the Emory University African American Vaginal, Oral, and Gut Microbiome in Pregnancy Cohort Study.
    BMC Pregnancy Childbirth Volume: 17 Page(s): 161
    06/01/2017 Authors: Corwin EJ; Hogue CJ; Pearce B; Hill CC; Read TD; Mulle J; Dunlop AL
  • Emergence of a new Neisseria meningitidis clonal complex 11 lineage 11.2 clade as an effective urogenital pathogen.
    Proc Natl Acad Sci U S A Volume: 114 Page(s): 4237 - 4242
    04/18/2017 Authors: Tzeng Y-L; Bazan JA; Turner AN; Wang X; Retchless AC; Read TD; Toh E; Nelson DE; Del Rio C; Stephens DS
  • Oral microbiome in HIV-associated periodontitis.
    Medicine (Baltimore) Volume: 96 Page(s): e5821
    03/01/2017 Authors: Noguera-Julian M; Guilln Y; Peterson J; Reznik D; Harris EV; Joseph SJ; Rivera J; Kannanganat S; Amara R; Nguyen ML
  • Correction: Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants.
    PLoS One Volume: 12 Page(s): e0186030
    01/01/2017 Authors: Diaz MH; Desai HP; Morrison SS; Benitez AJ; Wolff BJ; Caravas J; Read TD; Dean D; Winchell JM
  • Tet(C) Gene Transfer between Chlamydia suis Strains Occurs by Homologous Recombination after Co-infection: Implications for Spread of Tetracycline-Resistance among Chlamydiaceae.
    Front Microbiol Volume: 8 Page(s): 156
    01/01/2017 Authors: Marti H; Kim H; Joseph SJ; Dojiri S; Read TD; Dean D
  • Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants.
    PLoS One Volume: 12 Page(s): e0174701
    01/01/2017 Authors: Diaz MH; Desai HP; Morrison SS; Benitez AJ; Wolff BJ; Caravas J; Read TD; Dean D; Winchell JM
  • Rapid detection and strain typing of Chlamydia trachomatis using a highly multiplexed microfluidic PCR assay.
    PLoS One Volume: 12 Page(s): e0178653
    01/01/2017 Authors: Turingan RS; Kaplun L; Krautz-Peterson G; Norsworthy S; Zolotova A; Joseph SJ; Read TD; Dean D; Tan E; Selden RF
  • Dynamics of genome change among Legionella species.
    Sci Rep Volume: 6 Page(s): 33442
    09/16/2016 Authors: Joseph SJ; Cox D; Wolff B; Morrison SS; Kozak-Muiznieks NA; Frace M; Didelot X; Castillo-Ramirez S; Winchell J; Read TD
  • Tetracycline Selective Pressure and Homologous Recombination Shape the Evolution of Chlamydia suis: A Recently Identified Zoonotic Pathogen.
    Genome Biol Evol Volume: 8 Page(s): 2613 - 2623
    09/02/2016 Authors: Joseph SJ; Marti H; Didelot X; Read TD; Dean D
  • The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report.
    Microbiome Volume: 4 Page(s): 24
    06/03/2016 Authors: MetaSUB International Consortium
  • Antibiotic failure mediated by a resistant subpopulation in Enterobacter cloacae.
    Nat Microbiol Volume: 1 Page(s): 16053
    05/09/2016 Authors: Band VI; Crispell EK; Napier BA; Herrera CM; Tharp GK; Vavikolanu K; Pohl J; Read TD; Bosinger SE; Trent MS
  • The single-species metagenome: subtyping Staphylococcus aureus core genome sequences from shotgun metagenomic data.
    PeerJ Volume: 4 Page(s): e2571
    01/01/2016 Authors: Joseph SJ; Li B; Petit Iii RA; Qin ZS; Darrow L; Read TD
  • Draft Genome Sequence of the Pandoraea apista LMG 16407 Type Strain.
    Genome Announc Volume: 3
    11/12/2015 Authors: Millard AD; Westblade LF; LiPuma JJ; Vavikolanu K; Read TD; Pallen MJ; Burd EM; Constantinidou CI
  • Chlamydiaceae Genomics Reveals Interspecies Admixture and the Recent Evolution of Chlamydia abortus Infecting Lower Mammalian Species and Humans.
    Genome Biol Evol Volume: 7 Page(s): 3070 - 3084
    10/27/2015 Authors: Joseph SJ; Marti H; Didelot X; Castillo-Ramirez S; Read TD; Dean D
  • Characterization of a spermine/spermidine transport system reveals a novel DNA sequence duplication in Neisseria gonorrhoeae.
