Trey Ideker

ORCID

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 49

Top Venues

bioRxiv : the preprint server for biology

Nature communications

Nature cancer

Science (New York, N.Y.)

University of California San Diego

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of California San Diego

United States

Professor :: Medicine

Publications

Sungjoon Park, Erica Silva, Akshat Singhal, Marcus R Kelly, Kate Licon, Isabella Panagiotou, Catalina Fogg, Samson Fong, John J Y Lee, Xiaoyu Zhao, Robin E Bachelder, Barbara A Parker, Kay T Yeung, Trey Ideker
A deep learning model of tumor cell architecture elucidates response and resistance to CDK4/6 inhibitors. Nature cancer (2024)
Brenton P Munson, Michael Chen, Audrey Bogosian, Jason F Kreisberg, Katherine Licon, Ruben Abagyan, Brent M Kuenzi, Trey Ideker
De novo generation of multi-target compounds using deep generative chemistry. Nature communications 15 (1) (2024)
Brittany S Leger, John J Meredith, Trey Ideker, Sandra Sanchez-Roige, Abraham A Palmer
Rare and Common Variants Associated with Alcohol Consumption Identify a Conserved Molecular Network. bioRxiv : the preprint server for biology (2024)
Sungjoon Park, Erica Silva, Akshat Singhal, Marcus R Kelly, Kate Licon, Isabella Panagiotou, Catalina Fogg, Samson Fong, John J Y Lee, Xiaoyu Zhao, Robin E Bachelder, Barbara A Parker, Kay T Yeung, Trey Ideker
A deep learning model of tumor cell architecture elucidates response and resistance to CDK4/6 inhibitors. Nature cancer 5 (7) (2024)
Xin Yin, Yuan Pu, Shuofeng Yuan, Lars Pache, Christopher Churas, Stuart Weston, Laura Riva, Lacy M Simons, William J Cisneros, Thomas Clausen, Paul D De Jesus, Ha Na Kim, Daniel Fuentes, John Whitelock, Jeffrey D Esko, Megan Lord, Ignacio Mena, Adolfo García-Sastre, Judd F Hultquist, Matthew B Frieman, Trey Ideker, Dexter Pratt, Laura Martin-Sancho, Sumit K Chanda
Global siRNA Screen Reveals Critical Human Host Factors of SARS-CoV-2 Multicycle Replication. bioRxiv : the preprint server for biology (2024)
Sungjoon Park, Erica Silva, Akshat Singhal, Marcus R Kelly, Kate Licon, Isabella Panagiotou, Catalina Fogg, Samson Fong, John J Y Lee, Xiaoyu Zhao, Robin E Bachelder, Barbara A Parker, Kay T Yeung, Trey Ideker
A deep learning model of tumor cell architecture elucidates response and resistance to CDK4/6 inhibitors. Nature cancer 5 (7) (2024)
Sungjoon Park, Erica Silva, Akshat Singhal, Marcus R Kelly, Kate Licon, Isabella Panagiotou, Catalina Fogg, Samson Fong, John J Y Lee, Xiaoyu Zhao, Robin E Bachelder, Barbara A Parker, Kay T Yeung, Trey Ideker
A deep learning model of tumor cell architecture elucidates response and resistance to CDK4/6 inhibitors. Nature cancer (2024)
Timothy W Clark, Jillian Mohan, Michael R Shortreed, Kirsten Obernier, Mohammad Sadnan Al Manir, Christopher P Churas, Amir Dailamy, Yesh Doctor, Antoine Forget, Jan Niklas Hansen, Mengzhou Hu, Joanna Lenkiewicz, Maxwell Adam Levinson, Charlotte Marquez, Sami Nourreddine, Justin Niestroy, Dexter Pratt, Gege Qian, Swathi Thaker, Jean-Christophe Bélisle-Pipon, Cynthia A Brandt, Jake Chen, Ying Ding, Samah Jamal Fodeh, Nevan J Krogan, Emma Lundberg, Prashant Mali, Pamela Payne-Foster, Sarah Jane Ratcliffe, Vardit Ravitsky, Andrej Sali, Wade L Schulz, Trey Ideker
Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines. bioRxiv : the preprint server for biology (2024)
Timothy W Clark, Jillian Mohan, Michael R Shortreed, Kirsten Obernier, Mohammad Sadnan Al Manir, Christopher P Churas, Amir Dailamy, Yesh Doctor, Antoine Forget, Jan Niklas Hansen, Mengzhou Hu, Joanna Lenkiewicz, Maxwell Adam Levinson, Charlotte Marquez, Sami Nourreddine, Justin Niestroy, Dexter Pratt, Gege Qian, Swathi Thaker, Jean-Christophe Bélisle-Pipon, Cynthia A Brandt, Jake Chen, Ying Ding, Samah Jamal Fodeh, Nevan J Krogan, Emma Lundberg, Prashant Mali, Pamela Payne-Foster, Sarah Jane Ratcliffe, Vardit Ravitsky, Andrej Sali, Wade L Schulz, Trey Ideker
Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines. bioRxiv : the preprint server for biology (2024)
Brittany S Leger, John J Meredith, Trey Ideker, Sandra Sanchez-Roige, Abraham A Palmer
Rare and Common Variants Associated with Alcohol Consumption Identify a Conserved Molecular Network. bioRxiv : the preprint server for biology (2024)
Xiaoyu Zhao, Akshat Singhal, Sungjoon Park, JungHo Kong, Robin E Bachelder, Trey Ideker
Cancer Mutations Converge on a Collection of Protein Assemblies to Predict Resistance to Replication Stress. Cancer discovery 14 (3) (2024)
Xin Yin, Yuan Pu, Shuofeng Yuan, Lars Pache, Christopher Churas, Stuart Weston, Laura Riva, Lacy M Simons, William Cisneros, Thomas Clausen, Paul de Jesus, Ha Na Kim, Daniel Fuentes, John Whitelock, Jeffrey D Esko, Megan Lord, Ignacio Mena, Adolfo Garcia-Sastre, Judd Hultquist, Matthew Frieman, Trey Ideker, Dexter Pratt, Laura Martin-Sancho, Sumit Chanda
Global siRNA Screen Reveals Critical Human Host Factors of SARS-CoV-2 Multicycle Replication. bioRxiv : the preprint server for biology (2024)
Brittany S Leger, John J Meredith, Trey Ideker, Sandra Sanchez-Roige, Abraham A Palmer
Rare and common variants associated with alcohol consumption identify a conserved molecular network. Alcohol, clinical & experimental research (2024)
Xiaoyu Zhao, Akshat Singhal, Sungjoon Park, JungHo Kong, Robin E Bachelder, Trey Ideker
Cancer mutations converge on a collection of protein assemblies to predict resistance to replication stress. Cancer discovery (2024)
Timothy W Clark, Jillian Mohan, Michael R Shortreed, Kirsten Obernier, Mohammad Sadnan Al Manir, Christopher P Churas, Amir Dailamy, Yesh Doctor, Antoine Forget, Jan Niklas Hansen, Mengzhou Hu, Joanna Lenkiewicz, Maxwell Adam Levinson, Charlotte Marquez, Sami Nourreddine, Justin Niestroy, Dexter Pratt, Gege Qian, Swathi Thaker, Jean-Christophe Bélisle-Pipon, Cynthia A Brandt, Jake Chen, Ying Ding, Samah Jamal Fodeh, Nevan J Krogan, Emma Lundberg, Prashant Mali, Pamela Payne-Foster, Sarah Jane Ratcliffe, Vardit Ravitsky, Andrej Sali, Wade L Schulz, Trey Ideker
Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines. bioRxiv : the preprint server for biology (2024)
Brittany S Leger, John J Meredith, Trey Ideker, Sandra Sanchez-Roige, Abraham A Palmer
