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A

Avi Ma’ayan

mount sinai

86H-index
335Paper Count
5.8WCitation Count
Published Papers 144
Publication Date
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GSFM: A gene set foundation model pre-trained on a massive collection of diverse gene sets
errPatterns
IF7.4
err2026-05-21
err0
errOAAI
errDaniel J.B. Clarke; Giacomo B. Marino; Avi Ma’ayan
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ChEA-KG and ChEA-KG-TS: a network-based transcription factor enrichment analysis tool with an accompanying time-series workflow
errNucleic Acids Research
IF13.1
err2026-05-21
err0
errOAAI
errAnna I Byrd; John Erol Evangelista; Andrew Van Dusen; Daniel J B Clarke; Maha Berrada; Sherry L Jenkins; Avi Ma’ayan
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errSave
The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs
errJournal of Molecular Biology
IF4.5
err2026-01-06
err0
errOAAI
errJohn Erol Evangelista; Daniel J.B. Clarke; Anna I. Byrd; Shivaramakrishna Srinivasan; Sumana Srinivasan; Mano R. Maurya; Sherry L. Jenkins; Ido Diamant; Ethan Sanchez; Zhuorui Xie; Stephanie Olaiya; Heesu Kim; Giacomo B. Marino; Nasheath Ahmed; Srinivasan Ramachandran; Shankar Subramaniam; Avi Ma’ayan
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Molecular Signatures and Signaling Interactions of the Hair Follicle Stem Cell Niche
errJournal of Investigative Dermatology
IF5.7
err2025-12-15
err0
PREAI
errSangeeta Ghuwalewala; Jenny Cao; Amelie Rezza; Martina Rangl; Adrian Kwiatkowski; Alexia Brown; Laura Grisanti; Nicholas Heitman; Markus Schober; Zichen Wang; Avi Ma’ayan; Axel A. Almet; Maksim V. Plikus; Michael Rendl
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errSave
Creating an Interactive Web Interface for Networks Stored in Knowledge Graph Databases
errCURRENT PROTOCOLS
IF2.2
err2025-09-16
err0
errOAAI
errEvangelista, John Erol; Lutsky, Andrew D.; Byrd, Anna I.; Clarke, Daniel J. B.; Prabhakaran, Abinanda; Jenkins, Sherry L.; Ma'ayan, Avi
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Integrative analysis of lung adenocarcinoma across diverse ethnicities and exposures
errCancer Cell
IF44.5
err2025-07-31
err0
errOAAI
errShankha Satpathy; Natalie M. Clark; Yi-Ju Chen; Noshad Hosseini; Ya-Hsuan Chang; Yi Hsiao; Jonathan T. Lei; Francesca Petralia; Jin-Shing Chen; Yifat Geffen; David I. Heiman; Indranil Paul; Hanbyul Cho; Michelle Hollenberg; Giacomo B. Marino; Kuen-Tyng Lin; Rahul Mannan; C. Jackson White; Joe Allen; Shayan C. Avanessian; M. Harry Kane; Ashley Wolfe; Miloni Kinarivala; Wenke Liu; Shankara Anand; Mong-Wei Lin; Moe Haines; Erik J. Bergstrom; Grant Hussey; Ginny Xiaohe Li; Deepak C. Mani; Hao Fang; Eric J. Jaehnig; Hasmik Keshishian; Brecca Miller; Kang-Yi Su; Yi-Jing Hsiao; Hsao-Hsun Hsu; Min-Shu Hsieh; Kuo-Hsuan Hsu; Alexi Monovoukas; Simone Gohsman; John R. Thorup; Yamei Deng; Yo Akiyama; Eden Deng; Eric Sheng-Wen Chen; Azra Krek; Rodrigo Espinoza; Weiping Ma; Daniel Charytonowicz; Robert Sebra; Jyun-Hong Lin; Yan-Si Chen; Yin-Chen Hsu; Ze-Shiang Lin; Kun-Chieh Chen; Chang-Wei Yeh; Yu-Tai Wang; Alexander J. Lazar; Mehdi Mesri; Eunkyung An; Xu Zhang; Karl R. Clauser; David Fenyö; Arul M. Chinnaiyan; Bing Zhang; Li Ding; Kelly Ruggles; Chelsea Newton; Hui Zhang; Pei Wang; Galen Hostetter; Gilbert S. Omenn; Chandan Kumar-Sinha; Mathangi Thiagarajan; Ramaswamy Govindan; Paul Paik; Abhijit Parolia; Qing K. Li; Avi Ma’ayan; Gad A. Getz; Saravana M. Dhanasekaran; Ana I. Robles; Gee-Chen Chang; Pan-Chyr Yang; Sung-Liang Yu; Hsuan-Yu Chen; Alexey I. Nesvizhskii; Steven A. Carr; D.R. Mani; Marcin P. Cieslik; Yu-Ju Chen; Michael A. Gillette