    FEMS Microbiol Lett Volume: 362
    08/01/2015 Authors: Goytia M; Hawel L; Dhulipala VL; Joseph SJ; Read TD; Shafer WM
  • The effect of sample complexity and sequencing depth on DNA barcoding of mixed-species pollen samples
    GENOME Volume: 58 Page(s): 194 - 194
    05/01/2015 Authors: Bell KL; Burgess KS; Read TD; Brosi BJ
  • USA300 and USA500 clonal lineages of Staphylococcus aureus do not produce a capsular polysaccharide due to conserved mutations in the cap5 locus.
    mBio Volume: 6
    04/07/2015 Authors: Boyle-Vavra S; Li X; Alam MT; Read TD; Sieth J; Cywes-Bentley C; Dobbins G; David MZ; Kumar N; Eells SJ
  • Transmission and microevolution of USA300 MRSA in U.S. households: evidence from whole-genome sequencing.
    mBio Volume: 6 Page(s): e00054
    03/10/2015 Authors: Alam MT; Read TD; Petit RA; Boyle-Vavra S; Miller LG; Eells SJ; Daum RS; David MZ
  • Overproduction of the MtrCDE efflux pump in Neisseria gonorrhoeae produces unexpected changes in cellular transcription patterns.
    Antimicrob Agents Chemother Volume: 59 Page(s): 724 - 726
    01/01/2015 Authors: Ohneck EA; Goytia M; Rouquette-Loughlin CE; Joseph SJ; Read TD; Jerse AE; Shafer WM
  • Population structure of Neisseria gonorrhoeae based on whole genome data and its relationship with antibiotic resistance.
    PeerJ Volume: 3 Page(s): e806
    01/01/2015 Authors: Ezewudo MN; Joseph SJ; Castillo-Ramirez S; Dean D; Del Rio C; Didelot X; Dillon J-A; Selden RF; Shafer WM; Turingan RS
  • 'SEEDY' (Simulation of Evolutionary and Epidemiological Dynamics): An R Package to Follow Accumulation of Within-Host Mutation in Pathogens.
    PLoS One Volume: 10 Page(s): e0129745
    01/01/2015 Authors: Worby CJ; Read TD
  • Using crude whole-genome assemblies of Neisseria gonorrhoeae as a platform for strain analysis: clonal spread of gonorrhea infection in Saskatchewan, Canada.
    J Clin Microbiol Volume: 52 Page(s): 3772 - 3776
    10/01/2014 Authors: Vidovic S; Caron C; Taheri A; Thakur SD; Read TD; Kusalik A; Dillon J-AR
  • Using genomics to standardize population analysis profile-area under the curve ratio for vancomycin-intermediate Staphylococcus aureus.
    J Clin Microbiol Volume: 52 Page(s): 3824 - 3826
    10/01/2014 Authors: Read TD; Satola SW
  • High rates of sexually transmissible infections in HIV-positive patients in the Australian HIV Observational Database: a prospective cohort study.
    Sex Health Volume: 11 Page(s): 291 - 297
    09/01/2014 Authors: Mulhall BP; Wright S; Allen D; Brown K; Dickson B; Grotowski M; Jackson E; Petoumenos K; Read P; Read T
  • Development of oxacillin resistance in a patient with recurrent Staphylococcus aureus bacteremia.
    J Clin Microbiol Volume: 52 Page(s): 3114 - 3117
    08/01/2014 Authors: Burd EM; Alam MT; Passalacqua KD; Kalokhe AS; Eaton ME; Satola SW; Kraft CS; Read TD
  • Functional genomic characterization of virulence factors from necrotizing fasciitis-causing strains of Aeromonas hydrophila.
    Appl Environ Microbiol Volume: 80 Page(s): 4162 - 4183
    07/01/2014 Authors: Grim CJ; Kozlova EV; Ponnusamy D; Fitts EC; Sha J; Kirtley ML; van Lier CJ; Tiner BL; Erova TE; Joseph SJ
  • Phase-variable expression of lptA modulates the resistance of Neisseria gonorrhoeae to cationic antimicrobial peptides.
    Antimicrob Agents Chemother Volume: 58 Page(s): 4230 - 4233
    07/01/2014 Authors: Kandler JL; Joseph SJ; Balthazar JT; Dhulipala V; Read TD; Jerse AE; Shafer WM
  • WP 115 WHOLE GENOME SEQUENCING AS A TOOL FOR MULTILOCUS SEQUENCE TYPING OF NEISSERIA GONORRHOEAE ISOLATES
    Volume: 41 Page(s): S126 - S126
    06/01/2014 Authors: Caron C; Kusalik A; Read TD; Vidovic S; Dillon J-AR
  • IsdB-dependent hemoglobin binding is required for acquisition of heme by Staphylococcus aureus.
