Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: PATRIC, the bacterial bioinformatics database and analysis resource

Abstract

The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein– protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since itsmore » initial report in the 2007 NAR Database Issue.« less

Authors:
 [1];  [1];  [1];  [2];  [1];  [3];  [4];  [1];  [1];  [1];  [1];  [1];  [1];  [2];  [5];  [6];  [1];  [1];  [7];  [1] more »;  [6];  [1];  [1];  [1];  [1];  [1];  [1];  [8] « less
+ Show Author Affiliations
  1. Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States). Virginia Bioinformatics Inst.
  2. Univ. of Chicago, IL (United States). Computation Inst.; Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Division
  3. Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States). Virginia Bioinformatics Inst. and Grado Dept. of Industrial and Systems Engineering
  4. Univ. of Maryland School of Medicine, Baltimore, MD (United States). Dept. of Microbiology and Immunology
  5. Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Division; Fellowship for Interpretation of Genomes, Burr Ridge, IL (United States)
  6. Fellowship for Interpretation of Genomes, Burr Ridge, IL (United States)
  7. Univ. of Chicago, IL (United States). Computation Inst.; Argonne National Lab. (ANL), Argonne, IL (United States). Computing, Environment and Life Sciences
  8. Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States). Virginia Bioinformatics Inst.; Nestle Inst. of Health Sciences SA, Lausanne (Switzerland)
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; National Institutes of Health (NIH); National Institute of Allergy and Infectious Diseases (NIAID)
OSTI Identifier:
1625514
Grant/Contract Number:  
AC02-06CH11357; HHSN272200900040C
Resource Type:
Accepted Manuscript
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 42; Journal Issue: D1; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biochemistry & Molecular Biology

Citation Formats

Wattam, Alice R., Abraham, David, Dalay, Oral, Disz, Terry L., Driscoll, Timothy, Gabbard, Joseph L., Gillespie, Joseph J., Gough, Roger, Hix, Deborah, Kenyon, Ronald, Machi, Dustin, Mao, Chunhong, Nordberg, Eric K., Olson, Robert, Overbeek, Ross, Pusch, Gordon D., Shukla, Maulik, Schulman, Julie, Stevens, Rick L., Sullivan, Daniel E., Vonstein, Veronika, Warren, Andrew, Will, Rebecca, Wilson, Meredith J. C., Yoo, Hyun Seung, Zhang, Chengdong, Zhang, Yan, and Sobral, Bruno W. PATRIC, the bacterial bioinformatics database and analysis resource. United States: N. p., 2013. Web. doi:10.1093/nar/gkt1099.
Copy to clipboard
Wattam, Alice R., Abraham, David, Dalay, Oral, Disz, Terry L., Driscoll, Timothy, Gabbard, Joseph L., Gillespie, Joseph J., Gough, Roger, Hix, Deborah, Kenyon, Ronald, Machi, Dustin, Mao, Chunhong, Nordberg, Eric K., Olson, Robert, Overbeek, Ross, Pusch, Gordon D., Shukla, Maulik, Schulman, Julie, Stevens, Rick L., Sullivan, Daniel E., Vonstein, Veronika, Warren, Andrew, Will, Rebecca, Wilson, Meredith J. C., Yoo, Hyun Seung, Zhang, Chengdong, Zhang, Yan, & Sobral, Bruno W. PATRIC, the bacterial bioinformatics database and analysis resource. United States. https://doi.org/10.1093/nar/gkt1099
Copy to clipboard
Wattam, Alice R., Abraham, David, Dalay, Oral, Disz, Terry L., Driscoll, Timothy, Gabbard, Joseph L., Gillespie, Joseph J., Gough, Roger, Hix, Deborah, Kenyon, Ronald, Machi, Dustin, Mao, Chunhong, Nordberg, Eric K., Olson, Robert, Overbeek, Ross, Pusch, Gordon D., Shukla, Maulik, Schulman, Julie, Stevens, Rick L., Sullivan, Daniel E., Vonstein, Veronika, Warren, Andrew, Will, Rebecca, Wilson, Meredith J. C., Yoo, Hyun Seung, Zhang, Chengdong, Zhang, Yan, and Sobral, Bruno W. Tue . "PATRIC, the bacterial bioinformatics database and analysis resource". United States. https://doi.org/10.1093/nar/gkt1099. https://www.osti.gov/servlets/purl/1625514.
Copy to clipboard
@article{osti_1625514,
title = {PATRIC, the bacterial bioinformatics database and analysis resource},
author = {Wattam, Alice R. and Abraham, David and Dalay, Oral and Disz, Terry L. and Driscoll, Timothy and Gabbard, Joseph L. and Gillespie, Joseph J. and Gough, Roger and Hix, Deborah and Kenyon, Ronald and Machi, Dustin and Mao, Chunhong and Nordberg, Eric K. and Olson, Robert and Overbeek, Ross and Pusch, Gordon D. and Shukla, Maulik and Schulman, Julie and Stevens, Rick L. and Sullivan, Daniel E. and Vonstein, Veronika and Warren, Andrew and Will, Rebecca and Wilson, Meredith J. C. and Yoo, Hyun Seung and Zhang, Chengdong and Zhang, Yan and Sobral, Bruno W.},
abstractNote = {The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein– protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue.},
doi = {10.1093/nar/gkt1099},
journal = {Nucleic Acids Research},
number = D1,
volume = 42,
place = {United States},
year = {Tue Nov 12 00:00:00 EST 2013},
month = {Tue Nov 12 00:00:00 EST 2013}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1093/nar/gkt1099
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

PATRIC: The VBI PathoSystems Resource Integration Center
journal, January 2007

  • Snyder, E. E.; Kampanya, N.; Lu, J.
  • Nucleic Acids Research, Vol. 35, Issue Database
  • DOI: 10.1093/nar/gkl858

The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation
journal, January 2007

  • McNeil, L. K.; Reich, C.; Aziz, R. K.
  • Nucleic Acids Research, Vol. 35, Issue Database
  • DOI: 10.1093/nar/gkl947

GenBank
journal, November 2012

  • Benson, Dennis A.; Cavanaugh, Mark; Clark, Karen
  • Nucleic Acids Research, Vol. 41, Issue D1
  • DOI: 10.1093/nar/gks1195

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
journal, November 2011

  • Pruitt, K. D.; Tatusova, T.; Brown, G. R.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1079

The RAST Server: Rapid Annotations using Subsystems Technology
journal, January 2008

  • Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A.
  • BMC Genomics, Vol. 9, Issue 1, Article No. 75
  • DOI: 10.1186/1471-2164-9-75

FIGfams: yet another set of protein families
journal, September 2009

  • Meyer, Folker; Overbeek, Ross; Rodriguez, Alex
  • Nucleic Acids Research, Vol. 37, Issue 20
  • DOI: 10.1093/nar/gkp698

BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata
journal, December 2011

  • Barrett, T.; Clark, K.; Gevorgyan, R.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1163

NCBI GEO: archive for functional genomics data sets—update
journal, November 2012

  • Barrett, Tanya; Wilhite, Stephen E.; Ledoux, Pierre
  • Nucleic Acids Research, Vol. 41, Issue D1
  • DOI: 10.1093/nar/gks1193

ArrayExpress update—trends in database growth and links to data analysis tools
journal, November 2012

  • Rustici, Gabriella; Kolesnikov, Nikolay; Brandizi, Marco
  • Nucleic Acids Research, Vol. 41, Issue D1
  • DOI: 10.1093/nar/gks1174

The IntAct molecular interaction database in 2012
journal, November 2011

  • Kerrien, S.; Aranda, B.; Breuza, L.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1088

The Biomolecular Interaction Network Database and related tools 2005 update
journal, December 2004

  • Alfarano, C.
  • Nucleic Acids Research, Vol. 33, Issue Database issue
  • DOI: 10.1093/nar/gki051

The Database of Interacting Proteins: 2004 update
journal, January 2004

MINT: the Molecular INTeraction database
journal, January 2007

  • Chatr-aryamontri, A.; Ceol, A.; Palazzi, L. M.
  • Nucleic Acids Research, Vol. 35, Issue Database
  • DOI: 10.1093/nar/gkl950

PSICQUIC and PSISCORE: accessing and scoring molecular interactions
journal, June 2011

  • Aranda, Bruno; Blankenburg, Hagen; Kerrien, Samuel
  • Nature Methods, Vol. 8, Issue 7
  • DOI: 10.1038/nmeth.1637

The BioGRID interaction database: 2013 update
journal, November 2012

  • Chatr-aryamontri, Andrew; Breitkreutz, Bobby-Joe; Heinicke, Sven
  • Nucleic Acids Research, Vol. 41, Issue D1
  • DOI: 10.1093/nar/gks1158

The RCSB Protein Data Bank: new resources for research and education
journal, November 2012

  • Rose, Peter W.; Bi, Chunxiao; Bluhm, Wolfgang F.
  • Nucleic Acids Research, Vol. 41, Issue D1
  • DOI: 10.1093/nar/gks1200

MMDB: 3D structures and macromolecular interactions
journal, December 2011

  • Madej, T.; Addess, K. J.; Fong, J. H.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1162

Biomolecules in the computer: Jmol to the rescue
journal, July 2006

Structural genomics of infectious disease drug targets: the SSGCID
journal, August 2011

  • Stacy, Robin; Begley, Darren W.; Phan, Isabelle
  • Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 67, Issue 9
  • DOI: 10.1107/S1744309111029204

Structural Genomics and Drug Discovery for Infectious Diseases
journal, October 2009