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Playbook workflow builder: Interactive construction of bioinformatics workflows
errplos biology
IF3.6
err2025-04-03
err1
errOAAI
errClarke, Daniel J. B.; Evangelista, John Erol; Xie, Zhuorui; Marino, Giacomo B.; Byrd, Anna I.; Maurya, Mano R.; Srinivasan, Sumana; Yu, Keyang; Petrosyan, Varduhi; Roth, Matthew E.; Milinkov, Miroslav; King, Charles Hadley; Vora, Jeet Kiran; Keeney, Jonathon; Nemarich, Christopher; Khan, William; Lachmann, Alexander; Ahmed, Nasheath; Agris, Alexandra; Pan, Juncheng; Ramachandran, Srinivasan; Fahy, Eoin; Esquivel, Emmanuel; Mihajlovic, Aleksandar; Jevtic, Bosko; Milinovic, Vuk; Kim, Sean; McNeely, Patrick; Wang, Tianyi; Wenger, Eric; Brown, Miguel A.; Sickler, Alexander; Zhu, Yuankun; Jenkins, Sherry L.; Blood, Philip D.; Taylor, Deanne M.; Resnick, Adam C.; Mazumder, Raja; Milosavljevic, Aleksandar; Subramaniam, Shankar; Ma'ayan, Avi
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Harmonizome 3.0: integrated knowledge about genes and proteins from diverse multi-omics resources
errNUCLEIC ACIDS RESEARCH
IF13.1
err2024-11-20
err0
errOAAI
errDiamant, Ido; Clarke, Daniel J. B.; Evangelista, John Erol; Lingam, Nathania; Ma'ayan, Avi
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errSave
Causal inference can lead us to modifiable mechanisms and informative archetypes in sepsis
errINTENSIVE CARE MEDICINE
IF21.2
err2024-10-21
err0
PREAI
errBaillie, J. Kenneth; Angus, Derek; Burnham, Katie; Calandra, Thierry; Calfee, Carolyn; Gutteridge, Alex; Hacohen, Nir; Khatri, Purvesh; Langley, Raymond; Ma'ayan, Avi; Marshall, John; Maslove, David; Prescott, Hallie C.; Rowan, Kathy; Scicluna, Brendon P.; Seymour, Christopher; Shankar-Hari, Manu; Shapiro, Nathan; Wiersinga, W. Joost; Singer, Mervyn; Randolph, Adrienne G.
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errSave
RummaGEO: Automatic mining of human and mouse gene sets from GEO
errPATTERNS
IF7.4
err2024-10-01
err1
errOAAI
errMarino, Giacomo B.; Clarke, Daniel J. B.; Lachmann, Alexander; Deng, Eden Z.; Ma'ayan, Avi
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errSave
Multiomics2Targets identifies targets from cancer cohorts profiled with transcriptomics, proteomics, and phosphoproteomics
errCELL REPORTS METHODS
IF4.5
err2024-08-01
err1
errOAAI
errDeng, Eden Z.; Marino, Giacomo B.; Clarke, Daniel J. B.; Diamant, Ido; Resnick, Adam C.; Ma, Weiping; Wang, Pei; Maayan, Avi
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Rummagene: massive mining of gene sets from supporting materials of biomedical research publications
errCOMMUNICATIONS BIOLOGY
IF5.1
err2024-04-20
err4
errOAAI
errClarke, Daniel J. B.; Marino, Giacomo B.; Deng, Eden Z.; Xie, Zhuorui; Evangelista, John Erol; Ma'ayan, Avi
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errSave
Optimizing pan-cancer driver pathway analysis from patient transcriptomics and phosphoproteomics
errCANCER RESEARCH
IF16.6
err2024-03-22
err0
PREAI
errDeng, Eden Z.; Marino, Giacomo B.; Clarke, Daniel J.; Ma, Weiping; Wang, Pei; Ma'ayan, Avi
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errSave
Personalized cell surface target identification from pan-cancer RNA-seq and proteomics profiling of tumors
errCANCER RESEARCH
IF16.6
err2024-03-22
err0
PREAI
errMarino, Giacomo B.; Deng, Eden Z.; Clarke, Daniel J. B.; Ma, Weiping; Wang, Pei; Resnick, Adam C.; Ma'ayan, Avi
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errSave
A proteogenomic study of high-grade glioma among adolescents and young adults
errCANCER RESEARCH
IF16.6
err2024-03-22
err0
PREAI
