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Trey Ideker

university of california san diego

108H-index
629Paper Count
12.1WCitation Count
Published Papers 222
Publication Date
A genome-scale CRISPRi perturbation atlas of human induced pluripotent stem cells
err2026-07-01
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PREAI
errSami Nourreddine; Yesh Doctor; Amir Dailamy; Yi-Hung Lee; Jan N. Hansen; Rebecca Chinn; Antoine Forget; Benjamin Polacco; Monita Muralidharan; Alina Sigaeva; Sushant Sunder; Emily Pan; Jiahao Gao; Jake Y. Chen; Timothy Clark; Jillian Parker; Kirsten Obernier; Christian Metallo; Trey Ideker; Emma Lundberg; Nevan Krogan; Prashant Mali
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DREAM repressive activity links somatic mutation, lifespan and disease
err2026-06-02
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PREAI
errZane Koch; Shuvro P. Nandi; Kate Licon; Arturo Bujarrabal-Dueso; David H. Meyer; Safa Saeed; Pirunthan Perampalam; Frederick A. Dick; Björn Schumacher; Ludmil B. Alexandrov; Trey Ideker
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scLong: a billion-parameter foundation model for capturing long-range gene context in single-cell transcriptomics
err2026-02-05
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errOAAI
errDing Bai; Shentong Mo; Ruiyi Zhang; Yingtao Luo; Jiahao Gao; Jeremy Parker Yang; Qiuyang Wu; Hamidreza Rahmani; Tiffany Amariuta; Danielle Grotjahn; Sheng Zhong; Nathan Lewis; Wei Wang; Trey Ideker; Pengtao Xie; Eric Xing
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The ADAPT learning cancer treatment system: ARPA-H’s initiative to revolutionize cancer therapy
err2026-01-08
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PREAI
errAndrea H. Bild; Michelle C. Sangar; Jasmine A. McQuerry; Trey Ideker; Scott Kopetz; Lisa Carey; Aritro Nath; Daniel Marcus; Allison Regier; Naim Rashid; Regina Barzilay; Eric Winer; Ravi Salgia; Jyoti Malhotra; Andrew Gentles; Kenneth Buetow; Faisal Mahmood; David W. Markman; James A. Eddy
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Understanding emergence in complex systems using abductive AI
err2025-11-11
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PREAI
errJingtao Ding; Yu Zheng; Fengli Xu; Carlo Vittorio Cannistraci; Xiaowen Dong; Paolo Santi; Guido Caldarelli; Yizhou Sun; Qi R. Wang; Boleslaw K. Szymanski; Carlo Ratti; Trey Ideker; Jianxi Gao; Yong Li; Deliang Chen
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Towards the ethical development of functional genomics research
err2025-10-30
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PREAI
errIan Stevens; Danielle Pacia; Jan N. Hansen; Jillian Parker; Pamela Payne-Foster; Trey Ideker; Jean-Christophe Bélisle-Pipon; Vardit Ravitsky
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Publisher Correction: Multimodal cell maps as a foundation for structural and functional genomics
errNature
IF48.5
err2025-10-02
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errOAAI
errLeah V. Schaffer; Mengzhou Hu; Gege Qian; Kyung-Mee Moon; Abantika Pal; Neelesh Soni; Andrew P. Latham; Laura Pontano Vaites; Dorothy Tsai; Nicole M. Mattson; Katherine Licon; Robin Bachelder; Anthony Cesnik; Ishan Gaur; Trang Le; William Leineweber; Aji Palar; Ernst Pulido; Yue Qin; Xiaoyu Zhao; Christopher Churas; Joanna Lenkiewicz; Jing Chen; Keiichiro Ono; Dexter Pratt; Peter Zage; Ignacia Echeverria; Andrej Sali; J. Wade Harper; Steven P. Gygi; Leonard J. Foster; Edward L. Huttlin; Emma Lundberg; Trey Ideker
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Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks
err2025-07-16
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errOAAI
errSarah N. Wright; Brittany S. Leger; Sara Brin Rosenthal; Sophie N. Liu; Tongqiu Jia; Apurva S. Chitre; Oksana Polesskaya; Katie Holl; Jianjun Gao; Riyan Cheng; Angel Garcia Martinez; Anthony George; Alexander F. Gileta; Wenyan Han; Alesa H. Netzley; Christopher P. King; Alexander Lamparelli; Connor Martin; Celine L. St. Pierre; Tengfei Wang; Hannah Bimschleger; Jerry Richards; Keita Ishiwari; Hao Chen; Shelly B. Flagel; Paul Meyer; Terry E. Robinson; Leah C. Solberg Woods; Jason F. Kreisberg; Trey Ideker; Abraham A. Palmer
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Artificial Intelligence-Powered Insights into Polyclonality and Tumor Evolution
errResearch
IF10.7
err2025-07-02
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errOAAI
errHong Zhao; Trey Ideker; Stephen T. C. Wong
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Desmosome mutations impact the tumor microenvironment to promote melanoma proliferation
err2025-04-16
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errOAAI
errMaayan Baron; Mohita Tagore; Patrick Wall; Fan Zheng; Dalia Barkley; Itai Yanai; Jing Yang; Maija Kiuru; Richard M. White; Trey Ideker
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Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders
err2025-04-01
err1
errOAAI
errMei, Yuan; Gosztyla, Maya L.; Tan, Xinzhu; Dozier, Lara E.; Wilkinson, Brent; McKetney, Justin; Lee, John; Chen, Michael; Tsai, Dorothy; Kopalle, Hema; Gritsenko, Marina A.; Hartel, Nicolas; Graham, Nicholas A.; Flores, Ilse; Gilmore-Hall, Stephen K.; Xu, Shuhao; Marquez, Charlotte A.; Liu, Sophie N.; Fong, Dylan; Chen, Jing; Licon, Kate; Hong, Derek; Wright, Sarah N.; Kreisberg, Jason F.; Nott, Alexi; Smith, Richard D.; Qian, Wei-Jun; Swaney, Danielle L.; Iakoucheva, Lilia M.; Krogan, Nevan J.; Patrick, Gentry N.; Zhou, Yang; Feng, Guoping; Coba, Marcelo P.; Yeo, Gene W.; Ideker, Trey
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Plasma Lipid Metabolites, Clinical Glycemic Predictors, and Incident Type 2 Diabetes
err2025-01-06
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PREAI
errBegzati, Arjana; Godinez-Macias, Karla P.; Long, Tao; Watrous, Jeramie D.; Moranchel, Rafael; Kantz, Edward D.; Tuomilehto, Jaakko; Havulinna, Aki S.; Niiranen, Teemu J.; Jousilahti, Pekka; Salomaa, Veikko; Yu, Bing; Norby, Faye; Rebholz, Casey M.; Selvin, Elizabeth; Winzeler, Elizabeth A.; Cheng, Susan; Alotaibi, Mona; Goyal, Ravi; Ideker, Trey; Jain, Mohit; Majithia, Amit R.
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State of the interactomes: an evaluation of molecular networks for generating biological insights
err2024-12-09
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PREAI
errWright, Sarah N.; Colton, Scott; Schaffer, Leah, V; Pillich, Rudolf T.; Churas, Christopher; Pratt, Dexter; Ideker, Trey
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A multilineage screen identifies actionable synthetic lethal interactions in human cancers
err2024-11-18
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PREAI
errFong, Samson H.; Kuenzi, Brent M.; Mattson, Nicole M.; Lee, John; Sanchez, Kyle; Bojorquez-Gomez, Ana; Ford, Kyle; Munson, Brenton P.; Licon, Katherine; Bergendahl, Sarah; Shen, John Paul; Kreisberg, Jason F.; Mali, Prashant; Hager, Jeffrey H.; White, Michael A.; Ideker, Trey
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Putting proteins in context
err2024-10-01
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PREAI
errHu, Mengzhou; Ideker, Trey
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Prediction of immunotherapy response using mutations to cancer protein assemblies
err2024-09-20
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errOAAI
errKong, JungHo; Zhao, Xiaoyu; Singhal, Akshat; Park, Sungjoon; Bachelder, Robin; Shen, Jeanne; Zhang, Haiyu; Moon, Jimin; Ahn, Changho; Ock, Chan-Young; Carter, Hannah; Ideker, Trey
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Mapping the Multiscale Proteomic Organization of Cellular and Disease Phenotypes
err2024-08-23
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errOAAI
errCesnik, Anthony; V. Schaffer, Leah; Gaur, Ishan; Jain, Mayank; Ideker, Trey; Lundberg, Emma
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Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes
err2024-08-01
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errOAAI
errMegagiannis, Platon; Mei, Yuan; Yan, Rachel E.; Yuan, Lin; Wilde, Jonathan J.; Eckersberg, Hailey; Suresh, Rahul; Tan, Xinzhu; Chen, Hong; Farmer, W. Todd; Cha, Kuwook; Le, Phuong Uyen; Catoire, Helene; Rochefort, Daniel; Kwan, Tony; Yee, Brian A.; Dion, Patrick; Krishnaswamy, Arjun; Cloutier, Jean-Francois; Stifani, Stefano; Petrecca, Kevin; Yeo, Gene W.; Murai, Keith K.; Feng, Guoping; Rouleau, Guy A.; Ideker, Trey; Sanjana, Neville E.; Zhou, Yang
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Interface-guided phenotyping of coding variants in the transcription factor RUNX1
err2024-07-01
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errOAAI
errOzturk, Kivilcim; Panwala, Rebecca; Sheen, Jeanna; Ford, Kyle; Jayne, Nathan; Portell, Andrew; Zhang, Dong-Er; Hutter, Stephan; Haferlach, Torsten; Ideker, Trey; Mali, Prashant; Carter, Hannah
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Rare and common variants associated with alcohol consumption identify a conserved molecular network
err2024-06-21
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errOAAI
errLeger, Brittany S.; Meredith, John J.; Ideker, Trey; Sanchez-Roige, Sandra; Palmer, Abraham A.
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