Molecular Epidemiology: Focus on Infection
journal, June 2001

Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria
journal, January 2012

  • Larsen, M. V.; Cosentino, S.; Rasmussen, S.
  • Journal of Clinical Microbiology, Vol. 50, Issue 4
  • DOI: 10.1128/JCM.06094-11

Phylogeny of Gammaproteobacteria
journal, March 2010

  • Williams, K. P.; Gillespie, J. J.; Sobral, B. W. S.
  • Journal of Bacteriology, Vol. 192, Issue 9
  • DOI: 10.1128/JB.01480-09

A Robust Species Tree for the Alphaproteobacteria
journal, May 2007

  • Williams, K. P.; Sobral, B. W.; Dickerman, A. W.
  • Journal of Bacteriology, Vol. 189, Issue 13
  • DOI: 10.1128/JB.00269-07

Bacterial DNA Sifted from the Trichoplax adhaerens (Animalia: Placozoa) Genome Project Reveals a Putative Rickettsial Endosymbiont
journal, March 2013

  • Driscoll, Timothy; Gillespie, Joseph J.; Nordberg, Eric K.
  • Genome Biology and Evolution, Vol. 5, Issue 4
  • DOI: 10.1093/gbe/evt036

KEGG for integration and interpretation of large-scale molecular data sets
journal, November 2011

  • Kanehisa, M.; Goto, S.; Sato, Y.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr988

Visualizing next-generation sequencing data with JBrowse
journal, March 2012

  • Westesson, O.; Skinner, M.; Holmes, I.
  • Briefings in Bioinformatics, Vol. 14, Issue 2
  • DOI: 10.1093/bib/bbr078

EuPathDB: The Eukaryotic Pathogen database
journal, November 2012

  • Aurrecoechea, C.; Barreto, A.; Brestelli, J.
  • Nucleic Acids Research, Vol. 41, Issue D1
  • DOI: 10.1093/nar/gks1113

VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics
journal, December 2011

  • Megy, K.; Emrich, S. J.; Lawson, D.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1089

Integration and visualization of host–pathogen data related to infectious diseases
journal, June 2011

HealthMap: Global Infectious Disease Monitoring through Automated Classification and Visualization of Internet Media Reports
journal, March 2008

  • Freifeld, C. C.; Mandl, K. D.; Reis, B. Y.
  • Journal of the American Medical Informatics Association, Vol. 15, Issue 2
  • DOI: 10.1197/jamia.M2544

PIG--the pathogen interaction gateway
journal, January 2009

  • Driscoll, T.; Dyer, M. D.; Murali, T. M.
  • Nucleic Acids Research, Vol. 37, Issue Database
  • DOI: 10.1093/nar/gkn799

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013
journal, November 2012

  • Vizcaíno, Juan Antonio; Côté, Richard G.; Csordas, Attila
  • Nucleic Acids Research, Vol. 41, Issue D1
  • DOI: 10.1093/nar/gks1262

VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors
journal, November 2011

  • Chen, L.; Xiong, Z.; Sun, L.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr989

MvirDB--a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications
journal, January 2007

  • Zhou, C. E.; Smith, J.; Lam, M.
  • Nucleic Acids Research, Vol. 35, Issue Database
  • DOI: 10.1093/nar/gkl791

ARDB--Antibiotic Resistance Genes Database
journal, January 2009

  • Liu, B.; Pop, M.
  • Nucleic Acids Research, Vol. 37, Issue Database
  • DOI: 10.1093/nar/gkn656

Database resources of the National Center for Biotechnology Information
journal, October 2020

  • Sayers, Eric W.; Beck, Jeffrey; Bolton, Evan E.
  • Nucleic Acids Research, Vol. 49, Issue D1
  • DOI: 10.1093/nar/gkaa892

Database resources of the National Center for Biotechnology Information
journal, December 2007

  • Wheeler, D. L.; Barrett, T.; Benson, D. A.
  • Nucleic Acids Research, Vol. 36, Issue Database
  • DOI: 10.1093/nar/gkm1000

Database resources of the National Center for Biotechnology Information
journal, November 2018

  • Sayers, Eric W.; Agarwala, Richa; Bolton, Evan E.
  • Nucleic Acids Research, Vol. 47, Issue D1
  • DOI: 10.1093/nar/gky1069

Bacterial DNA Sifted from the Trichoplax adhaerens (Animalia: Placozoa) Genome Project Reveals a Putative Rickettsial Endosymbiont
journal, March 2013

  • Driscoll, Timothy; Gillespie, Joseph J.; Nordberg, Eric K.
  • Genome Biology and Evolution, Vol. 5, Issue 4
  • DOI: 10.1093/gbe/evt036
    Sort by:
    [ × clear filter / sort ]

    Works referencing / citing this record:

    In Vitro Gut Metabolism of [U- 13 C]-Quinic Acid, The Other Hydrolysis Product of Chlorogenic Acid
    journal, September 2018

    • Naranjo Pinta, Martine; Montoliu, Ivan; Aura, Anna-Marja
    • Molecular Nutrition & Food Research, Vol. 62, Issue 22
    • DOI: 10.1002/mnfr.201800396

    Bacterial reference genes for gene expression studies by RT-qPCR: survey and analysis
    journal, July 2015

    • Rocha, Danilo J. P.; Santos, Carolina S.; Pacheco, Luis G. C.
    • Antonie van Leeuwenhoek, Vol. 108, Issue 3
    • DOI: 10.1007/s10482-015-0524-1

    Variations on a theme: evolution of the phage-shock-protein system in Actinobacteria
    journal, February 2018

    Insights into the degradation capacities of Amycolatopsis tucumanensis DSM 45259 guided by microarray data
    journal, October 2016

    • Bourguignon, Natalia; Bargiela, Rafael; Rojo, David
    • World Journal of Microbiology and Biotechnology, Vol. 32, Issue 12
    • DOI: 10.1007/s11274-016-2163-8

    Germline-encoded neutralization of a Staphylococcus aureus virulence factor by the human antibody repertoire
    journal, November 2016

    • Yeung, Yik Andy; Foletti, Davide; Deng, Xiaodi
    • Nature Communications, Vol. 7, Issue 1
    • DOI: 10.1038/ncomms13376

    Dissemination of antibiotic resistance genes from antibiotic producers to pathogens
    journal, June 2017

    • Jiang, Xinglin; Ellabaan, Mostafa M. Hashim; Charusanti, Pep
    • Nature Communications, Vol. 8, Issue 1
    • DOI: 10.1038/ncomms15784

    Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits
    journal, September 2018

    Single-molecule sequencing detection of N6-methyladenine in microbial reference materials
    journal, February 2019

    • McIntyre, Alexa B. R.; Alexander, Noah; Grigorev, Kirill
    • Nature Communications, Vol. 10, Issue 1
    • DOI: 10.1038/s41467-019-08289-9

    Physiological and evolutionary implications of tetrameric photosystem I in cyanobacteria
    journal, December 2019

    Pluripotency and the origin of animal multicellularity
    journal, June 2019

    A workflow for generating multi-strain genome-scale metabolic models of prokaryotes
    journal, December 2019

    Whole genome sequencing reveals widespread distribution of typhoidal toxin genes and VirB/D4 plasmids in bovine-associated nontyphoidal Salmonella
    journal, June 2018

    • Delgado-Suárez, Enrique Jesús; Selem-Mojica, Nelly; Ortiz-López, Rocío
    • Scientific Reports, Vol. 8, Issue 1
    • DOI: 10.1038/s41598-018-28169-4

    Virulence gene profiles of Shigella species isolated from stool specimens in India: its association with clinical manifestation and antimicrobial resistance
    journal, May 2019

    • Sethuvel, Dhiviya Prabaa Muthuirulandi; Anandan, Shalini; Michael, Joy Sarojini
    • Pathogens and Global Health, Vol. 113, Issue 4
    • DOI: 10.1080/20477724.2019.1632062

    ResistoMap—online visualization of human gut microbiota antibiotic resistome
    journal, March 2017

    MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs)
    journal, November 2018

    TORMES: an automated pipeline for whole bacterial genome analysis
    journal, April 2019

    Investigating Transfusion-related Sepsis Using Culture-Independent Metagenomic Sequencing
    journal, September 2019

    • Crawford, Emily; Kamm, Jack; Miller, Steve
    • Clinical Infectious Diseases, Vol. 71, Issue 5
    • DOI: 10.1093/cid/ciz960

    HPIDB 2.0: a curated database for host–pathogen interactions
    journal, January 2016

    In vivo evolution of resistant subpopulations of KPC-producing Klebsiella pneumoniae during ceftazidime/avibactam treatment
    journal, March 2018

    • Gaibani, Paolo; Campoli, Caterina; Lewis, Russell E.
    • Journal of Antimicrobial Chemotherapy, Vol. 73, Issue 6
    • DOI: 10.1093/jac/dky082

    Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center
    journal, November 2016

    • Wattam, Alice R.; Davis, James J.; Assaf, Rida
    • Nucleic Acids Research, Vol. 45, Issue D1
    • DOI: 10.1093/nar/gkw1017

    The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes
    journal, January 2017

    • Galperin, Michael Y.; Fernández-Suárez, Xosé M.; Rigden, Daniel J.
    • Nucleic Acids Research, Vol. 45, Issue D1
    • DOI: 10.1093/nar/gkw1188

    proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes
    journal, October 2016

    • Mende, Daniel R.; Letunic, Ivica; Huerta-Cepas, Jaime
    • Nucleic Acids Research, Vol. 45, Issue D1
    • DOI: 10.1093/nar/gkw989

    The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities
    journal, October 2019