Rare and Common Variants Associated with Alcohol Consumption Identify a Conserved Molecular Network. bioRxiv : the preprint server for biology (2024)
Brittany S Leger, John J Meredith, Trey Ideker, Sandra Sanchez-Roige, Abraham A Palmer
Rare and Common Variants Associated with Alcohol Consumption Identify a Conserved Molecular Network. bioRxiv : the preprint server for biology (2024)
Sarah N Wright, Scott Colton, Michael R Shortreed, Rudolf T Pillich, Christopher P Churas, Dexter Pratt, Trey Ideker
State of the Interactomes: an evaluation of molecular networks for generating biological insights. bioRxiv : the preprint server for biology (2024)
Brittany S Leger, John J Meredith, Trey Ideker, Sandra Sanchez-Roige, Abraham A Palmer
Rare and common variants associated with alcohol consumption identify a conserved molecular network. Alcohol, clinical & experimental research (2024)
JungHo Kong, Xiaoyu Zhao, Akshat Singhal, Sungjoon Park, Robin Bachelder, Jeanne Shen, Haiyu Zhang, Jimin Moon, Chang Ho Ahn, Chan-Young Ock, Hannah Carter, Trey Ideker
Prediction of immunotherapy response using mutations to cancer protein assemblies. Science advances 10 (38) (2024)
Brenton P Munson, Michael Chen, Audrey Bogosian, Jason F Kreisberg, Katherine Licon, Ruben Abagyan, Brent M Kuenzi, Trey Ideker
De novo generation of multi-target compounds using deep generative chemistry. Nature communications 15 (1) (2024)
Brenton P Munson, Michael Chen, Audrey Bogosian, Jason F Kreisberg, Katherine Licon, Ruben Abagyan, Brent M Kuenzi, Trey Ideker
De novo generation of multi-target compounds using deep generative chemistry. Nature communications 15 (1) (2024)
Brenton P Munson, Michael Chen, Audrey Bogosian, Jason F Kreisberg, Katherine Licon, Ruben Abagyan, Brent M Kuenzi, Trey Ideker
De novo generation of multi-target compounds using deep generative chemistry. Nature communications 15 (1) (2024)
Zane Koch, Adam Li, Daniel S Evans, Steven Cummings, Trey Ideker
Somatic mutation as an explanation for epigenetic aging. bioRxiv : the preprint server for biology (2023)
Daniel E Carlin, Simon Jonas Larsen, Vikram Sirupurapu, Michael H Cho, Edwin K Silverman, Jan Baumbach, Trey Ideker
Hierarchical association of COPD to principal genetic components of biological systems. PloS one 18 (5) (2023)
Zane Koch, Adam Li, Daniel S Evans, Steven Cummings, Trey Ideker
Somatic mutation as an explanation for epigenetic aging. bioRxiv : the preprint server for biology (2023)
Mohita M Tagore, Emiliano Hergenreder, Sarah C Perlee, Nelly M Cruz, Laura Menocal, Shruthy Suresh, Eric Chan, Maayan Baron, Stephanie Melendez, Asim Dave, Walid K Chatila, Jeremie Nsengimana, Richard P Koche, Travis J Hollman, Trey Ideker, Lorenz Studer, Andrea Schietinger, Richard M White
GABA regulates electrical activity and tumor initiation in melanoma. Cancer discovery (2023)
