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Fangfang Xia · SciRah

Researcher profile · Semantic Scholar

Fangfang Xia

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Fangfang Xia — researcher profile on SciRah

h-index: 31
Works: 68
Citations: 15K

Most-cited papers

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
R. Overbeek, Robert Olson, G. Pusch, G. Olsen +10 more
2013Nucleic Acids Res.4,375 citations Open access
Semantic Scholar
RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes
T. Brettin, James J. Davis, T. Disz, R. Edwards +12 more
2015Scientific Reports2,641 citations Open access
Semantic Scholar
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center
A. Wattam, James J. Davis, Rida Assaf, S. Boisvert +24 more
2016Nucleic Acids Res.1,561 citations Open access
Semantic Scholar
KBase: The United States Department of Energy Systems Biology Knowledgebase
A. Arkin, R. Cottingham, C. Henry, N. Harris +77 more
2018Nature Biotechnology1,445 citations Open access
Semantic Scholar
Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR
Robert Olson, Rida Assaf, T. Brettin, Neal Conrad +36 more
2022Nucleic Acids Res.1,165 citations Open access
Semantic Scholar
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities
James J. Davis, A. Wattam, R. Aziz, T. Brettin +30 more
2019Nucleic Acids Res.872 citations Open access
Semantic Scholar
Assemblathon 1: a competitive assessment of de novo short read assembly methods.
D. Earl, K. Bradnam, J. S. St John, A. Darling +67 more
2011Genome Research548 citations Open access
Semantic Scholar
Converting tabular data into images for deep learning with convolutional neural networks
Yi-Tan Zhu, T. Brettin, Fangfang Xia, A. Partin +5 more
2021Scientific Reports259 citations Open access
Semantic Scholar
Recovering complete and draft population genomes from metagenome datasets
N. Sangwan, Fangfang Xia, J. Gilbert
2016Microbiome225 citations Open access
Semantic Scholar
Antimicrobial Resistance Prediction in PATRIC and RAST
James J. Davis, S. Boisvert, T. Brettin, R. Kenyon +9 more
2016Scientific Reports219 citations Open access
Semantic Scholar
SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models
R. Aziz, Scott Devoid, T. Disz, R. Edwards +9 more
2012PLoS ONE205 citations Open access
Semantic Scholar
Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae
M. Nguyen, M. Nguyen, M. Nguyen, T. Brettin +19 more
2017Scientific Reports174 citations Open access
Semantic Scholar
Predicting tumor cell line response to drug pairs with deep learning
Fangfang Xia, M. Shukla, T. Brettin, Cristina Garcia-Cardona +8 more
2018BMC Bioinformatics112 citations Open access
Semantic Scholar
PATRIC as a unique resource for studying antimicrobial resistance
D. Antonopoulos, Rida Assaf, R. Aziz, T. Brettin +25 more
2017Briefings Bioinform.109 citations Open access
Semantic Scholar
CholecTriplet2021: A benchmark challenge for surgical action triplet recognition
C. Nwoye, Deepak Alapatt, Tong Yu, A. Vardazaryan +58 more
2022Medical Image Anal.108 citations Open access
Semantic Scholar
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation
L. K. McNeil, C. Reich, R. Aziz, D. Bartels +25 more
2006Nucleic Acids Res.108 citations Open access
Semantic Scholar
Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model
Kosei Tanaka, C. Henry, Jenifer Zinner, E. Jolivet +6 more
2012Nucleic Acids Research94 citations Open access
Semantic Scholar
Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center.
A. Wattam, T. Brettin, James J. Davis, S. Gerdes +12 more
2018Methods in molecular biology93 citations
Semantic Scholar
A cross-study analysis of drug response prediction in cancer cell lines
Fangfang Xia, Jonathan E. Allen, Prasanna Balaprakash, T. Brettin +20 more
2021Briefings Bioinform.88 citations Open access
Semantic Scholar
Ensemble transfer learning for the prediction of anti-cancer drug response
Yi-Tan Zhu, T. Brettin, Yvonne A. Evrard, A. Partin +5 more
2020Scientific Reports85 citations Open access
Semantic Scholar
CANDLE/Supervisor: a workflow framework for machine learning applied to cancer research
J. Wozniak, R. Jain, Prasanna Balaprakash, J. Ozik +9 more
2018BMC Bioinformatics85 citations Open access
Semantic Scholar
The DOE Systems Biology Knowledgebase (KBase)
A. Arkin, Rick L. Stevens, R. Cottingham, S. Maslov +75 more
2016bioRxiv68 citations Open access
Semantic Scholar
Scalable Reinforcement-learning-Based Neural Architecture Search for Cancer Deep Learning Research
Prasanna Balaprakash, Romain Egele, Misha Salim, Stefan M. Wild +4 more
2019International Conference for High Performance Computing, Networking, Storage and Analysis60 citations Open access
Semantic Scholar
Genomes of the class Erysipelotrichia clarify the firmicute origin of the class Mollicutes
James J. Davis, Fangfang Xia, R. Overbeek, G. Olsen
2013International Journal of Systematic and Evolutionary Microbiology47 citations Open access
Semantic Scholar
Whole-Genome Sequence Analysis of Antimicrobial Resistance Genes in Streptococcus uberis and Streptococcus dysgalactiae Isolates from Canadian Dairy Herds
Julián Reyes Vélez, M. Cameron, J. Rodríguez-Lecompte, Fangfang Xia +4 more
2017Frontiers in Veterinary Science46 citations Open access
