Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations

por Way, Gregory P., Zietz, Michael, Rubinetti, Vincent, Himmelstein, Daniel S., Greene, Casey S.
Publicado 2020

Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic

por Chow, Yuen Ler, Singh, Shantanu, Carpenter, Anne E., Way, Gregory P.
Publicado 2022

Deconvolution of DNA methylation identifies differentially methylated gene regions on 1p36 across breast cancer subtypes

por Titus, Alexander J., Way, Gregory P., Johnson, Kevin C., Christensen, Brock C.
Publicado 2017

PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia

por Chen, Kathleen M., Tan, Jie, Way, Gregory P., Doing, Georgia, Hogan, Deborah A., Greene, Casey S.
Publicado 2018

A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma

por Way, Gregory P., Allaway, Robert J., Bouley, Stephanie J., Fadul, Camilo E., Sanchez, Yolanda, Greene, Casey S.
Publicado 2017

Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes

por Way, Gregory P., Rudd, James, Wang, Chen, Hamidi, Habib, Fridley, Brooke L., Konecny, Gottfried E., Goode, Ellen L., Greene, Casey S., Doherty, Jennifer A.
Publicado 2016

High-content microscopy reveals a morphological signature of bortezomib resistance

por Kelley, Megan E, Berman, Adi Y, Stirling, David R, Cimini, Beth A, Han, Yu, Singh, Shantanu, Carpenter, Anne E, Kapoor, Tarun M, Way, Gregory P
Publicado 2023

Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas

por Way, Gregory P., Sanchez-Vega, Francisco, La, Konnor, Armenia, Joshua, Chatila, Walid K., Luna, Augustin, Sander, Chris, Cherniack, Andrew D., Mina, Marco, Ciriello, Giovanni, Schultz, Nikolaus, Sanchez, Yolanda, Greene, Casey S.
Publicado 2018

Predicting cell health phenotypes using image-based morphology profiling

por Way, Gregory P., Kost-Alimova, Maria, Shibue, Tsukasa, Harrington, William F., Gill, Stanley, Piccioni, Federica, Becker, Tim, Shafqat-Abbasi, Hamdah, Hahn, William C., Carpenter, Anne E., Vazquez, Francisca, Singh, Shantanu
Publicado 2021

Epigenomic profiling of neuroblastoma cell lines

por Upton, Kristen, Modi, Apexa, Patel, Khushbu, Kendsersky, Nathan M., Conkrite, Karina L., Sussman, Robyn T., Way, Gregory P., Adams, Rebecca N., Sacks, Gregory I., Fortina, Paolo, Diskin, Sharon J., Maris, John M., Rokita, Jo Lynne
Publicado 2020

Immune landscapes associated with different glioblastoma molecular subtypes

por Martinez-Lage, Maria, Lynch, Timothy M., Bi, Yingtao, Cocito, Carolina, Way, Gregory P., Pal, Sharmistha, Haller, Josephine, Yan, Rachel E., Ziober, Amy, Nguyen, Aivi, Kandpal, Manoj, O’Rourke, Donald M., Greenfield, Jeffrey P., Greene, Casey S., Davuluri, Ramana V., Dahmane, Nadia
Publicado 2019

A field guide to cultivating computational biology

por Way, Gregory P., Greene, Casey S., Carninci, Piero, Carvalho, Benilton S., de Hoon, Michiel, Finley, Stacey D., Gosline, Sara J. C., Lȇ Cao, Kim-Anh, Lee, Jerry S. H., Marchionni, Luigi, Robine, Nicolas, Sindi, Suzanne S., Theis, Fabian J., Yang, Jean Y. H., Carpenter, Anne E., Fertig, Elana J.
Publicado 2021

A genome-wide atlas of human cell morphology

por Ramezani, Meraj, Bauman, Julia, Singh, Avtar, Weisbart, Erin, Yong, John, Lozada, Maria, Way, Gregory P., Kavari, Sanam L., Diaz, Celeste, Haghighi, Marzieh, Batista, Thiago M., Pérez-Schindler, Joaquín, Claussnitzer, Melina, Singh, Shantanu, Cimini, Beth A., Blainey, Paul C., Carpenter, Anne E., Jan, Calvin H., Neal, James T.
Publicado 2023

