Trey Ideker

120.6k citations

246 papers · 66.9k indexed · 19 hit papers · h-index 81

Impact in

Molecular Biology top 0.01%
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Gene Regulatory Network Analysis
- Microbial Metabolic Engineering and Bioproduction
- Epigenetics and DNA Methylation
- RNA modifications and cancer
Aging top 0.1%

Papers in

Aging 6
Biophysics 18

Co-authors: Owen Ozier Benno Schwikowski Nitin S. Baliga Paul Shannon Nada Amin Daniel Ramage Keiichiro Ono Pengliang Wang
Journals: Bioinformatics (17 papers)Molecular Cell (14 papers)Proceedings of the National Academy of Sciences (9 papers)Genome biology (8 papers)Cell Systems (8 papers)
Partner nations: United States Israel Germany

In The Last Decade

Trey Ideker

242 papers receiving 65.9k citations

Hit Papers

15 papers align trajectories log scale

Predicting Drug Response and Synergy Using a Deep Learning Model of Human Cancer Cells 2020 · 285 citations

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if any of the following hold:

it has ≥500 total citations;
it reaches ≥1.5× the top-1% citation threshold for papers in the same subfield and year (the threshold is the minimum needed to enter the top 1%, not the average within it);
it reaches the top citation threshold in at least one of its specific research topics.

2020 Cancer Cell
2018 Molecular Cell
2017 Nature Reviews Genetics
2013 Nature Reviews Genetics
2013 Nature Methods
2013 eLife
2012 Molecular Systems Biology
2012 Nature Methods
2012 Molecular Cell
2011 Cytoscape 2.8: new features for data integration and network
2010 Bioinformatics
2008 Genome Research
2007 Molecular Systems Biology
2005 Proceedings of the National Academy of Sciences
2003 Genome Research
2002 Bioinformatics
2002 Molecular & Cellular Proteomics
2001 Annual Review of Genomics and Human Genetics
2001 Science

Peers

Countries citing papers authored by Trey Ideker

Since Specialization

Citations

This map shows the geographic impact of Trey Ideker's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Trey Ideker with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Trey Ideker more than expected).

Fields of papers citing papers by Trey Ideker

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Trey Ideker. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Trey Ideker. The network helps show where Trey Ideker may publish in the future.

Co-authors

The 25 scholars most cited alongside Trey Ideker, linked wherever they have co-authored with each other. Click a name or a connecting line to browse the papers they share.

Border = papers with Trey Ideker Line = papers co-authored together Trey Ideker links everyone, so they are left out of the graph.

