Works by Stevens, Rick L.

Results: 21

Enhanced Co-Expression Extrapolation (COXEN) Gene Selection Method for Building Anti-Cancer Drug Response Prediction Models.

Published in:

Genes, 2020, v. 11, n. 9, p. 1070, doi. 10.3390/genes11091070

By:

Zhu, Yitan;
Brettin, Thomas;
Evrard, Yvonne A.;
Xia, Fangfang;
Partin, Alexander;
Shukla, Maulik;
Yoo, Hyunseung;
Doroshow, James H.;
Stevens, Rick L.

Publication type:

Article

Publisher Correction: Converting tabular data into images for deep learning with convolutional neural networks.

Published in:

2021

By:

Zhu, Yitan;
Brettin, Thomas;
Xia, Fangfang;
Partin, Alexander;
Shukla, Maulik;
Yoo, Hyunseung;
Evrard, Yvonne A.;
Doroshow, James H.;
Stevens, Rick L.

Publication type:

Correction Notice

SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models.

Published in:

PLoS ONE, 2012, v. 7, n. 10, p. 1, doi. 10.1371/journal.pone.0048053

By:

Aziz, Ramy K.;
Devoid, Scott;
Disz, Terrence;
Edwards, Robert A.;
Henry, Christopher S.;
Olsen, Gary J.;
Olson, Robert;
Overbeek, Ross;
Parrello, Bruce;
Pusch, Gordon D.;
Stevens, Rick L.;
Vonstein, Veronika;
Xia, Fangfang

Publication type:

Article

Large-Scale Modeling of Epileptic Seizures: Scaling Properties of Two Parallel Neuronal Network Simulation Algorithms.

Published in:

Computational & Mathematical Methods in Medicine, 2013, p. 1, doi. 10.1155/2013/182145

By:

Pesce, Lorenzo L.;
Lee, Hyong C.;
Hereld, Mark;
Visser, Sid;
Stevens, Rick L.;
Wildeman, Albert;
van Drongelen, Wim

Publication type:

Article

High-throughput generation, optimization and analysis of genome-scale metabolic models.

Published in:

Nature Biotechnology, 2010, v. 28, n. 9, p. 977, doi. 10.1038/nbt.1672

By:

Henry, Christopher S.;
DeJongh, Matthew;
Best, Aaron A.;
Frybarger, Paul M.;
Linsay, Ben;
Stevens, Rick L.

Publication type:

Article

Data imbalance in drug response prediction: multi-objective optimization approach in deep learning setting.

Published in:

Briefings in Bioinformatics, 2025, v. 26, n. 2, p. 1, doi. 10.1093/bib/bbaf134

By:

Narykov, Oleksandr;
Zhu, Yitan;
Brettin, Thomas;
Evrard, Yvonne A;
Partin, Alexander;
Xia, Fangfang;
Shukla, Maulik;
Vasanthakumari, Priyanka;
Doroshow, James H;
Stevens, Rick L

Publication type:

Article

Converting tabular data into images for deep learning with convolutional neural networks.

Published in:

Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-90923-y

By:

Zhu, Yitan;
Brettin, Thomas;
Xia, Fangfang;
Partin, Alexander;
Shukla, Maulik;
Yoo, Hyunseung;
Evrard, Yvonne A.;
Doroshow, James H.;
Stevens, Rick L.

Publication type:

Article

Ensemble transfer learning for the prediction of anti-cancer drug response.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-74921-0

By:

Zhu, Yitan;
Brettin, Thomas;
Evrard, Yvonne A.;
Partin, Alexander;
Xia, Fangfang;
Shukla, Maulik;
Yoo, Hyunseung;
Doroshow, James H.;
Stevens, Rick L.

Publication type:

Article

A Comprehensive Investigation of Active Learning Strategies for Conducting Anti-Cancer Drug Screening.

Published in:

Cancers, 2024, v. 16, n. 3, p. 530, doi. 10.3390/cancers16030530

By:

Vasanthakumari, Priyanka;
Zhu, Yitan;
Brettin, Thomas;
Partin, Alexander;
Shukla, Maulik;
Xia, Fangfang;
Narykov, Oleksandr;
Weil, Michael Ryan;
Stevens, Rick L.

Publication type:

Article

Integration of Computational Docking into Anti-Cancer Drug Response Prediction Models.

Published in:

Cancers, 2024, v. 16, n. 1, p. 50, doi. 10.3390/cancers16010050

By:

Narykov, Oleksandr;
Zhu, Yitan;
Brettin, Thomas;
Evrard, Yvonne A.;
Partin, Alexander;
Shukla, Maulik;
Xia, Fangfang;
Clyde, Austin;
Vasanthakumari, Priyanka;
Doroshow, James H.;
Stevens, Rick L.

Publication type:

Article

PRACTITIONER APPLICATION: Shifts in Medicaid and Uninsured Payer Mix at Safety-Net and Non-Safety-Net Hospitals During the Great Recession.

Published in:

Journal of Healthcare Management, 2018, v. 63, n. 3, p. 173, doi. 10.1097/JHM-D-18-00033

By:

Stevens, Rick L.

