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David Ussery

TitleProfessor
InstitutionUniversity of Arkansas for Medical Sciences
DepartmentBiomedical Informatics, College of Medicine
Address200 South Cedar
Mail Slot # 782
Little Rock AR 72202
Phone501-603-1766
ORCID ORCID Icon0000-0003-3632-5512 Additional info
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    Other Positions
    TitleProfessor
    InstitutionUniversity of Arkansas for Medical Sciences
    DepartmentPhysiology and Cell Biology, College of Medicine

    Other Roles
    Director, Arkansas Center for Ecological and Genomic Medicine (ArC-GEM)

    Collapse Overview 
    Collapse overview
    Founding Member, Genomic Standards Consortium (GSC)

    Associate Editor, Frontiers in Microbiology

    Advisory Board, EcoCyc, SRI, Palo Alto, California


    Collapse Biography 
    Collapse awards and honors
    2016Arkansas Research Alliance Fellow, Dept. Biomedical Informatics, COM
    2017Helen Adams & Arkansas Research Alliance Professor & Chair, Dept. Biomedical Informatics, COM

    Collapse Research 
    Collapse research activities and funding
    N/A - Advance Account     (OUNPRASEUTH, SONGTHIP T)Jun 1, 2024 - May 31, 2025
    NIH/National Institutes of Health - Pass Through: Duke University
    ECHO Supplement ESC Protocol 2024-2025
    Role: Principal Investigator
    1946391     (PRIOR, FRED)May 1, 2024 - Aug 31, 2024
    National Science Foundation - Pass Through: Arkansas Economic Development Commission
    DART Summer Undergraduate Research Experience-Autumn Gault
    Role: Co-Investigator
    1946391     (PRIOR, FRED)Jul 1, 2023 - Aug 31, 2024
    National Science Foundation - Pass Through: Arkansas Economic Development Commission
    Robust and Trusted Data Analytics (DART)
    Role: Principal Investigator
    24-EPS4-002     (USSERY, DAVID W)Jul 1, 2023 - Aug 31, 2024
    National Science Foundation - Pass Through: Arkansas Economic Development Commission
    DART GRA -Ussery year 4
    Role: Principal Investigator
    24-EPS4     (USSERY, DAVID W)Jul 1, 2023 - Jun 30, 2024
    National Science Foundation - Pass Through: Arkansas Economic Development Commission
    DART GRA -Ussery year 4
    Role: Principal Investigator
    P20GM121293     (BYRD, ALICIA K)Jul 1, 2022 - Jun 30, 2027
    NIH/Nat. Inst. of General Medical Sciences - Pass Through: Arkansas Children's Research Institute
    Role of HELB in the Replication Stress Response Dr. Tacketts COBRA through ACRI
    Role: Co-Investigator
    OIA-1946391     (PRIOR, FRED)Jul 1, 2022 - Aug 31, 2023
    National Science Foundation - Pass Through: Arkansas Economic Development Commission
    Robust and Trusted Data Analytics: From Smart Curation to Socially Aware Decision Making (Area 1, Coordinated Data Science Cyber Infrastructure) Year 3
    Role: Principal Investigator
    22-EPS4     (USSERY, DAVID W)Jul 1, 2021 - Aug 31, 2022
    National Science Foundation - Pass Through: Arkansas Economic Development Commission
    DART GRA - Originally was submitted as a continuation of FP54713
    Role: Principal Investigator
    22-EPS4-0012     (USSERY, DAVID W)Jul 1, 2021 - Aug 31, 2022
    National Science Foundation - Pass Through: Arkansas Economic Development Commission
    DART GRA - Originally was submitted as a continuation of FP54713
    Role: Principal Investigator
    U54TR001629     (JAMES, LAURA P)Sep 26, 2017 - Aug 31, 2019
    NIH
    Expanding Translational Research in Arkansas
    Role: Co-Investigator
    OIA     (LARSON-PRIOR, LINDA)Sep 1, 2016 - Aug 31, 2020
    National Science Foundation - Pass Through: Louisiana Tech University
    RII Track-2 FEC- Probing and Understanding the Brain: Micro and Macro Dynamics of Seizure and Memory Networks
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse additional bibliographic sources
    The links below are provided by the researcher to provide access to external online bibliographies that they keep independently from the Profiles System.
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions. Don't see publications published under other names? Login to add alternative names.
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    1. Wassenaar TM, Harville T, Chastain J, Wanchai V, Ussery DW. DNA structural features and variability of complete MHC locus sequences. Front Bioinform. 2024; 4:1392613. PMID: 39022183.
      View in: PubMed
    2. Kandel S, Hartzell SL, Ingold AK, Turner GA, Kennedy JL, Ussery DW. Genomic surveillance of SARS-CoV-2 using long-range PCR primers. Front Microbiol. 2024; 15:1272972. PMID: 38440140.
      View in: PubMed
    3. Kandel S, Hartzell SL, Ingold AK, Turner GA, Kennedy JL, Ussery DW. Genomic Surveillance of SARS-CoV-2 Using Long-Range PCR Primers. bioRxiv. 2023 Jul 11. PMID: 37502853.
      View in: PubMed
    4. Wong L, Randolph C, Kanwischer E, Ingold A, Boyanton BL, Taylor J, Frenner RA, Harley SE, Bird JT, Thurman TJ, Kandel S, Ussery DW, Byrum SD, Dinwiddie D, Domman D, Chalwadi UK, Kennedy J. Severe Acute Respiratory Syndrome Coronavirus-2 Lambda Variant Collected from a Child from Arkansas and Sequenced. Microbiol Resour Announc. 2023 Mar 16; 12(3):e0000723. PMID: 36779742.
      View in: PubMed
    5. Wassenaar TM, Ussery DW, Rosel AC. Big data in genomic research for big questions with examples from covid-19 and other zoonoses. J Appl Microbiol. 2023 Jan 23; 134(1). PMID: 36626787.
      View in: PubMed
    6. Wassenaar TM, Wanchai V, Ussery DW. Comparison of Monkeypox virus genomes from the 2017 Nigeria outbreak and the 2022 outbreak. J Appl Microbiol. 2022 Dec; 133(6):3690-3698. PMID: 36074056.
      View in: PubMed
    7. Wassenaar TM, Wanchai V, Buzard G, Ussery DW. The first three waves of the Covid-19 pandemic hint at a limited genetic repertoire for SARS-CoV-2. FEMS Microbiol Rev. 2022 05 06; 46(3). PMID: 35076068.
      View in: PubMed
    8. Alkam D, Wongsurawat T, Nookaew I, Richardson AR, Ussery D, Smeltzer MS, Jenjaroenpun P. Is amplification bias consequential in transposon sequencing (TnSeq) assays? A case study with a Staphylococcus aureus TnSeq library subjected to PCR-based and amplification-free enrichment methods. Microb Genom. 2021 10; 7(10). PMID: 34596508.
