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

Davis, James J.; Brettin, Thomas; Dietrich, Emily M.; Gerdes, Svetlana; Henry, Christopher S.; Murphy-Olson, Daniel E.; Olson, Robert; Parrello, Bruce D.; Pusch, Gordon D.; Shukla, Maulik P.; Vonstein, Veronika; Xia, Fangfang; Yoo, Hyunseung; Stevens, Rick L.

doi:10.1093/nar/gkw1017

Title: Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

Journal Article · Mon Nov 28 00:00:00 EST 2016 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkw1017· OSTI ID:1373595

Davis, James J.; Brettin, Thomas; Dietrich, Emily M.; Gerdes, Svetlana; Henry, Christopher S.; Murphy-Olson, Daniel E.; Olson, Robert; Parrello, Bruce D.; Pusch, Gordon D.; Shukla, Maulik P.; Vonstein, Veronika; Xia, Fangfang; Yoo, Hyunseung; Stevens, Rick L.

Here, the Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center. Recent changes to PATRIC include a redesign of the web interface and some new services that provide users with a platform that takes them from raw reads to an integrated analysis experience. The redesigned interface allows researchers direct access to tools and data, and the emphasis has changed to user-created genome-groups, with detailed summaries and views of the data that researchers have selected. Perhaps the biggest change has been the enhanced capability for researchers to analyze their private data and compare it to the available public data. Researchers can assemble their raw sequence reads and annotate the contigs using RASTtk. PATRIC also provides services for RNA-Seq, variation, model reconstruction and differential expression analysis, all delivered through an updated private workspace. Private data can be compared by `virtual integration' to any of PATRIC's public data. The number of genomes available for comparison in PATRIC has expanded to over 80 000, with a special emphasis on genomes with antimicrobial resistance data. PATRIC uses this data to improve both subsystem annotation and k-mer classification, and tags new genomes as having signatures that indicate susceptibility or resistance to specific antibiotics.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: National Institutes of Health (NIH), National Institute of Allergy and Infectious Diseases (NIAID)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1373595

Journal Information:: Nucleic Acids Research, Vol. 45, Issue D1; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 871 works

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PRAP: Pan Resistome analysis pipeline He, Yichen; Zhou, Xiujuan; Chen, Ziyan BMC Bioinformatics, Vol. 21, Issue 1 https://doi.org/10.1186/s12859-019-3335-y	journal	January 2020
Comparative genomics analysis to differentiate metabolic and virulence gene potential in gastric versus enterohepatic Helicobacter species Mannion, Anthony; Shen, Zeli; Fox, James G. BMC Genomics, Vol. 19, Issue 1 https://doi.org/10.1186/s12864-018-5171-2	journal	November 2018
Draft genome sequence of Enterococcus faecium SP15, a potential probiotic strain isolated from spring water Aziz, Fauzia; Khan, Muhammad Nasim; Ahmed, Safia BMC Research Notes, Vol. 12, Issue 1 https://doi.org/10.1186/s13104-019-4136-0	journal	February 2019
A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events Jaillard, Magali; Lima, Leandro; Tournoud, Maud PLOS Genetics, Vol. 14, Issue 11 https://doi.org/10.1371/journal.pgen.1007758	journal	November 2018
Genetic determinants of genus-level glycan diversity in a bacterial protein glycosylation system Hadjineophytou, Chris; Anonsen, Jan Haug; Wang, Nelson PLOS Genetics, Vol. 15, Issue 12 https://doi.org/10.1371/journal.pgen.1008532	journal	December 2019
Rapidly evolving changes and gene loss associated with host switching in Corynebacterium pseudotuberculosis Viana, Marcus Vinicius Canário; Sahm, Arne; Góes Neto, Aristóteles PLOS ONE, Vol. 13, Issue 11 https://doi.org/10.1371/journal.pone.0207304	journal	November 2018
The afc antifungal activity cluster, which is under tight regulatory control of ShvR, is essential for transition from intracellular persistence of Burkholderia cenocepacia to acute pro-inflammatory infection Gomes, Margarida C.; Tasrini, Yara; Subramoni, Sujatha PLOS Pathogens, Vol. 14, Issue 12 https://doi.org/10.1371/journal.ppat.1007473	journal	December 2018
Whole Genome Sequencing and Comparative Genomics of Two Nematicidal Bacillus Strains Reveals a Wide Range of Possible Virulence Factors Susič, Nik; Janežič, Sandra; Rupnik, Maja G3: Genes\|Genomes\|Genetics, Vol. 10, Issue 3 https://doi.org/10.1534/g3.119.400716	journal	January 2020
Brucella spp. of amphibians comprise genomically diverse motile strains competent for replication in macrophages and survival in mammalian hosts Al Dahouk, Sascha; Köhler, Stephan; Occhialini, Alessandra RWTH Aachen University https://doi.org/10.18154/rwth-conv-221967	text	January 2017
Plasmid-Mediated Quinolone Resistance in Shigella flexneri Isolated From Macaques Mannion, Anthony J.; Martin, Heather R.; Shen, Zeli Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00311	journal	March 2018
Revisiting the Taxonomy of the Genus Arcobacter: Getting Order From the Chaos Pérez-Cataluña, Alba; Salas-Massó, Nuria; Diéguez, Ana L. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02077	journal	September 2018
