AVIS: AJAX viewer of interactive signaling networks. - Seth I. Berger; Ravi Iyengar; Avi Ma'ayan (Bioinform., 2007)

Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. - Seth I. Berger; Jeremy M. Posner; Avi Ma'ayan (BMC Bioinform., 2007)

PubMedAlertMe - Standalone Windows-based PubMed SDI software application. - Avi Ma'ayan (Comput. Biol. Medicine, 2008)

KEA: kinase enrichment analysis. - Alexander Lachmann; Avi Ma'ayan (Bioinform., 2009)

SNAVI: Desktop application for analysis and visualization of large-scale signaling networks. - Avi Ma'ayan; Sherry L. Jenkins; Ryan L. Webb; Seth I. Berger; Sudarshan P. Purushothaman; Noura S. Abul-Husn; Jeremy M. Posner; Tony Flores; Ravi Iyengar (BMC Syst. Biol., 2009)

Inferring the Sign of Kinase-Substrate Interactions by Combining Quantitative Phosphoproteomics with a Literature-Based Mammalian Kinome Network. - Marylens Hernandez; Alexander Lachmann; Shan Zhao; Kunhong Xiao; Avi Ma'ayan (BIBE, 2010)

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. - Alexander Lachmann; Huilei Xu; Jayanth Krishnan; Seth I. Berger; Amin R. Mazloom; Avi Ma'ayan (Bioinform., 2010)

GATE: software for the analysis and visualization of high-dimensional time series expression data. - Ben D. MacArthur; Alexander Lachmann; Ihor Lemischka; Avi Ma'ayan (Bioinform., 2010)

Lists2Networks: Integrated analysis of gene/protein lists. - Alexander Lachmann; Avi Ma'ayan (BMC Bioinform., 2010)

SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells. - Huilei Xu; Ihor Lemischka; Avi Ma'ayan (BMC Syst. Biol., 2010)

Visualization of Patient Samples by Dimensionality Reduction of Genome-Wide Measurements. - Huilei Xu; Avi Ma'ayan (USAB, 2011)

FNV: light-weight flash-based network and pathway viewer. - Ruth Dannenfelser; Alexander Lachmann; Mariola Szenk; Avi Ma'ayan (Bioinform., 2011)

Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes. - Amin R. Mazloom; Ruth Dannenfelser; Neil R. Clark; Arsen V. Grigoryan; Kathryn M. Linder; Timothy Cardozo; Julia C. Bond; Aislyn D. W. Boran; Ravi Iyengar; Anna Malovannaya; Rainer B. Lanz; Avi Ma'ayan (PLoS Comput. Biol., 2011)

Genes2WordCloud: a quick way to identify biological themes from gene lists and free text. - Caroline Baroukh; Sherry L. Jenkins; Ruth Dannenfelser; Avi Ma'ayan (Source Code Biol. Medicine, 2011)

Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format. - Ryan L. Webb; Avi Ma'ayan (Source Code Biol. Medicine, 2011)

Connecting clusters of patient to drug responses of cell lines to suggest personalized therapeutics for breast cancer. - Simon Gordonov; Avi Ma'ayan (BIBM Workshops, 2012)

Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers. - Edward Y. Chen; Huilei Xu; Simon Gordonov; Maribel P. Lim; Matthew H. Perkins; Avi Ma'ayan (Bioinform., 2012)

Genes2FANs: connecting genes through functional association networks. - Ruth Dannenfelser; Neil R. Clark; Avi Ma'ayan (BMC Bioinform., 2012)

Sets2Networks: network inference from repeated observations of sets. - Neil R. Clark; Ruth Dannenfelser; Christopher M. Tan; Michael E. Komosinski; Avi Ma'ayan (BMC Syst. Biol., 2012)

ChEA2: Gene-Set Libraries from ChIP-X Experiments to Decode the Transcription Regulome. - Yan Kou; Edward Y. Chen; Neil R. Clark; Qiaonan Duan; Christopher M. Tan; Avi Ma'ayan (CD-ARES, 2013)

ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells. - Huilei Xu; Caroline Baroukh; Ruth Dannenfelser; Edward Y. Chen; Christopher M. Tan; Yan Kou; Yujin E. Kim; Ihor Lemischka; Avi Ma'ayan (Database J. Biol. Databases Curation, 2013)

Network2Canvas: network visualization on a canvas with enrichment analysis. - Christopher M. Tan; Edward Y. Chen; Ruth Dannenfelser; Neil R. Clark; Avi Ma'ayan (Bioinform., 2013)