Publication type:

Article

Modeling central metabolism and energy biosynthesis across microbial life.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-2887-8

By:

Edirisinghe, Janaka N.;
Weisenhorn, Pamela;
Conrad, Neal;
Fangfang Xia;
Overbeek, Ross;
Stevens, Rick L.;
Henry, Christopher S.

Publication type:

Article

Life Sciences and Cyberinfrastructure: Dual and Interacting Revolutions that will Drive Future Science.

Published in:

New Generation Computing, 2004, v. 22, n. 2, p. 97, doi. 10.1007/BF03040949

By:

Arzberger, Peter W.;
Farazdel, Abbas;
Konagaya, Akihiko;
Ang, Larry;
Shimojo, Shinji;
Stevens, Rick L.

Publication type:

Article

Identification of an Attenuated Substrain of Francisella tularensis SCHU S4 by Phenotypic and Genotypic Analyses.

Published in:

Pathogens, 2021, v. 10, n. 6, p. 638, doi. 10.3390/pathogens10060638

By:

Lovchik, Julie A.;
Reed, Douglas S.;
Hutt, Julie A.;
Xia, Fangfang;
Stevens, Rick L.;
Modise, Thero;
Barry, Eileen M.;
Wu, Terry H.

Publication type:

Article

Building the blueprint of life.

Published in:

Biotechnology Journal, 2010, v. 5, n. 7, p. 695, doi. 10.1002/biot.201000076

By:

Henry, Christopher;
Overbeek, Ross;
Stevens, Rick L.

Publication type:

Article

Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation.

Published in:

Frontiers in Microbiology, 2016, v. 7, p. 1, doi. 10.3389/fmicb.2016.01819

By:

Faria, José P.;
Davis, James J.;
Edirisinghe, Janaka N.;
Taylor, Ronald C.;
Weisenhorn, Pamela;
Olson, Robert D.;
Stevens, Rick L.;
Rocha, Miguel;
Rocha, Isabel;
Best, Aaron A.;
DeJongh, Matthew;
Tintle, Nathan L.;
Parrello, Bruce;
Overbeek, Ross;
Henry, Christopher S.

Publication type:

Article

Predicting tumor cell line response to drug pairs with deep learning.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 18, p. 71, doi. 10.1186/s12859-018-2509-3

By:

Xia, Fangfang;
Shukla, Maulik;
Brettin, Thomas;
Garcia-Cardona, Cristina;
Cohn, Judith;
Allen, Jonathan E.;
Maslov, Sergei;
Holbeck, Susan L.;
Doroshow, James H.;
Evrard, Yvonne A.;
Stahlberg, Eric A.;
Stevens, Rick L.

Publication type:

Article

PATRIC, the bacterial bioinformatics database and analysis resource.

Published in:

Nucleic Acids Research, 2014, v. 42, n. D1, p. D581, doi. 10.1093/nar/gkt1099

By:

Wattam, Alice R.;
Abraham, David;
Dalay, Oral;
Disz, Terry L.;
Driscoll, Timothy;
Gabbard, Joseph L.;
Gillespie, Joseph J.;
Gough, Roger;
Hix, Deborah;
Kenyon, Ronald;
Machi, Dustin;
Mao, Chunhong;
Nordberg, Eric K.;
Olson, Robert;
Overbeek, Ross;
Pusch, Gordon D.;
Shukla, Maulik;
Schulman, Julie;
Stevens, Rick L.;
Sullivan, Daniel E.

Publication type:

Article

Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model.

Published in:

Nucleic Acids Research, 2013, v. 41, n. 1, p. 687, doi. 10.1093/nar/gks963

By:

Tanaka, Kosei;
Henry, Christopher S.;
Zinner, Jenifer F.;
Jolivet, Edmond;
Cohoon, Matthew P.;
Xia, Fangfang;
Bidnenko, Vladimir;
Ehrlich, S. Dusko;
Stevens, Rick L.;
Noirot, Philippe

Publication type:

Article

KBase: The United States Department of Energy Systems Biology Knowledgebase.

Published in:

Nature Biotechnology, 2018, v. 36, n. 7, p. 566, doi. 10.1038/nbt.4163

By:

Arkin, Adam P;
Cottingham, Robert W;
Henry, Christopher S;
Harris, Nomi L;
Stevens, Rick L;
Maslov, Sergei;
Dehal, Paramvir;
Ware, Doreen;
Perez, Fernando;
Canon, Shane;
Sneddon, Michael W;
Henderson, Matthew L;
Riehl, William J;
Murphy-Olson, Dan;
Chan, Stephen Y;
Kamimura, Roy T;
Kumari, Sunita;
Drake, Meghan M;
Brettin, Thomas S;
Glass, Elizabeth M

Publication type:

Article

Learning curves for drug response prediction in cancer cell lines.

Published in:

BMC Bioinformatics, 2021, v. 22, p. 1, doi. 10.1186/s12859-021-04163-y

By:

Partin, Alexander;
Brettin, Thomas;
Evrard, Yvonne A.;
Zhu, Yitan;
Yoo, Hyunseung;
Xia, Fangfang;
Jiang, Songhao;
Clyde, Austin;
Shukla, Maulik;
Fonstein, Michael;
Doroshow, James H.;
Stevens, Rick L.

Publication type:

Article