Genome Structure of the Opportunistic Pathogen Paracoccus yeei (Alphaproteobacteria) and Identification of Putative Virulence Factors Lasek, Robert; Szuplewska, Magdalena; Mitura, Monika Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02553	journal	October 2018
Environmental and Clinical Strains of Vibrio cholerae Non-O1, Non-O139 From Germany Possess Similar Virulence Gene Profiles Schwartz, Keike; Hammerl, Jens Andre; Göllner, Cornelia Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00733	journal	April 2019
In-Depth Genomic and Phenotypic Characterization of the Antarctic Psychrotolerant Strain Pseudomonas sp. MPC6 Reveals Unique Metabolic Features, Plasticity, and Biotechnological Potential Orellana-Saez, Matias; Pacheco, Nicolas; Costa, José I. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01154	journal	May 2019
Shotgun Metagenomics Reveals the Benthic Microbial Community Response to Plastic and Bioplastic in a Coastal Marine Environment Pinnell, Lee J.; Turner, Jeffrey W. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01252	journal	June 2019
Using Genomics to Track Global Antimicrobial Resistance Hendriksen, Rene S.; Bortolaia, Valeria; Tate, Heather Frontiers in Public Health, Vol. 7 https://doi.org/10.3389/fpubh.2019.00242	journal	September 2019
First Report of Integrative Conjugative Elements in Riemerella anatipestifer Isolates From Ducks in China Zhu, Dekang; Wan, Jianbang; Yang, Zhishuang Frontiers in Veterinary Science, Vol. 6 https://doi.org/10.3389/fvets.2019.00128	journal	April 2019
Genome-Guided Characterization of Ochrobactrum sp. POC9 Enhancing Sewage Sludge Utilization—Biotechnological Potential and Biosafety Considerations Poszytek, Krzysztof; Karczewska-Golec, Joanna; Ciok, Anna International Journal of Environmental Research and Public Health, Vol. 15, Issue 7 https://doi.org/10.3390/ijerph15071501	journal	July 2018
Insights into the Phylogeny and Evolution of Cold Shock Proteins: From Enteropathogenic Yersinia and Escherichia coli to Eubacteria Yu, Tao; Keto-Timonen, Riikka; Jiang, Xiaojie International Journal of Molecular Sciences, Vol. 20, Issue 16 https://doi.org/10.3390/ijms20164059	journal	August 2019
Integrated Genome-Wide Analysis of an Isogenic Pair of Pseudomonas aeruginosa Clinical Isolates with Differential Antimicrobial Resistance to Ceftolozane/Tazobactam, Ceftazidime/Avibactam, and Piperacillin/Tazobactam Huang, Weihua; Hamouche, Joelle El; Wang, Guiqing International Journal of Molecular Sciences, Vol. 21, Issue 3 https://doi.org/10.3390/ijms21031026	journal	February 2020
Role of FAD-I in Fusobacterial Interspecies Interaction and Biofilm Formation Shokeen, Bhumika; Park, Jane; Duong, Emily Microorganisms, Vol. 8, Issue 1 https://doi.org/10.3390/microorganisms8010070	journal	January 2020
Genome-Wide Analyses Revealed Remarkable Heterogeneity in Pathogenicity Determinants, Antimicrobial Compounds, and CRISPR-Cas Systems of Complex Phytopathogenic Genus Pectobacterium Arizala, Dario; Arif, Mohammad Pathogens, Vol. 8, Issue 4 https://doi.org/10.3390/pathogens8040247	journal	November 2019
Mycobacterium tuberculosis SatS is a chaperone for the SecA2 protein export pathway Miller, Brittany K.; Hughes, Ryan; Ligon, Lauren S. eLife, Vol. 8 https://doi.org/10.7554/elife.40063	journal	January 2019
Extensive transmission of microbes along the gastrointestinal tract Schmidt, Thomas SB; Hayward, Matthew R.; Coelho, Luis P. eLife, Vol. 8 https://doi.org/10.7554/elife.42693	journal	February 2019
Differential efficiency of wild type rhizogenic strains for rol gene transformation of plants Desmet, Siel; De Keyser, Ellen; Van Vaerenbergh, Johan Applied Microbiology and Biotechnology, Vol. 103, Issue 16 https://doi.org/10.1007/s00253-019-10003-0	journal	July 2019
Description of ‘Ca. Methylobacter oryzae’ KRF1, a novel species from the environmentally important Methylobacter clade 2 Khatri, Kumal; Mohite, Jyoti A.; Pandit, Pranitha S. Antonie van Leeuwenhoek, Vol. 113, Issue 5 https://doi.org/10.1007/s10482-019-01369-2	journal	December 2019
Organic micropollutants paracetamol and ibuprofen—toxicity, biodegradation, and genetic background of their utilization by bacteria Żur, Joanna; Piński, Artur; Marchlewicz, Ariel Environmental Science and Pollution Research, Vol. 25, Issue 22 https://doi.org/10.1007/s11356-018-2517-x	journal	June 2018
The enemy from within: a prophage of Roseburia intestinalis systematically turns lytic in the mouse gut, driving bacterial adaptation by CRISPR spacer acquisition Cornuault, Jeffrey K.; Moncaut, Elisabeth; Loux, Valentin The ISME Journal, Vol. 14, Issue 3 https://doi.org/10.1038/s41396-019-0566-x	journal	December 2019
Pseudogene repair driven by selection pressure applied in experimental evolution Anand, Amitesh; Olson, Connor A.; Yang, Laurence Nature Microbiology, Vol. 4, Issue 3 https://doi.org/10.1038/s41564-018-0340-2	journal	January 2019
Brevibacterium from Austrian hard cheese harbor a putative histamine catabolism pathway and a plasmid for adaptation to the cheese environment Anast, Justin M.; Dzieciol, Monika; Schultz, Dylan L. Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-42525-y	journal	April 2019
Antimicrobial Resistance Prediction for Gram-Negative Bacteria via Game Theory-Based Feature Evaluation Chowdhury, Abu Sayed; Call, Douglas R.; Broschat, Shira L. Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-50686-z	journal	October 2019
Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319 Aminian-Dehkordi, Javad; Mousavi, Seyyed Mohammad; Jafari, Arezou Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-55041-w	journal	December 2019
A plastidial pantoate transporter with a potential role in pantothenate synthesis Huang, Lili; Pyc, Michal; Alseekh, Saleh Biochemical Journal, Vol. 475, Issue 4 https://doi.org/10.1042/BCJ20170883	journal	February 2018
Network-based methods for predicting essential genes or proteins: a survey Li, Xingyi; Li, Wenkai; Zeng, Min Briefings in Bioinformatics, Vol. 21, Issue 2 https://doi.org/10.1093/bib/bbz017	journal	February 2019
Predicting bacterial virulence factors – evaluation of machine learning and negative data strategies Rentzsch, Robert; Deneke, Carlus; Nitsche, Andreas Briefings in Bioinformatics, Vol. 21, Issue 5 https://doi.org/10.1093/bib/bbz076	journal	October 2019
The MACADAM database: a MetAboliC pAthways DAtabase for Microbial taxonomic groups for mining potential metabolic capacities of archaeal and bacterial taxonomic groups Le Boulch, Malo; Déhais, Patrice; Combes, Sylvie Database, Vol. 2019 https://doi.org/10.1093/database/baz049	journal	January 2019
MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments Oliveira, Francislon S.; Brestelli, John; Cade, Shon Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1027	journal	November 2017
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes Mende, Daniel R.; Letunic, Ivica; Maistrenko, Oleksandr M. Nucleic Acids Research https://doi.org/10.1093/nar/gkz1002	journal	October 2019
Indiicoccus explosivorum gen. nov., sp. nov., isolated from an explosives waste contaminated site Pal, Yash; Mayilraj, Shanmugam; Paul, Mohit International Journal of Systematic and Evolutionary Microbiology, Vol. 69, Issue 8 https://doi.org/10.1099/ijsem.0.003541	journal	August 2019
Micromonospora deserti sp. nov., isolated from the Karakum Desert Saygin, Hayrettin; Ay, Hilal; Guven, Kiymet International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 1 https://doi.org/10.1099/ijsem.0.003752	journal	January 2020
Natrialba swarupiae sp. nov., a halophilic archaeon isolated from a hypersaline lake in India Kajale, Swapnil; Deshpande, Neelima; Pali, Snigdha International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 3 https://doi.org/10.1099/ijsem.0.003986	journal	March 2020
A fast and agnostic method for bacterial genome-wide association studies: bridging the gap between kmers and genetic events Jaillard, Magali; Lima, Leandro; Tournoud, Maud PLOS Genetics https://doi.org/10.1101/297754	journal	April 2018
Bridging the divide: bacteria synthesizing archaeal membrane lipids Villanueva, Laura; von Meijenfeldt, F. A. Bastiaan; Westbye, Alexander B. BioRxiv https://doi.org/10.1101/448035	posted_content	October 2018
Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates Galata, Valentina; Laczny, Cédric C.; Backes, Christina Genomics, Proteomics & Bioinformatics https://doi.org/10.1101/463901	journal	November 2018
Streptococcus equi subsp. zooepidemicus associated with sudden death of swine in North America de Costa, Matheus O.; Lage, Brad Emerging Infectious Diseases https://doi.org/10.1101/812636	journal	October 2019
Characterization of Hypermutator Pseudomonas aeruginosa Isolates from Patients with Cystic Fibrosis in Australia Rees, Vanessa E.; Deveson Lucas, Deanna S.; López-Causapé, Carla Antimicrobial Agents and Chemotherapy, Vol. 63, Issue 4 https://doi.org/10.1128/aac.02538-18	journal	April 2019
Generation of a Prophage-Free Variant of the Fast-Growing Bacterium Vibrio natriegens Pfeifer, Eugen; Michniewski, Slawomir; Gätgens, Cornelia Applied and Environmental Microbiology, Vol. 85, Issue 17 https://doi.org/10.1128/aem.00853-19	journal	June 2019
Population Dynamics of Salmonella enterica within Beef Cattle Cohorts Followed from Single-Dose Metaphylactic Antibiotic Treatment until Slaughter Levent, Gizem; Schlochtermeier, Ashlynn; Ives, Samuel E. Applied and Environmental Microbiology, Vol. 85, Issue 23 https://doi.org/10.1128/aem.01386-19	journal	December 2019
Draft Genome Sequences of Pseudomonas sp. Strains Isolated from Wheat in Germany Hollmann, Jürgen; Brinks, Erik; Schwake-Anduschus, Christine Microbiology Resource Announcements, Vol. 8, Issue 19 https://doi.org/10.1128/mra.00178-19	journal	May 2019
Draft Genome Sequence of Pseudomonas sp. Strain MWU13-2860, Isolated from a Wild Cranberry Bog in Truro, Massachusetts Ebadzadsahrai, Ghazal; Thomson, Jonathon; Soby, Scott Microbiology Resource Announcements, Vol. 7, Issue 13 https://doi.org/10.1128/mra.01007-18	journal	October 2018
Complete Genome Sequence of Lactobacillus plantarum Strain JDARSH, Isolated from Sheep Milk Patil, Abhinandan; Dubey, Anamika; Malla, Muneer Ahmad Microbiology Resource Announcements, Vol. 9, Issue 2 https://doi.org/10.1128/mra.01199-19	journal	January 2020
Draft Genome Sequences of Four Metallo-Beta-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates, Including Two Colistin-Resistant Strains, from Cairo, Egypt Attia, Heba; Szubin, Richard; Yassin, Aymen S. Microbiology Resource Announcements, Vol. 8, Issue 7 https://doi.org/10.1128/mra.01418-18	journal	February 2019
