Avi Ma'ayan

Publication Activity (10 Years)

Years Active: 2007-2023
Publications (10 Years): 35

Top Topics

Gene Expression

Top Venues

Nucleic Acids Res.

Database J. Biol. Databases Curation

Publications

John Erol Evangelista, Zhuorui Xie, Giacomo B. Marino, Nhi Nguyen, Daniel J. B. Clarke, Avi Ma'ayan
Enrichr-KG: bridging enrichment analysis across multiple libraries. Nucleic Acids Res. 51 (W1) (2023)
Giacomo B. Marino, Michael Ngai, Daniel J. B. Clarke, Reid H. Fleishman, Eden Z. Deng, Zhuorui Xie, Nasheath Ahmed, Avi Ma'ayan
GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery. Nucleic Acids Res. 51 (W1) (2023)
Giacomo B. Marino, Megan L. Wojciechowicz, Daniel J. B. Clarke, Maxim V. Kuleshov, Zhuorui Xie, Minji Jeon, Alexander Lachmann, Avi Ma'ayan
lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs. Database J. Biol. Databases Curation 2023 (2023)
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, Avi Ma'ayan
SigCom LINCS: data and metadata search engine for a million gene expression signatures. Nucleic Acids Res. 50 (W1) (2022)
Minji Jeon, Zhuorui Xie, John Erol Evangelista, Megan L. Wojciechowicz, Daniel J. B. Clarke, Avi Ma'ayan
Transforming L1000 profiles to RNA-seq-like profiles with deep learning. BMC Bioinform. 23 (1) (2022)
Alexander Lachmann, Zhuorui Xie, Avi Ma'ayan
blitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation. Bioinform. 38 (8) (2022)
Eryk Kropiwnicki, Alexander Lachmann, Daniel J. B. Clarke, Zhuorui Xie, Kathleen M. Jagodnik, Avi Ma'ayan
DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules. BMC Bioinform. 23 (1) (2022)
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, Serena Zhang, Christine Yoon, Tahmid Ahamed, Samantha Bhuiyan, Minxuan Cheng, Julie Karam, Kathleen M. Jagodnik, Ingrid Shu, Alexander Lachmann, Sam Ayling, Sherry L. Jenkins, Avi Ma'ayan
Appyters: Turning Jupyter Notebooks into data-driven web apps. Patterns 2 (3) (2021)
Maxim V. Kuleshov, Zhuorui Xie, Alexandra B. K. London, Janice Yang, John Erol Evangelista, Alexander Lachmann, Ingrid Shu, Denis Torre, Avi Ma'ayan
KEA3: improved kinase enrichment analysis via data integration. Nucleic Acids Res. 49 (Webserver-Issue) (2021)
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
Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning. Database J. Biol. Databases Curation 2021 (2021)
Alon Bartal, Alexander Lachmann, Daniel J. B. Clarke, Allison H. Seiden, Kathleen M. Jagodnik, Avi Ma'ayan
EnrichrBot: Twitter bot tracking tweets about human genes. Bioinform. 36 (12) (2020)
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, Alexander Lachmann, Avi Ma'ayan
The COVID-19 Drug and Gene Set Library. Patterns 1 (6) (2020)
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, John Erol Evangelista, Avi Ma'ayan, Mario Medvedovic, Stephan C. Schürer
LINCS Data Portal 2.0: next generation access point for perturbation-response signatures. Nucleic Acids Res. 48 (Database-Issue) (2020)
Behrouz Shamsaei, Szymon Chojnacki, Marcin Pilarczyk, Mehdi Fazel-Najafabadi, Wen Niu, Chuming Chen, Karen Ross, Andrea Matlock, Jeremy Muhlich, Somchai Chutipongtanate, Jie Zheng, John Turner, Dusica Vidovic, Jake Jaffe, Michael J. MacCoss, Cathy Wu, Ajay Pillai, Avi Ma'ayan, Stephan C. Schürer, Michal Kouril, Mario Medvedovic, Jarek Meller
piNET: a versatile web platform for downstream analysis and visualization of proteomics data. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
Alexandra B. Keenan, Denis Torre, Alexander Lachmann, Ariel K. Leong, Megan L. Wojciechowicz, Vivian Utti, Kathleen M. Jagodnik, Eryk Kropiwnicki, Zichen Wang, Avi Ma'ayan
ChEA3: transcription factor enrichment analysis by orthogonal omics integration. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Alexander Lachmann, Brian M. Schilder, Megan L. Wojciechowicz, Denis Torre, Maxim V. Kuleshov, Alexandra B. Keenan, Avi Ma'ayan
Geneshot: search engine for ranking genes from arbitrary text queries. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Randall J. Ellis, Zichen Wang, Nicholas Genes, Avi Ma'ayan
Predicting opioid dependence from electronic health records with machine learning. BioData Min. 12 (1) (2019)
Zichen Wang, Edward He, Kevin Sani, Kathleen M. Jagodnik, Moshe C. Silverstein, Avi Ma'ayan
Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures. Bioinform. 35 (7) (2019)
