iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations

por Henry, Christopher S, Zinner, Jenifer F, Cohoon, Matthew P, Stevens, Rick L
Publicado 2009

Image-based configuration and interaction for large neural network simulations

por Hereld, Mark, Lee, Hyong C, van Drongelen, Wim, Stevens, Rick L
Publicado 2007

Simulated-annealing as a tool to identify parameter values associated with epileptiform activity in single-neuron and network compartmental models

por Benayoun, Marc, Dwyer, Jennifer, Lee, Hyong C, Herald, Mark, Stevens, Rick L, van Drongelen, Wim
Publicado 2007

Deep learning methods for drug response prediction in cancer: Predominant and emerging trends

por Partin, Alexander, Brettin, Thomas S., Zhu, Yitan, Narykov, Oleksandr, Clyde, Austin, Overbeek, Jamie, Stevens, Rick L.
Publicado 2023

Modeling central metabolism and energy biosynthesis across microbial life

por Edirisinghe, Janaka N., Weisenhorn, Pamela, Conrad, Neal, Xia, Fangfang, Overbeek, Ross, Stevens, Rick L., Henry, Christopher S.
Publicado 2016

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

por Pesce, Lorenzo L., Lee, Hyong C., Hereld, Mark, Visser, Sid, Stevens, Rick L., Wildeman, Albert, van Drongelen, Wim
Publicado 2013

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

por Zhu, Yitan, Brettin, Thomas, Evrard, Yvonne A., Xia, Fangfang, Partin, Alexander, Shukla, Maulik, Yoo, Hyunseung, Doroshow, James H., Stevens, Rick L.
Publicado 2020

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

por Zhu, Yitan, Brettin, Thomas, Evrard, Yvonne A., Partin, Alexander, Xia, Fangfang, Shukla, Maulik, Yoo, Hyunseung, Doroshow, James H., Stevens, Rick L.
Publicado 2020

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

por Zhu, Yitan, Brettin, Thomas, Xia, Fangfang, Partin, Alexander, Shukla, Maulik, Yoo, Hyunseung, Evrard, Yvonne A., Doroshow, James H., Stevens, Rick L.
Publicado 2021

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

por Lovchik, Julie A., Reed, Douglas S., Hutt, Julie A., Xia, Fangfang, Stevens, Rick L., Modise, Thero, Barry, Eileen M., Wu, Terry H.
Publicado 2021

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

por Zhu, Yitan, Brettin, Thomas, Xia, Fangfang, Partin, Alexander, Shukla, Maulik, Yoo, Hyunseung, Evrard, Yvonne A., Doroshow, James H., Stevens, Rick L.
Publicado 2021

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

por 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
Publicado 2013

Data augmentation and multimodal learning for predicting drug response in patient-derived xenografts from gene expressions and histology images

por Partin, Alexander, Brettin, Thomas, Zhu, Yitan, Dolezal, James M., Kochanny, Sara, Pearson, Alexander T., Shukla, Maulik, Evrard, Yvonne A., Doroshow, James H., Stevens, Rick L.
Publicado 2023

Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae

por Nguyen, Marcus, Brettin, Thomas, Long, S. Wesley, Musser, James M., Olsen, Randall J., Olson, Robert, Shukla, Maulik, Stevens, Rick L., Xia, Fangfang, Yoo, Hyunseung, Davis, James J.
Publicado 2018

Learning curves for drug response prediction in cancer cell lines

por 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.
Publicado 2021

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

por 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
Publicado 2012

Predicting tumor cell line response to drug pairs with deep learning

por 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.
Publicado 2018

Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation

por 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.
Publicado 2016

PATRIC, the bacterial bioinformatics database and analysis resource

por 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., Vonstein, Veronika, Warren, Andrew, Will, Rebecca, Wilson, Meredith J.C., Yoo, Hyun Seung, Zhang, Chengdong, Zhang, Yan, Sobral, Bruno W.
Publicado 2014

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

por Wattam, Alice R., Davis, James J., Assaf, Rida, Boisvert, Sébastien, Brettin, Thomas, Bun, Christopher, Conrad, Neal, Dietrich, Emily M., Disz, Terry, Gabbard, Joseph L., Gerdes, Svetlana, Henry, Christopher S., Kenyon, Ronald W., Machi, Dustin, Mao, Chunhong, Nordberg, Eric K., Olsen, Gary J., Murphy-Olson, Daniel E., Olson, Robert, Overbeek, Ross, Parrello, Bruce, Pusch, Gordon D., Shukla, Maulik, Vonstein, Veronika, Warren, Andrew, Xia, Fangfang, Yoo, Hyunseung, Stevens, Rick L.
Publicado 2017