Characterization of agr Groups of Staphylococcus pseudintermedius Isolates from Dogs in Texas Little, Sara V.; Bryan, Laura K.; Hillhouse, Andrew E. mSphere, Vol. 4, Issue 2 https://doi.org/10.1128/msphere.00033-19	journal	April 2019
Comparative Genomics Reveals a Well-Conserved Intrinsic Resistome in the Emerging Multidrug-Resistant Pathogen Cupriavidus gilardii Ruiz, Cristian; McCarley, Ashley; Espejo, Manuel Luis mSphere, Vol. 4, Issue 5 https://doi.org/10.1128/msphere.00631-19	journal	October 2019
Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes Papudeshi, Bhavya; Haggerty, J. Matthew; Doane, Michael BMC Genomics, Vol. 18, Issue 1 https://doi.org/10.1186/s12864-017-4294-1	journal	November 2017
Identifying genomic islands with deep neural networks Assaf, Rida; Xia, Fangfang; Stevens, Rick BMC Genomics, Vol. 22, Issue S3 https://doi.org/10.1186/s12864-021-07575-5	journal	June 2021
Genomic characterization of Listeria monocytogenes isolates reveals that their persistence in a pig slaughterhouse is linked to the presence of benzalkonium chloride resistance genes Cherifi, Tamazight; Carrillo, Catherine; Lambert, Dominic BMC Microbiology, Vol. 18, Issue 1 https://doi.org/10.1186/s12866-018-1363-9	journal	December 2018
Determination of virulence and fitness genes associated with the pheU, pheV and selC integration sites of LEE-negative food-borne Shiga toxin-producing Escherichia coli strains Saile, Nadja; Schuh, Elisabeth; Semmler, Torsten Gut Pathogens, Vol. 10, Issue 1 https://doi.org/10.1186/s13099-018-0271-8	journal	October 2018
High contiguity genome sequence of a multidrug-resistant hospital isolate of Enterobacter hormaechei Monahan, Leigh G.; DeMaere, Matthew Z.; Cummins, Max L. Gut Pathogens, Vol. 11, Issue 1 https://doi.org/10.1186/s13099-019-0288-7	journal	February 2019
ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates Schwengers, Oliver; Hoek, Andreas; Fritzenwanker, Moritz PLOS Computational Biology, Vol. 16, Issue 3 https://doi.org/10.1371/journal.pcbi.1007134	journal	March 2020
Desiccation tolerance in Acinetobacter baumannii is mediated by the two-component response regulator BfmR Farrow, John M.; Wells, Greg; Pesci, Everett C. PLOS ONE, Vol. 13, Issue 10 https://doi.org/10.1371/journal.pone.0205638	journal	October 2018
Comparative Genomics Reveals the Regulatory Complexity of Bifidobacterial Arabinose and Arabino-Oligosaccharide Utilization Arzamasov, Aleksandr A.; van Sinderen, Douwe; Rodionov, Dmitry A. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00776	journal	April 2018
Genome-Wide Profiling of Enterotoxigenic Staphylococcus aureus Strains Used for the Production of Naturally Contaminated Cheeses Macori, Guerrino; Bellio, Alberto; Bianchi, Daniela Manila Genes, Vol. 11, Issue 1 https://doi.org/10.3390/genes11010033	journal	December 2019
Genomic Analysis of Shewanella sp. O23S—The Natural Host of the pSheB Plasmid Carrying Genes for Arsenic Resistance and Dissimilatory Reduction Uhrynowski, Witold; Radlinska, Monika; Drewniak, Lukasz International Journal of Molecular Sciences, Vol. 20, Issue 5 https://doi.org/10.3390/ijms20051018	journal	February 2019
Isolation and Characterization of a Novel Pathogenic Strain of Ehrlichia minasensis Moura de Aguiar, Daniel; Pessoa Araújo Junior, João; Nakazato, Luciano Microorganisms, Vol. 7, Issue 11 https://doi.org/10.3390/microorganisms7110528	journal	November 2019
The Role of Iron in the P-Acquisition Mechanisms of the Unicellular N2-Fixing Cyanobacteria Halothece sp., Found in Association with the Mediterranean Seagrass Posidonia oceanica Fernández-Juárez, Víctor; Bennasar-Figueras, Antoni; Tovar-Sanchez, Antonio Prime Archives in Microbiology https://doi.org/10.37247/pamic.1.2020.7	book	January 2020
The afc antifungal activity cluster, which is under tight regulatory control of ShvR, is essential for transition from intracellular persistence of Burkholderia cenocepacia to acute pro-inflammatory infection Gomes, Margarida C.; Tasrini, Yara; Subramoni, Sujatha Public Library of Science (PLoS) https://doi.org/10.5167/uzh-167662	text	January 2018
Greedy de novo motif discovery to construct motif repositories for bacterial proteomes Khakzad, Hamed; Malmstroem, Johan; Malmstroem, Lars Zenodo https://doi.org/10.5281/zenodo.1403142	text	January 2019
Insights on genomic diversity of Vibrio spp. through Pan-genome analysis Nathamuni, Suganya; Jangam, Ashok Kumar; Katneni, Vinaya Kumar Annals of Microbiology, Vol. 69, Issue 13 https://doi.org/10.1007/s13213-019-01539-7	journal	December 2019
GABA-modulating bacteria of the human gut microbiota Strandwitz, Philip; Kim, Ki Hyun; Terekhova, Darya Nature Microbiology, Vol. 4, Issue 3 https://doi.org/10.1038/s41564-018-0307-3	journal	December 2018
Bioinformatics Analysis of Metabolism Pathways of Archaeal Energy Reserves Wang, Liang; Liu, Qinghua; Wu, Xiang Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-018-37768-0	journal	January 2019
Selection of hyperproduction of AmpC and SME-1 in a carbapenem-resistant Serratia marcescens isolate during antibiotic therapy Hemarajata, Peera; Amick, Thomas; Yang, Shangxin Journal of Antimicrobial Chemotherapy, Vol. 73, Issue 5 https://doi.org/10.1093/jac/dky028	journal	February 2018
