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| 36350631 | Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRDÂ and ViPR. | Nucleic Acids Res | 2023 |
| 37314210 | Predicting variable gene content in <i>Escherichia coli</i> using conserved genes. | mSystems | 2023 |
| 34774517 | Delta Variants of SARS-CoV-2 Cause Significantly Increased Vaccine Breakthrough COVID-19 Cases in Houston, Texas. | Am J Pathol | 2022 |
| 35382558 | PlasmidHostFinder: Prediction of Plasmid Hosts Using Random Forest. | mSystems | 2022 |
| 35840592 | Transmission history of SARS-CoV-2 in humans and white-tailed deer. | Sci Rep | 2022 |
| 36525447 | Classification of bacterial plasmid and chromosome derived sequences using machine learning. | PLoS One | 2022 |
| 36451881 | GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics. | bioRxiv | 2022 |
| 36560774 | SARS-CoV-2 Omicron (B.1.1.529) Infection of Wild White-Tailed Deer in New York City. | Viruses | 2022 |
| 36353215 | Early detection of emerging SARS-CoV-2 variants of interest for experimental evaluation. | Front Bioinform | 2022 |
| 36377945 | SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies. | Microbiol Spectr | 2022 |
| 35123975 | Signals of Significantly Increased Vaccine Breakthrough, Decreased Hospitalization Rates, and Less Severe Disease in Patients with Coronavirus Disease 2019 Caused by the Omicron Variant of Severe Acute Respiratory Syndrome Coronavirus 2 in Houston, Texas. | Am J Pathol | 2022 |
| 35169802 | Detection of SARS-CoV-2 Omicron variant (B.1.1.529) infection of white-tailed deer. | bioRxiv | 2022 |
| 35078920 | Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer. | Proc Natl Acad Sci U S A | 2022 |
| 33010049 | Predicting antimicrobial susceptibility from the bacterial genome: A new paradigm for one health resistance monitoring. | J Vet Pharmacol Ther | 2021 |
| 33741335 | Sequence Analysis of 20,453 Severe Acute Respiratory Syndrome Coronavirus 2 Genomes from the Houston Metropolitan Area Identifies the Emergence and Widespread Distribution of Multiple Isolates of All Major Variants of Concern. | Am J Pathol | 2021 |
| 33622735 | Erratum for Pincus et al., "A Genome-Based Model to Predict the Virulence of Pseudomonas aeruginosa Isolates". | mBio | 2021 |
| 34878296 | Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein. | Microbiol Spectr | 2021 |
| 34379107 | A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes. | Brief Bioinform | 2021 |
| 34303698 | Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. | Am J Pathol | 2021 |
| 32843552 | A Genome-Based Model to Predict the Virulence of Pseudomonas aeruginosa Isolates. | mBio | 2020 |
| 31667520 | The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. | Nucleic Acids Res | 2020 |
| 33024977 | Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area. | medRxiv | 2020 |
| 33075053 | Predicting antimicrobial resistance using conserved genes. | PLoS Comput Biol | 2020 |
| 33127862 | Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area. | mBio | 2020 |
| 33093601 | Carbapenems drive the collateral resistance to ceftaroline in cystic fibrosis patients with MRSA. | Commun Biol | 2020 |
| 28968762 | PATRIC as a unique resource for studying antimicrobial resistance. | Brief Bioinform | 2019 |
| 30333126 | Using Machine Learning To Predict Antimicrobial MICs and Associated Genomic Features for Nontyphoidal <i>Salmonella</i>. | J Clin Microbiol | 2019 |
| 29323230 | Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae. | Sci Rep | 2018 |
| 29979655 | KBase: The United States Department of Energy Systems Biology Knowledgebase. | Nat Biotechnol | 2018 |
| 29277864 | Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center. | Methods Mol Biol | 2018 |
| 27899627 | Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. | Nucleic Acids Res | 2017 |
| 29051239 | Whole-Genome Sequencing of a Human Clinical Isolate of the Novel Species <i>Klebsiella quasivariicola</i> sp. nov. | Genome Announc | 2017 |
| 28512093 | Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing <i>Klebsiella pneumoniae</i> Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307. | mBio | 2017 |
| 28776045 | Whole-Genome Sequencing of Human Clinical <i>Klebsiella pneumoniae</i> Isolates Reveals Misidentification and Misunderstandings of <i>Klebsiella pneumoniae</i>, <i>Klebsiella variicola</i>, and <i>Klebsiella quasipneumoniae</i>. | mSphere | 2017 |
| 26903996 | PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database. | Front Microbiol | 2016 |
| 27933038 | Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation. | Front Microbiol | 2016 |
| 27297683 | Antimicrobial Resistance Prediction in PATRIC and RAST. | Sci Rep | 2016 |
| 25666585 | RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. | Sci Rep | 2015 |
| 28324362 | Enabling comparative modeling of closely related genomes: example genus Brucella. | 3 Biotech | 2015 |
| 24293654 | The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). | Nucleic Acids Res | 2014 |
| 28324432 | In search of genome annotation consistency: solid gene clusters and how to use them. | 3 Biotech | 2014 |
| 23606477 | Genomes of the class Erysipelotrichia clarify the firmicute origin of the class Mollicutes. | Int J Syst Evol Microbiol | 2013 |
| 20679093 | Characterizing the native codon usages of a genome: an axis projection approach. | Mol Biol Evol | 2011 |
| 22128332 | Similarity of genes horizontally acquired by Escherichia coli and Salmonella enterica is evidence of a supraspecies pangenome. | Proc Natl Acad Sci U S A | 2011 |
| 20018979 | Modal codon usage: assessing the typical codon usage of a genome. | Mol Biol Evol | 2010 |