    • Davis, James J.; Wattam, Alice R.; Aziz, Ramy K.
    • Nucleic Acids Research
    • DOI: 10.1093/nar/gkz943

    Molecular convergence and positive selection associated with the evolution of symbiont transmission mode in stony corals
    journal, April 2019

    • Dixon, Groves B.; Kenkel, Carly D.
    • Proceedings of the Royal Society B: Biological Sciences, Vol. 286, Issue 1901
    • DOI: 10.1098/rspb.2019.0111

    The mechanisms of in vivo commensal control of Clostridioides difficile virulence
    journal, May 2021

    Selection removes Shine-Dalgarno-like sequences from within protein coding genes
    journal, March 2018

    • Hockenberry, Adam J.; Amaral, Luίs AN; Jewett, Michael C.
    • Molecular Biology and Evolution
    • DOI: 10.1101/278689

    Molecular Evolution of Pseudomonas syringae Type III Secreted Effector Proteins
    journal, December 2018

    • Dillon, Marcus M.; Almeida, Renan N. D.; Laflamme, Bradley
    • Frontiers in Plant Science
    • DOI: 10.1101/503219

    Physiological and Evolutionary Implications of Tetrameric Photosystem I in Cyanobacteria
    posted_content, February 2019

    • Li, Meng; Calteau, Alexandra; Semchonok, Dmitry A.
    • Nature Plants
    • DOI: 10.1101/544353

    Identification and characterization of putative Aeromonas spp. T3SS effectors
    journal, March 2019

    • Rangel, Luiz Thiberio; Marden, Jeremiah; Colston, Sophie
    • PLOS ONE
    • DOI: 10.1101/570887

    Investigating Transfusion-Related Sepsis using Culture-Independent Metagenomic Sequencing
    journal, September 2019

    • Crawford, Emily; Kamm, Jack; Miller, Steve
    • Clinical Infectious Diseases
    • DOI: 10.1101/653337

    An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography
    journal, October 2016

    • Nayfach, Stephen; Rodriguez-Mueller, Beltran; Garud, Nandita
    • Genome Research, Vol. 26, Issue 11
    • DOI: 10.1101/gr.201863.115

    Focusing the diversity of Gardnerella vaginalis through the lens of ecotypes
    journal, November 2017

    • Cornejo, Omar E.; Hickey, Roxana J.; Suzuki, Haruo
    • Evolutionary Applications, Vol. 11, Issue 3
    • DOI: 10.1111/eva.12555

    High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis
    journal, January 2018

    • Chen, Eric C. H.; Morin, Emmanuelle; Beaudet, Denis
    • New Phytologist, Vol. 220, Issue 4
    • DOI: 10.1111/nph.14989

    Genomic epidemiology of multidrug-resistant Gram-negative organisms: Translational genomics of resistant Gram-negatives
    journal, March 2018

    • Hawken, Shawn E.; Snitkin, Evan S.
    • Annals of the New York Academy of Sciences, Vol. 1435, Issue 1
    • DOI: 10.1111/nyas.13672

    Durable coexistence of donor and recipient strains after fecal microbiota transplantation
    journal, April 2016

    Commensal orthologs of the human autoantigen Ro60 as triggers of autoimmunity in lupus
    journal, March 2018

    Real-Time PCR Targeting the penA Mosaic XXXIV Type for Prediction of Extended-Spectrum-Cephalosporin Susceptibility in Clinical Neisseria gonorrhoeae Isolates
    journal, November 2017

    • Wong, L. K.; Hemarajata, P.; Soge, O. O.
    • Antimicrobial Agents and Chemotherapy, Vol. 61, Issue 11
    • DOI: 10.1128/aac.01339-17

    A Standard Method To Inactivate Bacillus anthracis Spores to Sterility via Gamma Irradiation
    journal, June 2018

    • Cote, Christopher K.; Buhr, Tony; Bernhards, Casey B.
    • Applied and Environmental Microbiology, Vol. 84, Issue 12
    • DOI: 10.1128/aem.00106-18

    Long-Term Colonization Dynamics of Enterococcus faecalis in Implanted Devices in Research Macaques
    journal, September 2018

    • Lieberman, Mia T.; Van Tyne, Daria; Dzink-Fox, JoAnn
    • Applied and Environmental Microbiology, Vol. 84, Issue 18
    • DOI: 10.1128/aem.01336-18

    Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections
    journal, March 2016

    • Soto-Giron, Maria J.; Rodriguez-R, Luis M.; Luo, Chengwei
    • Applied and Environmental Microbiology, Vol. 82, Issue 9
    • DOI: 10.1128/aem.03529-15

    Closed Genome Sequence of Phytopathogen Biocontrol Agent Bacillus velezensis Strain AGVL-005, Isolated from Soybean
    journal, February 2018

    • Pylro, Victor Satler; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini
    • Genome Announcements, Vol. 6, Issue 7
    • DOI: 10.1128/genomea.00057-18

    Genome Sequence of the Red Pigment-Forming Meiothermus taiwanensis Strain RP Isolated from Paniphala Hot Spring, India
    journal, June 2016

    • Mukherjee, Trinetra; Bose, Sucharita; Sen, Urmimala
    • Genome Announcements, Vol. 4, Issue 3
    • DOI: 10.1128/genomea.00629-16

    Draft Genome Sequence of a Red-Pigmented Janthinobacterium sp. Native to the Hudson Valley Watershed
    journal, January 2018

    • O’Brien, Kelsey; Perron, Gabriel G.; Jude, Brooke A.
    • Genome Announcements, Vol. 6, Issue 1
    • DOI: 10.1128/genomea.01429-17

    Consolidating and Exploring Antibiotic Resistance Gene Data Resources
    journal, January 2016

    • Xavier, Basil Britto; Das, Anupam J.; Cochrane, Guy
    • Journal of Clinical Microbiology, Vol. 54, Issue 4
    • DOI: 10.1128/jcm.02717-15

    Draft Genome Sequences of Four Antibiotic-Resistant Salmonella Strains Isolated from Australian Red Meat Animal Species
    journal, August 2019

    • Sarjit, Amreeta; Ravensdale, Joshua T.; Coorey, Ranil
    • Microbiology Resource Announcements, Vol. 8, Issue 35
    • DOI: 10.1128/mra.00925-19

    Draft Genome Sequences of 27 Salmonella enterica Serovar Schwarzengrund Isolates from Clinical Sources
    journal, March 2019

    • Khajanchi, Bijay K.; Yoskowitz, Noah C.; Han, Jing
    • Microbiology Resource Announcements, Vol. 8, Issue 12
    • DOI: 10.1128/mra.01687-18

    Convergent Evolution Driven by Rifampin Exacerbates the Global Burden of Drug-Resistant Staphylococcus aureus
    journal, February 2018

    Functional Changes in the Gut Microbiome Contribute to Transforming Growth Factor β-Deficient Colon Cancer
    journal, October 2017

    Comprehensive Virulence Gene Profiling of Bovine Non- aureus Staphylococci Based on Whole-Genome Sequencing Data
    journal, April 2019

    Phylogenomic and Molecular Demarcation of the Core Members of the Polyphyletic Pasteurellaceae Genera Actinobacillus , Haemophilus , and Pasteurella
    journal, January 2015

    • Naushad, Sohail; Adeolu, Mobolaji; Goel, Nisha
    • International Journal of Genomics, Vol. 2015
    • DOI: 10.1155/2015/198560

    Pathogen metadata platform: software for accessing and analyzing pathogen strain information
    journal, September 2016

    • Chang, Wenling E.; Peterson, Matthew W.; Garay, Christopher D.
    • BMC Bioinformatics, Vol. 17, Issue 1
    • DOI: 10.1186/s12859-016-1231-2

    Full genome SNP-based phylogenetic analysis reveals the origin and global spread of Brucella melitensis
    journal, February 2015

    Development of ListeriaBase and comparative analysis of Listeria monocytogenes
    journal, October 2015

    Identification of two different chemosensory pathways in representatives of the genus Halomonas
    journal, April 2018

    • Gasperotti, Ana Florencia; Revuelta, María Victoria; Studdert, Claudia Alicia
    • BMC Genomics, Vol. 19, Issue 1
    • DOI: 10.1186/s12864-018-4655-4

    Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes
    journal, February 2020

    • Silveira, Cynthia B.; Coutinho, Felipe H.; Cavalcanti, Giselle S.
    • BMC Genomics, Vol. 21, Issue 1
    • DOI: 10.1186/s12864-020-6523-2

    Visual programming for next-generation sequencing data analytics
    journal, April 2016

    Analysis of Vibrio cholerae genomes identifies new type VI secretion system gene clusters
    journal, August 2019

    DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data
    journal, February 2018

    Mobile resistome of human gut and pathogen drives anthropogenic bloom of antibiotic resistance
    journal, January 2020

    Structural host-microbiota interaction networks
    journal, October 2017

    Lack of the PGA exopolysaccharide in Salmonella as an adaptive trait for survival in the host
    journal, May 2017

    Vikodak - A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets
    journal, February 2016

    Whole-genome comparison between reference sequences and oyster Vibrio vulnificus C-genotype strains
    journal, July 2019

    • Guerrero, Abraham; Licea-Navarro, Alexei Fedorovish; González-Sánchez, Ricardo
    • PLOS ONE, Vol. 14, Issue 7
    • DOI: 10.1371/journal.pone.0220385

    A Brucella spp. Isolate from a Pac-Man Frog (Ceratophrys ornata) Reveals Characteristics Departing from Classical Brucellae
    journal, September 2016