Maxim V. Kuleshov, Jennifer E. L. Diaz, Zachary N. Flamholz, Alexandra B. Keenan, Alexander Lachmann, Megan L. Wojciechowicz, Ross L. Cagan, Avi Ma'ayan
modEnrichr: a suite of gene set enrichment analysis tools for model organisms. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Rachel Hodos, Ping Zhang, Hao-Chih Lee, Qiaonan Duan, Zichen Wang, Neil R. Clark, Avi Ma'ayan, Fei Wang, Brian A. Kidd, Jianying Hu, David A. Sontag, Joel Dudley
Cell-specific prediction and application of drug-induced gene expression . PSB (2018)
Simon Koplev, Katie Lin, Anders B. Dohlman, Avi Ma'ayan
Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition. PLoS Comput. Biol. 14 (1) (2018)
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, Kathleen M. Jagodnik, Lily Wang, Sherry L. Jenkins, Christopher Mader, Wen Niu, Mehdi Fazel, Naim Al Mahi, Marcin Pilarczyk, Nicholas A. Clark, Behrouz Shamsaei, Jarek Meller, Juozas Vasiliauskas, John Reichard, Mario Medvedovic, Avi Ma'ayan, Ajay Pillai, Stephan C. Schürer
Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data. Nucleic Acids Res. 46 (Database-Issue) (2018)
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, Avi Ma'ayan
eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Zichen Wang, Alexander Lachmann, Alexandra B. Keenan, Avi Ma'ayan
L1000FWD: fireworks visualization of drug-induced transcriptomic signatures. Bioinform. 34 (12) (2018)
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, Avi Ma'ayan, Joel T. Dudley
Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning. Briefings Bioinform. 19 (4) (2018)
Avi Ma'ayan
The Art of Connectivity Mapping. BCB (2018)
Kathleen M. Jagodnik, Simon Koplev, Sherry L. Jenkins, Lucila Ohno-Machado, Benedict Paten, Stephan C. Schürer, Michel Dumontier, Ruben Verborgh, Alex Bui, Peipei Ping, Neil J. McKenna, Ravi K. Madduri, Ajay Pillai, Avi Ma'ayan
Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop. J. Biomed. Informatics 71 (2017)
Zichen Wang, Li Li, Benjamin S. Glicksberg, Ariel Israel, Joel T. Dudley, Avi Ma'ayan
Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age. J. Biomed. Informatics 76 (2017)
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, Geetha Mandava, Subramani Mani, Saurabh Mehta, John P. Overington, Juhee Patel, Andrew D. Rouillard, Stephan C. Schürer, Timothy Sheils, Anton Simeonov, Larry A. Sklar, Noel Southall, Oleg Ursu, Dusica Vidovic, Anna Waller, Jeremy J. Yang, Ajit Jadhav, Tudor I. Oprea, Rajarshi Guha
Pharos: Collating protein information to shed light on the druggable genome. Nucleic Acids Res. 45 (Database-Issue) (2017)
Avi Ma'ayan, Neil R. Clark
Large Collection of Diverse Gene Set Search Queries Recapitulate Known Protein-Protein Interactions and Gene-Gene Functional Associations. CoRR (2016)
Zichen Wang, Neil R. Clark, Avi Ma'ayan
Drug-induced adverse events prediction with the LINCS L1000 data. Bioinform. 32 (15) (2016)
Zichen Wang, Avi Ma'ayan
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study. F1000Research 5 (2016)
Andrew D. Rouillard, Gregory W. Gundersen, Nicolas F. Fernandez, Zichen Wang, Caroline D. Monteiro, Michael G. McDermott, Avi Ma'ayan
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database J. Biol. Databases Curation 2016 (2016)
Maxim V. Kuleshov, Matthew R. Jones, Andrew D. Rouillard, Nicolas F. Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L. Jenkins, Kathleen M. Jagodnik, Alexander Lachmann, Michael G. McDermott, Caroline D. Monteiro, Gregory W. Gundersen, Avi Ma'ayan
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
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
GEN3VA: aggregation and analysis of gene expression signatures from related studies. BMC Bioinform. 17 (2016)
Gregory W. Gundersen, Matthew R. Jones, Andrew D. Rouillard, Yan Kou, Caroline D. Monteiro, Axel S. Feldmann, Kevin S. Hu, Avi Ma'ayan
GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions. Bioinform. 31 (18) (2015)
Zichen Wang, Neil R. Clark, Avi Ma'ayan
Dynamics of the discovery process of protein-protein interactions from low content studies. BMC Syst. Biol. 9 (2015)
Neil R. Clark, Maciej Szymkiewicz, Zichen Wang, Caroline D. Monteiro, Matthew R. Jones, Avi Ma'ayan
Principle Angle Enrichment Analysis (PAEA): Dimensionally reduced multivariate gene set enrichment analysis tool. BIBM (2015)
Andrew D. Rouillard, Zichen Wang, Avi Ma'ayan
Reprint of "Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction". Comput. Biol. Chem. 59 (2015)