Belinda Wang, Rasika Vartak, Yefim Zaltsman, Zun Zar Chi Naing, Kelsey M Hennick, Benjamin J Polacco, Ali Bashir, Manon Eckhardt, Mehdi Bouhaddou, Jiewei Xu, Nawei Sun, Micaela Lasser, Yuan Zhou, Keelan Z Guiley, Una Chan, Julia A Kaye, Prachi Khare, Sam Drake, Vanessa Drury, David Francis Burke, Silvano Gonzalez, Sahar Alkhairy, Reuben Thomas, Stephanie Lam, Montana Morris, Ethel Bader, Meghan Seyler, Tierney Baum, Rebecca Krasnoff, Sheng Wang, Presley Pham, Juan Arbalaez, Dexter Pratt, Shivali Chag, Thomas Rolland, Thomas Bourgeron, Steven Finkbeiner, Sourav Bandyopadhyay, Trey Ideker, Pedro Beltrao, Nadir Moohmood, Helen Rankin Willsey, Kirsten Obernier, Tomasz Jan Nowakowski, Ruth Hüttenhain, Matthew W State, A Jeremy Willsey, Nevan J Krogan
A foundational atlas of autism protein interactions reveals molecular convergence. bioRxiv : the preprint server for biology (2023)
Zane Koch, Adam Li, Daniel S Evans, Steven Cummings, Trey Ideker
Somatic mutation as an explanation for epigenetic aging. bioRxiv : the preprint server for biology (2023)
Naoki Konno, Yusuke Kijima, Keito Watano, Soh Ishiguro, Keiichiro Ono, Mamoru Tanaka, Hideto Mori, Nanami Masuyama, Dexter Pratt, Trey Ideker, Wataru Iwasaki, Nozomu Yachie
Deep distributed computing to reconstruct extremely large lineage trees. Nature biotechnology 40 (4) (2022)
Minkyu Kim, Jisoo Park, Mehdi Bouhaddou, Kyumin Kim, Ajda Rojc, Maya Modak, Margaret Soucheray, Michael J McGregor, Patrick C O'Leary, Denise Wolf, Erica Stevenson, Tzeh Keong Foo, Dominique C Mitchell, Kari A Herrington, Denise P Muñoz, Beril Tutuncuoglu, Kuei-Ho Chen, Fan Zheng, Jason F Kreisberg, Morgan E Diolati, John D Gordan, Jean-Philippe Coppé, Danielle L Swaney, Bing Xia, Laura van 't Veer, Alan Ashworth, Trey Ideker, Nevan J Krogan
A protein interaction landscape of breast cancer. Science (New York, N.Y.) 374 (6563) (2021)
Jianzhu Ma, Samson H Fong, Yunan Luo, Christopher J Bakkenist, John Paul Shen, Soufiane Mourragui, Lodewyk F A Wessels, Marc Hafner, Roded Sharan, Jian Peng, Trey Ideker
Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients. Nature cancer 2 (2) (2021)
Laura Martin-Sancho, Shashank Tripathi, Ariel Rodriguez-Frandsen, Lars Pache, María Teresa Sánchez-Aparicio, Michael J McGregor, Kelsey M Haas, Danielle L Swaney, Thong T Nguyen, João I Mamede, Christopher Churas, Dexter Pratt, Sara B Rosenthal, Laura Riva, Courtney Nguyen, Nish Beltran-Raygoza, Stephen Soonthornvacharin, Guojun Wang, David Jimenez-Morales, Paul D De Jesus, Hong M Moulton, David A Stein, Max W Chang, Christopher W Benner, Trey Ideker, Randy A Albrecht, Judd F Hultquist, Nevan J Krogan, Adolfo García-Sastre, Sumit K Chanda
Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy. Nature microbiology 6 (10) (2021)
Danielle L Swaney, Dana J Ramms, Zhiyong Wang, Jisoo Park, Yusuke Goto, Margaret Soucheray, Neil Bhola, Kyumin Kim, Fan Zheng, Yan Zeng, Michael J McGregor, Kari A Herrington, Rachel A O'Keefe, Nan Jin, Nathan K VanLandingham, Helene Foussard, John Von Dollen, Mehdi Bouhaddou, David Jimenez-Morales, Kirsten Obernier, Jason F Kreisberg, Minkyu Kim, Daniel E Johnson, Natalia Jura, Jennifer R Grandis, Jorge Silvio Gutkind, Trey Ideker, Nevan J Krogan
A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity. Science (New York, N.Y.) 374 (6563) (2021)