    J Infect Dis Volume: 209 Page(s): 1764 - 1772
    06/01/2014 Authors: Pishchany G; Sheldon JR; Dickson CF; Alam MT; Read TD; Gell DA; Heinrichs DE; Skaar EP
  • Predicting the virulence of MRSA from its genome sequence.
    Genome Res Volume: 24 Page(s): 839 - 849
    05/01/2014 Authors: Laabei M; Recker M; Rudkin JK; Aldeljawi M; Gulay Z; Sloan TJ; Williams P; Endres JL; Bayles KW; Fey PD
  • Dissecting vancomycin-intermediate resistance in staphylococcus aureus using genome-wide association.
    Genome Biol Evol Volume: 6 Page(s): 1174 - 1185
    04/30/2014 Authors: Alam MT; Petit RA; Crispell EK; Thornton TA; Conneely KN; Jiang Y; Satola SW; Read TD
  • Genetic evidence for the involvement of the S-layer protein gene sap and the sporulation genes spo0A, spo0B, and spo0F in Phage AP50c infection of Bacillus anthracis.
    J Bacteriol Volume: 196 Page(s): 1143 - 1154
    03/01/2014 Authors: Plaut RD; Beaber JW; Zemansky J; Kaur AP; George M; Biswas B; Henry M; Bishop-Lilly KA; Mokashi V; Hannah RM
  • Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology.
    Genome Med Volume: 6 Page(s): 109
    01/01/2014 Authors: Read TD; Massey RC
  • Direct amplification, sequencing and profiling of Chlamydia trachomatis strains in single and mixed infection clinical samples.
    PLoS One Volume: 9 Page(s): e99290
    01/01/2014 Authors: Joseph SJ; Li B; Ghonasgi T; Haase CP; Qin ZS; Dean D; Read TD
  • Genome Sequencing of Four Strains of Rickettsia prowazekii, the Causative Agent of Epidemic Typhus, Including One Flying Squirrel Isolate.
    Genome Announc Volume: 1
    06/27/2013 Authors: Bishop-Lilly KA; Ge H; Butani A; Osborne B; Verratti K; Mokashi V; Nagarajan N; Pop M; Read TD; Richards AL
  • Characterization of Aeromonas hydrophila wound pathotypes by comparative genomic and functional analyses of virulence genes.
    mBio Volume: 4 Page(s): e00064 - e00013
    04/23/2013 Authors: Grim CJ; Kozlova EV; Sha J; Fitts EC; van Lier CJ; Kirtley ML; Joseph SJ; Read TD; Burd EM; Tall BD
  • Comparative analysis of Chlamydia psittaci genomes reveals the recent emergence of a pathogenic lineage with a broad host range.
    mBio Volume: 4
    03/26/2013 Authors: Read TD; Joseph SJ; Didelot X; Liang B; Patel L; Dean D
  • Population genomics of Chlamydia trachomatis: insights on drift, selection, recombination, and population structure.
    Mol Biol Evol Volume: 29 Page(s): 3933 - 3946
    12/01/2012 Authors: Joseph SJ; Didelot X; Rothschild J; de Vries HJC; Morr SA; Read TD; Dean D
  • Whole genome sequencing of phage resistant Bacillus anthracis mutants reveals an essential role for cell surface anchoring protein CsaB in phage AP50c adsorption.
    Virol J Volume: 9 Page(s): 246
    10/26/2012 Authors: Bishop-Lilly KA; Plaut RD; Chen PE; Akmal A; Willner KM; Butani A; Dorsey S; Mokashi V; Mateczun AJ; Chapman C
  • A mutation in the PP2C phosphatase gene in a Staphylococcus aureus USA300 clinical isolate with reduced susceptibility to vancomycin and daptomycin.
    Antimicrob Agents Chemother Volume: 56 Page(s): 5212 - 5223
    10/01/2012 Authors: Passalacqua KD; Satola SW; Crispell EK; Read TD
  • Genomic characterization of the Bacillus cereus sensu lato species: backdrop to the evolution of Bacillus anthracis.
    Genome Res Volume: 22 Page(s): 1512 - 1524
    08/01/2012 Authors: Zwick ME; Joseph SJ; Didelot X; Chen PE; Bishop-Lilly KA; Stewart AC; Willner K; Nolan N; Lentz S; Thomason MK
  • Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium.
    Genome Biol Volume: 13 Page(s): R30
    04/26/2012 Authors: Kristoffersen SM; Haase C; Weil MR; Passalacqua KD; Niazi F; Hutchison SK; Desany B; Kolst A-B; Tourasse NJ; Read TD
  • Genome-wide recombination in Chlamydia trachomatis.