    • Soler-Lloréns, Pedro F.; Quance, Chris R.; Lawhon, Sara D.
    • Frontiers in Cellular and Infection Microbiology, Vol. 6
    • DOI: 10.3389/fcimb.2016.00116

    Functional Annotations of Paralogs: A Blessing and a Curse
    journal, September 2016

    • Zallot, Rémi; Harrison, Katherine; Kolaczkowski, Bryan
    • Life, Vol. 6, Issue 3
    • DOI: 10.3390/life6030039

    Evolution of BACON Domain Tandem Repeats in crAssphage and Novel Gut Bacteriophage Lineages
    journal, November 2019

    • de Jonge, Patrick A.; von Meijenfeldt, F. A. Bastiaan; van Rooijen, Laura E.
    • Viruses, Vol. 11, Issue 12
    • DOI: 10.3390/v11121085

    Brucella, nitrogen and virulence
    text, January 2014

    Diverse deep-sea anglerfishes share a genetically reduced luminous symbiont that is acquired from the environment
    journal, October 2019

    Accelerating the Drug Development Pipeline with Genome-Scale Metabolic Network Reconstructions
    book, January 2017

    A comprehensive phylogenetic analysis of copper transporting P 1B ATPases from bacteria of the Rhizobiales order uncovers multiplicity, diversity and novel taxonomic subtypes
    journal, February 2017

    • Cubillas, Ciro; Miranda-Sánchez, Fabiola; González-Sánchez, Antonio
    • MicrobiologyOpen, Vol. 6, Issue 4
    • DOI: 10.1002/mbo3.452

    Role of a membrane-bound aldehyde dehydrogenase complex AldFGH in acetic acid fermentation with Acetobacter pasteurianus SKU1108
    journal, April 2018

    • Yakushi, Toshiharu; Fukunari, Seiya; Kodama, Tomohiro
    • Applied Microbiology and Biotechnology, Vol. 102, Issue 10
    • DOI: 10.1007/s00253-018-8940-6

    A Randomized Trait Community Clustering approach to unveil consistent environmental thresholds in community assembly
    journal, June 2019

    • Triadó-Margarit, Xavier; Capitán, José A.; Menéndez-Serra, Mateu
    • The ISME Journal, Vol. 13, Issue 11
    • DOI: 10.1038/s41396-019-0454-4

    Distinct Campylobacter fetus lineages adapted as livestock pathogens and human pathobionts in the intestinal microbiota
    journal, November 2017

    Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance
    journal, October 2018

    Natural product diversity associated with the nematode symbionts Photorhabdus and Xenorhabdus
    journal, October 2017

    • Tobias, Nicholas J.; Wolff, Hendrik; Djahanschiri, Bardya
    • Nature Microbiology, Vol. 2, Issue 12
    • DOI: 10.1038/s41564-017-0039-9

    Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae
    journal, January 2018

    Draft genome and description of Merdibacter massiliensis gen.nov., sp. nov., a new bacterium genus isolated from the human ileum
    journal, May 2019

    The commensal infant gut meta-mobilome as a potential reservoir for persistent multidrug resistance integrons
    journal, October 2015

    • Ravi, Anuradha; Avershina, Ekaterina; Foley, Steven L.
    • Scientific Reports, Vol. 5, Issue 1
    • DOI: 10.1038/srep15317

    Antimicrobial Resistance Prediction in PATRIC and RAST
    journal, June 2016

    • Davis, James J.; Boisvert, Sébastien; Brettin, Thomas
    • Scientific Reports, Vol. 6, Issue 1
    • DOI: 10.1038/srep27930

    Omics and bioinformatics applied to vaccine development against Borrelia
    journal, January 2018

    • Bencurova, Elena; Gupta, Shishir K.; Oskoueian, Ehsan
    • Molecular Omics, Vol. 14, Issue 5
    • DOI: 10.1039/c8mo00130h

    Phylogenomics with paralogs
    journal, February 2015

    • Hellmuth, Marc; Wieseke, Nicolas; Lechner, Marcus
    • Proceedings of the National Academy of Sciences, Vol. 112, Issue 7
    • DOI: 10.1073/pnas.1412770112

    Noncanonical SMC protein in Mycobacterium smegmatis restricts maintenance of Mycobacterium fortuitum plasmids
    journal, September 2014

    • Panas, Michael W.; Jain, Paras; Yang, Hui
    • Proceedings of the National Academy of Sciences, Vol. 111, Issue 37
    • DOI: 10.1073/pnas.1414207111

    Comparative genomics identifies potential virulence factors in Clostridium tertium and C. paraputrificum
    journal, January 2019

    Curation, integration and visualization of bacterial virulence factors in PATRIC
    journal, September 2014

    Pantoea: insights into a highly versatile and diverse genus within the Enterobacteriaceae
    journal, June 2015

    • Walterson, Alyssa M.; Stavrinides, John
    • FEMS Microbiology Reviews, Vol. 39, Issue 6
    • DOI: 10.1093/femsre/fuv027

    Phylogenomic Analysis of β-Lactamase in Archaea and Bacteria Enables the Identification of Putative New Members
    journal, March 2018

    • Keshri, Vivek; Panda, Arup; Levasseur, Anthony
    • Genome Biology and Evolution, Vol. 10, Issue 4
    • DOI: 10.1093/gbe/evy028

    Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements
    journal, October 2016

    • Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon
    • Nucleic Acids Research, Vol. 45, Issue D1
    • DOI: 10.1093/nar/gkw992

    proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes
    journal, October 2019

    • Mende, Daniel R.; Letunic, Ivica; Maistrenko, Oleksandr M.
    • Nucleic Acids Research
    • DOI: 10.1093/nar/gkz1002

    Sequencing of the variable region of rpsB to discriminate between Streptococcus pneumoniae and other streptococcal species
    journal, September 2017

    • Wyllie, Anne L.; Pannekoek, Yvonne; Bovenkerk, Sandra
    • Open Biology, Vol. 7, Issue 9
    • DOI: 10.1098/rsob.170074

    Identification of Klebsiella capsule synthesis loci from whole genome data
    journal, December 2016

    • Wyres, Kelly L.; Wick, Ryan R.; Gorrie, Claire
    • Microbial Genomics, Vol. 2, Issue 12
    • DOI: 10.1099/mgen.0.000102

    Modification of the Streptococcus mutans transcriptome by LrgAB and environmental stressors
    journal, February 2017

    • Rice, Kelly C.; Turner, Matthew E.; Carney, O’neshia V.
    • Microbial Genomics, Vol. 3, Issue 2
    • DOI: 10.1099/mgen.0.000104

    Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris
    journal, August 2017

    • Schatschneider, Sarah; Schneider, Jessica; Blom, Jochen
    • Microbiology, Vol. 163, Issue 8
    • DOI: 10.1099/mic.0.000473

    Evolutionary changes of an intestinal Lactobacillus reuteri during probiotic manufacture
    journal, March 2019

    • López, Lázaro; Cardenas, Paúl; Prado, María B.
    • MicrobiologyOpen
    • DOI: 10.1101/567974

    Distinct polysaccharide growth profiles of human intestinal Prevotella copri isolates
    journal, September 2019

    • Fehlner-Peach, Hannah; Magnabosco, Cara; Raghavan, Varsha
    • Cell Host & Microbe
    • DOI: 10.1101/750802

    Novel insights into the taxonomic diversity and molecular mechanisms of bacterial Mn( III ) reduction
    journal, August 2020

    • Szeinbaum, Nadia; Nunn, Brook L.; Cavazos, Amanda R.
    • Environmental Microbiology Reports, Vol. 12, Issue 5
    • DOI: 10.1111/1758-2229.12867

    Capreomycin resistance prediction in two species of Mycobacterium using a stacked ensemble method
    journal, June 2019

    • Chowdhury, A. S.; Khaledian, E.; Broschat, S. L.
    • Journal of Applied Microbiology, Vol. 127, Issue 6
    • DOI: 10.1111/jam.14413

    Essentiality of threonylcarbamoyladenosine (t 6 A), a universal tRNA modification, in bacteria : t
    journal, October 2015

    • Thiaville, Patrick C.; El Yacoubi, Basma; Köhrer, Caroline
    • Molecular Microbiology, Vol. 98, Issue 6
    • DOI: 10.1111/mmi.13209

    Phylogenomics of Endogonaceae and evolution of mycorrhizas within Mucoromycota
    journal, January 2019

    • Chang, Ying; Desirò, Alessandro; Na, Hyunsoo
    • New Phytologist, Vol. 222, Issue 1
    • DOI: 10.1111/nph.15613

    Comparative genomics of Rhizophagus irregularis , R. cerebriforme , R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina
    journal, February 2019

    • Morin, Emmanuelle; Miyauchi, Shingo; San Clemente, Hélène
    • New Phytologist, Vol. 222, Issue 3
    • DOI: 10.1111/nph.15687

    Genome Sequences of 15 Klebsiella sp. Isolates from Sugarcane Fields in Colombia’s Cauca Valley
    journal, March 2018

    • Medina-Cordoba, Luz K.; Chande, Aroon T.; Rishishwar, Lavanya
    • Genome Announcements, Vol. 6, Issue 12
    • DOI: 10.1128/genomea.00104-18

    Databases for Microbiologists: TABLE 1
    journal, May 2015

    Whole-Genome Sequences of 66 Incompatibility Group FIB Plasmid-Carrying Salmonella enterica Serovar Typhimurium Isolates from Food Animal Sources
    journal, January 2020