Semantic Scholar
Biomedical image analysis competitions: The state of current participation practice
M. Eisenmann, A. Reinke, V. Weru, M. Tizabi +350 more
2022arXiv.org37 citations Open access
Semantic Scholar
Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models
José P. Faria, R. Overbeek, Fangfang Xia, Miguel P. Rocha +2 more
2014Briefings Bioinform.35 citations Open access
Semantic Scholar
Why is the Winner the Best?
M. Eisenmann, A. Reinke, V. Weru, M. Tizabi +121 more
2023Computer Vision and Pattern Recognition34 citations Open access
Semantic Scholar
Modeling central metabolism and energy biosynthesis across microbial life
J. Edirisinghe, P. Weisenhorn, Neal Conrad, Fangfang Xia +3 more
2016BMC Genomics34 citations Open access
Semantic Scholar
Connecting genotype to phenotype in the era of high-throughput sequencing.
C. Henry, R. Overbeek, Fangfang Xia, Aaron A. Best +17 more
2011Biochimica et Biophysica Acta34 citations
Semantic Scholar
Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli
M. Oberhardt, Raphy Zarecki, L. Reshef, Fangfang Xia +7 more
2016PLoS Comput. Biol.31 citations Open access
Semantic Scholar
Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers
Agastya P. Bhati, S. Wan, Dario Alfè, Austin R. Clyde +25 more
2021Interface Focus30 citations Open access
Semantic Scholar
AI Meets Exascale Computing: Advancing Cancer Research With Large-Scale High Performance Computing
Tanmoy Bhattacharya, T. Brettin, J. Doroshow, Yvonne A. Evrard +12 more
2019Frontiers in Oncology29 citations Open access
Semantic Scholar
Comparison of the Genome Sequences of “Candidatus Portiera aleyrodidarum” Primary Endosymbionts of the Whitefly Bemisia tabaci B and Q Biotypes
Zi-Feng Jiang, Fangfang Xia, Kipp W. Johnson, Christopher D. Brown +7 more
2013Applied and Environmental Microbiology29 citations Open access
Semantic Scholar
Performance, Energy, and Scalability Analysis and Improvement of Parallel Cancer Deep Learning CANDLE Benchmarks
Xingfu Wu, V. Taylor, J. Wozniak, R. Stevens +2 more
2019International Conference on Parallel Processing28 citations
Semantic Scholar
Machine Learning for Antimicrobial Resistance
John Santerre, James J. Davis, Fangfang Xia, Rick L. Stevens
201628 citations
Semantic Scholar
AgEBO-Tabular: Joint Neural Architecture and Hyperparameter Search with Autotuned Data-Parallel Training for Tabular Data
Romain Egele, Prasanna Balaprakash, Isabelle M Guyon, V. Vishwanath +3 more
2020International Conference for High Performance Computing, Networking, Storage and Analysis25 citations Open access
Semantic Scholar
Learning curves for drug response prediction in cancer cell lines
A. Partin, T. Brettin, Yvonne A. Evrard, Yi-Tan Zhu +8 more
2020BMC Bioinformatics22 citations Open access
Semantic Scholar
Mutation in an Unannotated Protein Confers Carbapenem Resistance in Mycobacterium tuberculosis
Pankaj Kumar, A. Kaushik, D. Bell, Varsha Chauhan +3 more
2017Antimicrobial Agents and Chemotherapy16 citations Open access
Semantic Scholar
Detecting operons in bacterial genomes via visual representation learning
Rida Assaf, Fangfang Xia, Rick L. Stevens
2019Scientific Reports13 citations Open access
Semantic Scholar
Application of high-performance computing to the reconstruction, analysis, and optimization of genome-scale metabolic models
C. Henry, Fangfang Xia, Rick L. Stevens
200913 citations Open access
Semantic Scholar
Enhanced Co-Expression Extrapolation (COXEN) Gene Selection Method for Building Anti-Cancer Drug Response Prediction Models
Yi-Tan Zhu, T. Brettin, Yvonne A. Evrard, Fangfang Xia +5 more
2020Genes12 citations Open access
Semantic Scholar
REMap: Operon Map of M. tuberculosis
Shaaretha Pelly, K. Winglee, Fangfang Xia, Rick L. Stevens +2 more
2016Tuberculosis12 citations Open access
Semantic Scholar
Crowd-sourced machine learning prediction of long COVID using data from the National COVID Cohort Collaborative
T. Bergquist, Johanna Loomba, E. Pfaff, Fangfang Xia +36 more
2024EBioMedicine8 citations Open access
Semantic Scholar
Publisher Correction: Converting tabular data into images for deep learning with convolutional neural networks
Yi-Tan Zhu, T. Brettin, Fangfang Xia, A. Partin +5 more
2021Scientific Reports8 citations Open access
Semantic Scholar
Identifying genomic islands with deep neural networks
Rida Assaf, Fangfang Xia, Rick L. Stevens
2019BMC Genomics8 citations Open access
Semantic Scholar
TULIP: An RNA-seq-based Primary Tumor Type Prediction Tool Using Convolutional Neural Networks
Sara E. Jones, M. Beyers, M. Shukla, Fangfang Xia +4 more
2022Cancer Informatics7 citations Open access
Semantic Scholar
A Systematic Approach to Featurization for Cancer Drug Sensitivity Predictions with Deep Learning
Austin R. Clyde, T. Brettin, A. Partin, Maulik Shaulik +5 more
2020arXiv.org7 citations
Semantic Scholar
In search of genome annotation consistency: solid gene clusters and how to use them
James J. Davis, G. Olsen, R. Overbeek, V. Vonstein +1 more
20133 Biotech7 citations Open access
Semantic Scholar
Contextual Active Model Selection
Xuefeng Liu, Fangfang Xia, R. Stevens, Yuxin Chen
2022Neural Information Processing Systems6 citations Open access
Semantic Scholar

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