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. - Edward Y. Chen; Christopher M. Tan; Yan Kou; Qiaonan Duan; Zichen Wang 002; Gabriela Vaz Meirelles; Neil R. Clark; Avi Ma'ayan (BMC Bioinform., 2013)

Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets. - Qiaonan Duan; Zichen Wang 002; Nicolas F. Fernandez; Andrew D. Rouillard; Christopher M. Tan; Cyril H. Benes; Avi Ma'ayan (Bioinform., 2014)

The characteristic direction: a geometrical approach to identify differentially expressed genes. - Neil R. Clark; Kevin S. Hu; Axel S. Feldmann; Yan Kou; Edward Y. Chen; Qiaonan Duan; Avi Ma'ayan (BMC Bioinform., 2014)

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. - Qiaonan Duan; Corey Flynn; Mario Niepel; Marc Hafner; Jeremy Muhlich; Nicolas F. Fernandez; Andrew D. Rouillard; Christopher M. Tan; Edward Y. Chen; Todd R. Golub; Peter K. Sorger; Aravind Subramanian; et al. (Nucleic Acids Res., 2014)

Construction and Validation of a Regulatory Network for Pluripotency and Self-Renewal of Mouse Embryonic Stem Cells. - Huilei Xu; Yen-Sin Ang; Ana Sevilla; Ihor Lemischka; Avi Ma'ayan (PLoS Comput. Biol., 2014)

Principle Angle Enrichment Analysis (PAEA): Dimensionally reduced multivariate gene set enrichment analysis tool. - Neil R. Clark; Maciej Szymkiewicz; Zichen Wang 002; Caroline D. Monteiro; Matthew R. Jones; Avi Ma'ayan (BIBM, 2015)

GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions. - Gregory W. Gundersen; Matthew R. Jones; Andrew D. Rouillard; Yan Kou; Caroline D. Monteiro; Axel S. Feldmann; Kevin S. Hu; Avi Ma'ayan (Bioinform., 2015)

Dynamics of the discovery process of protein-protein interactions from low content studies. - Zichen Wang 002; Neil R. Clark; Avi Ma'ayan (BMC Syst. Biol., 2015)

Reprint of "Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction". - Andrew D. Rouillard; Zichen Wang 002; Avi Ma'ayan (Comput. Biol. Chem., 2015)

The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. - Andrew D. Rouillard; Gregory W. Gundersen; Nicolas F. Fernandez; Zichen Wang 002; Caroline D. Monteiro; Michael G. McDermott; Avi Ma'ayan (Database J. Biol. Databases Curation, 2016)

Drug-induced adverse events prediction with the LINCS L1000 data. - Zichen Wang 002; Neil R. Clark; Avi Ma'ayan (Bioinform., 2016)

GEN3VA: aggregation and analysis of gene expression signatures from related studies. - Gregory W. Gundersen; Kathleen M. Jagodnik; Holly Woodland; Nicolas F. Fernandez; Kevin Sani; Anders B. Dohlman; Peter Man-Un Ung; Caroline D. Monteiro; Avner Schlessinger; Avi Ma'ayan (BMC Bioinform., 2016)

Large Collection of Diverse Gene Set Search Queries Recapitulate Known Protein-Protein Interactions and Gene-Gene Functional Associations. - Avi Ma'ayan; Neil R. Clark (CoRR, 2016)

An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study. - Zichen Wang 002; Avi Ma'ayan (F1000Research, 2016)

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. - Maxim V. Kuleshov; Matthew R. Jones; Andrew D. Rouillard; Nicolas F. Fernandez; Qiaonan Duan; Zichen Wang 002; Simon Koplev; Sherry L. Jenkins; Kathleen M. Jagodnik; Alexander Lachmann; Michael G. McDermott; Caroline D. Monteiro; et al. (Nucleic Acids Res., 2016)

Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop. - Kathleen M. Jagodnik; Simon Koplev; Sherry L. Jenkins; Lucila Ohno-Machado; Benedict Paten; Stephan C. Schürer; Michel Dumontier; Ruben Verborgh; Alex A. T. Bui; Peipei Ping; Neil J. McKenna; Ravi K. Madduri; et al. (J. Biomed. Informatics, 2017)

Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age. - Zichen Wang 002; Li Li 062; Benjamin S. Glicksberg; Ariel Israel; Joel T. Dudley; Avi Ma'ayan (J. Biomed. Informatics, 2017)