VFDB 2019: a comparative pathogenomic platform with an interactive web interface Liu, Bo; Zheng, Dandan; Jin, Qi Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1080	journal	November 2018
Gut Microbiota and Clinical Features Distinguish Colonization With Klebsiella pneumoniae Carbapenemase-Producing Klebsiella pneumoniae at the Time of Admission to a Long-term Acute Care Hospital Seekatz, Anna M.; Bassis, Christine M.; Fogg, Louis Open Forum Infectious Diseases, Vol. 5, Issue 8 https://doi.org/10.1093/ofid/ofy190	journal	July 2018
Yersinia kristensenii subsp. rochesterensis subsp. nov., isolated from human feces Cunningham, Scott A.; Jeraldo, Patricio; Patel, Robin International Journal of Systematic and Evolutionary Microbiology, Vol. 69, Issue 8 https://doi.org/10.1099/ijsem.0.003464	journal	August 2019
Afifella aestuarii sp. nov., a phototrophic bacterium Buddhi, Sailaja; G., Suresh; Gupta, Deepshikha International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 1 https://doi.org/10.1099/ijsem.0.003756	journal	January 2020
Complete genome sequence and comparative genomics of the fish pathogen Streptococcus iniae QMA0248 Alsheikh-Hussain, Areej S.; Ben Zakour, Nouri L.; Forde, Brian M. Microbial Genomics https://doi.org/10.1101/2019.12.17.880476	journal	July 2020
Appearance of synthetic vector-associated antibiotic resistance genes in next-generation sequences Taiaroa, George; Cook, Gregory M.; Williamson, Deborah A. https://doi.org/10.1101/392225	posted_content	August 2018
Improving the usability and comprehensiveness of microbial databases Loeffler, Caitlin; Karlsberg, Aaron; Martin, Lana S. BMC Biology https://doi.org/10.1101/497867	journal	February 2020
Genome-wide assessment of Mycobacterium tuberculosis conditionally essential metabolic pathways Minato, Yusuke; Gohl, Daryl M.; Thiede, Joshua M. mSystems https://doi.org/10.1101/534289	journal	May 2019
The Helicobacter pylori cell shape promoting protein Csd5 interacts with the cell wall, MurF, and the bacterial cytoskeleton Blair, Kris M.; Mears, Kevin S.; Taylor, Jennifer A. Molecular Microbiology, Vol. 110, Issue 1 https://doi.org/10.1111/mmi.14087	journal	September 2018
Draft Genome Sequence of Bacillus sp. Strain UFRGS-B20, a Hydrocarbon Degrader Dörr de Quadros, Patricia; Fulthorpe, Roberta; Saati, Rosemary Genome Announcements, Vol. 6, Issue 8 https://doi.org/10.1128/genomea.00052-18	journal	February 2018
Genome Sequences of Escherichia Bacteriophages Isolated from Raw Wastewater Keely, Scott P.; Herrmann, Michael P.; Korajkic, Asja Microbiology Resource Announcements, Vol. 8, Issue 26 https://doi.org/10.1128/mra.00135-19	journal	June 2019
Draft Genome Sequences of Pseudomonas MWU13-2625 and MWU12-2115, Isolated from a Wild Cranberry Bog at the Cape Cod National Seashore Ebadzadsahrai, Ghazal; Thomson, Jonathon; Soby, Scott Microbiology Resource Announcements, Vol. 7, Issue 12 https://doi.org/10.1128/mra.00992-18	journal	September 2018
Draft Genome Sequence of the Type Strain Streptomyces armeniacus ATCC 15676 Labana, Puneet; Gosse, Jessica T.; Boddy, Christopher N. Microbiology Resource Announcements, Vol. 7, Issue 11 https://doi.org/10.1128/mra.01107-18	journal	September 2018
Genome Sequence of “ Candidatus Rickettsia colombianensi,” a Novel Tick-Associated Bacterium Distributed in Colombia Miranda, Jorge; Mattar, Salim; Puerta-González, Andrés Microbiology Resource Announcements, Vol. 8, Issue 14 https://doi.org/10.1128/mra.01433-18	journal	April 2019
Draft Genome Sequence of Aquitalea sp. Strain MWU14-2217, Isolated from a Wild Cranberry Bog in Provincetown, Massachusetts Ebadzadsahrai, Ghazal; Soby, Scott Microbiology Resource Announcements, Vol. 7, Issue 21 https://doi.org/10.1128/mra.01493-18	journal	November 2018
VraSR and Virulence Trait Modulation during Daptomycin Resistance in Methicillin-Resistant Staphylococcus aureus Infection Taglialegna, Agustina; Varela, Maria C.; Rosato, Roberto R. mSphere, Vol. 4, Issue 1 https://doi.org/10.1128/msphere.00557-18	journal	February 2019
Identification and molecular epidemiology of methicillin resistant Staphylococcus pseudintermedius strains isolated from canine clinical samples in Argentina Gagetti, Paula; Wattam, Alice R.; Giacoboni, Gabriela BMC Veterinary Research, Vol. 15, Issue 1 https://doi.org/10.1186/s12917-019-1990-x	journal	July 2019
Cytotoxic Escherichia coli strains encoding colibactin and cytotoxic necrotizing factor (CNF) colonize laboratory macaques Feng, Yan; Mannion, Anthony; Madden, Carolyn M. Gut Pathogens, Vol. 9, Issue 1 https://doi.org/10.1186/s13099-017-0220-y	journal	December 2017
Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection Yan, Jinyuan; Estanbouli, Henri; Liao, Chen PLOS Computational Biology, Vol. 15, Issue 12 https://doi.org/10.1371/journal.pcbi.1007562	journal	December 2019
Understanding the Representative Gut Microbiota Dysbiosis in Metformin-Treated Type 2 Diabetes Patients Using Genome-Scale Metabolic Modeling Rosario, Dorines; Benfeitas, Rui; Bidkhori, Gholamreza Frontiers in Physiology, Vol. 9 https://doi.org/10.3389/fphys.2018.00775	journal	June 2018
Genome Mining and Comparative Pathogenomic Analysis of An Endemic Methicillin-Resistant Staphylococcus Aureus (MRSA) Clone, ST612-CC8-t1257-SCCmec_IVd(2B), Isolated in South Africa Amoako, Daniel Gyamfi; Somboro, Anou M.; Abia, Akebe Luther King Pathogens, Vol. 8, Issue 4 https://doi.org/10.3390/pathogens8040166	journal	September 2019