Yue Qin, Edward L Huttlin, Casper F Winsnes, Maya L Gosztyla, Ludivine Wacheul, Marcus R Kelly, Steven M Blue, Fan Zheng, Michael Chen, Leah V Schaffer, Katherine Licon, Anna Bäckström, Laura Pontano Vaites, John J Lee, Wei Ouyang, Sophie N Liu, Tian Zhang, Erica Silva, Jisoo Park, Adriana Pitea, Jason F Kreisberg, Steven P Gygi, Jianzhu Ma, J Wade Harper, Gene W Yeo, Denis L J Lafontaine, Emma Lundberg, Trey Ideker
A multi-scale map of cell structure fusing protein images and interactions. Nature (2021)
Hidenori Tanaka, Jason F Kreisberg, Trey Ideker
Genetic dissection of complex traits using hierarchical biological knowledge. PLoS computational biology 17 (9) (2021)
Fan Zheng, Marcus R Kelly, Dana J Ramms, Marissa L Heintschel, Kai Tao, Beril Tutuncuoglu, John J Lee, Keiichiro Ono, Helene Foussard, Michael Chen, Kari A Herrington, Erica Silva, Sophie N Liu, Jing Chen, Christopher P Churas, Nicholas Wilson, Anton Kratz, Rudolf T Pillich, Devin N Patel, Jisoo Park, Brent M Kuenzi, Michael K Yu, Katherine Licon, Dexter Pratt, Jason F Kreisberg, Minkyu Kim, Danielle L Swaney, Xiaolin Nan, Stephanie I Fraley, Jorge Silvio Gutkind, Nevan J Krogan, Trey Ideker
Interpretation of cancer mutations using a multiscale map of protein systems. Science (New York, N.Y.) 374 (6563) (2021)
Laura Martin-Sancho, Mary K Lewinski, Lars Pache, Charlotte A Stoneham, Xin Yin, Dexter Pratt, Christopher Churas, Sara B Rosenthal, Sophie Liu, Paul D De Jesus, Alan M O'Neill, Anshu P Gounder, Courtney Nguyen, Yuan Pu, Aaron L Oom, Lisa Miorin, Ariel Rodriguez-Frandsen, Matthew Urbanowski, Megan L Shaw, Max W Chang, Christopher Benner, Matthew B Frieman, Adolfo García-Sastre, Trey Ideker, Judd F Hultquist, John Guatelli, Sumit K Chanda
Functional Landscape of SARS-CoV-2 Cellular Restriction. bioRxiv : the preprint server for biology (2020)
Erica Silva, Manuel Michaca, Brenton Munson, Gordon J Bean, Philipp A Jaeger, Katherine Licon, Elizabeth A Winzeler, Trey Ideker
Genome-Wide Dynamic Evaluation of the UV-Induced DNA Damage Response. G3 (Bethesda, Md.) 10 (9) (2020)
Brent M Kuenzi, Trey Ideker
A census of pathway maps in cancer systems biology. Nature reviews. Cancer 20 (4) (2020)
Nikolaos Vakirlis, Omer Acar, Brian Hsu, Nelson C Coelho, S Branden Van Oss, Aaron Wacholder, Kate Medetgul-Ernar, Ray W Bowman, Cameron P Hines, John Iannotta, Saurin Bipin Parikh, Aoife McLysaght, Carlos Jaime Camacho, Allyson F O'Donnell, Trey Ideker, Anne-Ruxandra Carvunis
De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nature communications 11 (1) (2020)
Su Ming Sun, Amandine Batté, Mireille Elmer, Sophie C van der Horst, Tibor van Welsem, Gordon Bean, Trey Ideker, Fred van Leeuwen, Haico van Attikum
A genetic interaction map centered on cohesin reveals auxiliary factors involved in sister chromatid cohesion in S. cerevisiae. Journal of cell science 133 (10) (2020)