    • Aljahdali, Nesreen H.; Foley, Steven L.; Han, Jing
    • Microbiology Resource Announcements, Vol. 9, Issue 5
    • DOI: 10.1128/MRA.01435-19

    Closed Genome Sequence of Bacillus paralicheniformis Strain CBMAI 1303, a Bacterium Applied for Phytopathogen Biocontrol
    journal, January 2019

    • Pylro, Victor Satler; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini
    • Microbiology Resource Announcements, Vol. 8, Issue 3
    • DOI: 10.1128/mra.01507-18

    Dormant non-culturable Mycobacterium tuberculosis retains stable low-abundant mRNA
    journal, November 2015

    Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia
    journal, March 2016

    Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers
    journal, October 2018

    Prevailing clone (ST69) of Vibrio cholerae O139 in India over 10 years
    journal, November 2017

    • Anandan, Shalini; Devanga Ragupathi, Naveen Kumar; Muthuirulandi Sethuvel, Dhiviya Prabaa
    • Gut Pathogens, Vol. 9, Issue 1
    • DOI: 10.1186/s13099-017-0210-0

    Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data
    journal, October 2017

    Biomarker panels for characterizing microbial community biofilm formation as composite molecular process
    journal, August 2018

    Identification and characterization of putative Aeromonas spp. T3SS effectors
    journal, June 2019

    iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE
    journal, April 2018

    Evidence for Ecological Flexibility in the Cosmopolitan Genus Curtobacterium
    journal, November 2016

    Subspecies in the global human gut microbiome
    text, January 2017

    Urban metagenomics uncover antibiotic resistance reservoirs in coastal beach and sewage waters
    text, January 2019

    Brucella, nitrogen and virulence
    text, January 2014

    Comparative assessment of the therapeutic drug targets of C. botulinum ATCC 3502 and C. difficile str. 630 using in silico subtractive proteomics approach
    journal, May 2019

    • Bhardwaj, Tulika; Haque, Shafiul; Somvanshi, Pallavi
    • Journal of Cellular Biochemistry, Vol. 120, Issue 9
    • DOI: 10.1002/jcb.28897

    Evolutionary changes of an intestinal Lactobacillus reuteri during probiotic manufacture
    journal, November 2019

    • López, Lázaro; Calderón, Diana; Cardenas, Paúl
    • MicrobiologyOpen, Vol. 9, Issue 2
    • DOI: 10.1002/mbo3.972

    A framework towards data analytics on host–pathogen protein–protein interactions
    journal, January 2020

    • Chen, Huaming; Shen, Jun; Wang, Lei
    • Journal of Ambient Intelligence and Humanized Computing, Vol. 11, Issue 11
    • DOI: 10.1007/s12652-020-01715-7

    Phylogenomic analysis of Candidatus ‘Izimaplasma’ species: free-living representatives from a Tenericutes clade found in methane seeps
    journal, April 2016

    • Skennerton, Connor T.; Haroon, Mohamed F.; Briegel, Ariane
    • The ISME Journal, Vol. 10, Issue 11
    • DOI: 10.1038/ismej.2016.55

    Ancient pathogen genomics as an emerging tool for infectious disease research
    journal, April 2019

    • Spyrou, Maria A.; Bos, Kirsten I.; Herbig, Alexander
    • Nature Reviews Genetics, Vol. 20, Issue 6
    • DOI: 10.1038/s41576-019-0119-1

    New insights from uncultivated genomes of the global human gut microbiome
    journal, March 2019

    Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields
    journal, April 2021

    • Medina-Cordoba, Luz K.; Chande, Aroon T.; Rishishwar, Lavanya
    • Scientific Reports, Vol. 11, Issue 1
    • DOI: 10.1038/s41598-021-88380-8

    Global profiling of protein complexes: current approaches and their perspective in biomedical research
    journal, September 2016

    • Rudashevskaya, Elena L.; Sickmann, Albert; Markoutsa, Stavroula
    • Expert Review of Proteomics, Vol. 13, Issue 10
    • DOI: 10.1080/14789450.2016.1233064

    EffectiveDB—updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems
    journal, November 2015

    • Eichinger, Valerie; Nussbaumer, Thomas; Platzer, Alexander
    • Nucleic Acids Research, Vol. 44, Issue D1
    • DOI: 10.1093/nar/gkv1269

    EuPathDB: the eukaryotic pathogen genomics database resource
    journal, November 2016

    • Aurrecoechea, Cristina; Barreto, Ana; Basenko, Evelina Y.
    • Nucleic Acids Research, Vol. 45, Issue D1
    • DOI: 10.1093/nar/gkw1105

    Victors: a web-based knowledge base of virulence factors in human and animal pathogens
    journal, October 2018

    • Sayers, Samantha; Li, Li; Ong, Edison
    • Nucleic Acids Research, Vol. 47, Issue D1
    • DOI: 10.1093/nar/gky999

    Borrelia maritima sp. nov., a novel species of the Borrelia burgdorferi sensu lato complex, occupying a basal position to North American species
    journal, February 2020

    • Margos, Gabriele; Fedorova, Natalia; Becker, Noémie S.
    • International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 2
    • DOI: 10.1099/ijsem.0.003833

    High diversity in SCCmec elements among multidrug-resistant Staphylococcus haemolyticus strains originating from paediatric patients; characterization of a new composite island
    journal, July 2018

    • Hosseinkhani, Farideh; Tammes Buirs, Matthias; Jabalameli, Fereshteh
    • Journal of Medical Microbiology, Vol. 67, Issue 7
    • DOI: 10.1099/jmm.0.000776

    Strain typing and characterization of virulence genes in clinical Staphylococcus aureus isolates from Kenya
    posted_content, August 2018

    • Kyany’a, Cecilia; Nyasinga, Justin; Matano, Daniel
    • BioRxiv
    • DOI: 10.1101/390955

    Functional and Comparative Genomics of Niche-Specific Adapted Actinomycetes Kocuria rhizophila Strain D2 Isolated from Healthy Human Gut
    posted_content, August 2018

    • Ghattargi, Vikas C.; Nimonkar, Yogesh S.; Sape, Kamala
    • BioRxiv
    • DOI: 10.1101/400242

    A newly recorded Rickettsia of the Torix group is a recent intruder and an endosymbiont in the whitefly Bemisia tabaci
    journal, April 2020

    • Wang, Hua‐Ling; Lei, Teng; Wang, Xiao‐Wei
    • Environmental Microbiology, Vol. 22, Issue 4
    • DOI: 10.1111/1462-2920.14927

    Small RNA Transcriptome of the Oral Microbiome during Periodontitis Progression
    journal, October 2015

    • Duran-Pinedo, Ana E.; Yost, Susan; Frias-Lopez, Jorge
    • Applied and Environmental Microbiology, Vol. 81, Issue 19
    • DOI: 10.1128/aem.01782-15

    Comparative Phylogenomics and Evolution of the Brucellae Reveal a Path to Virulence
    journal, December 2013

    • Wattam, A. R.; Foster, J. T.; Mane, S. P.
    • Journal of Bacteriology, Vol. 196, Issue 5
    • DOI: 10.1128/jb.01091-13

    Application of Whole-Genome Sequencing Data for O-Specific Antigen Analysis and In Silico Serotyping of Pseudomonas aeruginosa Isolates
    journal, July 2016

    • Thrane, Sandra Wingaard; Taylor, Véronique L.; Lund, Ole
    • Journal of Clinical Microbiology, Vol. 54, Issue 7
    • DOI: 10.1128/jcm.00349-16

    Whole-Genome Sequences of 35 Incompatibility Group I1 Plasmid-Carrying Salmonella enterica Isolates from Food Animal and Clinical Sources
    journal, August 2019

    • Aljahdali, Nesreen H.; Kaldhone, Pravin R.; Foley, Steven L.
    • Microbiology Resource Announcements, Vol. 8, Issue 35
    • DOI: 10.1128/mra.00831-19

    Draft Genome Sequence of Freshwater-Derived Streptomyces
    journal, October 2019

    • Zothanpuia, ; Passari, Ajit Kumar; Deka, Purbajyoti
    • Microbiology Resource Announcements, Vol. 8, Issue 43
    • DOI: 10.1128/mra.00874-19

    Draft Genome Sequences of Violacein-Producing Duganella sp. Isolates from a Waterway in Eastern Pennsylvania
    journal, September 2018

    • Lamendella, Regina; Jude, Brooke A.
    • Microbiology Resource Announcements, Vol. 7, Issue 12
    • DOI: 10.1128/mra.01196-18

    Listeriomics: an Interactive Web Platform for Systems Biology of Listeria
    journal, April 2017

    Prediction of Acquired Antimicrobial Resistance for Multiple Bacterial Species Using Neural Networks
    journal, January 2020

    A novel approach to probe host-pathogen interactions of bovine digital dermatitis, a model of a complex polymicrobial infection
    journal, December 2016

    • Marcatili, Paolo; Nielsen, Martin W.; Sicheritz-Pontén, Thomas
    • BMC Genomics, Vol. 17, Issue 1
    • DOI: 10.1186/s12864-016-3341-7

    Comparative genomics of whole-cell pertussis vaccine strains from India
    journal, May 2020

    Origins and global context of Brucella abortus in Italy
    journal, February 2017

    • Garofolo, Giuliano; Di Giannatale, Elisabetta; Platone, Ilenia
    • BMC Microbiology, Vol. 17, Issue 1
    • DOI: 10.1186/s12866-017-0939-0

    gyrA and parC mutations in fluoroquinolone-resistant Neisseria gonorrhoeae isolates from Kenya
    journal, April 2019