      View in: PubMed
    9. Abram K, Udaondo Z, Bleker C, Wanchai V, Wassenaar TM, Robeson MS, Ussery DW. Mash-based analyses of Escherichia coli genomes reveal 14 distinct phylogroups. Commun Biol. 2021 01 26; 4(1):117. PMID: 33500552.
      View in: PubMed
    10. Jenjaroenpun P, Wongsurawat T, Wadley TD, Wassenaar TM, Liu J, Dai Q, Wanchai V, Akel NS, Jamshidi-Parsian A, Franco AT, Boysen G, Jennings ML, Ussery DW, He C, Nookaew I. Decoding the epitranscriptional landscape from native RNA sequences. Nucleic Acids Res. 2021 01 25; 49(2):e7. PMID: 32710622.
      View in: PubMed
    11. Jenjaroenpun P, Wanchai V, Ono-Moore KD, Laudadio J, James LP, Adams SH, Prior F, Nookaew I, Ussery DW, Wongsurawat T. Two SARS-CoV-2 Genome Sequences of Isolates from Rural U.S. Patients Harboring the D614G Mutation, Obtained Using Nanopore Sequencing. Microbiol Resour Announc. 2020 Dec 17; 10(1). PMID: 33334896.
      View in: PubMed
    12. Wanchai V, Nookaew I, Ussery DW. ProdMX: Rapid query and analysis of protein functional domain based on compressed sparse matrices. Comput Struct Biotechnol J. 2020; 18:3890-3896. PMID: 33335686.
      View in: PubMed
    13. Patel L, Shukla T, Huang X, Ussery DW, Wang S. Machine Learning Methods in Drug Discovery. Molecules. 2020 Nov 12; 25(22). PMID: 33198233.
      View in: PubMed
    14. Wongsurawat T, Jenjaroenpun P, De Loose A, Alkam D, Ussery DW, Nookaew I, Leung YK, Ho SM, Day JD, Rodriguez A. A novel Cas9-targeted long-read assay for simultaneous detection of IDH1/2 mutations and clinically relevant MGMT methylation in fresh biopsies of diffuse glioma. Acta Neuropathol Commun. 2020 06 20; 8(1):87. PMID: 32563269.
      View in: PubMed
    15. Kandel S, Sripiboon S, Jenjaroenpun P, Ussery DW, Nookaew I, Robeson MS, Wongsurawat T. 16S rRNA Gene Amplicon Profiling of Baby and Adult Captive Elephants in Thailand. Microbiol Resour Announc. 2020 Jun 11; 9(24). PMID: 32527771.
      View in: PubMed
    16. Udaondo Z, Jenjaroenpun P, Wongsurawat T, Meyers E, Anderson C, Lopez J, Mohan M, Tytarenko R, Walker B, Ussery D, Kothari A, Jun SR. Two Cases of Vancomycin-Resistant Enterococcus faecium Bacteremia With Development of Daptomycin-Resistant Phenotype and its Detection Using Oxford Nanopore Sequencing. Open Forum Infect Dis. 2020 Jun; 7(6):ofaa180. PMID: 32550237.
      View in: PubMed
    17. Cleveland MH, Anekella B, Brewer M, Chin PJ, Couch H, Delwart E, Huggett J, Jackson S, Martin J, Monpoeho S, Morrison T, Ng SHS, Ussery D, Khan AS. Report of the 2019 NIST-FDA workshop on standards for next generation sequencing detection of viral adventitious agents in biologics and biomanufacturing. Biologicals. 2020 Mar; 64:76-82. PMID: 32094072.
      View in: PubMed
    18. Jenjaroenpun P, Wongsurawat T, Udaondo Z, Anderson C, Lopez J, Mohan M, Tytarenko R, Walker B, Nookaew I, Ussery D, Kothari A, Jun SR. Complete Genome Sequences of Four Isolates of Vancomycin-Resistant Enterococcus faecium with the vanA Gene and Two Daptomycin Resistance Mutations, Obtained from Two Inpatients with Prolonged Bacteremia. Microbiol Resour Announc. 2020 Feb 06; 9(6). PMID: 32029568.
      View in: PubMed
    19. Wassenaar TM, Jun SR, Robeson M, Ussery DW. Comparative genomics of hepatitis A virus, hepatitis C virus, and hepatitis E virus provides insights into the evolutionary history of Hepatovirus species. Microbiologyopen. 2020 02; 9(2):e973. PMID: 31742930.
      View in: PubMed
    20. Wongsurawat T, Nakagawa M, Atiq O, Coleman HN, Jenjaroenpun P, Allred JI, Trammel A, Puengrang P, Ussery DW, Nookaew I. An assessment of Oxford Nanopore sequencing for human gut metagenome profiling: A pilot study of head and neck cancer patients. J Microbiol Methods. 2019 11; 166:105739. PMID: 31626891.
      View in: PubMed
    21. Gomez-Acevedo H, Patterson JD, Sardar S, Gokden M, Das BC, Ussery DW, Rodriguez A. SMARC-B1 deficient sinonasal carcinoma metastasis to the brain with next generation sequencing data: a case report of perineural invasion progressing to leptomeningeal invasion. BMC Cancer. 2019 Aug 22; 19(1):827. PMID: 31438887.
      View in: PubMed
    22. Alkam D, Jenjaroenpun P, Wongsurawat T, Udaondo Z, Patumcharoenpol P, Robeson M, Haselow D, Mason W, Nookaew I, Ussery D, Jun SR. Genomic characterization of mumps viruses from a large-scale mumps outbreak in Arkansas, 2016. Infect Genet Evol. 2019 11; 75:103965. PMID: 31319177.
      View in: PubMed
    23. Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Mu?oz AR, Roberts RJ, Rossell?-M?ra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I. Consent insufficient for data release-Response. Science. 2019 05 03; 364(6439):446. PMID: 31048484.
      View in: PubMed
    24. Wassenaar TM, Wanchai V, Buzard GS, Ussery DW. In silico Selection of Amplification Targets for Rapid Polymorphism Screening in Ebola Virus Outbreaks. Front Microbiol. 2019; 10:857. PMID: 31080442.
      View in: PubMed
    25. Udaondo Z, Wongsurawat T, Jenjaroenpun P, Anderson C, Lopez J, Mohan M, Tytarenko R, Walker B, Nookaew I, Ussery D, Kothari A, Jun SR. Draft Genome Sequences of 48 Vancomycin-Resistant Enterococcus faecium Strains Isolated from Inpatients with Bacteremia and Urinary Tract Infection. Microbiol Resour Announc. 2019 Apr 11; 8(15). PMID: 30975810.
      View in: PubMed
    26. Bavineni M, Wassenaar TM, Agnihotri K, Ussery DW, L?scher TF, Mehta JL. Mechanisms linking preterm birth to onset of cardiovascular disease later in adulthood. Eur Heart J. 2019 04 07; 40(14):1107-1112. PMID: 30753448.
      View in: PubMed
    27. Gurley BJ, Miousse IR, Nookaew I, Ewing LE, Skinner CM, Jenjaroenpun P, Wongsurawat T, Kennon-McGill S, Avula B, Bae JY, McGill MR, Ussery D, Khan IA, Koturbash I. Decaffeinated Green Tea Extract Does Not Elicit Hepatotoxic Effects and Modulates the Gut Microbiome in Lean B6C3F1 Mice. Nutrients. 2019 Apr 03; 11(4). PMID: 30987244.
      View in: PubMed
    28. Wadley TD, Jenjaroenpun P, Wongsurawat T, Ussery DW, Nookaew I. Complete Genome and Plasmid Sequences of Escherichia coli Type Strain ATCC 11775. Microbiol Resour Announc. 2019 Feb; 8(9). PMID: 30834378.
      View in: PubMed
    29. Wongsurawat T, Jenjaroenpun P, Taylor MK, Lee J, Tolardo AL, Parvathareddy J, Kandel S, Wadley TD, Kaewnapan B, Athipanyasilp N, Skidmore A, Chung D, Chaimayo C, Whitt M, Kantakamalakul W, Sutthent R, Horthongkham N, Ussery DW, Jonsson CB, Nookaew I. Rapid Sequencing of Multiple RNA Viruses in Their Native Form. Front Microbiol. 2019; 10:260. PMID: 30858830.
      View in: PubMed
    30. Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Mu?oz AR, Roberts RJ, Rossell?-M?ra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I. Toward unrestricted use of public genomic data. Science. 2019 01 25; 363(6425):350-352. PMID: 30679363.
      View in: PubMed
    31. Wongsurawat T, Jenjaroenpun P, Athipanyasilp N, Kaewnapan B, Leelahakorn N, Angkasekwinai N, Kantakamalakul W, Sutthent R, Ussery DW, Horthongkham N, Nookaew I. Genome Sequences of Zika Virus Strains Recovered from Amniotic Fluid, Placenta, and Fetal Brain of a Microcephaly Patient in Thailand, 2017. Microbiol Resour Announc. 2018 Sep; 7(11). PMID: 30533643.
      View in: PubMed
    32. Wongsurawat T, Athipanyasilp N, Jenjaroenpun P, Jun SR, Kaewnapan B, Wassenaar TM, Leelahakorn N, Angkasekwinai N, Kantakamalakul W, Ussery DW, Sutthent R, Nookaew I, Horthongkham N. Case of Microcephaly after Congenital Infection with Asian Lineage Zika Virus, Thailand. Emerg Infect Dis. 2018 09; 24(9). PMID: 29985788.
      View in: PubMed
    33. Apopa PL, Alley L, Penney RB, Arnaoutakis K, Steliga MA, Jeffus S, Bircan E, Gopalan B, Jin J, Patumcharoenpol P, Jenjaroenpun P, Wongsurawat T, Shah N, Boysen G, Ussery D, Nookaew I, Fagan P, Bebek G, Orloff MS. PARP1 Is Up-Regulated in Non-small Cell Lung Cancer Tissues in the Presence of the Cyanobacterial Toxin Microcystin. Front Microbiol. 2018; 9:1757. PMID: 30127774.
      View in: PubMed
    34. Jenjaroenpun P, Wongsurawat T, Pereira R, Patumcharoenpol P, Ussery DW, Nielsen J, Nookaew I. Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D. Nucleic Acids Res. 2018 04 20; 46(7):e38. PMID: 29346625.
      View in: PubMed
    35. Cabal A, Jun SR, Jenjaroenpun P, Wanchai V, Nookaew I, Wongsurawat T, Burgess MJ, Kothari A, Wassenaar TM, Ussery DW. Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes. Microb Ecol. 2018 Oct; 76(3):801-813. PMID: 29445826.
      View in: PubMed
    36. Wanchai V, Patumcharoenpol P, Nookaew I, Ussery D. dBBQs: dataBase of Bacterial Quality scores. BMC Bioinformatics. 2017 12 28; 18(Suppl 14):483. PMID: 29297289.
      View in: PubMed
    37. Jun SR, Wassenaar TM, Wanchai V, Patumcharoenpol P, Nookaew I, Ussery DW. Suggested mechanisms for Zika virus causing microcephaly: what do the genomes tell us? BMC Bioinformatics. 2017 12 28; 18(Suppl 14):471. PMID: 29297281.
      View in: PubMed
    38. Alkam D, Wongsurawat T, Jenjaroenpun P, Connor S, Hobbs C, Wassenaar TM, Jun SR, Nookaew I, Ussery D. Three Complete Genome Sequences of Genotype G Mumps Virus from the 2016 Outbreak in Arkansas, USA. Genome Announc. 2017 Aug 10; 5(32). PMID: 28798162.
      View in: PubMed
    39. Zhang Q, Jun SR, Leuze M, Ussery D, Nookaew I. Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer. Sci Rep. 2017 01 19; 7:40712. PMID: 28102365.
      View in: PubMed
    40. Poudel S, Giannone RJ, Rodriguez M, Raman B, Martin MZ, Engle NL, Mielenz JR, Nookaew I, Brown SD, Tschaplinski TJ, Ussery D, Hettich RL. Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass. Biotechnol Biofuels. 2017; 10:14. PMID: 28077967.
      View in: PubMed
    41. Wassenaar TM, Ussery DW, Ingmer H. The qacC Gene Has Recently Spread between Rolling Circle Plasmids of Staphylococcus, Indicative of a Novel Gene Transfer Mechanism. Front Microbiol. 2016; 7:1528. PMID: 27729906.
      View in: PubMed
    42. Leekitcharoenphon P, Hendriksen RS, Le Hello S, Weill FX, Baggesen DL, Jun SR, Ussery DW, Lund O, Crook DW, Wilson DJ, Aarestrup FM. Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104. Appl Environ Microbiol. 2016 Apr; 82(8):2516-26. PMID: 26944846.
      View in: PubMed
    43. Jun SR, Wassenaar TM, Nookaew I, Hauser L, Wanchai V, Land M, Timm CM, Lu TY, Schadt CW, Doktycz MJ, Pelletier DA, Ussery DW. Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis. Appl Environ Microbiol. 2016 01 01; 82(1):375-83. PMID: 26519390.
      View in: PubMed
    44. Timm CM, Campbell AG, Utturkar SM, Jun SR, Parales RE, Tan WA, Robeson MS, Lu TY, Jawdy S, Brown SD, Ussery DW, Schadt CW, Tuskan GA, Doktycz MJ, Weston DJ, Pelletier DA. Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment. Front Microbiol. 2015; 6:1118. PMID: 26528266.
      View in: PubMed
    45. Espinoza-Valles I, Vora GJ, Lin B, Leekitcharoenphon P, Gonz?lez-Castillo A, Ussery D, H?j L, Gomez-Gil B. Unique and conserved genome regions in Vibrio harveyi and related species in comparison with the shrimp pathogen Vibrio harveyi CAIM 1792. Microbiology (Reading). 2015 Sep; 161(9):1762-1779. PMID: 26198743.