David E Gordon, Gwendolyn M Jang, Mehdi Bouhaddou, Jiewei Xu, Kirsten Obernier, Kris M White, Matthew J O'Meara, Veronica V Rezelj, Jeffrey Z Guo, Danielle L Swaney, Tia A Tummino, Ruth Hüttenhain, Robyn M Kaake, Alicia L Richards, Beril Tutuncuoglu, Helene Foussard, Jyoti Batra, Kelsey Haas, Maya Modak, Minkyu Kim, Paige Haas, Benjamin J Polacco, Hannes Braberg, Jacqueline M Fabius, Manon Eckhardt, Margaret Soucheray, Melanie J Bennett, Merve Cakir, Michael J McGregor, Qiongyu Li, Bjoern Meyer, Ferdinand Roesch, Thomas Vallet, Alice Mac Kain, Lisa Miorin, Elena Moreno, Zun Zar Chi Naing, Yuan Zhou, Shiming Peng, Ying Shi, Ziyang Zhang, Wenqi Shen, Ilsa T Kirby, James E Melnyk, John S Chorba, Kevin Lou, Shizhong A Dai, Inigo Barrio-Hernandez, Danish Memon, Claudia Hernandez-Armenta, Jiankun Lyu, Christopher J P Mathy, Tina Perica, Kala Bharath Pilla, Sai J Ganesan, Daniel J Saltzberg, Ramachandran Rakesh, Xi Liu, Sara Brin Rosenthal, Lorenzo Calviello, Srivats Venkataramanan, José M Liboy-Lugo, Yizhu Lin, Xi-Ping Huang, YongFeng Liu, Stephanie A Wankowicz, Markus Bohn, Maliheh Safari, Fatima S Ugur, Cassandra Koh, Nastaran Sadat Savar, Quang Dinh Tran, Djoshkun Shengjuler, Sabrina J Fletcher, Michael C O'Neal, Yiming Cai, Jason C J Chang, David J Broadhurst, Saker Klippsten, Phillip P Sharp, Nicole A Wenzell, Duygu Kuzuoglu-Ozturk, Hao-Yuan Wang, Raphael Trenker, Janet M Young, Devin A Cavero, Joseph Hiatt, Theodore L Roth, Ujjwal Rathore, Advait Subramanian, Julia Noack, Mathieu Hubert, Robert M Stroud, Alan D Frankel, Oren S Rosenberg, Kliment A Verba, David A Agard, Melanie Ott, Michael Emerman, Natalia Jura, Mark Von Zastrow, Eric Verdin, Alan Ashworth, Olivier Schwartz, Christophe D'Enfert, Shaeri Mukherjee, Matthew P Jacobson, Harmit Singh Malik, Danica G Fujimori, Trey Ideker, Charles S Craik, Stephen N Floor, Brian K Shoichet, John D Gross, Andrej Sali, Bryan L Roth, Davide Ruggero, Jack Taunton, Tanja Kortemme, Pedro Beltrao, Marco Vignuzzi, Adolfo García-Sastre, Kevan M Shokat, Brian K Shoichet, Nevan J Krogan
A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 583 (7816) (2020)
Akshat Singhal, Song Cao, Christopher P Churas, Dexter Pratt, Santo Fortunato, Fan Zheng, Trey Ideker
Multiscale community detection in Cytoscape. PLoS computational biology 16 (10) (2020)
David E Gordon, Joseph Hiatt, Mehdi Bouhaddou, Veronica V Rezelj, Svenja Ulferts, Hannes Braberg, Alexander S Jureka, Kirsten Obernier, Jeffrey Z Guo, Jyoti Batra, Robyn M Kaake, Andrew R Weckstein, Tristan W Owens, Meghna Gupta, Sergei Pourmal, Erron W Titus, Merve Cakir, Margaret Soucheray, Michael J McGregor, Zeynep Cakir, Gwendolyn M Jang, Matthew J O'Meara, Tia A Tummino, Ziyang Zhang, Helene Foussard, Ajda Rojc, Yuan Zhou, Dmitry Kuchenov, Ruth Hüttenhain, Jiewei Xu, Manon Eckhardt, Danielle L Swaney, Jacqueline M Fabius, Manisha Ummadi, Beril Tutuncuoglu, Ujjwal Rathore, Maya Modak, Paige Haas, Kelsey M Haas, Zun Zar Chi Naing, Ernst H Pulido, Ying Shi, Inigo Barrio-Hernandez, Danish Memon, Eirini Petsalaki, Alistair S Dunham, Miguel Correa Marrero, David Francis Burke, Cassandra Koh, Thomas Vallet, Jesus A Silvas, Caleigh M Azumaya, Christian B Billesbølle, Axel F Brilot, Melody G Campbell, Amy Diallo, Miles Sasha Dickinson, Devan Diwanji, Nadia Herrera, Nicholas Hoppe, Huong T Kratochvil, Yanxin Liu, Gregory E Merz, Michelle Moritz, Henry C Nguyen, Carlos A Nowotny, Cristina Puchades, Alexandrea N Rizo, Ursula