    Nat Genet Volume: 44 Page(s): 364 - 366
    03/28/2012 Authors: Joseph SJ; Read TD
  • Strand-specific RNA-seq reveals ordered patterns of sense and antisense transcription in Bacillus anthracis.
    PLoS One Volume: 7 Page(s): e43350
    01/01/2012 Authors: Passalacqua KD; Varadarajan A; Weist C; Ondov BD; Byrd B; Read TD; Bergman NH
  • A multiplexed microfluidic PCR assay for sensitive and specific point-of-care detection of Chlamydia trachomatis.
    PLoS One Volume: 7 Page(s): e51685
    01/01/2012 Authors: Dean D; Turingan RS; Thomann H-U; Zolotova A; Rothschild J; Joseph SJ; Read TD; Tan E; Selden RF
  • Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample.
    PLoS One Volume: 7 Page(s): e30087
    01/01/2012 Authors: Luo C; Tsementzi D; Kyrpides N; Read T; Konstantinidis KT
  • Unity in variety--the pan-genome of the Chlamydiae.
    Mol Biol Evol Volume: 28 Page(s): 3253 - 3270
    12/01/2011 Authors: Collingro A; Tischler P; Weinmaier T; Penz T; Heinz E; Brunham RC; Read TD; Bavoil PM; Sachse K; Kahane S
  • Combined proteomic and transcriptomic analysis of the response of Bacillus anthracis to oxidative stress.
    Proteomics Volume: 11 Page(s): 3036 - 3055
    08/01/2011 Authors: Pohl S; Tu WY; Aldridge PD; Gillespie C; Hahne H; Mder U; Read TD; Harwood CR
  • Genome sequences of the zoonotic pathogens Chlamydia psittaci 6BC and Cal10.
    J Bacteriol Volume: 193 Page(s): 4039 - 4040
    08/01/2011 Authors: Grinblat-Huse V; Drabek EF; Creasy HH; Daugherty SC; Jones KM; Santana-Cruz I; Tallon LJ; Read TD; Hatch TP; Bavoil P
  • The evolution of infectious agents in relation to sex in animals and humans: brief discussions of some individual organisms.
    Volume: 1230 Page(s): 74 - 107
    08/01/2011 Authors: Reed DL; Currier RW; Walton SF; Conrad M; Sullivan SA; Carlton JM; Read TD; Severini A; Tyler S; Eberle R
  • Genome sequence of the obligate intracellular animal pathogen Chlamydia pecorum E58.
    J Bacteriol Volume: 193 Page(s): 3690
    07/01/2011 Authors: Mojica S; Huot Creasy H; Daugherty S; Read TD; Kim T; Kaltenboeck B; Bavoil P; Myers GSA
  • Interplay of recombination and selection in the genomes of Chlamydia trachomatis.
    Biol Direct Volume: 6 Page(s): 28
    05/26/2011 Authors: Joseph SJ; Didelot X; Gandhi K; Dean D; Read TD
  • PheMaDB: a solution for storage, retrieval, and analysis of high throughput phenotype data.
    BMC Bioinformatics Volume: 12 Page(s): 109
    04/20/2011 Authors: Chang WE; Sarver K; Higgs BW; Read TD; Nolan NM; Chapman CE; Bishop-Lilly KA; Sozhamannan S
  • Genomic signatures of strain selection and enhancement in Bacillus atrophaeus var. globigii, a historical biowarfare simulant.
    PLoS One Volume: 6 Page(s): e17836
    03/25/2011 Authors: Gibbons HS; Broomall SM; McNew LA; Daligault H; Chapman C; Bruce D; Karavis M; Krepps M; McGregor PA; Hong C
  • Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation.
    Proc Natl Acad Sci U S A Volume: 108 Page(s): 5027 - 5032
    03/22/2011 Authors: Rasko DA; Worsham PL; Abshire TG; Stanley ST; Bannan JD; Wilson MR; Langham RJ; Decker RS; Jiang L; Read TD
  • Investigating the Arenyl-Diene Double [3+2] Photocycloaddition Reaction
    JOURNAL OF ORGANIC CHEMISTRY Volume: 76 Page(s): 1295 - 1304
    03/04/2011 Authors: Penkett CS; Woolford JA; Read TW; Kahan RJ
  • Uncovering the Genomic Architecture of Male Pair-bonding Behaviour in an Emerging Model Organism, the Prairie Vole (Microtus ochrogaster)
    ATLA-ALTERNATIVES TO LABORATORY ANIMALS Volume: 39 Page(s): 68 - 69
    03/01/2011 Authors: McGraw LA; Davis JK; Lowman JJ; Ten Hallers BFH; Koriabine M; de Jong PJ; Read TD; Rudd MK; Thomas JW; Young LJ
  • Hypervirulent Chlamydia trachomatis clinical strain is a recombinant between lymphogranuloma venereum (L(2)) and D lineages.
    mBio Volume: 2 Page(s): e00045 - e00011
    01/01/2011 Authors: Somboonna N; Wan R; Ojcius DM; Pettengill MA; Joseph SJ; Chang A; Hsu R; Read TD; Dean D
  • Genetic variation and linkage disequilibrium in Bacillus anthracis.