    • Kivata, Mary Wandia; Mbuchi, Margaret; Eyase, Fredrick Lunyagi
    • BMC Microbiology, Vol. 19, Issue 1
    • DOI: 10.1186/s12866-019-1439-1

    Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in the Pseudomonas syringae species complex
    journal, January 2019

    Functional signatures of oral dysbiosis during periodontitis progression revealed by microbial metatranscriptome analysis
    journal, April 2015

    Genome sequencing and analysis of the first spontaneous Nanosilver resistant bacterium Proteus mirabilis strain SCDR1
    journal, November 2017

    • Saeb, Amr T. M.; Al-Rubeaan, Khalid A.; Abouelhoda, Mohamed
    • Antimicrobial Resistance & Infection Control, Vol. 6, Issue 1
    • DOI: 10.1186/s13756-017-0277-x

    A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments
    journal, July 2019

    Complete genome of Arthrobacter alpinus strain R3.8, bioremediation potential unraveled with genomic analysis
    journal, September 2017

    Diversity and distribution of nuclease bacteriocins in bacterial genomes revealed using Hidden Markov Models
    journal, July 2017

    Genomic insights on heterogeneous resistance to vancomycin and teicoplanin in Methicillin-resistant Staphylococcus aureus: A first report from South India
    journal, December 2019

    Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates
    collection, January 2019

    • Galata, Valentina; Laczny, Cédric C.; Backes, Christina
    • Universität des Saarlandes
    • DOI: 10.22028/d291-33737

    Brucella , nitrogen and virulence
    journal, December 2014

    Characterization of Antimicrobial-Producing Beneficial Bacteria Isolated from Huanglongbing Escape Citrus Trees
    journal, December 2017

    Plasmid-Mediated Quinolone Resistance in Shigella flexneri Isolated From Macaques
    journal, March 2018

    Characterization of Stackebrandtia nassauensis GH 20 Beta-Hexosaminidase, a Versatile Biocatalyst for Chitobiose Degradation
    journal, March 2019

    • Wang, Meng; Zheng, Feng; Wang, Ting
    • International Journal of Molecular Sciences, Vol. 20, Issue 5
    • DOI: 10.3390/ijms20051243

    Comparative Study on A Novel Pathogen of European Seabass. Diversity of Aeromonas veronii in the Aegean Sea
    journal, October 2019

    Staphylococcus aureus viewed from the perspective of 40,000+ genomes
    journal, January 2018

    Comparative transcriptomics of sympatric species of coral reef fishes (genus: Haemulon )
    journal, January 2019

    • Bernal, Moisés A.; Dixon, Groves B.; Matz, Mikhail V.
    • PeerJ, Vol. 7
    • DOI: 10.7717/peerj.6541

    Genomic Insights into Evolution of AdpA Family Master Regulators of Morphological Differentiation and Secondary Metabolism in Streptomyces
    journal, March 2018

    • Rabyk, Mariia; Yushchuk, Oleksandr; Rokytskyy, Ihor
    • Journal of Molecular Evolution, Vol. 86, Issue 3-4
    • DOI: 10.1007/s00239-018-9834-z

    Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates
    journal, April 2019

    • Galata, Valentina; Laczny, Cédric C.; Backes, Christina
    • Genomics, Proteomics & Bioinformatics, Vol. 17, Issue 2
    • DOI: 10.1016/j.gpb.2018.11.002

    Community-wide transcriptome of the oral microbiome in subjects with and without periodontitis
    journal, March 2014

    • Duran-Pinedo, Ana E.; Chen, Tsute; Teles, Ricardo
    • The ISME Journal, Vol. 8, Issue 8
    • DOI: 10.1038/ismej.2014.23

    Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession
    journal, February 2018

    • Ortiz-Álvarez, Rüdiger; Fierer, Noah; de los Ríos, Asunción
    • The ISME Journal, Vol. 12, Issue 7
    • DOI: 10.1038/s41396-018-0076-2

    Insights into the skin microbiome dynamics of leprosy patients during multi-drug therapy and in healthy individuals from Brazil
    journal, June 2018

    Enzymatic glycosylation of indoxyglycosides catalyzed by a novel maltose phosphorylase from Emticicia oligotrophica
    journal, July 2016

    Insights from protein-protein interaction studies on bacterial pathogenesis
    journal, August 2017

    VIM-1-producing Salmonella Infantis isolated from swine and minced pork meat in Germany
    journal, March 2017

    • Borowiak, Maria; Szabo, Istvan; Baumann, Beatrice
    • Journal of Antimicrobial Chemotherapy, Vol. 72, Issue 7
    • DOI: 10.1093/jac/dkx101

    BacWGSTdb, a database for genotyping and source tracking bacterial pathogens
    journal, October 2015

    IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis: Figure 1.
    journal, April 2015

    • Dhillon, Bhavjinder K.; Laird, Matthew R.; Shay, Julie A.
    • Nucleic Acids Research, Vol. 43, Issue W1
    • DOI: 10.1093/nar/gkv401

    Application of whole genome sequencing to query a potential outbreak of Elizabethkingia anophelis in Ontario, Canada
    journal, April 2019

    • McTaggart, Lisa R.; Stapleton, Patrick J.; Eshaghi, AliReza
    • Access Microbiology, Vol. 1, Issue 2
    • DOI: 10.1099/acmi.0.000017

    Origins and Global Context of Brucella abortus in Italy
    journal, October 2016

    • Garofolo, Giuliano; Di Giannatale, Elisabetta; Platone, Ilenia
    • BMC Microbiology
    • DOI: 10.1101/077529

    Pan-genome and phylogeny of Bacillus cereus sensu lato
    journal, June 2017

    Pluripotency and the origin of animal multicellularity
    journal, March 2019

    • Sogabe, Shunske; Hatleberg, William L.; Kocot, Kevin M.
    • Nature
    • DOI: 10.1101/564518

    Phylogenomics of Enterococcus faecalis from wild birds: new insights into host‐associated differences in core and accessory genomes of the species
    journal, July 2019

    • León‐Sampedro, Ricardo; del Campo, Rosa; Rodriguez‐Baños, Mercedes
    • Environmental Microbiology, Vol. 21, Issue 8
    • DOI: 10.1111/1462-2920.14702

    Draft Genome Sequence of the Extremely Desiccation-Tolerant Cyanobacterium Gloeocapsopsis sp. Strain AAB1
    journal, April 2018

    • Puente-Sánchez, Fernando; González-Silva, Carlos; Parro, Victor
    • Genome Announcements, Vol. 6, Issue 17
    • DOI: 10.1128/genomea.00216-18

    Draft Genome Sequences of Strains TRE 1, TRE D, TRE H, and TRI 7, Isolated from Tamarins and Belonging to Four Putative Novel Bifidobacterium Species
    journal, January 2018

    • Puglisi, Edoardo; Mattarelli, Paola; Modesto, Monica
    • Genome Announcements, Vol. 6, Issue 3
    • DOI: 10.1128/genomea.01449-17

    Whole-Genome Shotgun Sequencing of Cephalosporin-Resistant Salmonella enterica Serovar Typhi
    journal, March 2017

    Genome Sequence of Pseudomonas sp. Strain ST1, Isolated from Olive (Olea europaea L.) Knot Galls in Croatia
    journal, November 2019

    • Vuletin Selak, Gabriela; Raboteg, Marina; Fournier, Pascale
    • Microbiology Resource Announcements, Vol. 8, Issue 46
    • DOI: 10.1128/mra.00986-19

    Enterococcus faecium TIR-Domain Genes Are Part of a Gene Cluster Which Promotes Bacterial Survival in Blood
    journal, December 2018

    • Wagner, Theresa M.; Janice, Jessin; Paganelli, Fernanda L.
    • International Journal of Microbiology, Vol. 2018
    • DOI: 10.1155/2018/1435820

    Isolation and Characterization of Two Novel Plasmids from Pathogenic Leptospira interrogans Serogroup Canicola Serovar Canicola Strain Gui44
    journal, August 2014

    Subspecies in the global human gut microbiome
    journal, December 2017

    • Costea, Paul I.; Coelho, Luis Pedro; Sunagawa, Shinichi
    • Molecular Systems Biology, Vol. 13, Issue 12
    • DOI: 10.15252/msb.20177589

    A review on computational systems biology of pathogen–host interactions
    journal, April 2015

    • DurmuÅŸ, Saliha; Çakır, Tunahan; Özgür, Arzucan
    • Frontiers in Microbiology, Vol. 6
    • DOI: 10.3389/fmicb.2015.00235

    iVikodak—A Platform and Standard Workflow for Inferring, Analyzing, Comparing, and Visualizing the Functional Potential of Microbial Communities
    journal, January 2019

    • Nagpal, Sunil; Haque, Mohammed Monzoorul; Singh, Rashmi
    • Frontiers in Microbiology, Vol. 9
    • DOI: 10.3389/fmicb.2018.03336

    Staphylococcus aureus viewed from the perspective of 40,000+ genomes
    journal, April 2018

    Network representations of immune system complexity: Immune networks
    journal, January 2015

    • Subramanian, Naeha; Torabi-Parizi, Parizad; Gottschalk, Rachel A.
    • Wiley Interdisciplinary Reviews: Systems Biology and Medicine, Vol. 7, Issue 1
    • DOI: 10.1002/wsbm.1288

    Virulence factor activity relationships (VFARs): a bioinformatics perspective
    journal, January 2017

    • Waseem, Hassan; Williams, Maggie R.; Stedtfeld, Tiffany
    • Environmental Science: Processes & Impacts, Vol. 19, Issue 3
    • DOI: 10.1039/c6em00689b

    phylogenize: correcting for phylogeny reveals genes associated with microbial distributions
    journal, October 2019