Schulze-Gahmen, Amber M Smith, Ming Sun, Iris D Young, Jianhua Zhao, Daniel Asarnow, Justin T Biel, Alisa Bowen, Julian R Braxton, Jen Chen, Cynthia M Chio, Un Seng Chio, Ishan Deshpande, Loan Doan, Bryan Faust, Sebastian Flores, Mingliang Jin, Sun Kyung Kim, Victor L Lam, Fei Li, Junrui Li, Grant J Jensen, Yang Li, Xi Liu, Megan Lo, Kyle E Lopez, Arthur A Melo, Frank R Moss, Phuong Nguyen, Joana Paulino, Komal Ishwar Pawar, Jessica K Peters, Thomas H Pospiech, Maliheh Safari, Smriti Sangwan, Kaitlin Schaefer, Paul V Thomas, Aye C Thwin, Raphael Trenker, Eric Tse, Tsz Kin Martin Tsui, Feng Wang, Natalie Whitis, Zanlin Yu, Kaihua Zhang, Sunny Zhang, Fengbo Zhou, Daniel J Saltzberg, null null, Anthony J Hodder, Amber S Shun-Shion, Daniel M Williams, Kris M White, Romel Rosales, Thomas Kehrer, Lisa Miorin, Elena Moreno, Arvind H Patel, Suzannah J Rihn, Mir Mubashir Khalid, Albert Vallejo-Gracia, Parinaz Fozouni, Camille R Simoneau, Theodore L Roth, David Wu, Mohd Anisul Karim, Maya Ghoussaini, Ian Dunham, Francesco Berardi, Sebastian Weigang, Maxime Chazal, Jisoo Park, James P Logue, Marisa E McGrath, Stuart M Weston, Robert E Haupt, C James Hastie, Matthew Elliott, Fiona Brown, Kerry A Burness, Elaine Reid, Mark Dorward, Clare Johnson, Stuart G Wilkinson, Anna Geyer, Daniel M Giesel, Carla Baillie, Samantha Raggett, Hannah Leech, Rachel Toth, Nicola Goodman, Kathleen C Keough, Abigail L Lind, null null, Reyna J Klesh, Kafi R Hemphill, Jared Carlson-Stevermer, Jennifer Oki, Kevin Holden, Travis Maures, Katherine S Pollard, Andrej Sali, David A Agard, Yifan Cheng, Brian K Shoichet, Adam Frost, Natalia Jura, Tanja Kortemme, Aashish Manglik, Daniel R Southworth, Robert M Stroud, Dario R Alessi, Paul Davies, Matthew B Friemann, Trey Ideker, Carmen Abate, Nolwenn Jouvenet, Georg Kochs, Brian K Shoichet, Melanie M Ott, Massimo Palmarini, Kevan M Shokat, Adolfo García-Sastre, Jeremy A Rassen, Robert Grosse, Oren S Rosenberg, Kliment A Verba, Christopher F Basler, Marco Vignuzzi, Andrew A Peden, Pedro Beltrao, Nevan J Krogan
Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science (New York, N.Y.) 370 (6521) (2020)
Jonathan Flint, Trey Ideker
The great hairball gambit. PLoS genetics 15 (11) (2019)
Jianzhu Ma, Michael Ku Yu, Samson Fong, Keiichiro Ono, Eric Sage, Barry Demchak, Roded Sharan, Trey Ideker
Using deep learning to model the hierarchical structure and function of a cell. Nature methods 15 (4) (2018)
Sheng Wang, Jianzhu Ma, Wei Zhang, John Paul Shen, Justin Huang, Jian Peng, Trey Ideker
Typing tumors using pathways selected by somatic evolution. Nature communications 9 (1) (2018)
Wei Zhang, Ana Bojorquez-Gomez, Daniel Ortiz Velez, Guorong Xu, Kyle S Sanchez, John Paul Shen, Kevin Chen, Katherine Licon, Collin Melton, Katrina M Olson, Michael Ku Yu, Justin K Huang, Hannah Carter, Emma K Farley, Michael Snyder, Stephanie I Fraley, Jason F Kreisberg, Trey Ideker
A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nature genetics 50 (4) (2018)

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Publication Activity (10 Years)

Top Topics

Top Venues

Trey Ideker