Impact of bedaquiline and capreomycin on the gene expression patterns of multidrug‐resistant Mycobacterium tuberculosis H37Rv strain and understanding the molecular mechanism of antibiotic resistance Miryala, Sravan Kumar; Anbarasu, Anand; Ramaiah, Sudha Journal of Cellular Biochemistry, Vol. 120, Issue 9 https://doi.org/10.1002/jcb.28711	journal	April 2019
Brucella spp. of amphibians comprise genomically diverse motile strains competent for replication in macrophages and survival in mammalian hosts Al Dahouk, Sascha; Köhler, Stephan; Occhialini, Alessandra Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/srep44420	journal	March 2017
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Mechanisms and phenotypic consequences of acquisition of tigecycline resistance by Stenotrophomonas maltophilia Blanco, Paula; Corona, Fernando; Martinez, José Luis Journal of Antimicrobial Chemotherapy, Vol. 74, Issue 11 https://doi.org/10.1093/jac/dkz326	journal	August 2019
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis Vallenet, David; Calteau, Alexandra; Dubois, Mathieu Nucleic Acids Research https://doi.org/10.1093/nar/gkz926	journal	October 2019
Deciphering the unexplored Leptospira diversity from soils uncovers genomic evolution to virulence Thibeaux, Roman; Iraola, Gregorio; Ferrés, Ignacio Microbial Genomics, Vol. 4, Issue 1 https://doi.org/10.1099/mgen.0.000144	journal	January 2018
Universal scaling across biochemical networks on Earth Kim, Hyunju; Smith, Harrison B.; Mathis, Cole Science Advances https://doi.org/10.1101/212118	posted_content	March 2018
Real-Time PCR Targeting the penA Mosaic XXXIV Type for Prediction of Extended-Spectrum-Cephalosporin Susceptibility in Clinical Neisseria gonorrhoeae Isolates Wong, L. K.; Hemarajata, P.; Soge, O. O. Antimicrobial Agents and Chemotherapy, Vol. 61, Issue 11 https://doi.org/10.1128/aac.01339-17	journal	November 2017
Cyanuric Acid Biodegradation via Biuret: Physiology, Taxonomy, and Geospatial Distribution Aukema, Kelly G.; Tassoulas, Lambros J.; Robinson, Serina L. Applied and Environmental Microbiology, Vol. 86, Issue 2 https://doi.org/10.1128/aem.01964-19	journal	January 2020
Stenotrophomonas maltophilia Differential Gene Expression in Synthetic Cystic Fibrosis Sputum Reveals Shared and Cystic Fibrosis Strain-Specific Responses to the Sputum Environment Willsey, Graham G.; Eckstrom, Korin; LaBauve, Annette E. Journal of Bacteriology, Vol. 201, Issue 15 https://doi.org/10.1128/jb.00074-19	journal	May 2019
Genome Sequence of Bordetella pertussis Vaccine Strain BP 165 Alai, Shweta; Ghattargi, Vikas C.; Gautam, Manish Microbiology Resource Announcements, Vol. 8, Issue 16 https://doi.org/10.1128/mra.00150-19	journal	April 2019
Draft Genome Sequences of Klebsiella pneumoniae Strains Isolated from Immunocompromised NOD-scid Gamma Research Mice Mannion, Anthony; Fabian, Niora; Stair, Melissa Microbiology Resource Announcements, Vol. 8, Issue 42 https://doi.org/10.1128/mra.00869-19	journal	October 2019
Draft Genome Sequence of Pseudomonas sp. Strain MWU12-2534b, Isolated from a Wild Cranberry Bog in Truro, Massachusetts Ebadzadsahrai, Ghazal; Thomson, Jonathon; Soby, Scott Microbiology Resource Announcements, Vol. 7, Issue 13 https://doi.org/10.1128/mra.01005-18	journal	October 2018
Draft Genome Sequences of Lactobacillus helveticus, Lactobacillus fermentum, and Lactobacillus delbrueckii Strains from African Fermented Nono Cho, Gyu-Sung; Fagbemigun, Olakunle; Brinks, Erik Microbiology Resource Announcements, Vol. 9, Issue 1 https://doi.org/10.1128/mra.01342-19	journal	January 2020
Draft Genome Sequence of Pseudomonas sp. Strain MWU12-2323, Isolated from a Wild Cranberry Bog in Truro, Massachusetts Ebadzadsahrai, Ghazal; Soby, Scott Microbiology Resource Announcements, Vol. 9, Issue 2 https://doi.org/10.1128/mra.01387-19	journal	January 2020
The recombination-cold region as an epidemiological marker of recombinogenic opportunistic pathogen Mycobacterium avium Yano, Hirokazu; Suzuki, Haruo; Maruyama, Fumito BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-6078-2	journal	October 2019
Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom Bhatnagar, Srijak; Cowley, Elise S.; Kopf, Sebastian H. Environmental Microbiome, Vol. 15, Issue 1 https://doi.org/10.1186/s40793-019-0348-0	journal	January 2020
Pangenome guided pharmacophore modelling of enterohemorrhagic Escherichia coli sdiA Bandoy, DJ Darwin F1000Research, Vol. 8 https://doi.org/10.12688/f1000research.17620.1	journal	January 2019
Evolutionary dynamics of bacteria in the gut microbiome within and across hosts Garud, Nandita R.; Good, Benjamin H.; Hallatschek, Oskar PLOS Biology, Vol. 17, Issue 1 https://doi.org/10.1371/journal.pbio.3000102	journal	January 2019
Phylogeographic diversity and mosaicism of the Helicobacter pylori tfs integrative and conjugative elements. Delahay, Robin M.; Croxall, Nicola J.; Stephens, Amberley D. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.18200	collection	January 2018
Greedy de novo motif discovery to construct motif repositories for bacterial proteomes Khakzad, Hamed; Malmström, Johan; Malmström, Lars BioMed Central https://doi.org/10.5167/uzh-171124	text	January 2019