    A Pan-Genomic Approach to Understand the Basis of Host Adaptation in Achromobacter
    journal, April 2017

    • Jeukens, Julie; Freschi, Luca; Vincent, Antony T.
    • Genome Biology and Evolution, Vol. 9, Issue 4
    • DOI: 10.1093/gbe/evx061

    Global ecotypes in the ubiquitous marine clade SAR86
    journal, May 2019

    • Hoarfrost, Adrienne; Nayfach, Stephen; Ladau, Joshua
    • The ISME Journal
    • DOI: 10.1101/635185

    Complete Genome Sequence of the Endophytic Biocontrol Strain Bacillus velezensis CC09
    journal, October 2016

    Draft Genome Sequence of a Violacein-Producing Iodobacter sp. from the Hudson Valley Watershed
    journal, January 2018

    • Doing, Georgia; Perron, Gabriel G.; Jude, Brooke A.
    • Genome Announcements, Vol. 6, Issue 1
    • DOI: 10.1128/genomea.01428-17

    Cystic Fibrosis-Associated Stenotrophomonas maltophilia Strain-Specific Adaptations and Responses to pH
    journal, April 2019

    • Gallagher, Tara; Phan, Joann; Oliver, Andrew
    • Journal of Bacteriology, Vol. 201, Issue 7
    • DOI: 10.1128/jb.00478-18

    Draft Genome Sequence of Plant Growth-Promoting Endophytic Microbacterium hydrothermale BPSAC84, Isolated from the Medicinal Plant Mirabilis jalapa
    journal, May 2019

    • Passari, Ajit Kumar; Rajput, Vinay
    • Microbiology Resource Announcements, Vol. 8, Issue 22
    • DOI: 10.1128/mra.00406-19

    Characterization of Burkholderia pseudomallei protein BPSL1375 validates the Putative hemolytic activity of the COG3176 N-Acyltransferase family
    journal, November 2015

    A method for automated pathogenic content estimation with application to rheumatoid arthritis
    journal, November 2016

    Urban metagenomics uncover antibiotic resistance reservoirs in coastal beach and sewage waters
    journal, February 2019

    Phylogeny-corrected identification of microbial gene families relevant to human gut colonization
    journal, August 2018

    • Bradley, Patrick H.; Nayfach, Stephen; Pollard, Katherine S.
    • PLOS Computational Biology, Vol. 14, Issue 8
    • DOI: 10.1371/journal.pcbi.1006242

    VAMPr: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning
    journal, January 2020

    Protection induced by a Francisella tularensis subunit vaccine delivered by glucan particles
    journal, October 2018

    Approximate Search for Known Gene Clusters in New Genomes Using PQ-Trees
    text, January 2020

    • Zimerman, Galia R.; Svetlitsky, Dina; Zehavi, Meirav
    • Schloss Dagstuhl - Leibniz-Zentrum für Informatik
    • DOI: 10.4230/lipics.wabi.2020.1

    An enhanced genome-scale metabolic reconstruction of Streptomyces clavuligerus identifies novel strain improvement strategies
    journal, February 2018

    • Toro, León; Pinilla, Laura; Avignone-Rossa, Claudio
    • Bioprocess and Biosystems Engineering, Vol. 41, Issue 5
    • DOI: 10.1007/s00449-018-1900-9

    Collaborative Effort for a Centralized Worldwide Tuberculosis Relational Sequencing Data Platform: Figure 1.
    journal, September 2015

    • Starks, Angela M.; Avilés, Enrique; Cirillo, Daniela M.
    • Clinical Infectious Diseases, Vol. 61, Issue suppl 3
    • DOI: 10.1093/cid/civ610

    Fast automated reconstruction of genome-scale metabolic models for microbial species and communities
    journal, June 2018

    • Machado, Daniel; Andrejev, Sergej; Tramontano, Melanie
    • Nucleic Acids Research, Vol. 46, Issue 15
    • DOI: 10.1093/nar/gky537

    Analysis of Vibrio cholerae genomes using a novel bioinformatic tool identifies new, active Type VI Secretion System gene clusters
    posted_content, January 2019

    • Crisan, Cristian V.; Chande, Aroon T.; Williams, Kenneth
    • BioRxiv
    • DOI: 10.1101/526723

    Disentangling the impact of environmental and phylogenetic constraints on prokaryotic strain diversity
    journal, August 2019

    • Maistrenko, Oleksandr M.; Mende, Daniel R.; Luetge, Mechthild
    • The ISME Journal
    • DOI: 10.1101/735696

    Emergence of soil bacterial ecotypes along a climate gradient: Soil ecotypes along a climate gradient
    journal, October 2018

    • Chase, Alexander B.; Gomez-Lunar, Zulema; Lopez, Alberto E.
    • Environmental Microbiology, Vol. 20, Issue 11
    • DOI: 10.1111/1462-2920.14405

    First report of Klebsiella quasipneumoniae harboring blaKPC-2 in Saudi Arabia
    journal, December 2019

    • Hala, Sharif; Antony, Chakkiath Paul; Alshehri, Mohammed
    • Antimicrobial Resistance & Infection Control, Vol. 8, Issue 1
    • DOI: 10.1186/s13756-019-0653-9

    Genotypic differences between strains of the opportunistic pathogen Corynebacterium bovis isolated from humans, cows, and rodents
    journal, December 2018

    PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database
    journal, February 2016

    Phylogenomics with Paralogs
    text, January 2017

    Editorial: Computational Systems Biology of Pathogen-Host Interactions
    journal, February 2016

    New Algorithms for Structure Informed Genome Rearrangement
    text, January 2022

    Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway
    journal, June 2014

    • de Crécy-Lagard, Valérie
    • Computational and Structural Biotechnology Journal, Vol. 10, Issue 16
    • DOI: 10.1016/j.csbj.2014.05.008

    Whole genome shotgun sequencing of Indian strains of Streptococcus agalactiae
    journal, December 2017

    Insights into the pan-microbiome: skin microbial communities of Chinese individuals differ from other racial groups
    journal, July 2015

    • Leung, Marcus H. Y.; Wilkins, David; Lee, Patrick K. H.
    • Scientific Reports, Vol. 5, Issue 1
    • DOI: 10.1038/srep11845

    MycoCAP - Mycobacterium Comparative Analysis Platform
    journal, December 2015

    • Choo, Siew Woh; Ang, Mia Yang; Dutta, Avirup
    • Scientific Reports, Vol. 5, Issue 1
    • DOI: 10.1038/srep18227

    Metabolic and genetic basis for auxotrophies in Gram-negative species
    journal, March 2020

    • Seif, Yara; Choudhary, Kumari Sonal; Hefner, Ying
    • Proceedings of the National Academy of Sciences, Vol. 117, Issue 11
    • DOI: 10.1073/pnas.1910499117

    RNA-Rocket: an RNA-Seq analysis resource for infectious disease research
    journal, January 2015

    A Pan-Genomic Approach to Understand the Basis of Host Adaptation in Achromobacter
    journal, April 2017

    • Jeukens, Julie; Freschi, Luca; Vincent, Antony T.
    • Genome Biology and Evolution, Vol. 9, Issue 4
    • DOI: 10.1093/gbe/evx061

    MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes
    journal, November 2016

    • Vallenet, David; Calteau, Alexandra; Cruveiller, Stéphane
    • Nucleic Acids Research, Vol. 45, Issue D1
    • DOI: 10.1093/nar/gkw1101

    EuPathDB: the eukaryotic pathogen genomics database resource
    journal, November 2016

    • Aurrecoechea, Cristina; Barreto, Ana; Basenko, Evelina Y.
    • Nucleic Acids Research, Vol. 45, Issue D1
    • DOI: 10.1093/nar/gkw1105

    The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes
    journal, January 2017

    • Galperin, Michael Y.; Fernández-Suárez, Xosé M.; Rigden, Daniel J.
    • Nucleic Acids Research
    • DOI: 10.1093/nar/gkx021

    Bergeyella cardium: Clinical Characteristics and Draft Genome of an Emerging Pathogen in Native and Prosthetic Valve Endocarditis
    journal, March 2019

    • Mulliken, Jennifer S.; Langelier, Charles; Budak, Jehan Z.
    • Open Forum Infectious Diseases, Vol. 6, Issue 4
    • DOI: 10.1093/ofid/ofz134

    Genome Sequence of Hypervirulent Aeromonas hydrophila Strain HZAUAH
    journal, March 2017

    Complete Genome Sequence of an Escherichia coli O157:H7 Strain Isolated from a Super-Shedder Steer
    journal, April 2016

    Draft Genome Sequence of Organophosphate-Degrading Ochrobactrum anthropi FRAF13
    journal, April 2016

    Genome Sequence of a Proteus mirabilis Strain Isolated from the Salivary Glands of Larval Lucilia sericata
    journal, August 2016

    First Report on the Draft Genome Sequences of Corynebacterium diphtheriae Isolates from India
    journal, December 2016

    • Veeraraghavan, Balaji; Anandan, Shalini; Rajamani Sekar, Suresh Kumar
    • Genome Announcements, Vol. 4, Issue 6
    • DOI: 10.1128/genomea.01316-16

    First Report on a Cluster of Colistin-Resistant Klebsiella pneumoniae Strains Isolated from a Tertiary Care Center in India: Whole-Genome Shotgun Sequencing
    journal, February 2017

    • Mathur, Purva; Veeraraghavan, Balaji; Devanga Ragupathi, Naveen Kumar
    • Genome Announcements, Vol. 5, Issue 5
    • DOI: 10.1128/genomea.01466-16