      View in: PubMed
    46. Jun SR, Leuze MR, Nookaew I, Uberbacher EC, Land M, Zhang Q, Wanchai V, Chai J, Nielsen M, Trolle T, Lund O, Buzard GS, Pedersen TD, Wassenaar TM, Ussery DW. Ebolavirus comparative genomics. FEMS Microbiol Rev. 2015 Sep; 39(5):764-78. PMID: 26175035.
      View in: PubMed
    47. Wassenaar TM, Ussery D, Nielsen LN, Ingmer H. Review and phylogenetic analysis of qac genes that reduce susceptibility to quaternary ammonium compounds in Staphylococcus species. Eur J Microbiol Immunol (Bp). 2015 Mar; 5(1):44-61. PMID: 25883793.
      View in: PubMed
    48. Land M, Hauser L, Jun SR, Nookaew I, Leuze MR, Ahn TH, Karpinets T, Lund O, Kora G, Wassenaar T, Poudel S, Ussery DW. Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics. 2015 Mar; 15(2):141-61. PMID: 25722247.
      View in: PubMed
    49. Beatson SA, Ben Zakour NL, Totsika M, Forde BM, Watts RE, Mabbett AN, Szubert JM, Sarkar S, Phan MD, Peters KM, Petty NK, Alikhan NF, Sullivan MJ, Gawthorne JA, Stanton-Cook M, Nhu NT, Chong TM, Yin WF, Chan KG, Hancock V, Ussery DW, Ulett GC, Schembri MA. Molecular analysis of asymptomatic bacteriuria Escherichia coli strain VR50 reveals adaptation to the urinary tract by gene acquisition. Infect Immun. 2015 May; 83(5):1749-64. PMID: 25667270.
      View in: PubMed
    50. Ali A, Naz A, Soares SC, Bakhtiar M, Tiwari S, Hassan SS, Hanan F, Ramos R, Pereira U, Barh D, Figueiredo HC, Ussery DW, Miyoshi A, Silva A, Azevedo V. Pan-genome analysis of human gastric pathogen H. pylori: comparative genomics and pathogenomics approaches to identify regions associated with pathogenicity and prediction of potential core therapeutic targets. Biomed Res Int. 2015; 2015:139580. PMID: 25705648.
      View in: PubMed
    51. Thompson CC, Amaral GR, Campe?o M, Edwards RA, Polz MF, Dutilh BE, Ussery DW, Sawabe T, Swings J, Thompson FL. Microbial taxonomy in the post-genomic era: rebuilding from scratch? Arch Microbiol. 2015 Apr; 197(3):359-70. PMID: 25533848.
      View in: PubMed
    52. Land ML, Hyatt D, Jun SR, Kora GH, Hauser LJ, Lukjancenko O, Ussery DW. Quality scores for 32,000 genomes. Stand Genomic Sci. 2014; 9:20. PMID: 25780509.
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    53. Haugum K, Johansen J, Gabrielsen C, Brandal LT, Bergh K, Ussery DW, Drabl?s F, Afset JE. Comparative genomics to delineate pathogenic potential in non-O157 Shiga toxin-producing Escherichia coli (STEC) from patients with and without haemolytic uremic syndrome (HUS) in Norway. PLoS One. 2014; 9(10):e111788. PMID: 25360710.
      View in: PubMed
    54. Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Dor? J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, L?onard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, S?rensen S, Tap J, Tims S, Ussery DW, Yamada T, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat Biotechnol. 2014 Aug; 32(8):822-8. PMID: 24997787.
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    55. Lukjancenko O, Ussery DW. Vibrio chromosome-specific families. Front Microbiol. 2014; 5:73. PMID: 24672511.
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    56. Larsen MV, Cosentino S, Lukjancenko O, Saputra D, Rasmussen S, Hasman H, Sicheritz-Pont?n T, Aarestrup FM, Ussery DW, Lund O. Benchmarking of methods for genomic taxonomy. J Clin Microbiol. 2014 May; 52(5):1529-39. PMID: 24574292.
      View in: PubMed
    57. Field D, Sterk P, Kottmann R, De Smet JW, Amaral-Zettler L, Cochrane G, Cole JR, Davies N, Dawyndt P, Garrity GM, Gilbert JA, Gl?ckner FO, Hirschman L, Klenk HP, Knight R, Kyrpides N, Meyer F, Karsch-Mizrachi I, Morrison N, Robbins R, San Gil I, Sansone S, Schriml L, Tatusova T, Ussery D, Yilmaz P, White O, Wooley J, Caporaso G. Genomic standards consortium projects. Stand Genomic Sci. 2014 Jun 15; 9(3):599-601. PMID: 25197446.
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    58. Vesth T, Ozen A, Andersen SC, Kaas RS, Lukjancenko O, Bohlin J, Nookaew I, Wassenaar TM, Ussery DW. Veillonella, Firmicutes: Microbes disguised as Gram negatives. Stand Genomic Sci. 2013 Dec 20; 9(2):431-48. PMID: 24976898.
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    59. Jensen DB, Ussery DW. Bayesian prediction of microbial oxygen requirement. F1000Res. 2013; 2:184. PMID: 26913185.
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    60. Cook H, Ussery DW. Sigma factors in a thousand E. coli genomes. Environ Microbiol. 2013 Dec; 15(12):3121-9. PMID: 23992563.
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    61. Bohlin J, Brynildsrud O, Vesth T, Skjerve E, Ussery DW. Amino acid usage is asymmetrically biased in AT- and GC-rich microbial genomes. PLoS One. 2013; 8(7):e69878. PMID: 23922837.
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    62. Vesth T, Lagesen K, Acar ?, Ussery D. CMG-biotools, a free workbench for basic comparative microbial genomics. PLoS One. 2013; 8(4):e60120. PMID: 23577086.
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    63. Holch A, Webb K, Lukjancenko O, Ussery D, Rosenthal BM, Gram L. Genome sequencing identifies two nearly unchanged strains of persistent Listeria monocytogenes isolated at two different fish processing plants sampled 6 years apart. Appl Environ Microbiol. 2013 May; 79(9):2944-51. PMID: 23435887.
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    64. Jensen DB, Vesth TC, Hallin PF, Pedersen AG, Ussery DW. Bayesian prediction of bacterial growth temperature range based on genome sequences. BMC Genomics. 2012; 13 Suppl 7:S3. PMID: 23282160.
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    65. Acevedo-Rocha CG, Fang G, Schmidt M, Ussery DW, Danchin A. From essential to persistent genes: a functional approach to constructing synthetic life. Trends Genet. 2013 May; 29(5):273-9. PMID: 23219343.
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    66. Kaas RS, Friis C, Ussery DW, Aarestrup FM. Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes. BMC Genomics. 2012 Oct 31; 13:577. PMID: 23114024.