Jiangella anatolica sp. nov. isolated from coastal lake soil Ay, Hilal; Nouioui, Imen; Carro, Lorena Antonie van Leeuwenhoek, Vol. 112, Issue 6 https://doi.org/10.1007/s10482-018-01222-y	journal	January 2019
Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium Hill, David R.; Huang, Sha; Nagy, Melinda S. eLife https://doi.org/10.1101/144568	journal	October 2017
The enemy from within: a prophage of Roseburia intestinalis systematically turns lytic in the mouse gut, driving bacterial adaptation by CRISPR spacer acquisition Cornuault, Jeffrey K.; Moncaut, Elisabeth; Loux, Valentin The ISME Journal https://doi.org/10.1101/575076	journal	March 2019
Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom Bhatnagar, Srijak; Cowley, Elise S.; Kopf, Sebastian H. Environmental Microbiome https://doi.org/10.1101/604504	journal	September 2019
Draft Genome Sequence of a Violacein-Producing Iodobacter sp. from the Hudson Valley Watershed Doing, Georgia; Perron, Gabriel G.; Jude, Brooke A. Genome Announcements, Vol. 6, Issue 1 https://doi.org/10.1128/genomea.01428-17	journal	January 2018
A Carbonic Anhydrase Pseudogene Sensitizes Select Brucella Lineages to Low CO ₂ Tension Varesio, Lydia M.; Willett, Jonathan W.; Fiebig, Aretha Journal of Bacteriology, Vol. 201, Issue 22 https://doi.org/10.1128/jb.00509-19	journal	November 2019
Complete Genome Sequence of Bacillus mycoides TH26, Isolated from a Permafrost Thaw Gradient Haan, Tracie; McDougall, Scout; Drown, Devin M. Microbiology Resource Announcements, Vol. 8, Issue 24 https://doi.org/10.1128/mra.00507-19	journal	June 2019
Environmentally-driven gene content convergence and the Bacillus phylogeny Hernández-González, Ismael L.; Moreno-Hagelsieb, Gabriel; Olmedo-Álvarez, Gabriela BMC Evolutionary Biology, Vol. 18, Issue 1 https://doi.org/10.1186/s12862-018-1261-7	journal	October 2018
Antibiotics resistance and toxin profiles of Bacillus cereus-group isolates from fresh vegetables from German retail markets Fiedler, Gregor; Schneider, Carmen; Igbinosa, Etinosa O. BMC Microbiology, Vol. 19, Issue 1 https://doi.org/10.1186/s12866-019-1632-2	journal	November 2019
Improving the usability and comprehensiveness of microbial databases Loeffler, Caitlin; Karlsberg, Aaron; Martin, Lana S. BMC Biology, Vol. 18, Issue 1 https://doi.org/10.1186/s12915-020-0756-z	journal	April 2020
Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT von Meijenfeldt, F. A. Bastiaan; Arkhipova, Ksenia; Cambuy, Diego D. Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1817-x	journal	October 2019
Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome Rodionov, Dmitry A.; Arzamasov, Aleksandr A.; Khoroshkin, Matvei S. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01316	journal	June 2019
Extensive transmission of microbes along the gastrointestinal tract Schmidt, Thomas S. B.; Hayward, Matthew R.; Coelho, Luis P. ETH Zurich https://doi.org/10.3929/ethz-b-000334551	text	January 2019
Potentiated In Vitro Probiotic Activities of Lactobacillus fermentum LfQi6 Biofilm Biomass Versus Planktonic Culture Berkes, Eva; Liao, Yu-Hsien; Neef, Daniel Probiotics and Antimicrobial Proteins, Vol. 12, Issue 3 https://doi.org/10.1007/s12602-019-09624-8	journal	December 2019
Streptococcal inhibitor of complement (SIC) modulates fibrinolysis and enhances bacterial survival within fibrin clots Frick, Inga-Maria; Shannon, Oonagh; Neumann, Ariane Journal of Biological Chemistry, Vol. 293, Issue 35 https://doi.org/10.1074/jbc.ra118.001988	journal	August 2018
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities Davis, James J.; Wattam, Alice R.; Aziz, Ramy K. Nucleic Acids Research https://doi.org/10.1093/nar/gkz943	journal	October 2019
Kribbella turkmenica sp. nov., isolated from the Karakum Desert Saygin, Hayrettin; Ay, Hilal; Guven, Kiymet International Journal of Systematic and Evolutionary Microbiology, Vol. 69, Issue 8 https://doi.org/10.1099/ijsem.0.003538	journal	August 2019
Metabolic mechanisms of interaction within a defined gut microbiota Medlock, Gregory L.; Carey, Maureen A.; McDuffie, Dennis G. https://doi.org/10.1101/250860	posted_content	January 2018
Capreomycin resistance prediction in two species of Mycobacterium using a stacked ensemble method Chowdhury, A. S.; Khaledian, E.; Broschat, S. L. Journal of Applied Microbiology, Vol. 127, Issue 6 https://doi.org/10.1111/jam.14413	journal	June 2019
Universal scaling across biochemical networks on Earth Kim, Hyunju; Smith, Harrison B.; Mathis, Cole Science Advances, Vol. 5, Issue 1 https://doi.org/10.1126/sciadv.aau0149	journal	January 2019
Parallel Evolution of Tobramycin Resistance across Species and Environments Scribner, Michelle R.; Santos-Lopez, Alfonso; Marshall, Christopher W. mBio, Vol. 11, Issue 3 https://doi.org/10.1128/mbio.00932-20	journal	June 2020
Draft Genome Sequences of Violacein-Producing Duganella sp. Isolates from a Waterway in Eastern Pennsylvania Lamendella, Regina; Jude, Brooke A. Microbiology Resource Announcements, Vol. 7, Issue 12 https://doi.org/10.1128/mra.01196-18	journal	September 2018
Greedy de novo motif discovery to construct motif repositories for bacterial proteomes Khakzad, Hamed; Malmstroem, Johan; Malmstroem, Lars Zenodo https://doi.org/10.5281/zenodo.1403141	text	January 2019