    Sci Rep Volume: 1 Page(s): 169
    01/01/2011 Authors: Zwick ME; Thomason MK; Chen PE; Johnson HR; Sozhamannan S; Mateczun A; Read TD
  • Bacterial population genomics and infectious disease diagnostics.
    Trends Biotechnol Volume: 28 Page(s): 611 - 618
    12/01/2010 Authors: Joseph SJ; Read TD
  • High-redundancy draft sequencing of 15 clinical and environmental Burkholderia strains.
    J Bacteriol Volume: 192 Page(s): 6313 - 6314
    12/01/2010 Authors: Mukhopadhyay S; Thomason MK; Lentz S; Nolan N; Willner K; Gee JE; Glass MB; Inglis TJJ; Merritt A; Levy A
  • Arbovirus detection in insect vectors by rapid, high-throughput pyrosequencing.
    PLoS Negl Trop Dis Volume: 4 Page(s): e878
    11/09/2010 Authors: Bishop-Lilly KA; Turell MJ; Willner KM; Butani A; Nolan NME; Lentz SM; Akmal A; Mateczun A; Brahmbhatt TN; Sozhamannan S
  • Rapid identification of genetic modifications in Bacillus anthracis using whole genome draft sequences generated by 454 pyrosequencing.
    PLoS One Volume: 5 Page(s): e12397
    08/25/2010 Authors: Chen PE; Willner KM; Butani A; Dorsey S; George M; Stewart A; Lentz SM; Cook CE; Akmal A; Price LB
  • Rapid multi-locus sequence typing using microfluidic biochips.
    PLoS One Volume: 5 Page(s): e10595
    05/12/2010 Authors: Read TD; Turingan RS; Cook C; Giese H; Thomann UH; Hogan CC; Tan E; Selden RF
  • Finishing genomes with limited resources: lessons from an ensemble of microbial genomes.
    BMC Genomics Volume: 11 Page(s): 242
    04/16/2010 Authors: Nagarajan N; Cook C; Di Bonaventura M; Ge H; Richards A; Bishop-Lilly KA; DeSalle R; Read TD; Pop M
  • Genomic characterization of the Yersinia genus.
    Genome Biol Volume: 11 Page(s): R1
    01/04/2010 Authors: Chen PE; Cook C; Stewart AC; Nagarajan N; Sommer DD; Pop M; Thomason B; Thomason MPK; Lentz S; Nolan N
  • Quantitative characterization of quantum dot-labeled lambda phage for Escherichia coli detection.
    Biotechnol Bioeng Volume: 104 Page(s): 1059 - 1067
    12/15/2009 Authors: Yim PB; Clarke ML; McKinstry M; De Paoli Lacerda SH; Pease LF; Dobrovolskaia MA; Kang H; Read TD; Sozhamannan S; Hwang J
  • Evidence that human Chlamydia pneumoniae was zoonotically acquired.
    J Bacteriol Volume: 191 Page(s): 7225 - 7233
    12/01/2009 Authors: Myers GSA; Mathews SA; Eppinger M; Mitchell C; O'Brien KK; White OR; Benahmed F; Brunham RC; Read TD; Ravel J
  • Genomics. Genome project standards in a new era of sequencing.
    Science Volume: 326 Page(s): 236 - 237
    10/09/2009 Authors: Chain PSG; Grafham DV; Fulton RS; Fitzgerald MG; Hostetler J; Muzny D; Ali J; Birren B; Bruce DC; Buhay C
  • Predicting phenotype and emerging strains among Chlamydia trachomatis infections.
    Emerg Infect Dis Volume: 15 Page(s): 1385 - 1394
    09/01/2009 Authors: Dean D; Bruno WJ; Wan R; Gomes JP; Devignot S; Mehari T; de Vries HJC; Morr SA; Myers G; Read TD
  • Identification of Bacillus anthracis spore component antigens conserved across diverse Bacillus cereus sensu lato strains.
    Mol Cell Proteomics Volume: 8 Page(s): 1174 - 1191
    06/01/2009 Authors: Mukhopadhyay S; Akmal A; Stewart AC; Hsia R-C; Read TD
  • DIYA: a bacterial annotation pipeline for any genomics lab.