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    67. Mekalanos JJ, Robins W, Ussery DW, Davis BM, Schadt E, Waldor MK. Non-O1 Vibrio cholerae unlinked to cholera in Haiti. Proc Natl Acad Sci U S A. 2012 Nov 20; 109(47):E3206; author reply E3207. PMID: 23035253.
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    68. Snipen LG, Ussery DW. A domain sequence approach to pangenomics: applications to Escherichia coli. F1000Res. 2012; 1:19. PMID: 24555018.
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    69. Rodriguez-Valera F, Ussery DW. Is the pan-genome also a pan-selectome? F1000Res. 2012; 1:16. PMID: 24358823.
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    70. Zakham F, Aouane O, Ussery D, Benjouad A, Ennaji MM. Computational genomics-proteomics and Phylogeny analysis of twenty one mycobacterial genomes (Tuberculosis & non Tuberculosis strains). Microb Inform Exp. 2012 Aug 28; 2(1):7. PMID: 22929624.
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    71. Snipen L, Wassenaar TM, Altermann E, Olson J, Kathariou S, Lagesen K, Takamiya M, Kn?chel S, Ussery DW, Meinersmann RJ. Analysis of evolutionary patterns of genes in Campylobacter jejuni and C. coli. Microb Inform Exp. 2012 Aug 28; 2(1):8. PMID: 22929701.
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    72. Ali A, Soares SC, Santos AR, Guimar?es LC, Barbosa E, Almeida SS, Abreu VA, Carneiro AR, Ramos RT, Bakhtiar SM, Hassan SS, Ussery DW, On S, Silva A, Schneider MP, Lage AP, Miyoshi A, Azevedo V. Campylobacter fetus subspecies: comparative genomics and prediction of potential virulence targets. Gene. 2012 Oct 25; 508(2):145-56. PMID: 22890137.
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    73. Dillon SC, Espinosa E, Hokamp K, Ussery DW, Casades?s J, Dorman CJ. LeuO is a global regulator of gene expression in Salmonella enterica serovar Typhimurium. Mol Microbiol. 2012 Sep; 85(6):1072-89. PMID: 22804842.
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    74. Kr?ger C, Dillon SC, Cameron AD, Papenfort K, Sivasankaran SK, Hokamp K, Chao Y, Sittka A, H?brard M, H?ndler K, Colgan A, Leekitcharoenphon P, Langridge GC, Lohan AJ, Loftus B, Lucchini S, Ussery DW, Dorman CJ, Thomson NR, Vogel J, Hinton JC. The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium. Proc Natl Acad Sci U S A. 2012 May 15; 109(20):E1277-86. PMID: 22538806.
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    75. Ussery DW, Gordon SV. Two novel methods for using genome sequences to infer taxonomy. Microbiology (Reading). 2012 Jun; 158(Pt 6):1414. PMID: 22504434.
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    76. Leekitcharoenphon P, Lukjancenko O, Friis C, Aarestrup FM, Ussery DW. Genomic variation in Salmonella enterica core genes for epidemiological typing. BMC Genomics. 2012 Mar 12; 13:88. PMID: 22409488.
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    77. Bohlin J, van Passel MW, Snipen L, Kristoffersen AB, Ussery D, Hardy SP. Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands. BMC Genomics. 2012 Feb 10; 13:66. PMID: 22325062.
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    78. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Pont?n T, Ussery DW, Aarestrup FM, Lund O. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol. 2012 Apr; 50(4):1355-61. PMID: 22238442.
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    79. Gonzaga A, Martin-Cuadrado AB, L?pez-P?rez M, Megumi Mizuno C, Garc?a-Heredia I, Kimes NE, Lopez-Garc?a P, Moreira D, Ussery D, Zaballos M, Ghai R, Rodriguez-Valera F. Polyclonality of concurrent natural populations of Alteromonas macleodii. Genome Biol Evol. 2012; 4(12):1360-74. PMID: 23212172.
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    80. Lukjancenko O, Ussery DW, Wassenaar TM. Comparative genomics of Bifidobacterium, Lactobacillus and related probiotic genera. Microb Ecol. 2012 Apr; 63(3):651-73. PMID: 22031452.
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    81. Takamiya M, Ozen A, Rasmussen M, Alter T, Gilbert T, Ussery DW, Kn?chel S. Genome sequences of two stress-tolerant Campylobacter jejuni poultry strains, 305 and DFVF1099. J Bacteriol. 2011 Oct; 193(19):5546-7. PMID: 21914871.
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    82. ?zen AI, Ussery DW. Defining the Pseudomonas genus: where do we draw the line with Azotobacter? Microb Ecol. 2012 Feb; 63(2):239-48. PMID: 21811795.
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    83. Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, Garrity GM, Gilbert J, Gl?ckner FO, Hirschman L, Karsch-Mizrachi I, Klenk HP, Knight R, Kottmann R, Kyrpides N, Meyer F, San Gil I, Sansone SA, Schriml LM, Sterk P, Tatusova T, Ussery DW, White O, Wooley J. The Genomic Standards Consortium. PLoS Biol. 2011 Jun; 9(6):e1001088. PMID: 21713030.
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    84. Jacobsen A, Hendriksen RS, Aaresturp FM, Ussery DW, Friis C. The Salmonella enterica pan-genome. Microb Ecol. 2011 Oct; 62(3):487-504. PMID: 21643699.
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    85. Takamiya M, Ozen A, Rasmussen M, Alter T, Gilbert T, Ussery DW, Kn?chel S. Genome Sequence of Campylobacter jejuni strain 327, a strain isolated from a turkey slaughterhouse. Stand Genomic Sci. 2011 Apr 29; 4(2):113-22. PMID: 21677848.
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    86. Brede DA, Snipen LG, Ussery DW, Nederbragt AJ, Nes IF. Complete genome sequence of the commensal Enterococcus faecalis 62, isolated from a healthy Norwegian infant. J Bacteriol. 2011 May; 193(9):2377-8. PMID: 21398545.
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    87. Karlsson FH, Ussery DW, Nielsen J, Nookaew I. A closer look at bacteroides: phylogenetic relationship and genomic implications of a life in the human gut. Microb Ecol. 2011 Apr; 61(3):473-85. PMID: 21222211.
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    88. Friis C, Wassenaar TM, Javed MA, Snipen L, Lagesen K, Hallin PF, Newell DG, Toszeghy M, Ridley A, Manning G, Ussery DW. Genomic characterization of Campylobacter jejuni strain M1. PLoS One. 2010 Aug 26; 5(8):e12253. PMID: 20865039.
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    89. Bohlin J, Snipen L, Cloeckaert A, Lagesen K, Ussery D, Kristoffersen AB, Godfroid J. Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods. BMC Evol Biol. 2010 Aug 13; 10:249. PMID: 20707916.
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    90. Bohlin J, Snipen L, Hardy SP, Kristoffersen AB, Lagesen K, D?nsvik T, Skjerve E, Ussery DW. Analysis of intra-genomic GC content homogeneity within prokaryotes. BMC Genomics. 2010 Aug 06; 11:464. PMID: 20691090.
