|
| 36350631 | Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRDÂ and ViPR. | Nucleic Acids Res | 2023 |
| 37064526 | Causal Discovery and Optimal Experimental Design for Genome-Scale Biological Network Recovery. | ArXiv | 2023 |
| 34524425 | A cross-study analysis of drug response prediction in cancer cell lines. | Brief Bioinform | 2022 |
| 36451881 | GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics. | bioRxiv | 2022 |
| 36353215 | Early detection of emerging SARS-CoV-2 variants of interest for experimental evaluation. | Front Bioinform | 2022 |
| 34001007 | Learning curves for drug response prediction in cancer cell lines. | BMC Bioinformatics | 2021 |
| 33483546 | Detecting operons in bacterial genomes via visual representation learning. | Sci Rep | 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 |
| 34956592 | Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers. | Interface Focus | 2021 |
| 34379107 | A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes. | Brief Bioinform | 2021 |
| 34078279 | Identifying genomic islands with deep neural networks. | BMC Genomics | 2021 |
| 34128695 | Predicting Antimicrobial Resistance Using Partial Genome Alignments. | mSystems | 2021 |
| 34067337 | Identification of an Attenuated Substrain of <i>Francisella tularensis</i> SCHU S4 by Phenotypic and Genotypic Analyses. | Pathogens | 2021 |
| 34211076 | Publisher Correction: Converting tabular data into images for deep learning with convolutional neural networks. | Sci Rep | 2021 |
| 34059739 | Converting tabular data into images for deep learning with convolutional neural networks. | Sci Rep | 2021 |
| 32933072 | Enhanced Co-Expression Extrapolation (COXEN) Gene Selection Method for Building Anti-Cancer Drug Response Prediction Models. | Genes (Basel) | 2020 |
| 31667520 | The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities. | Nucleic Acids Res | 2020 |
| 31955678 | Exascale applications: skin in the game. | Philos Trans A Math Phys Eng Sci | 2020 |
| 33093487 | Ensemble transfer learning for the prediction of anti-cancer drug response. | Sci Rep | 2020 |
| 28968762 | PATRIC as a unique resource for studying antimicrobial resistance. | Brief Bioinform | 2019 |
| 31632915 | AI Meets Exascale Computing: Advancing Cancer Research With Large-Scale High Performance Computing. | Front Oncol | 2019 |
| 30679363 | Toward unrestricted use of public genomic data. | Science | 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 |
| 30577754 | Predicting tumor cell line response to drug pairs with deep learning. | BMC Bioinformatics | 2018 |
| 30577736 | CANDLE/Supervisor: a workflow framework for machine learning applied to cancer research. | BMC Bioinformatics | 2018 |
| 29734278 | Practitioner Application: Shifts in Medicaid and Uninsured Payer Mix at Safety-Net and Non-Safety-Net Hospitals During the Great Recession. | J Healthc Manag | 2018 |
| 29277864 | Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center. | Methods Mol Biol | 2018 |
| 28069655 | Mutation in an Unannotated Protein Confers Carbapenem Resistance in Mycobacterium tuberculosis. | Antimicrob Agents Chemother | 2017 |
| 29088705 | A communal catalogue reveals Earth's multiscale microbial diversity. | Nature | 2017 |
| 27899627 | Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. | Nucleic Acids Res | 2017 |
| 27297683 | Antimicrobial Resistance Prediction in PATRIC and RAST. | Sci Rep | 2016 |
| 27933038 | Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation. | Front Microbiol | 2016 |
| 27502787 | Modeling central metabolism and energy biosynthesis across microbial life. | BMC Genomics | 2016 |
| 27450008 | REMap: Operon map of M. tuberculosis based on RNA sequence data. | Tuberculosis (Edinb) | 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 |
| 24225323 | PATRIC, the bacterial bioinformatics database and analysis resource. | Nucleic Acids Res | 2014 |
| 25093819 | Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. | PLoS Biol | 2014 |
| 24927599 | High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource. | Proc Natl Acad Sci U S A | 2014 |
| 24936976 | Standardized metadata for human pathogen/vector genomic sequences. | PLoS One | 2014 |
| 24293654 | The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). | Nucleic Acids Res | 2014 |
| 23109554 | Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model. | Nucleic Acids Res | 2013 |
| 24416069 | Large-scale modeling of epileptic seizures: scaling properties of two parallel neuronal network simulation algorithms. | Comput Math Methods Med | 2013 |
| 23315735 | Comparison of the genome sequences of "Candidatus Portiera aleyrodidarum" primary endosymbionts of the whitefly Bemisia tabaci B and Q biotypes. | Appl Environ Microbiol | 2013 |
| 22678395 | Unlocking the potential of metagenomics through replicated experimental design. | Nat Biotechnol | 2012 |
| 23144417 | Genome sequences of the primary endosymbiont "Candidatus Portiera aleyrodidarum" in the whitefly Bemisia tabaci B and Q biotypes. | J Bacteriol | 2012 |
| 23110173 | SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models. | PLoS One | 2012 |
| 23047562 | Real time metagenomics: using k-mers to annotate metagenomes. | Bioinformatics | 2012 |
| 21421023 | Connecting genotype to phenotype in the era of high-throughput sequencing. | Biochim Biophys Acta | 2011 |