errTignor, Nicole; Koptyra, Mateusz P.; Chowdhury, Shrabanti; Ma, Weiping; Rokita, Jo Lynne; Gritsenko, Marina; Song, Xiaoyu; Marino, Giacomo B.; Deng, Eden Z.; Petralia, Francesca; Krek, Azra; Rykunov, Dmitry; Leprevost, Felipe da Veiga; Hosseini, Noshad; Rathi, Komal S.; Hu, Yingwei; Migliozzi, Simona; Yaron, Tomer; Fu, Weijia; Zhang, Bo; Zhu, Yuankun; Brown, Miguel A.; Whiteaker, Jeffrey R.; Mesri, Mehdi; Robles, Ana I.; Rodland, Karin; Cantley, Lewis C.; Iavarone, Antonio; Aldape, Kenneth; Cieslik, Marcin; Nesvizhskii, Alexey I.; Ippolito, Joseph E.; Rubin, Joshua B.; Paulovich, Amanda G.; Zhang, Hui; Ma'ayan, Avi; Liu, Tao; Storm, Phillip B.; Resnick, Adam C.; Rood, Brian R.; Wang, Pei
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Programming a Ferroptosis-to-Apoptosis Transition Landscape Revealed Ferroptosis Biomarkers and Repressors for Cancer Therapy
errADVANCED SCIENCE
IF14.1
err2024-03-05
err8
errOAAI
errVinik, Yaron; Maimon, Avi; Dubey, Vinay; Raj, Harsha; Abramovitch, Ifat; Malitsky, Sergey; Itkin, Maxim; Ma'ayan, Avi; Westermann, Frank; Gottlieb, Eyal; Ruppin, Eytan; Lev, Sima
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Toxicology knowledge graph for structural birth defects
errCOMMUNICATIONS MEDICINE
IF6.3
err2023-07-17
err4
errOAAI
errEvangelista, John Erol; Clarke, Daniel J. B.; Xie, Zhuorui; Marino, Giacomo B.; Utti, Vivian; Jenkins, Sherry L.; Ahooyi, Taha Mohseni; Bologa, Cristian G.; Yang, Jeremy J.; Binder, Jessica L.; Kumar, Praveen; Lambert, Christophe G.; Grethe, Jeffrey S.; Wenger, Eric; Taylor, Deanne; Oprea, Tudor, I; de Bono, Bernard; Ma'ayan, Avi
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errSave
Systems immunology-based drug repurposing framework to target inflammation in atherosclerosis (vol 2, pg 550, 2023)
errcardiovascular research
IF10.8
err2023-07-04
err0
errOAAI
errAmadori, Letizia; Calcagno, Claudia; Fernandez, Dawn M.; Koplev, Simon; Fernandez, Nicolas; Kaur, Ravneet; Mury, Pauline; Khan, Nayaab S.; Sajja, Swathy; Shamailova, Roza; Cyr, Yannick; Jeon, Minji; Hill, Christopher A.; Chong, Peik Sean; Naidu, Sonum; Sakurai, Ken; Ghotbi, Adam Ali; Soler, Raphael; Eberhardt, Natalia; Rahman, Adeeb; Faries, Peter; Moore, Kathryn J.; Fayad, Zahi A.; Ma'ayan, Avi; Giannarelli, Chiara
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Systems immunology-based drug repurposing framework to target inflammation in atherosclerosis
errcardiovascular research
IF10.8
err2023-06-08
err13
errOAAI
errAmadori, Letizia; Calcagno, Claudia; Fernandez, Dawn M.; Koplev, Simon; Fernandez, Nicolas; Kaur, Ravneet; Mury, Pauline; Khan, Nayaab S.; Sajja, Swathy; Shamailova, Roza; Cyr, Yannick; Jeon, Minji; Hill, Christopher A.; Chong, Peik Sean; Naidu, Sonum; Sakurai, Ken; Ghotbi, Adam Ali; Soler, Raphael; Eberhardt, Natalia; Rahman, Adeeb; Faries, Peter; Moore, Kathryn J.; Fayad, Zahi A.; Ma'ayan, Avi; Giannarelli, Chiara
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Enrichr-KG: bridging enrichment analysis across multiple libraries
errNUCLEIC ACIDS RESEARCH
IF13.1
err2023-05-11
err40
errOAAI
errEvangelista, John Erol; Xie, Zhuorui; Marino, Giacomo B.; Nguyen, Nhi; Clarke, Daniel J. B.; Ma'ayan, Avi
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Research Directions

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Co-authors
Cooperation Journals
G
Gad Getz
H-index: 248 · Papers: 1.8K
G
Gordon B. Mills
H-index: 231 · Papers: 3.5K
L
Lewis C. Cantley
H-index: 214 · Papers: 1.4K
J
Joshua M. Stuart
H-index: 170 · Papers: 578
N
Nico van Rooijen
H-index: 165 · Papers: 1.0K
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