Identification and characterization of OmpT‐like proteases in uropathogenic Escherichia coli clinical isolates Desloges, Isabelle; Taylor, James A.; Leclerc, Jean‐Mathieu MicrobiologyOpen, Vol. 8, Issue 11 https://doi.org/10.1002/mbo3.915	journal	April 2019
Data on genome sequencing, assembly, annotation and genomic analysis of Rhodococcus rhodochrous strain SPC17 isolated from Lonar Lake Kumar, Satish; Paul, Dhiraj; Shouche, Yogesh Data in Brief, Vol. 29 https://doi.org/10.1016/j.dib.2020.105336	journal	April 2020
Polyphyly in 16S rRNA-based LVTree Versus Monophyly in Whole-genome-based CVTree Zuo, Guanghong; Qi, Ji; Hao, Bailin Genomics, Proteomics & Bioinformatics, Vol. 16, Issue 5 https://doi.org/10.1016/j.gpb.2018.06.005	journal	October 2018
GeneHunt for rapid domain-specific annotation of glycoside hydrolases Nguyen, S. N.; Flores, A.; Talamantes, D. Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-46290-w	journal	July 2019
Population Structure and Local Adaptation of MAC Lung Disease Agent Mycobacterium avium subsp. hominissuis Yano, Hirokazu; Iwamoto, Tomotada; Nishiuchi, Yukiko Genome Biology and Evolution, Vol. 9, Issue 9 https://doi.org/10.1093/gbe/evx183	journal	September 2017
Identification of a novel transposon-associated phosphoethanolamine transferase gene, mcr-5, conferring colistin resistance in d-tartrate fermenting Salmonella enterica subsp. enterica serovar Paratyphi B Borowiak, Maria; Fischer, Jennie; Hammerl, Jens A. Journal of Antimicrobial Chemotherapy, Vol. 72, Issue 12 https://doi.org/10.1093/jac/dkx327	journal	September 2017
OxyR Is a Convergent Target for Mutations Acquired during Adaptation to Oxidative Stress-Prone Metabolic States Anand, Amitesh; Chen, Ke; Catoiu, Edward Molecular Biology and Evolution, Vol. 37, Issue 3 https://doi.org/10.1093/molbev/msz251	journal	October 2019
MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments Oliveira, Francislon S.; Brestelli, John; Cade, Shon Nucleic Acids Research https://doi.org/10.1101/176784	journal	August 2017
Complete Genome Sequence of Listeria monocytogenes Strain MR310, Isolated from a Pastured-Flock Poultry Farm System Rothrock, Michael J.; Fan, Peixin; Jeong, Kwangcheol C. Genome Announcements, Vol. 6, Issue 10 https://doi.org/10.1128/genomea.00171-18	journal	March 2018
Draft Genome Sequence of a Wohlfahrtiimonas chitiniclastica Strain Isolated from Frozen Chicken in Rio De Janeiro, Brazil Matos, Jorge; Faria, Adriana Rocha; Carvalho Assef, Ana Paula D’Alincourt Microbiology Resource Announcements, Vol. 8, Issue 49 https://doi.org/10.1128/mra.00352-19	journal	December 2019
Draft Genome Sequences of Helcococcus ovis Strains Isolated at Time of Metritis Diagnosis from the Uterus of Holstein Dairy Cows Cunha, Federico; Jeon, Soo Jin; Kutzer, Peter Microbiology Resource Announcements, Vol. 8, Issue 22 https://doi.org/10.1128/mra.00402-19	journal	May 2019
Draft Genome Sequence of Massilia sp. Strain MC02, Isolated from a Sandy Loam Maize Soil Raths, Rachel; Peta, Vincent; Bücking, Heike Microbiology Resource Announcements, Vol. 8, Issue 32 https://doi.org/10.1128/mra.00410-19	journal	August 2019
Draft Genome Sequence of Duganella sp. Strain DN04, Isolated from Cultivated Soil Raths, Rachel; Peta, Vincent; Bücking, Heike Microbiology Resource Announcements, Vol. 8, Issue 32 https://doi.org/10.1128/mra.00848-19	journal	August 2019
Draft Genome Sequence of Marine Bacillus sp. Strain ISO11, a Candidate Finfish and Shellfish Probiotic Schreier, Harold J. Microbiology Resource Announcements, Vol. 7, Issue 15 https://doi.org/10.1128/mra.01227-18	journal	October 2018
Draft Genome Sequence of Megaplasmid-Bearing Staphylococcus sciuri Strain B9-58B, Isolated from Retail Pork Neyaz, Leena; Karki, Anand B.; Fakhr, Mohamed K. Microbiology Resource Announcements, Vol. 9, Issue 1 https://doi.org/10.1128/mra.01474-19	journal	January 2020
Phylogeographic diversity and mosaicism of the Helicobacter pylori tfs integrative and conjugative elements Delahay, Robin M.; Croxall, Nicola J.; Stephens, Amberley D. Mobile DNA, Vol. 9, Issue 1 https://doi.org/10.1186/s13100-018-0109-4	journal	January 2018
New Aspects on Listeria monocytogenes ST5-ECVI Predominance in a Heavily Contaminated Cheese Processing Environment Muhterem-Uyar, Meryem; Ciolacu, Luminita; Wagner, Karl-Heinz Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00064	journal	February 2018
Distribution Patterns of Polyphosphate Metabolism Pathway and Its Relationships With Bacterial Durability and Virulence Wang, Liang; Yan, Jiawei; Wise, Michael J. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00782	journal	April 2018
Predictable Molecular Adaptation of Coevolving Enterococcus faecium and Lytic Phage EfV12-phi1 Wandro, Stephen; Oliver, Andrew; Gallagher, Tara Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.03192	journal	January 2019
Constructing and Characterizing Bacteriophage Libraries for Phage Therapy of Human Infections Gibson, Shelley B.; Green, Sabrina I.; Liu, Carmen Gu Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02537	journal	November 2019
Prediction of bacterial E₃ ubiquitin ligase effectors using reduced amino acid peptide fingerprinting McDermott, Jason; Cort, John; Nakayasu, Ernesto PeerJ Preprints https://doi.org/10.7287/peerj.preprints.27292v1	journal	October 2018

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