    Databases for Microbiologists: TABLE 1
    journal, May 2015

    Cystic Fibrosis-Associated Stenotrophomonas maltophilia Strain-Specific Adaptations and Responses to pH
    journal, April 2019

    • Gallagher, Tara; Phan, Joann; Oliver, Andrew
    • Journal of Bacteriology, Vol. 201, Issue 7
    • DOI: 10.1128/jb.00478-18

    Identification of a New Lipoprotein Export Signal in Gram-Negative Bacteria
    journal, November 2016

    • Lauber, Frédéric; Cornelis, Guy Richard; Renzi, Francesco
    • mBio, Vol. 7, Issue 5
    • DOI: 10.1128/mbio.01232-16

    Recovery of a Medieval Brucella melitensis Genome Using Shotgun Metagenomics
    journal, August 2014

    • Kay, Gemma L.; Sergeant, Martin J.; Giuffra, Valentina
    • mBio, Vol. 5, Issue 4
    • DOI: 10.1128/mbio.01337-14

    Release of Nonstop Ribosomes Is Essential
    journal, December 2014

    • Feaga, Heather A.; Viollier, Patrick H.; Keiler, Kenneth C.
    • mBio, Vol. 5, Issue 6
    • DOI: 10.1128/mbio.01916-14

    Genome-Wide Screening for Enteric Colonization Factors in Carbapenem-Resistant ST258 Klebsiella pneumoniae
    journal, April 2019

    Whole-Genome Sequences of 35 Incompatibility Group I1 Plasmid-Carrying Salmonella enterica Isolates from Food Animal and Clinical Sources
    journal, August 2019

    • Aljahdali, Nesreen H.; Kaldhone, Pravin R.; Foley, Steven L.
    • Microbiology Resource Announcements, Vol. 8, Issue 35
    • DOI: 10.1128/mra.00831-19

    Draft Genomic Sequences of Streptomyces misionensis ACT66 and Streptomyces albidoflavus ACT77, Bacteria with Potential Application for Phytopathogen Biocontrol
    journal, September 2019

    • Pylro, Victor Satler; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini
    • Microbiology Resource Announcements, Vol. 8, Issue 36
    • DOI: 10.1128/mra.00949-19

    Draft Genome Sequences of Violacein-Producing Duganella sp. Isolates from a Waterway in Eastern Pennsylvania
    journal, September 2018

    • Lamendella, Regina; Jude, Brooke A.
    • Microbiology Resource Announcements, Vol. 7, Issue 12
    • DOI: 10.1128/mra.01196-18

    Comprehensive Virulence Gene Profiling of Bovine Non- aureus Staphylococci Based on Whole-Genome Sequencing Data
    journal, April 2019

    Listeriomics: an Interactive Web Platform for Systems Biology of Listeria
    journal, April 2017

    Prediction of Acquired Antimicrobial Resistance for Multiple Bacterial Species Using Neural Networks
    journal, January 2020

    Phylogenomic and Molecular Demarcation of the Core Members of the Polyphyletic Pasteurellaceae Genera Actinobacillus , Haemophilus , and Pasteurella
    journal, January 2015

    • Naushad, Sohail; Adeolu, Mobolaji; Goel, Nisha
    • International Journal of Genomics, Vol. 2015
    • DOI: 10.1155/2015/198560

    BorreliaBase: a phylogeny-centered browser of Borrelia genomes
    journal, July 2014

    GWAMAR: Genome-wide assessment of mutations associated with drug resistance in bacteria
    journal, December 2014

    PhyTB: Phylogenetic tree visualisation and sample positioning for M. tuberculosis
    journal, May 2015

    Full genome SNP-based phylogenetic analysis reveals the origin and global spread of Brucella melitensis
    journal, February 2015

    Dormant non-culturable Mycobacterium tuberculosis retains stable low-abundant mRNA
    journal, November 2015

    Correction to: Identification of two different chemosensory pathways in representatives of the genus Halomonas
    journal, June 2018

    • Gasperotti, Ana Florencia; Revuelta, María Victoria; Studdert, Claudia Alicia
    • BMC Genomics, Vol. 19, Issue 1
    • DOI: 10.1186/s12864-018-4811-x

    Complete nontuberculous mycobacteria whole genomes using an optimized DNA extraction protocol for long-read sequencing
    journal, October 2019

    Characterization of Burkholderia pseudomallei protein BPSL1375 validates the Putative hemolytic activity of the COG3176 N-Acyltransferase family
    journal, November 2015

    The Brucella TIR domain containing proteins BtpA and BtpB have a structural WxxxE motif important for protection against microtubule depolymerisation
    journal, October 2014

    • Felix, Christine; Kaplan Türköz, Burcu; Ranaldi, Sebastien
    • Cell Communication and Signaling, Vol. 12, Issue 1
    • DOI: 10.1186/s12964-014-0053-y

    Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers
    journal, October 2018

    Associations between digital dermatitis lesion grades in dairy cattle and the quantities of four Treponema species
    journal, October 2018

    Genome sequencing and analysis of the first spontaneous Nanosilver resistant bacterium Proteus mirabilis strain SCDR1
    journal, November 2017

    • Saeb, Amr T. M.; Al-Rubeaan, Khalid A.; Abouelhoda, Mohamed
    • Antimicrobial Resistance & Infection Control, Vol. 6, Issue 1
    • DOI: 10.1186/s13756-017-0277-x

    Urban metagenomics uncover antibiotic resistance reservoirs in coastal beach and sewage waters
    journal, February 2019

    A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments
    journal, July 2019

    Complete genome of Arthrobacter alpinus strain R3.8, bioremediation potential unraveled with genomic analysis
    journal, September 2017

    Structural host-microbiota interaction networks
    journal, October 2017

    Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens
    journal, March 2020

    Standardized Metadata for Human Pathogen/Vector Genomic Sequences
    journal, June 2014

    Vikodak - A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets
    journal, February 2016

    Biomarker panels for characterizing microbial community biofilm formation as composite molecular process
    journal, August 2018

    Correcting Inconsistencies and Errors in Bacterial Genome Metadata Using an Automated Curation Tool in Excel (AutoCurE)
    journal, September 2015

    • Schmedes, Sarah E.; King, Jonathan L.; Budowle, Bruce
    • Frontiers in Bioengineering and Biotechnology, Vol. 3
    • DOI: 10.3389/fbioe.2015.00138

    A Brucella spp. Isolate from a Pac-Man Frog (Ceratophrys ornata) Reveals Characteristics Departing from Classical Brucellae
    journal, September 2016

    • Soler-Lloréns, Pedro F.; Quance, Chris R.; Lawhon, Sara D.
    • Frontiers in Cellular and Infection Microbiology, Vol. 6
    • DOI: 10.3389/fcimb.2016.00116

    Hidden state prediction: a modification of classic ancestral state reconstruction algorithms helps unravel complex symbioses
    journal, August 2014

    Composite mobile genetic elements disseminating macrolide resistance in Streptococcus pneumoniae
    journal, February 2015

    Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation
    journal, November 2016

    • Faria, José P.; Davis, James J.; Edirisinghe, Janaka N.
    • Frontiers in Microbiology, Vol. 7
    • DOI: 10.3389/fmicb.2016.01819

    Evidence for Ecological Flexibility in the Cosmopolitan Genus Curtobacterium
    journal, November 2016

    The Potential of Systems Biology to Discover Antibacterial Mechanisms of Plant Phenolics
    journal, March 2017

    • Rempe, Caroline S.; Burris, Kellie P.; Lenaghan, Scott C.
    • Frontiers in Microbiology, Vol. 8
    • DOI: 10.3389/fmicb.2017.00422

    Plasmid-Mediated Quinolone Resistance in Shigella flexneri Isolated From Macaques
    journal, March 2018

    Distribution Patterns of Polyphosphate Metabolism Pathway and Its Relationships With Bacterial Durability and Virulence
    journal, April 2018

    Quantitative RNA-seq Analysis Unveils Osmotic and Thermal Adaptation Mechanisms Relevant for Ectoine Production in Chromohalobacter salexigens
    journal, August 2018

    • Salvador, Manuel; Argandoña, Montserrat; Naranjo, Emilia
    • Frontiers in Microbiology, Vol. 9
    • DOI: 10.3389/fmicb.2018.01845

    A Comparison of Microbial Genome Web Portals
    journal, February 2019

    • Karp, Peter D.; Ivanova, Natalia; Krummenacker, Markus
    • Frontiers in Microbiology, Vol. 10
    • DOI: 10.3389/fmicb.2019.00208

    Plasmid profiles among some ESKAPE pathogens in a tertiary care centre in south India
    journal, January 2019

    • Veeraraghavan, Balaji; Ragupathi, NaveenKumar Devanga; Bakthavatchalam, YamunaDevi
    • Indian Journal of Medical Research, Vol. 149, Issue 2
    • DOI: 10.4103/ijmr.ijmr_2098_17

    Identification of nonserotypeable Shigella spp. using genome sequencing: a step forward
    journal, November 2017

    • Dhiviya Prabaa, Muthuirulandi Sethuvel; Naveen Kumar, Devanga Ragupathi; Yesurajan, Inbanathan Francis
    • Future Science OA, Vol. 3, Issue 4
    • DOI: 10.4155/fsoa-2017-0063

    Current Bioinformatics resources in combating infectious diseases
    journal, January 2018

      Sort by:
      [ × clear filter / sort ]

      Similar Records in DOE PAGES and OSTI.GOV collections: