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Ideker’s research laboratory has led seminal studies establishing the theory and practice of systems biology, including systematic techniques for elucidating human cell architecture and its molecular networks. From 2001–present, his laboratory produced numerous maps of protein-protein, transcriptional, and genetic networks in model organisms and humans (in collaboration with trainees and co-investigators), along with widely used Cytoscape network analysis software (with Gary Bader and others). His studies introduced core concepts in bioinformatics, including generation of transcriptional networks to explain genome-wide expression patterns (with Leroy Hood), network alignment and evolutionary comparison (with Richard Karp and Roded Sharan), and network biomarkers, which enable multigenic definitions of patient subtypes and treatment responses. He also introduced experimental mapping techniques, including synthetic-lethal interaction mapping with CRISPR/Cas9 (with Prashant Mali) and characterization of differential interactions across conditions and time (with Nevan Krogan). These technologies have broadly informed the mechanisms by which diverse genetic alterations drive cancer, neurological disorders, and drug resistance. Recently, Ideker and Emma Lundberg demonstrated an end-to-end pipeline for mapping the structure of human cells over a broad scale range (10–9 to 10–5 m) based on fusion of protein networks with immunofluorescence imaging. Ideker has also recently shown that network maps provide a substrate for deep learning models of cell structure and function, with basic implications for the construction of intelligent systems in precision medicine (with Jianzhu Ma and co-investigators). Finally, Ideker and collaborators showed that large parts of the methylome are remodeled with age, leading to the first epigenetic clock and the rapidly expanding field of epigenetic aging.
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论文共 440 篇作者统计合作学者相似作者
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Leah V. Schaffer, Mengzhou Hu,Edward L. Huttlin, Gege Qian, Abantika Pal,Neelesh Soni, Andrew Latham,Laura Pontano Vaites,Trang Le,Yue Qin,Christopher Churas,Dexter Pratt,
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Kivilcim Ozturk,Rebecca Panwala, Jeanna Sheen,Kyle Ford, Nathan Jayne,Dong-Er Zhang, Stephan Hutter, Torsten Haferlach,Trey Ideker,Prashant Mali,Hannah Carter
Cancer Researchno. 6_Supplement (2024): 4899-4899
Mengzhou Hu,Leah V. Schaffer,Edward L. Huttlin, Gege Qian, Andrew Latham, Abantika Pal,Laura Pontano Vaites,Trang Le,Yue Qin,Christopher Churas,Dexter Pratt,Robin Bachelder,
Cancer Researchno. 6_Supplement (2024): 6543-6543
Cancer Researchno. 6_Supplement (2024): 4918-4918
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 C Lasser,
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 Bachelder,Barbara A. Parker,
Gege Qian,Leah Schaffer,Kyung-Mee Moon,Leonard Foster,Trey Ideker, Mengzhou Hu, Sahar Alkhairy, Emma Lundberg
Cancer Researchno. 6_Supplement (2024): 7101-7101
CELL GENOMICSno. 1 (2024): 100466-100466
Sungjoon Park,Erica Silva,Akshat Singhal,Marcus R. Kelly,Kate Licon, Isabella Panagiotou, Catalina Fogg,Samson Fong,John J. Y. Lee,Xiaoyu Zhao, Robin Bachelder,Barbara A. Parker,
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