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Author Details

Fangfang Xia
University of Chicago
2007
46
21
PMIDPaper TitleJournal TitlePublished Year
36350631Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR.Nucleic Acids Res2023
37004378CholecTriplet2021: A benchmark challenge for surgical action triplet recognition.Med Image Anal2023
34524425A cross-study analysis of drug response prediction in cancer cell lines.Brief Bioinform2022
36507076TULIP: An RNA-seq-based Primary Tumor Type Prediction Tool Using Convolutional Neural Networks.Cancer Inform2022
34001007Learning curves for drug response prediction in cancer cell lines.BMC Bioinformatics2021
33483546Detecting operons in bacterial genomes via visual representation learning.Sci Rep2021
34956592Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers.Interface Focus2021
34078279Identifying genomic islands with deep neural networks.BMC Genomics2021
34067337Identification of an Attenuated Substrain of <i>Francisella tularensis</i> SCHU S4 by Phenotypic and Genotypic Analyses.Pathogens2021
34211076Publisher Correction: Converting tabular data into images for deep learning with convolutional neural networks.Sci Rep2021
34059739Converting tabular data into images for deep learning with convolutional neural networks.Sci Rep2021
32933072Enhanced Co-Expression Extrapolation (COXEN) Gene Selection Method for Building Anti-Cancer Drug Response Prediction Models.Genes (Basel)2020
31667520The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities.Nucleic Acids Res2020
33093487Ensemble transfer learning for the prediction of anti-cancer drug response.Sci Rep2020
28968762PATRIC as a unique resource for studying antimicrobial resistance.Brief Bioinform2019
31632915AI Meets Exascale Computing: Advancing Cancer Research With Large-Scale High Performance Computing.Front Oncol2019
29323230Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae.Sci Rep2018
29979655KBase: The United States Department of Energy Systems Biology Knowledgebase.Nat Biotechnol2018
30577754Predicting tumor cell line response to drug pairs with deep learning.BMC Bioinformatics2018
30577736CANDLE/Supervisor: a workflow framework for machine learning applied to cancer research.BMC Bioinformatics2018
29277864Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center.Methods Mol Biol2018
28069655Mutation in an Unannotated Protein Confers Carbapenem Resistance in Mycobacterium tuberculosis.Antimicrob Agents Chemother2017
28232424Genome Sequences of Three <i>Brucella canis</i> Strains Isolated from Humans and a Dog.Genome Announc2017
28254974Genome Sequences of Two <i>Brucella suis</i> Strains Isolated from the Same Patient, 8 Years Apart.Genome Announc2017
28512093Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing <i>Klebsiella pneumoniae</i> Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307.mBio2017
28589129Whole-Genome Sequence Analysis of Antimicrobial Resistance Genes in <i>Streptococcus uberis</i> and <i>Streptococcus dysgalactiae</i> Isolates from Canadian Dairy Herds.Front Vet Sci2017
27899627Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center.Nucleic Acids Res2017
26951112Recovering complete and draft population genomes from metagenome datasets.Microbiome2016
27502787Modeling central metabolism and energy biosynthesis across microbial life.BMC Genomics2016
27450008REMap: Operon map of M. tuberculosis based on RNA sequence data.Tuberculosis (Edinb)2016
27297683Antimicrobial Resistance Prediction in PATRIC and RAST.Sci Rep2016
26821166Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in E. coli.PLoS Comput Biol2016
25666585RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes.Sci Rep2015
23422247Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models.Brief Bioinform2014
28324432In search of genome annotation consistency: solid gene clusters and how to use them.3 Biotech2014
25178782Tapping the wealth of microbial data in high-throughput metabolic model reconstruction.Methods Mol Biol2014
24293654The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).Nucleic Acids Res2014
23109554Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model.Nucleic Acids Res2013
27447255Human Analysts at Superhuman Scales: What Has Friendly Software To Do?Big Data2013
23606477Genomes of the class Erysipelotrichia clarify the firmicute origin of the class Mollicutes.Int J Syst Evol Microbiol2013
23315735Comparison of the genome sequences of "Candidatus Portiera aleyrodidarum" primary endosymbionts of the whitefly Bemisia tabaci B and Q biotypes.Appl Environ Microbiol2013
23110173SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models.PLoS One2012
23144417Genome sequences of the primary endosymbiont "Candidatus Portiera aleyrodidarum" in the whitefly Bemisia tabaci B and Q biotypes.J Bacteriol2012
21421023Connecting genotype to phenotype in the era of high-throughput sequencing.Biochim Biophys Acta2011
21926179Assemblathon 1: a competitive assessment of de novo short read assembly methods.Genome Res2011
17145713The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation.Nucleic Acids Res2007
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Collaborators

Argonne National Laboratory
Co-authored papers 32
University of Chicago
Co-authored papers 23
University of Chicago
Co-authored papers 18
University of Chicago
Co-authored papers 13
Translational Research Center, Inha University Hospital
Co-authored papers 13
University of Chicago
Co-authored papers 13
University of Illinois
Co-authored papers 11
Argonne National Laboratory
Co-authored papers 9
University of Chicago
Co-authored papers 9
Frederick National Laboratory for Cancer Research, Inc.
Co-authored papers 8
National Cancer Institute, National Institutes of Health
Co-authored papers 8
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University of Chicago
Co-authored papers 6
University of Chicago
Co-authored papers 5
Co-authored papers 4
Argonne National Laboratory
Co-authored papers 4
Institute for Artificial Intelligence, University of Duisburg-Essen
Co-authored papers 3
Argonne National Laboratory
Co-authored papers 3
Argonne National Laboratory
Co-authored papers 3
University of Illinois Urbana-Champaign
Co-authored papers 3
Computation Institute, University of Chicago
Co-authored papers 3
Argonne National Laboratory
Co-authored papers 3
USDA-ARS Laboratory at Cold Spring Harbor Laboratory
Co-authored papers 2
Johns Hopkins University
Co-authored papers 2
Hope College
Co-authored papers 2
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University of Chicago
Co-authored papers 2
Argonne National Laboratory
Co-authored papers 2
Scripps Institution of Oceanography, University of California San Diego
Co-authored papers 2