Reproducible image-based profiling with Pycytominer

por Serrano, Erik, Chandrasekaran, Srinivas Niranj, Bunten, Dave, Brewer, Kenneth I., Tomkinson, Jenna, Kern, Roshan, Bornholdt, Michael, Fleming, Stephen, Pei, Ruifan, Arevalo, John, Tsang, Hillary, Rubinetti, Vincent, Tromans-Coia, Callum, Becker, Tim, Weisbart, Erin, Bunne, Charlotte, Kalinin, Alexandr A., Senft, Rebecca, Taylor, Stephen J., Jamali, Nasim, Adeboye, Adeniyi, Abbasi, Hamdah Shafqat, Goodman, Allen, Caicedo, Juan C., Carpenter, Anne E., Cimini, Beth A., Singh, Shantanu, Way, Gregory P.
Publicado 2023

Genome-wide association study implicates novel loci and reveals candidate effector genes for longitudinal pediatric bone accrual

por Cousminer, Diana L., Wagley, Yadav, Pippin, James A., Elhakeem, Ahmed, Way, Gregory P., Pahl, Matthew C., McCormack, Shana E., Chesi, Alessandra, Mitchell, Jonathan A., Kindler, Joseph M., Baird, Denis, Hartley, April, Howe, Laura, Kalkwarf, Heidi J., Lappe, Joan M., Lu, Sumei, Leonard, Michelle E., Johnson, Matthew E., Hakonarson, Hakon, Gilsanz, Vicente, Shepherd, John A., Oberfield, Sharon E., Greene, Casey S., Kelly, Andrea, Lawlor, Deborah A., Voight, Benjamin F., Wells, Andrew D., Zemel, Babette S., Hankenson, Kurt D., Grant, Struan F. A.
Publicado 2021

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

por Knijnenburg, Theo A., Wang, Linghua, Zimmermann, Michael T., Chambwe, Nyasha, Gao, Galen F., Cherniack, Andrew D., Fan, Huihui, Shen, Hui, Way, Gregory P., Greene, Casey S., Liu, Yuexin, Akbani, Rehan, Feng, Bin, Donehower, Lawrence A., Miller, Chase, Shen, Yang, Karimi, Mostafa, Chen, Haoran, Kim, Pora, Jia, Peilin, Shinbrot, Eve, Zhang, Shaojun, Liu, Jianfang, Hu, Hai, Bailey, Matthew H., Yau, Christina, Wolf, Denise, Zhao, Zhongming, Weinstein, John N., Li, Lei, Ding, Li, Mills, Gordon B., Laird, Peter W., Wheeler, David A., Shmulevich, Ilya, Monnat, Raymond J, Xiao, Yonghong, Wang, Chen
Publicado 2018

Discovering cellular programs of intrinsic and extrinsic drivers of metabolic traits using LipocyteProfiler

por Laber, Samantha, Strobel, Sophie, Mercader, Josep M., Dashti, Hesam, dos Santos, Felipe R.C., Kubitz, Phil, Jackson, Maya, Ainbinder, Alina, Honecker, Julius, Agrawal, Saaket, Garborcauskas, Garrett, Stirling, David R., Leong, Aaron, Figueroa, Katherine, Sinnott-Armstrong, Nasa, Kost-Alimova, Maria, Deodato, Giacomo, Harney, Alycen, Way, Gregory P., Saadat, Alham, Harken, Sierra, Reibe-Pal, Saskia, Ebert, Hannah, Zhang, Yixin, Calabuig-Navarro, Virtu, McGonagle, Elizabeth, Stefek, Adam, Dupuis, Josée, Cimini, Beth A., Hauner, Hans, Udler, Miriam S., Carpenter, Anne E., Florez, Jose C., Lindgren, Cecilia, Jacobs, Suzanne B.R., Claussnitzer, Melina
Publicado 2023

Opportunities and obstacles for deep learning in biology and medicine

por Ching, Travers, Himmelstein, Daniel S., Beaulieu-Jones, Brett K., Kalinin, Alexandr A., Do, Brian T., Way, Gregory P., Ferrero, Enrico, Agapow, Paul-Michael, Zietz, Michael, Hoffman, Michael M., Xie, Wei, Rosen, Gail L., Lengerich, Benjamin J., Israeli, Johnny, Lanchantin, Jack, Woloszynek, Stephen, Carpenter, Anne E., Shrikumar, Avanti, Xu, Jinbo, Cofer, Evan M., Lavender, Christopher A., Turaga, Srinivas C., Alexandari, Amr M., Lu, Zhiyong, Harris, David J., DeCaprio, Dave, Qi, Yanjun, Kundaje, Anshul, Peng, Yifan, Wiley, Laura K., Segler, Marwin H. S., Boca, Simina M., Swamidass, S. Joshua, Huang, Austin, Gitter, Anthony, Greene, Casey S.
Publicado 2018

OpenPBTA: The Open Pediatric Brain Tumor Atlas

por Shapiro, Joshua A., Gaonkar, Krutika S., Spielman, Stephanie J., Savonen, Candace L., Bethell, Chante J., Jin, Run, Rathi, Komal S., Zhu, Yuankun, Egolf, Laura E., Farrow, Bailey K., Miller, Daniel P., Yang, Yang, Koganti, Tejaswi, Noureen, Nighat, Koptyra, Mateusz P., Duong, Nhat, Santi, Mariarita, Kim, Jung, Robins, Shannon, Storm, Phillip B., Mack, Stephen C., Lilly, Jena V., Xie, Hongbo M., Jain, Payal, Raman, Pichai, Rood, Brian R., Lulla, Rishi R., Nazarian, Javad, Kraya, Adam A., Vaksman, Zalman, Heath, Allison P., Kline, Cassie, Scolaro, Laura, Viaene, Angela N., Huang, Xiaoyan, Way, Gregory P., Foltz, Steven M., Zhang, Bo, Poetsch, Anna R., Mueller, Sabine, Ennis, Brian M., Prados, Michael, Diskin, Sharon J., Zheng, Siyuan, Guo, Yiran, Kannan, Shrivats, Waanders, Angela J., Margol, Ashley S., Kim, Meen Chul, Hanson, Derek, Van Kuren, Nicholas, Wong, Jessica, Kaufman, Rebecca S., Coleman, Noel, Blackden, Christopher, Cole, Kristina A., Mason, Jennifer L., Madsen, Peter J., Koschmann, Carl J., Stewart, Douglas R., Wafula, Eric, Brown, Miguel A., Resnick, Adam C., Greene, Casey S., Rokita, Jo Lynne, Taroni, Jaclyn N.
Publicado 2023

Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design

por Rokita, Jo Lynne, Rathi, Komal S., Cardenas, Maria F., Upton, Kristen A., Jayaseelan, Joy, Cross, Katherine L., Pfeil, Jacob, Egolf, Laura E., Way, Gregory P., Farrel, Alvin, Kendsersky, Nathan M., Patel, Khushbu, Gaonkar, Krutika S., Modi, Apexa, Berko, Esther R., Lopez, Gonzalo, Vaksman, Zalman, Mayoh, Chelsea, Nance, Jonas, McCoy, Kristyn, Haber, Michelle, Evans, Kathryn, McCalmont, Hannah, Bendak, Katerina, Böhm, Julia W., Marshall, Glenn M., Tyrrell, Vanessa, Kalletla, Karthik, Braun, Frank K., Qi, Lin, Du, Yunchen, Zhang, Huiyuan, Lindsay, Holly B., Zhao, Sibo, Shu, Jack, Baxter, Patricia, Morton, Christopher, Kurmashev, Dias, Zheng, Siyuan, Chen, Yidong, Bowen, Jay, Bryan, Anthony C., Leraas, Kristen M., Coppens, Sara E., Doddapaneni, HarshaVardhan, Momin, Zeineen, Zhang, Wendong, Sacks, Gregory I., Hart, Lori S., Krytska, Kateryna, Mosse, Yael P., Gatto, Gregory J., Sanchez, Yolanda, Greene, Casey S., Diskin, Sharon J., Vaske, Olena Morozova, Haussler, David, Gastier-Foster, Julie M., E. Anders, Kolb, Gorlick, Richard, Li, Xiao-Nan, Reynolds, C. Patrick, Kurmasheva, Raushan T., Houghton, Peter J., Smith, Malcolm A., Lock, Richard B., Raman, Pichai, Wheeler, David A., Maris, John M.
Publicado 2019