    Bioinformatics Volume: 25 Page(s): 962 - 963
    04/01/2009 Authors: Stewart AC; Osborne B; Read TD
  • The complete genome sequence of Bacillus anthracis Ames "Ancestor".
    J Bacteriol Volume: 191 Page(s): 445 - 446
    01/01/2009 Authors: Ravel J; Jiang L; Stanley ST; Wilson MR; Decker RS; Read TD; Worsham P; Keim PS; Salzberg SL; Fraser-Liggett CM
  • Characterization of two Campylobacter jejuni strains for use in volunteer experimental-infection studies.
    Infect Immun Volume: 76 Page(s): 5655 - 5667
    12/01/2008 Authors: Poly F; Read TD; Chen Y-H; Monteiro MA; Serichantalergs O; Pootong P; Bodhidatta L; Mason CJ; Rockabrand D; Baqar S
  • Molecular characterization of a variant of Bacillus anthracis-specific phage AP50 with improved bacteriolytic activity.
    Appl Environ Microbiol Volume: 74 Page(s): 6792 - 6796
    11/01/2008 Authors: Sozhamannan S; McKinstry M; Lentz SM; Jalasvuori M; McAfee F; Smith A; Dabbs J; Ackermann H-W; Bamford JKH; Mateczun A
  • A Bacillus thuringiensis strain producing a polyglutamate capsule resembling that of Bacillus anthracis.
    FEMS Microbiol Lett Volume: 285 Page(s): 220 - 226
    08/01/2008 Authors: Cachat E; Barker M; Read TD; Priest FG
  • Genotyping of Bacillus cereus strains by microarray-based resequencing.
    PLoS One Volume: 3 Page(s): e2513
    07/02/2008 Authors: Zwick ME; Kiley MP; Stewart AC; Mateczun A; Read TD
  • Scaffolding and validation of bacterial genome assemblies using optical restriction maps.
    Bioinformatics Volume: 24 Page(s): 1229 - 1235
    05/15/2008 Authors: Nagarajan N; Read TD; Pop M
  • Genome sequence of a clinical isolate of Campylobacter jejuni from Thailand.
    Infect Immun Volume: 75 Page(s): 3425 - 3433
    07/01/2007 Authors: Poly F; Read T; Tribble DR; Baqar S; Lorenzo M; Guerry P
  • Genomic plasticity of the rrn-nqrF intergenic segment in the Chlamydiaceae.
    J Bacteriol Volume: 189 Page(s): 2128 - 2132
    03/01/2007 Authors: Liu Z; Rank R; Kaltenboeck B; Magnino S; Dean D; Burall L; Plaut RD; Read TD; Myers G; Bavoil PM
  • Whole genome comparisons of Campylobacter jejuni strains for use as human vaccine challenge strains
    ZOONOSES AND PUBLIC HEALTH Volume: 54 Page(s): 59 - 60
    01/01/2007 Authors: Poly F; Read T; Bodhidatta L; Serichantalergs O; Mason C; Darsley M; Monteiro M; Guerry P
  • PATHOGENOMICS OF BACTERIAL BIOTHREAT AGENTS
    Page(s): 232 - 266
    01/01/2007 Authors: Read TD; Thomason B
  • Strain-specific single-nucleotide polymorphism assays for the Bacillus anthracis Ames strain.
    J Clin Microbiol Volume: 45 Page(s): 47 - 53
    01/01/2007 Authors: Van Ert MN; Easterday WR; Simonson TS; U'Ren JM; Pearson T; Kenefic LJ; Busch JD; Huynh LY; Dukerich M; Trim CB
  • Sequencing Bacillus anthracis typing phages gamma and cherry reveals a common ancestry.
    J Bacteriol Volume: 188 Page(s): 3402 - 3408
    05/01/2006 Authors: Fouts DE; Rasko DA; Cer RZ; Jiang L; Fedorova NB; Shvartsbeyn A; Vamathevan JJ; Tallon L; Althoff R; Arbogast TS
  • The Bacillus anthracis chromosome contains four conserved, excision-proficient, putative prophages.
    BMC Microbiol Volume: 6 Page(s): 34
    04/06/2006 Authors: Sozhamannan S; Chute MD; McAfee FD; Fouts DE; Akmal A; Galloway DR; Mateczun A; Baillie LW; Read TD
  • Shuffling bacterial metabolomes.
    Genome Biol Volume: 7 Page(s): 204
    01/01/2006 Authors: Thomason B; Read TD
  • Microarray-based resequencing of multiple Bacillus anthracis isolates.