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    91. Lukjancenko O, Wassenaar TM, Ussery DW. Comparison of 61 sequenced Escherichia coli genomes. Microb Ecol. 2010 Nov; 60(4):708-20. PMID: 20623278.
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    92. Lav?n JL, Binnewies TT, Pisabarro AG, Ussery DW, Garc?a-Lobo JM, Oguiza JA. Differences in two-component signal transduction proteins among the genus Brucella: implications for host preference and pathogenesis. Vet Microbiol. 2010 Aug 26; 144(3-4):478-83. PMID: 20153589.
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    93. Snipen L, Ussery DW. Standard operating procedure for computing pangenome trees. Stand Genomic Sci. 2010 Jan 28; 2(1):135-41. PMID: 21304685.
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    94. Davenport C, Ussery DW, T?mmler B. Comparative genomics of green sulfur bacteria. Photosynth Res. 2010 Jun; 104(2-3):137-52. PMID: 20099081.
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    95. Lav?n JL, Ram?rez L, Ussery DW, Pisabarro AG, Oguiza JA. Genomic analysis of two-component signal transduction proteins in basidiomycetes. J Mol Microbiol Biotechnol. 2010; 18(2):63-73. PMID: 20110730.
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    96. Lagesen K, Ussery DW, Wassenaar TM. Genome update: the 1000th genome--a cautionary tale. Microbiology (Reading). 2010 Mar; 156(Pt 3):603-608. PMID: 20093288.
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    97. Vesth T, Wassenaar TM, Hallin PF, Snipen L, Lagesen K, Ussery DW. On the origins of a Vibrio species. Microb Ecol. 2010 Jan; 59(1):1-13. PMID: 19830476.
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    98. Thompson CC, Vicente AC, Souza RC, Vasconcelos AT, Vesth T, Alves N, Ussery DW, Iida T, Thompson FL. Genomic taxonomy of Vibrios. BMC Evol Biol. 2009 Oct 27; 9:258. PMID: 19860885.
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    99. Bohlin J, Skjerve E, Ussery DW. Analysis of genomic signatures in prokaryotes using multinomial regression and hierarchical clustering. BMC Genomics. 2009 Oct 21; 10:487. PMID: 19845945.
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    100. Hallin PF, St?rfeldt HH, Rotenberg E, Binnewies TT, Benham CJ, Ussery DW. GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes. Stand Genomic Sci. 2009 Sep 25; 1(2):204-15. PMID: 21304658.
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    101. Snipen L, Alm?y T, Ussery DW. Microbial comparative pan-genomics using binomial mixture models. BMC Genomics. 2009 Aug 19; 10:385. PMID: 19691844.
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    102. Wassenaar TM, Bohlin J, Binnewies TT, Ussery DW. Genome comparison of bacterial pathogens. Genome Dyn. 2009; 6:1-20. PMID: 19696490.
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    103. Ussery DW, Kiil K, Lagesen K, Sicheritz-Pont?n T, Bohlin J, Wassenaar TM. The genus burkholderia: analysis of 56 genomic sequences. Genome Dyn. 2009; 6:140-157. PMID: 19696499.
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    104. Bohlin J, Hardy SP, Ussery DW. Stretches of alternating pyrimidine/purines and purines are respectively linked with pathogenicity and growth temperature in prokaryotes. BMC Genomics. 2009 Jul 31; 10:346. PMID: 19646265.
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    105. Garrity GM, Thompson LM, Ussery DW, Paskin N, Baker D, Desmeth P, Schindel DE, Ong PS. Studies on monitoring and tracking genetic resources: an executive summary. Stand Genomic Sci. 2009 Jul 20; 1(1):78-86. PMID: 21304641.
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    106. Wortman JR, Gilsenan JM, Joardar V, Deegan J, Clutterbuck J, Andersen MR, Archer D, Bencina M, Braus G, Coutinho P, von D?hren H, Doonan J, Driessen AJ, Durek P, Espeso E, Fekete E, Flipphi M, Estrada CG, Geysens S, Goldman G, de Groot PW, Hansen K, Harris SD, Heinekamp T, Helmstaedt K, Henrissat B, Hofmann G, Homan T, Horio T, Horiuchi H, James S, Jones M, Karaffa L, Kar?nyi Z, Kato M, Keller N, Kelly DE, Kiel JA, Kim JM, van der Klei IJ, Klis FM, Kovalchuk A, Krasevec N, Kubicek CP, Liu B, Maccabe A, Meyer V, Mirabito P, Miskei M, Mos M, Mullins J, Nelson DR, Nielsen J, Oakley BR, Osmani SA, Pakula T, Paszewski A, Paulsen I, Pilsyk S, P?csi I, Punt PJ, Ram AF, Ren Q, Robellet X, Robson G, Seiboth B, van Solingen P, Specht T, Sun J, Taheri-Talesh N, Takeshita N, Ussery D, vanKuyk PA, Visser H, van de Vondervoort PJ, de Vries RP, Walton J, Xiang X, Xiong Y, Zeng AP, Brandt BW, Cornell MJ, van den Hondel CA, Visser J, Oliver SG, Turner G. The 2008 update of the Aspergillus nidulans genome annotation: a community effort. Fungal Genet Biol. 2009 Mar; 46 Suppl 1:S2-13. PMID: 19146970.
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    107. Wang K, Ussery DW, Brunak S. Analysis and prediction of gene splice sites in four Aspergillus genomes. Fungal Genet Biol. 2009 Mar; 46 Suppl 1:S14-8. PMID: 18948220.
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    108. Boyd EF, Cohen AL, Naughton LM, Ussery DW, Binnewies TT, Stine OC, Parent MA. Molecular analysis of the emergence of pandemic Vibrio parahaemolyticus. BMC Microbiol. 2008 Jun 30; 8:110. PMID: 18590559.
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    109. Lee KB, De Backer P, Aono T, Liu CT, Suzuki S, Suzuki T, Kaneko T, Yamada M, Tabata S, Kupfer DM, Najar FZ, Wiley GB, Roe B, Binnewies TT, Ussery DW, D'Haeze W, Herder JD, Gevers D, Vereecke D, Holsters M, Oyaizu H. The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571. BMC Genomics. 2008 Jun 04; 9:271. PMID: 18522759.
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    110. Garrity GM, Field D, Kyrpides N, Hirschman L, Sansone SA, Angiuoli S, Cole JR, Gl?ckner FO, Kolker E, Kowalchuk G, Moran MA, Ussery D, White O. Toward a standards-compliant genomic and metagenomic publication record. OMICS. 2008 Jun; 12(2):157-60. PMID: 18564916.
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    111. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Gl?ckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008 May; 26(5):541-7. PMID: 18464787.
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    112. Hancock V, Seshasayee AS, Ussery DW, Luscombe NM, Klemm P. Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972. Mol Genet Genomics. 2008 May; 279(5):523-34. PMID: 18317809.
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    113. Bohlin J, Skjerve E, Ussery DW. Investigations of oligonucleotide usage variance within and between prokaryotes. PLoS Comput Biol. 2008 Apr 18; 4(4):e1000057. PMID: 18421372.
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    114. Hallin PF, Binnewies TT, Ussery DW. The genome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology. Mol Biosyst. 2008 May; 4(5):363-71. PMID: 18414733.
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    115. Bohlin J, Skjerve E, Ussery DW. Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes. BMC Genomics. 2008 Feb 28; 9:104. PMID: 18307761.
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    116. Miller WG, Parker CT, Rubenfield M, Mendz GL, W?sten MM, Ussery DW, Stolz JF, Binnewies TT, Hallin PF, Wang G, Malek JA, Rogosin A, Stanker LH, Mandrell RE. The complete genome sequence and analysis of the epsilonproteobacterium Arcobacter butzleri. PLoS One. 2007 Dec 26; 2(12):e1358. PMID: 18159241.
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    117. Reva ON, Hallin PF, Willenbrock H, Sicheritz-Ponten T, T?mmler B, Ussery DW. Global features of the Alcanivorax borkumensis SK2 genome. Environ Microbiol. 2008 Mar; 10(3):614-25. PMID: 18081853.
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    118. Coenye T, Drevinek P, Mahenthiralingam E, Shah SA, Gill RT, Vandamme P, Ussery DW. Identification of putative noncoding RNA genes in the Burkholderia cenocepacia J2315 genome. FEMS Microbiol Lett. 2007 Nov; 276(1):83-92. PMID: 17937666.
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    119. Lav?n JL, Kiil K, Resano O, Ussery DW, Oguiza JA. Comparative genomic analysis of two-component regulatory proteins in Pseudomonas syringae. BMC Genomics. 2007 Oct 31; 8:397. PMID: 17971244.
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    120. Arvas M, Kivioja T, Mitchell A, Saloheimo M, Ussery D, Penttila M, Oliver S. Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina. BMC Genomics. 2007 Sep 17; 8:325. PMID: 17868481.
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    121. Lagesen K, Hallin P, R?dland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007; 35(9):3100-8. PMID: 17452365.
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    122. Willenbrock H, Ussery DW. Prediction of highly expressed genes in microbes based on chromatin accessibility. BMC Mol Biol. 2007 Feb 13; 8:11. PMID: 17295928.
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    123. Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, Turner G, de Vries RP, Albang R, Albermann K, Andersen MR, Bendtsen JD, Benen JA, van den Berg M, Breestraat S, Caddick MX, Contreras R, Cornell M, Coutinho PM, Danchin EG, Debets AJ, Dekker P, van Dijck PW, van Dijk A, Dijkhuizen L, Driessen AJ, d'Enfert C, Geysens S, Goosen C, Groot GS, de Groot PW, Guillemette T, Henrissat B, Herweijer M, van den Hombergh JP, van den Hondel CA, van der Heijden RT, van der Kaaij RM, Klis FM, Kools HJ, Kubicek CP, van Kuyk PA, Lauber J, Lu X, van der Maarel MJ, Meulenberg R, Menke H, Mortimer MA, Nielsen J, Oliver SG, Olsthoorn M, Pal K, van Peij NN, Ram AF, Rinas U, Roubos JA, Sagt CM, Schmoll M, Sun J, Ussery D, Varga J, Vervecken W, van de Vondervoort PJ, Wedler H, W?sten HA, Zeng AP, van Ooyen AJ, Visser J, Stam H. Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nat Biotechnol. 2007 Feb; 25(2):221-31. PMID: 17259976.
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    124. Willenbrock H, Hallin PF, Wassenaar TM, Ussery DW. Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray. Genome Biol. 2007; 8(12):R267. PMID: 18088402.
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    125. Ussery DW. Leaner and meaner genomes in Escherichia coli. Genome Biol. 2006; 7(10):237. PMID: 17076878.
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    126. Willenbrock H, Petersen A, Sekse C, Kiil K, Wasteson Y, Ussery DW. Design of a seven-genome Escherichia coli microarray for comparative genomic profiling. J Bacteriol. 2006 Nov; 188(22):7713-21. PMID: 16963574.
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    127. Reen FJ, Almagro-Moreno S, Ussery D, Boyd EF. The genomic code: inferring Vibrionaceae niche specialization. Nat Rev Microbiol. 2006 09; 4(9):697-704. PMID: 16894340.
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    128. Binnewies TT, Motro Y, Hallin PF, Lund O, Dunn D, La T, Hampson DJ, Bellgard M, Wassenaar TM, Ussery DW. Ten years of bacterial genome sequencing: comparative-genomics-based discoveries. Funct Integr Genomics. 2006 Jul; 6(3):165-85. PMID: 16773396.
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    129. Champ PC, Binnewies TT, Nielsen N, Zinman G, Kiil K, Wu H, Bohlin J, Ussery DW. Genome update: purine strand bias in 280 bacterial genomes. Microbiology (Reading). 2006 Mar; 152(Pt 3):579-583. PMID: 16514138.
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    130. Stanke F, Becker T, Cuppens H, Kumar V, Cassiman JJ, Jansen S, Radojkovic D, Siebert B, Yarden J, Ussery DW, Wienker TF, T?mmler B. The TNFalpha receptor TNFRSF1A and genes encoding the amiloride-sensitive sodium channel ENaC as modulators in cystic fibrosis. Hum Genet. 2006 Apr; 119(3):331-43. PMID: 16463024.
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    131. Worning P, Jensen LJ, Hallin PF, Staerfeldt HH, Ussery DW. Origin of replication in circular prokaryotic chromosomes. Environ Microbiol. 2006 Feb; 8(2):353-61. PMID: 16423021.
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    132. Willenbrock H, Friis C, Juncker AS, Ussery DW. An environmental signature for 323 microbial genomes based on codon adaptation indices. Genome Biol. 2006; 7(12):R114. PMID: 17156429.
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    133. Kiil K, Ferchaud JB, David C, Binnewies TT, Wu H, Sicheritz-Pont?n T, Willenbrock H, Ussery DW. Genome update: distribution of two-component transduction systems in 250 bacterial genomes. Microbiology (Reading). 2005 Nov; 151(Pt 11):3447-3452. PMID: 16272367.
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    134. Oguiza JA, Kiil K, Ussery DW. Extracytoplasmic function sigma factors in Pseudomonas syringae. Trends Microbiol. 2005 Dec; 13(12):565-8. PMID: 16257528.
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    135. Kill K, Binnewies TT, Sicheritz-Pont?n T, Willenbrock H, Hallin PF, Wassenaar TM, Ussery DW. Genome update: sigma factors in 240 bacterial genomes. Microbiology (Reading). 2005 Oct; 151(Pt 10):3147-3150. PMID: 16207898.
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    136. Bendtsen JD, Binnewies TT, Hallin PF, Ussery DW. Genome update: prediction of membrane proteins in prokaryotic genomes. Microbiology (Reading). 2005 Jul; 151(Pt 7):2119-2121. PMID: 16000701.
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    137. Bendtsen JD, Binnewies TT, Hallin PF, Sicheritz-Pont?n T, Ussery DW. Genome update: prediction of secreted proteins in 225 bacterial proteomes. Microbiology (Reading). 2005 Jun; 151(Pt 6):1725-1727. PMID: 15941981.
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    138. Ussery DW, de Lichtenberg U, Jensen LJ. Crystal ball. Systems biology: in the broadest sense of the word. Environ Microbiol. 2005 Apr; 7(4):482-3. PMID: 15816924.
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    139. Binnewies TT, Bendtsen JD, Hallin PF, Nielsen N, Wassenaar TM, Pedersen MB, Klemm P, Ussery DW. Genome Update: Protein secretion systems in 225 bacterial genomes. Microbiology (Reading). 2005 Apr; 151(Pt 4):1013-1016. PMID: 15817770.
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    140. Hallin PF, Nielsen N, Devine KM, Binnewies TT, Willenbrock H, Ussery DW. Genome update: base skews in 200+ bacterial chromosomes. Microbiology (Reading). 2005 Mar; 151(Pt 3):633-637. PMID: 15758208.
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    141. Willenbrock H, Binnewies TT, Hallin PF, Ussery DW. Genome update: 2D clustering of bacterial genomes. Microbiology (Reading). 2005 Feb; 151(Pt 2):333-336. PMID: 15699184.
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    142. Binnewies TT, Hallin PF, St?rfeldt HH, Ussery DW. Genome Update: proteome comparisons. Microbiology (Reading). 2005 Jan; 151(Pt 1):1-4. PMID: 15632419.
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    143. Willenbrock H, Ussery DW. Chromatin architecture and gene expression in Escherichia coli. Genome Biol. 2004; 5(12):252. PMID: 15575978.
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    144. Hallin PF, Coenye T, Binnewies TT, Jarmer H, Saerfeldt HH, Ussery DW. Genome update: correlation of bacterial genomic properties. Microbiology (Reading). 2004 Dec; 150(Pt 12):3899-903. PMID: 15583141.
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    145. Ussery DW, Binnewies TT, Gouveia-Oliveira R, Jarmer H, Hallin PF. Genome update: DNA repeats in bacterial genomes. Microbiology (Reading). 2004 Nov; 150(Pt 11):3519-3521. PMID: 15528640.
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    146. Hallin PF, Binnewies TT, Ussery DW. Genome update: chromosome atlases. Microbiology (Reading). 2004 Oct; 150(Pt 10):3091-3. PMID: 15470087.
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    147. Ussery DW, Tindb?k N, Hallin PF. Genome update: promoter profiles. Microbiology (Reading). 2004 Sep; 150(Pt 9):2791-2793. PMID: 15347738.
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    148. Ussery DW, Jensen MS, Poulsen TR, Hallin PF. Genome update: alignment of bacterial chromosomes. Microbiology (Reading). 2004 Aug; 150(Pt 8):2491-2493. PMID: 15289544.
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    149. Hallin PF, Ussery DW. CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data. Bioinformatics. 2004 Dec 12; 20(18):3682-6. PMID: 15256401.
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    150. Ussery DW, Hallin PF. Genome Update: annotation quality in sequenced microbial genomes. Microbiology (Reading). 2004 Jul; 150(Pt 7):2015-2017. PMID: 15256543.
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    151. Ussery DW, Hallin PF, Lagesen K, Wassenaar TM. Genome update: tRNAs in sequenced microbial genomes. Microbiology (Reading). 2004 Jun; 150(Pt 6):1603-1606. PMID: 15184546.
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    152. Ussery DW, Hallin PF, Lagesen K, Coenye T. Genome update: rRNAs in sequenced microbial genomes. Microbiology (Reading). 2004 May; 150(Pt 5):1113-1115. PMID: 15133066.
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    153. Ussery DW, Hallin PF. Genome Update: AT content in sequenced prokaryotic genomes. Microbiology (Reading). 2004 Apr; 150(Pt 4):749-752. PMID: 15073284.
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    154. Ussery DW, Hallin PF. Genome update: Length distributions of sequenced prokaryotic genomes. Microbiology (Reading). 2004 Mar; 150(Pt 3):513-516. PMID: 14993295.
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    155. Ussery DW. Genome update: 161 prokaryotic genomes sequenced, and counting. Microbiology (Reading). 2004 Feb; 150(Pt 2):261-263. PMID: 14766901.
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    156. Barnard FM, Loughlin MF, Fainberg HP, Messenger MP, Ussery DW, Williams P, Jenks PJ. Global regulation of virulence and the stress response by CsrA in the highly adapted human gastric pathogen Helicobacter pylori. Mol Microbiol. 2004 Jan; 51(1):15-32. PMID: 14651608.
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    157. Cases I, Ussery DW, de Lorenzo V. The sigma54 regulon (sigmulon) of Pseudomonas putida. Environ Microbiol. 2003 Dec; 5(12):1281-93. PMID: 14641574.
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    158. M?lbak L, Tett A, Ussery DW, Wall K, Turner S, Bailey M, Field D. The plasmid genome database. Microbiology (Reading). 2003 Nov; 149(Pt 11):3043-3045. PMID: 14600215.
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    159. Jensen LJ, Ussery DW, Brunak S. Functionality of system components: conservation of protein function in protein feature space. Genome Res. 2003 Nov; 13(11):2444-9. PMID: 14559779.
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    160. van Noort V, Worning P, Ussery DW, Rosche WA, Sinden RR. Strand misalignments lead to quasipalindrome correction. Trends Genet. 2003 Jul; 19(7):365-9. PMID: 12850440.
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    161. Jensen LJ, Skovgaard M, Sicheritz-Pont?n T, J?rgensen MK, Lundegaard C, Pedersen CC, Petersen N, Ussery D. Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome. BMC Genomics. 2003 Apr 02; 4(1):12. PMID: 12697059.
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    162. Petersen L, Larsen TS, Ussery DW, On SL, Krogh A. RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box. J Mol Biol. 2003 Mar 07; 326(5):1361-72. PMID: 12595250.
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    163. Ussery D, Soumpasis DM, Brunak S, Staerfeldt HH, Worning P, Krogh A. Bias of purine stretches in sequenced chromosomes. Comput Chem. 2002 Jul; 26(5):531-41. PMID: 12144181.
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    164. Petersen RF, Langkjaer RB, Hvidtfeldt J, Gartner J, Palmen W, Ussery DW, Piskur J. Inheritance and organisation of the mitochondrial genome differ between two Saccharomyces yeasts. J Mol Biol. 2002 May 03; 318(3):627-36. PMID: 12054811.
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    165. Phylactides M, Rowntree R, Nuthall H, Ussery D, Wheeler A, Harris A. Evaluation of potential regulatory elements identified as DNase I hypersensitive sites in the CFTR gene. Eur J Biochem. 2002 Jan; 269(2):553-9. PMID: 11856314.
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