Qiaonan Duan, Zichen Wang, Nicolas F. Fernandez, Andrew D. Rouillard, Christopher M. Tan, Cyril H. Benes, Avi Ma'ayan
Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets. Bioinform. 30 (22) (2014)
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, Avi Ma'ayan
LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
Huilei Xu, Yen-Sin Ang, Ana Sevilla, Ihor Lemischka, Avi Ma'ayan
Construction and Validation of a Regulatory Network for Pluripotency and Self-Renewal of Mouse Embryonic Stem Cells. PLoS Comput. Biol. 10 (8) (2014)
Neil R. Clark, Kevin S. Hu, Axel S. Feldmann, Yan Kou, Edward Y. Chen, Qiaonan Duan, Avi Ma'ayan
The characteristic direction: a geometrical approach to identify differentially expressed genes. BMC Bioinform. 15 (2014)
Huilei Xu, Caroline Baroukh, Ruth Dannenfelser, Edward Y. Chen, Christopher M. Tan, Yan Kou, Yujin E. Kim, Ihor Lemischka, Avi Ma'ayan
ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells. Database J. Biol. Databases Curation 2013 (2013)
Edward Y. Chen, Christopher M. Tan, Yan Kou, Qiaonan Duan, Zichen Wang, Gabriela Vaz Meirelles, Neil R. Clark, Avi Ma'ayan
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinform. 14 (2013)
Christopher M. Tan, Edward Y. Chen, Ruth Dannenfelser, Neil R. Clark, Avi Ma'ayan
Network2Canvas: network visualization on a canvas with enrichment analysis. Bioinform. 29 (15) (2013)
Yan Kou, Edward Y. Chen, Neil R. Clark, Qiaonan Duan, Christopher M. Tan, Avi Ma'ayan
ChEA2: Gene-Set Libraries from ChIP-X Experiments to Decode the Transcription Regulome. CD-ARES (2013)
Neil R. Clark, Ruth Dannenfelser, Christopher M. Tan, Michael E. Komosinski, Avi Ma'ayan
Sets2Networks: network inference from repeated observations of sets. BMC Syst. Biol. 6 (2012)
Ruth Dannenfelser, Neil R. Clark, Avi Ma'ayan
Genes2FANs: connecting genes through functional association networks. BMC Bioinform. 13 (2012)
Edward Y. Chen, Huilei Xu, Simon Gordonov, Maribel P. Lim, Matthew H. Perkins, Avi Ma'ayan
Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers. Bioinform. 28 (1) (2012)
Simon Gordonov, Avi Ma'ayan
Connecting clusters of patient to drug responses of cell lines to suggest personalized therapeutics for breast cancer. BIBM Workshops (2012)
Caroline Baroukh, Sherry L. Jenkins, Ruth Dannenfelser, Avi Ma'ayan
Genes2WordCloud: a quick way to identify biological themes from gene lists and free text. Source Code Biol. Medicine 6 (2011)
Huilei Xu, Avi Ma'ayan
Visualization of Patient Samples by Dimensionality Reduction of Genome-Wide Measurements. USAB (2011)
Ruth Dannenfelser, Alexander Lachmann, Mariola Szenk, Avi Ma'ayan
FNV: light-weight flash-based network and pathway viewer. Bioinform. 27 (8) (2011)
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
Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes. PLoS Comput. Biol. 7 (12) (2011)
Ryan L. Webb, Avi Ma'ayan
Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format. Source Code Biol. Medicine 6 (2011)
Alexander Lachmann, Huilei Xu, Jayanth Krishnan, Seth I. Berger, Amin R. Mazloom, Avi Ma'ayan
ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinform. 26 (19) (2010)
Alexander Lachmann, Avi Ma'ayan
Lists2Networks: Integrated analysis of gene/protein lists. BMC Bioinform. 11 (2010)
Huilei Xu, Ihor Lemischka, Avi Ma'ayan
SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells. BMC Syst. Biol. 4 (2010)
Marylens Hernandez, Alexander Lachmann, Shan Zhao, Kunhong Xiao, Avi Ma'ayan
Inferring the Sign of Kinase-Substrate Interactions by Combining Quantitative Phosphoproteomics with a Literature-Based Mammalian Kinome Network. BIBE (2010)
Ben D. MacArthur, Alexander Lachmann, Ihor Lemischka, Avi Ma'ayan
GATE: software for the analysis and visualization of high-dimensional time series expression data. Bioinform. 26 (1) (2010)
Alexander Lachmann, Avi Ma'ayan
KEA: kinase enrichment analysis. Bioinform. 25 (5) (2009)
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
SNAVI: Desktop application for analysis and visualization of large-scale signaling networks. BMC Syst. Biol. 3 (2009)
Avi Ma'ayan
PubMedAlertMe - Standalone Windows-based PubMed SDI software application. Comput. Biol. Medicine 38 (5) (2008)
Seth I. Berger, Ravi Iyengar, Avi Ma'ayan
AVIS: AJAX viewer of interactive signaling networks. Bioinform. 23 (20) (2007)
Seth I. Berger, Jeremy M. Posner, Avi Ma'ayan
Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. BMC Bioinform. 8 (2007)