    Genome Biol Volume: 6 Page(s): R10
    01/01/2005 Authors: Zwick ME; Mcafee F; Cutler DJ; Read TD; Ravel J; Bowman GR; Galloway DR; Mateczun A
  • The bcr1 DNA repeat element is specific to the Bacillus cereus group and exhibits mobile element characteristics.
    J Bacteriol Volume: 186 Page(s): 7714 - 7725
    11/01/2004 Authors: kstad OA; Tourasse NJ; Stabell FB; Sundfaer CK; Egge-Jacobsen W; Risen PA; Read TD; Kolst A-B
  • Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath).
    PLoS Biol Volume: 2 Page(s): e303
    10/01/2004 Authors: Ward N; Larsen ; Sakwa J; Bruseth L; Khouri H; Durkin AS; Dimitrov G; Jiang L; Scanlan D; Kang KH
  • Phylogenetic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing.
    Proc Natl Acad Sci U S A Volume: 101 Page(s): 13536 - 13541
    09/14/2004 Authors: Pearson T; Busch JD; Ravel J; Read TD; Rhoton SD; U'Ren JM; Simonson TS; Kachur SM; Leadem RR; Cardon ML
  • Identification of anthrax toxin genes in a Bacillus cereus associated with an illness resembling inhalation anthrax.
    Proc Natl Acad Sci U S A Volume: 101 Page(s): 8449 - 8454
    06/01/2004 Authors: Hoffmaster AR; Ravel J; Rasko DA; Chapman GD; Chute MD; Marston CK; De BK; Sacchi CT; Fitzgerald C; Mayer LW
  • Comparative genomics of the Bacillus anthracis family: insights into physiology and evolution of a pathogenic species
    Volume: 18 Page(s): C225 - C226
    05/14/2004 Authors: Fraser C; Ravel J; Rasko D; Peterson S; Read T; Shumway M; Salzberg S
  • Horizontal transfer of CS1 pilin genes of enterotoxigenic Escherichia coli.
    J Bacteriol Volume: 186 Page(s): 3230 - 3237
    05/01/2004 Authors: Froehlich B; Holtzapple E; Read TD; Scott JR
  • Formation and composition of the Bacillus anthracis endospore.
    J Bacteriol Volume: 186 Page(s): 164 - 178
    01/01/2004 Authors: Liu H; Bergman NH; Thomason B; Shallom S; Hazen A; Crossno J; Rasko DA; Ravel J; Read TD; Peterson SN
  • The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1.
    Nucleic Acids Res Volume: 32 Page(s): 977 - 988
    01/01/2004 Authors: Rasko DA; Ravel J; kstad OA; Helgason E; Cer RZ; Jiang L; Shores KA; Fouts DE; Tourasse NJ; Angiuoli SV
  • The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria.
    Nature Volume: 423 Page(s): 81 - 86
    05/01/2003 Authors: Read TD; Peterson SN; Tourasse N; Baillie LW; Paulsen IT; Nelson KE; Tettelin H; Fouts DE; Eisen JA; Gill SR
  • Complete genome sequence of the Q-fever pathogen Coxiella burnetii.
    Proc Natl Acad Sci U S A Volume: 100 Page(s): 5455 - 5460
    04/29/2003 Authors: Seshadri R; Paulsen IT; Eisen JA; Read TD; Nelson KE; Nelson WC; Ward NL; Tettelin H; Davidsen TM; Beanan MJ
  • Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae.
    Nucleic Acids Res Volume: 31 Page(s): 2134 - 2147
    04/15/2003 Authors: Read TD; Myers GSA; Brunham RC; Nelson WC; Paulsen IT; Heidelberg J; Holtzapple E; Khouri H; Federova NB; Carty HA
  • Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis.
    Science Volume: 299 Page(s): 2071 - 2074
    03/28/2003 Authors: Paulsen IT; Banerjei L; Myers GSA; Nelson KE; Seshadri R; Read TD; Fouts DE; Eisen JA; Gill SR; Heidelberg JF
  • Molecular analysis of the multiple GroEL proteins of Chlamydiae.
    J Bacteriol Volume: 185 Page(s): 1958 - 1966
    03/01/2003 Authors: Karunakaran KP; Noguchi Y; Read TD; Cherkasov A; Kwee J; Shen C; Nelson CC; Brunham RC
  • Identification and characterization of the gerH operon of Bacillus anthracis endospores: a differential role for purine nucleosides in germination.
    J Bacteriol Volume: 185 Page(s): 1462 - 1464
    02/01/2003 Authors: Weiner MA; Read TD; Hanna PC
  • Microbial genome jambalaya.
    Genome Biol Volume: 4 Page(s): 314
    01/01/2003 Authors: Read TD
  • Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis.