Pharos: Collating protein information to shed light on the druggable genome. - Dac-Trung Nguyen; Stephen L. Mathias; Cristian Bologa; Søren Brunak; Nicolas F. Fernandez; Anna Gaulton; Anne Hersey; Jayme Holmes; Lars Juhl Jensen; Anneli Karlsson; Guixia Liu; Avi Ma'ayan; et al. (Nucleic Acids Res., 2017)

The Art of Connectivity Mapping. - Avi Ma'ayan (BCB, 2018)

Cell-specific prediction and application of drug-induced gene expression . - Rachel Hodos; Ping Zhang 016; Hao-Chih Lee; Qiaonan Duan; Zichen Wang 002; Neil R. Clark; Avi Ma'ayan; Fei Wang 001; Brian A. Kidd; Jianying Hu; David A. Sontag; Joel Dudley (PSB, 2018)

Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning. - Khader Shameer; Benjamin S. Glicksberg; Rachel Hodos; Kipp W. Johnson; Marcus A. Badgeley; Ben Readhead; Max S. Tomlinson; Timothy O'Connor; Riccardo Miotto; Brian A. Kidd; Rong Chen 006; Avi Ma'ayan; et al. (Briefings Bioinform., 2018)

L1000FWD: fireworks visualization of drug-induced transcriptomic signatures. - Zichen Wang 002; Alexander Lachmann; Alexandra B. Keenan; Avi Ma'ayan (Bioinform., 2018)

eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks. - Daniel J. B. Clarke; Maxim V. Kuleshov; Brian M. Schilder; Denis Torre; Mary E. Duffy; Alexandra B. Keenan; Alexander Lachmann; Axel S. Feldmann; Gregory W. Gundersen; Moshe C. Silverstein; Zichen Wang 002; Avi Ma'ayan (Nucleic Acids Res., 2018)

Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data. - Amar Koleti; Raymond Terryn; Vasileios Stathias; Caty Chung; Daniel J. Cooper; John Paul Turner; Dusica Vidovic; Michele Forlin; Tanya T. Kelley; Alessandro D'Urso; Bryce K. Allen; Denis Torre; et al. (Nucleic Acids Res., 2018)

Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition. - Simon Koplev; Katie Lin; Anders B. Dohlman; Avi Ma'ayan (PLoS Comput. Biol., 2018)

Predicting opioid dependence from electronic health records with machine learning. - Randall J. Ellis; Zichen Wang 002; Nicholas Genes; Avi Ma'ayan (BioData Min., 2019)

Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures. - Zichen Wang 002; Edward He 002; Kevin Sani; Kathleen M. Jagodnik; Moshe C. Silverstein; Avi Ma'ayan (Bioinform., 2019)

ChEA3: transcription factor enrichment analysis by orthogonal omics integration. - Alexandra B. Keenan; Denis Torre; Alexander Lachmann; Ariel K. Leong; Megan L. Wojciechowicz; Vivian Utti; Kathleen M. Jagodnik; Eryk Kropiwnicki; Zichen Wang 002; Avi Ma'ayan (Nucleic Acids Res., 2019)

modEnrichr: a suite of gene set enrichment analysis tools for model organisms. - Maxim V. Kuleshov; Jennifer E. L. Diaz; Zachary N. Flamholz; Alexandra B. Keenan; Alexander Lachmann; Megan L. Wojciechowicz; Ross L. Cagan; Avi Ma'ayan (Nucleic Acids Res., 2019)

Geneshot: search engine for ranking genes from arbitrary text queries. - Alexander Lachmann; Brian M. Schilder; Megan L. Wojciechowicz; Denis Torre; Maxim V. Kuleshov; Alexandra B. Keenan; Avi Ma'ayan (Nucleic Acids Res., 2019)

EnrichrBot: Twitter bot tracking tweets about human genes. - Alon Bartal; Alexander Lachmann; Daniel J. B. Clarke; Allison H. Seiden; Kathleen M. Jagodnik; Avi Ma'ayan (Bioinform., 2020)

piNET: a versatile web platform for downstream analysis and visualization of proteomics data. - Behrouz Shamsaei; Szymon Chojnacki; Marcin Pilarczyk; Mehdi Fazel-Najafabadi; Wen Niu; Chuming Chen; Karen Ross; Andrea Matlock; Jeremy Muhlich; Somchai Chutipongtanate; Jie Zheng 001; John Turner; et al. (Nucleic Acids Res., 2020)

