Predicting antimicrobial resistance using conserved genes

por Nguyen, Marcus, Olson, Robert, Shukla, Maulik, VanOeffelen, Margo, Davis, James J.
Publicado 2020

TULIP: An RNA-seq-based Primary Tumor Type Prediction Tool Using Convolutional Neural Networks

por Jones, Sara, Beyers, Matthew, Shukla, Maulik, Xia, Fangfang, Brettin, Thomas, Stevens, Rick, Weil, M Ryan, Ranganathan Ganakammal, Satishkumar
Publicado 2022

Curation, integration and visualization of bacterial virulence factors in PATRIC

por Mao, Chunhong, Abraham, David, Wattam, Alice R., Wilson, Meredith J.C., Shukla, Maulik, Yoo, Hyun Seung, Sobral, Bruno W.
Publicado 2015

637. Whole-Genome Sequencing (WGS) of Isolates from Resolving (RB) and Persistent (PB) Methicillin-Resistant Staphylococcus aureus Bacteremia

por Sharma-Kuinkel, Batu K, Medie, Felix, Ruffin, Felicia, Wattam, Rebecca, Shukla, Maulik, Davis, James, Yeaman, Michael, Fowler, Vance G
Publicado 2019

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

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

PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database

por Davis, James J., Gerdes, Svetlana, Olsen, Gary J., Olson, Robert, Pusch, Gordon D., Shukla, Maulik, Vonstein, Veronika, Wattam, Alice R., Yoo, Hyunseung
Publicado 2016

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

por Davis, James J., Long, S. Wesley, Christensen, Paul A., Olsen, Randall J., Olson, Robert, Shukla, Maulik, Subedi, Sishir, Stevens, Rick, Musser, James M.
Publicado 2021

Early detection of emerging SARS-CoV-2 variants of interest for experimental evaluation

por Wallace, Zachary S., Davis, James, Niewiadomska, Anna Maria, Olson, Robert D., Shukla, Maulik, Stevens, Rick, Zhang, Yun, Zmasek, Christian M., Scheuermann, Richard H.
Publicado 2022

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

Antimicrobial Resistance Prediction in PATRIC and RAST

por Davis, James J., Boisvert, Sébastien, Brettin, Thomas, Kenyon, Ronald W., Mao, Chunhong, Olson, Robert, Overbeek, Ross, Santerre, John, Shukla, Maulik, Wattam, Alice R., Will, Rebecca, Xia, Fangfang, Stevens, Rick
Publicado 2016

Enabling comparative modeling of closely related genomes: example genus Brucella

por Faria, José P., Edirisinghe, Janaka N., Davis, James J., Disz, Terrence, Hausmann, Anna, Henry, Christopher S., Olson, Robert, Overbeek, Ross A., Pusch, Gordon D., Shukla, Maulik, Vonstein, Veronika, Wattam, Alice R.
Publicado 2014

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

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

por Overbeek, Ross, Olson, Robert, Pusch, Gordon D., Olsen, Gary J., Davis, James J., Disz, Terry, Edwards, Robert A., Gerdes, Svetlana, Parrello, Bruce, Shukla, Maulik, Vonstein, Veronika, Wattam, Alice R., Xia, Fangfang, Stevens, Rick
Publicado 2014

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

por Brettin, Thomas, Davis, James J., Disz, Terry, Edwards, Robert A., Gerdes, Svetlana, Olsen, Gary J., Olson, Robert, Overbeek, Ross, Parrello, Bruce, Pusch, Gordon D., Shukla, Maulik, Thomason, James A., Stevens, Rick, Vonstein, Veronika, Wattam, Alice R., Xia, Fangfang
Publicado 2015

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research

por Warren, Andrew S., Aurrecoechea, Cristina, Brunk, Brian, Desai, Prerak, Emrich, Scott, Giraldo-Calderón, Gloria I., Harb, Omar, Hix, Deborah, Lawson, Daniel, Machi, Dustin, Mao, Chunhong, McClelland, Michael, Nordberg, Eric, Shukla, Maulik, Vosshall, Leslie B., Wattam, Alice R., Will, Rebecca, Yoo, Hyun Seung, Sobral, Bruno
Publicado 2015