    Nat Biotechnol Volume: 20 Page(s): 1118 - 1123
    11/01/2002 Authors: Heidelberg JF; Paulsen IT; Nelson KE; Gaidos EJ; Nelson WC; Read TD; Eisen JA; Seshadri R; Ward N; Methe B
  • The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts.
    Proc Natl Acad Sci U S A Volume: 99 Page(s): 13148 - 13153
    10/01/2002 Authors: Paulsen IT; Seshadri R; Nelson KE; Eisen JA; Heidelberg JF; Read TD; Dodson RJ; Umayam L; Brinkac LM; Beanan MJ
  • Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae.
    Proc Natl Acad Sci U S A Volume: 99 Page(s): 12391 - 12396
    09/17/2002 Authors: Tettelin H; Masignani V; Cieslewicz MJ; Eisen JA; Peterson S; Wessels MR; Paulsen IT; Nelson KE; Margarit I; Read TD
  • Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis.
    Science Volume: 296 Page(s): 2028 - 2033
    06/14/2002 Authors: Read TD; Salzberg SL; Pop M; Shumway M; Umayam L; Jiang L; Holtzapple E; Busch JD; Smith KL; Schupp JM
  • Restricting genome data won't stop bioterrorism.
    Nature Volume: 417 Page(s): 379
    05/23/2002 Authors: Read TD; Parkhill J
  • Finding drug targets in microbial genomes.
    Drug Discov Today Volume: 6 Page(s): 887 - 892
    09/01/2001 Authors: Read TD; Gill SR; Tettelin H; Dougherty BA
  • Complete genome sequence of a virulent isolate of Streptococcus pneumoniae.
    Science Volume: 293 Page(s): 498 - 506
    07/20/2001 Authors: Tettelin H; Nelson KE; Paulsen IT; Eisen JA; Read TD; Peterson S; Heidelberg J; DeBoy RT; Haft DH; Dodson RJ
  • Bacillus anthracis, a bug with attitude!
    Curr Opin Microbiol Volume: 4 Page(s): 78 - 81
    02/01/2001 Authors: Baillie L; Read TD
  • Nucleotide sequence analysis of hypervariable junctions of Haemophilus influenzae pilus gene clusters.
    Infect Immun Volume: 68 Page(s): 6896 - 6902
    12/01/2000 Authors: Read TD; Satola SW; Farley MM
  • DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae.
    Nature Volume: 406 Page(s): 477 - 483
    08/03/2000 Authors: Heidelberg JF; Eisen JA; Nelson WC; Clayton RA; Gwinn ML; Dodson RJ; Haft DH; Hickey EK; Peterson JD; Umayam L
  • Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39.
    Nucleic Acids Res Volume: 28 Page(s): 1397 - 1406
    03/15/2000 Authors: Read TD; Brunham RC; Shen C; Gill SR; Heidelberg JF; White O; Hickey EK; Peterson J; Utterback T; Berry K
  • Comparative analysis of Chlamydia bacteriophages reveals variation localized to a putative receptor binding domain.
    Microb Comp Genomics Volume: 5 Page(s): 223 - 231
    01/01/2000 Authors: Read TD; Fraser CM; Hsia RC; Bavoil PM
  • Copy number of pilus gene clusters in Haemophilus influenzae and variation in the hifE pilin gene.
    Infect Immun Volume: 66 Page(s): 1622 - 1631
    04/01/1998 Authors: Read TD; Satola SW; Opdyke JA; Farley MM
  • Genetic variation of haemophilus influenzae pilus adhesin genes
    JOURNAL OF INVESTIGATIVE MEDICINE Volume: 46 Page(s): 217A - 217A
    03/01/1998 Authors: Read TD; Satola SW; Opdyke JA; Farley MM
  • Conserved extragenic DNA elements in Haemophilus influenzae.
    Mol Microbiol Volume: 23 Page(s): 627 - 628
    02/01/1997 Authors: Read TD; Farley MM
  • Duplication of pilus gene complexes of Haemophilus influenzae biogroup aegyptius.
    J Bacteriol Volume: 178 Page(s): 6564 - 6570
    11/01/1996 Authors: Read TD; Dowdell M; Satola SW; Farley MM
  • Evasion of type I and type II DNA restriction systems by IncI1 plasmid CoIIb-P9 during transfer by bacterial conjugation.
    Mol Microbiol Volume: 6 Page(s): 1933 - 1941
    07/01/1992 Authors: Read TD; Thomas AT; Wilkins BM
  • SPENDTHRIFT TRUSTS IN WASHINGTON - THE STATUTORY RESTRAINT UPON INVOLUNTARY ALIENATION
    WASHINGTON LAW REVIEW Volume: 58 Page(s): 831 - 852
    01/01/1983 Authors: READ TW
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