LINCS Data Portal 2.0: next generation access point for perturbation-response signatures. - Vasileios Stathias; John Paul Turner; Amar Koleti; Dusica Vidovic; Daniel J. Cooper; Mehdi Fazel-Najafabadi; Marcin Pilarczyk; Raymond Terryn; Caty Chung; Afoma Umeano; Daniel J. B. Clarke; Alexander Lachmann; et al. (Nucleic Acids Res., 2020)

The COVID-19 Drug and Gene Set Library. - Maxim V. Kuleshov; Daniel J. Stein; Daniel J. B. Clarke; Eryk Kropiwnicki; Kathleen M. Jagodnik; Alon Bartal; John Erol Evangelista; Jason Hom; Minxuan Cheng; Allison Bailey; Abigail Zhou; Laura B. Ferguson; et al. (Patterns, 2020)

Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning. - Eryk Kropiwnicki; John Erol Evangelista; Daniel J. Stein; Daniel J. B. Clarke; Alexander Lachmann; Maxim V. Kuleshov; Minji Jeon; Kathleen M. Jagodnik; Avi Ma'ayan (Database J. Biol. Databases Curation, 2021)

KEA3: improved kinase enrichment analysis via data integration. - Maxim V. Kuleshov; Zhuorui Xie; Alexandra B. K. London; Janice Yang; John Erol Evangelista; Alexander Lachmann; Ingrid Shu; Denis Torre; Avi Ma'ayan (Nucleic Acids Res., 2021)

Appyters: Turning Jupyter Notebooks into data-driven web apps. - Daniel J. B. Clarke; Minji Jeon; Daniel J. Stein; Nicole Moiseyev; Eryk Kropiwnicki; Charles Dai; Zhuorui Xie; Megan L. Wojciechowicz; Skylar Litz; Jason Hom; John Erol Evangelista; Lucas Goldman; et al. (Patterns, 2021)

blitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation. - Alexander Lachmann; Zhuorui Xie; Avi Ma'ayan (Bioinform., 2022)

Transforming L1000 profiles to RNA-seq-like profiles with deep learning. - Minji Jeon; Zhuorui Xie; John Erol Evangelista; Megan L. Wojciechowicz; Daniel J. B. Clarke; Avi Ma'ayan (BMC Bioinform., 2022)

DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules. - Eryk Kropiwnicki; Alexander Lachmann; Daniel J. B. Clarke; Zhuorui Xie; Kathleen M. Jagodnik; Avi Ma'ayan (BMC Bioinform., 2022)

SigCom LINCS: data and metadata search engine for a million gene expression signatures. - John Erol Evangelista; Daniel J. B. Clarke; Zhuorui Xie; Alexander Lachmann; Minji Jeon; Kerwin Chen; Kathleen M. Jagodnik; Sherry L. Jenkins; Maxim V. Kuleshov; Megan L. Wojciechowicz; Stephan C. Schürer; Mario Medvedovic; et al. (Nucleic Acids Res., 2022)

lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs. - Giacomo B. Marino; Megan L. Wojciechowicz; Daniel J. B. Clarke; Maxim V. Kuleshov; Zhuorui Xie; Minji Jeon; Alexander Lachmann; Avi Ma'ayan (Database J. Biol. Databases Curation, 2023)

Enrichr-KG: bridging enrichment analysis across multiple libraries. - John Erol Evangelista; Zhuorui Xie; Giacomo B. Marino; Nhi Nguyen; Daniel J. B. Clarke; Avi Ma'ayan (Nucleic Acids Res., 2023)

GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery. - Giacomo B. Marino; Michael Ngai; Daniel J. B. Clarke; Reid H. Fleishman; Eden Z. Deng; Zhuorui Xie; Nasheath Ahmed; Avi Ma'ayan (Nucleic Acids Res., 2023)

RummaGEO: Automatic mining of human and mouse gene sets from GEO. - Giacomo B. Marino; Daniel J. B. Clarke; Alexander Lachmann; Eden Z. Deng; Avi Ma'ayan (Patterns, 2024)

Playbook workflow builder: Interactive construction of bioinformatics workflows. - Daniel J. B. Clarke; John Erol Evangelista; Zhuorui Xie; Giacomo B. Marino; Anna I. Byrd; Mano Ram Maurya; Sumana Srinivasan; Keyang Yu; Varduhi Petrosyan; Matthew E. Roth; Miroslav Milinkov; Charles Hadley King; et al. (PLoS Comput. Biol., 2025)