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个人简介
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.
研究兴趣
论文共 483 篇作者统计合作学者相似作者
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Cancer Researchno. 6_Supplement (2024): 2348-2348
Timothy Clark, Jillian Mohan,Leah Schaffer,Kirsten Obernier,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 Brandt,Jake Chen, Ying Ding,Samah Fodeh,Nevan Krogan,Emma Lundberg,Prashant Mali,Pamela Payne-Foster,Sarah Ratcliffe, Vardit Ravitsky,Andrej Sali,Wade Schulz,Trey Ideker
bioRxiv : the preprint server for biology (2024)
Cancer Researchno. 6_Supplement (2024): 7383-7383
JungHo Kong, Xiaoyu Zhao,Akshat Singhal,Sungjoon Park, Robin Bachelder,Jeanne Shen,Haiyu Zhang, Jimin Moon, Changho Ahn,Chan-Young Ock,Hannah Carter,Trey Ideker
Science advancesno. 38 (2024): eado9746-eado9746
Annual review of biomedical data science (2024)
Bioinformatics (Oxford, England)no. Suppl 2 (2024): ii105-ii110
Mingjia Huo, Han Guo,Xingyi Cheng, Digvijay Singh, Hamidreza Rahmani,Shen Li, Philipp Gerlof,Trey Ideker, Danielle A. Grotjahn, Elizabeth Villa,Le Song,Pengtao Xie
biorxiv(2024)
CANCER DISCOVERYno. 3 (2024): 508-523
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作者统计
#Papers: 483
#Citation: 109998
H-Index: 102
G-Index: 331
Sociability: 8
Diversity: 0
Activity: 3
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