All Works

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20 of 20 papers shown

#	Work
1	Rare and common variants associated with alcohol consumption identify a conserved molecular network Alcohol Clinical and Experimental Research ·Catalina Popescu, 周東森照, Trey Ideker, Sandra Sanchez‐Roige, Abraham A. Palmer	2024	1
2	A deep learning model of tumor cell architecture elucidates response and resistance to CDK4/6 inhibitors Nature Cancer ·Kristina Zdolec, Sidra Hassan, Niemen Tayebi, Marcus R. Kelly, Archam Zahidin, Yong-Ping Kang, Takushi Takada, Samson Fong, John J. Y. Lee, Xiaoyu Zhao, Robin E. Bachelder, Barbara A. Parker, Kay T. Yeung, Trey Ideker	2024	20
3	Cancer Mutations Converge on a Collection of Protein Assemblies to Predict Resistance to Replication Stress Cancer Discovery ·Xiaoyu Zhao, Niemen Tayebi, Kristina Zdolec, JungHo Kong, Robin E. Bachelder, Trey Ideker	2024	15
4	De novo generation of multi-target compounds using deep generative chemistry Nature Communications ·Y Goth, Mike Y. Chen, Конкина Юлия Александровна, Jason F. Kreisberg, Katherine Licon, Ruben Abagyan, Brent M. Kuenzi, Trey Ideker	2024	38
5	Opportunities for basic, clinical, and bioethics research at the intersection of machine learning and genomics Cell Genomics ·Shurjo K. Sen, Eric D. Green, Carolyn M. Hutter, Mark Craven, Trey Ideker, Valentina Di Francesco	2023	5
6	GABA Regulates Electrical Activity and Tumor Initiation in Melanoma Cancer Discovery ·Mohita Tagore, Ton Crijnen, Rashad L. Reid, Nelly M. Cruz, Laura Menocal, Shruthy Suresh, Eric Chan, Maayan Baron, 明夫原田, Alec Chunta, Walid K. Chatila, Jérémie Nsengimana, Richard P. Koche, Travis J. Hollmann, Trey Ideker, Lorenz Studer, Andrea Schietinger, Richard M. White	2023	24
7	Understudied proteins: opportunities and challenges for functional proteomics Nature Methods ·Georg Kustatscher, Tom Collins, Anne‐Claude Gingras, Tiannan Guo, Henning Hermjakob, Trey Ideker, Kathryn S. Lilley, Emma Lundberg, Edward M. Marcotte, Markus Ralser, Juri Rappsilber	2022	110
8	Unveiling Complexity and Multipotentiality of Early Heart Fields Circulation Research ·Qingquan Zhang, Daniel E. Carlin, Fugui Zhu, Paola Cattaneo, Trey Ideker, Sylvia Μ. Evans, Joshua Bloomekatz, C. Neil	2021	55
9	Thousands of missing variants in the UK Biobank are recoverable by genome realignment Annals of Human Genetics ·Jurgen Spieb, Y Goth, Hana Lango Allen, Trey Ideker, Amit R. Majithia	2020	12
10	Predicting Drug Response and Synergy Using a Deep Learning Model of Human Cancer Cells Cancer Cell ·Brent M. Kuenzi, Jisoo Park, Samson Fong, Kyle S. Sanchez, John J. Y. Lee, Jason F. Kreisberg, Jianzhu Ma, Trey Ideker Hit paper breakdown →	2020	285
11	Disruption of NSD1 in Head and Neck Cancer Promotes Favorable Chemotherapeutic Responses Linked to Hypomethylation Molecular Cancer Therapeutics ·Nam Q. Bui, Justin K. Huang, Ana Bojorquez-Gomez, Katherine Licon, Kyle S. Sanchez, Чистякова Ирина Александровна, Alexandra Beckett, Tina Wang, Wei Zhang, John Paul Shen, Jason F. Kreisberg, Trey Ideker	2018	50
12	Dot1 promotes H2B ubiquitination by a methyltransferase-independent mechanism Nucleic Acids Research ·Tibor van Welsem, María Olga Álvarez Huerta, Reggy Ekkebus, Μιχαήλ Ζησίου, Francesco Antonio Astore, Jeong-Hong Kim, Vijay Sharathi Jayakumar, Su Ming Sun, Tineke L. Lenstra, Rohith Srivas, Trey Ideker, Frank C. P. Holstege, Haico van Attikum, Farid El Oualid, Huib Ovaa, I.J.E. Stulemeijer, Hanneke Vlaming, Fred van Leeuwen	2018	26
13	Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus–Host Protein Network Cancer Discovery ·Manon Eckhardt, Wei Zhang, Andrew M. Gross, John Von Dollen, Jeffrey R. Johnson, Kathleen E. Franks-Skiba, Danielle L. Swaney, Tasha L. Johnson, Gwendolyn Μ. Jang, Priya S. Shah, Toni M. Brand, Jacques Archambault, Jason F. Kreisberg, Jennifer R. Grandis, Trey Ideker, Nevan J. Krogan	2018	63
14	Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer Cancer Discovery ·Hannah Carter, Rachel Marty, Matan Hofree, Andrew M. Gross, James Jensen, Kathleen M. Fisch, Xingyu Wu, Christopher DeBoever, Eric L. Van Nostrand, Yan Song, Emily C. Wheeler, Jason F. Kreisberg, Scott M. Lippman, G Yeo, J. Silvio Gutkind, Trey Ideker	2017	87
15	NDEx 2.0: A Clearinghouse for Research on Cancer Pathways Cancer Research ·Dexter Pratt, Jing Chen, Rudolf Pillich, Vladimir Rynkov, Gossie M. Powae, Barry Demchak, Trey Ideker	2017	38
16	Challenges in identifying cancer genes by analysis of exome sequencing data Nature Communications ·Matan Hofree, Hannah Carter, Jason F. Kreisberg, Sourav Bandyopadhyay, Paul S. Mischel, Stephen Friend, Trey Ideker	2016	29
17	Combined TP53 mutation/3p loss correlates with decreased radiosensitivity and increased matrix-metalloproteinase activity in head and neck carcinoma Oral Oncology ·K Ohgushi, Samantha J. Hauff, My Nguyen Thi Xuan, Ryan K. Orosco, Andrew M. Gross, Linda Nguyen, J. Vahidibenehkohal, William J. Moss, Michael Whitney, Ezra E.W. Cohen, Scott M. Lippman, Roger Y. Tsien, Trey Ideker, Sunil J. Advani, Quyen T. Nguyen	2015	15
18	Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p Proceedings of the National Academy of Sciences ·Joel F. Moxley, Michael C. Jewett, Maciek R. Antoniewicz, Silas G. Villas‐Bôas, Hal S. Alper, Robert T. Wheeler, L. Tong, Alan G. Hinnebusch, Trey Ideker, Jens Nielsen, Gregory Stephanopoulos	2009	129
19	A systems approach to delineate functions of paralogous transcription factors: Role of the Yap family in the DNA damage response Proceedings of the National Academy of Sciences ·Kai Tan, Maura Ysela, Colin Luo, Carmen Cobos Lama, Timothy Ravasi, Trey Ideker	2008	49
20	Conserved patterns of protein interaction in multiple species Proceedings of the National Academy of Sciences ·Roded Sharan, Silpa Suthram, Ryan Kelley, Riri Agnestri, Scott McCuine, Peter Uetz, Taylor Sittler, Richard M. Karp, Trey Ideker Hit paper breakdown →	2005	507

About Trey Ideker

Trey Ideker is a scholar working on Aging, Biophysics, Molecular Biology, Cancer Research and Computational Theory and Mathematics, having authored 246 papers that have together received 66.9k indexed citations. Recurring topics across this work include Bioinformatics and Genomic Networks (106 papers), Gene Regulatory Network Analysis (36 papers), Microbial Metabolic Engineering and Bioproduction (33 papers), Fungal and yeast genetics research (31 papers), Gene expression and cancer classification (26 papers), Cancer Genomics and Diagnostics (25 papers), Computational Drug Discovery Methods (25 papers) and Genomics and Chromatin Dynamics (21 papers). The work is most often cited by research in Molecular Biology (46.8k citations), Aging (1.0k citations), Cancer Research (8.2k citations), Computational Theory and Mathematics (5.0k citations) and Genetics (6.4k citations). Trey Ideker has collaborated with scholars based in United States, Israel and Germany. Frequent co-authors include Owen Ozier, Benno Schwikowski, Nitin S. Baliga, Paul Shannon, Nada Amin, Daniel Ramage, Keiichiro Ono, Pengliang Wang, Roded Sharan and Michael Smoot. Their work appears in journals such as Bioinformatics, Molecular Cell, Proceedings of the National Academy of Sciences, Genome biology and Cell Systems.

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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