Avi Ma'ayan

发表

Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center

Vasileios Stathias, Amar Koleti, Dušica Vidović, 2018, Scientific Data.

Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning

Rong Chen, Riccardo Miotto, Marcus A. Badgeley, 2017, Briefings Bioinform..

Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format

Avi Ma'ayan, Ryan L. Webb, Avi Ma’ayan, 2011, Source Code for Biology and Medicine.

Towards Intelligent Integration and Sharing of Stem Cell Research Data.

Avi Ma'ayan, Joseph Finkelstein, Kirill Borziak, 2020, Studies in health technology and informatics.

FNV: light-weight flash-based network and pathway viewer

Avi Ma'ayan, Ruth Dannenfelser, Alexander Lachmann, 2011, Bioinform..

Microdynamics and Criticality in Evolving Random Graphs

Avi Ma'ayan, Ben D. MacArthur, Rubén J. Sánchez-García, 2009 .

The Signaling Pathways Project: an integrated ‘omics knowledgebase for mammalian cellular signaling pathways

Wei Ding, Avi Ma'ayan, Kirt Martin, 2018, bioRxiv.

Abstract B1-28: GEO2Enrichr: A Google Chrome extension to extract gene sets from the Gene Expression Omnibus and analyze these lists for common biological functions

Avi Ma'ayan, Matthew R. Jones, Gregory W. Gundersen, 2015 .

Network2Canvas: network visualization on a canvas with enrichment analysis

Avi Ma'ayan, Ruth Dannenfelser, Christopher M. Tan, 2013, Bioinform..

Visualization of Patient Samples by Dimensionality Reduction of Genome-Wide Measurements

Avi Ma'ayan, Huilei Xu, Avi Ma’ayan, 2011, USAB.

Genes2FANs: connecting genes through functional association networks

Avi Ma'ayan, Ruth Dannenfelser, Neil R. Clark, 2011, BMC Bioinformatics.

Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd

Kathleen M Jagodnik, Avi Ma'ayan, Pablo Gamallo, 2016, Nature Communications.

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures

Andrew D. Rouillard, Avi Ma'ayan, Marc Hafner, 2014, Nucleic Acids Res..

Massive Mining of Publicly Available RNA-seq Data from Human and Mouse

Denis Torre, Avi Ma'ayan, Kathleen M. Jagodnik, 2017 .

Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition

Avi Ma'ayan, Simon Koplev, Katie Lin, 2018, PLoS Comput. Biol..

Interoperable RNA-Seq analysis in the cloud.

Denis Torre, Avi Ma'ayan, Daniel J B Clarke, 2020, Biochimica et biophysica acta. Gene regulatory mechanisms.

Cloud-based drag-and-drop scalable RNA sequencing pipeline

Avi Ma'ayan, Alexander Lachmann, Troy Goff, 2016 .

The characteristic direction: a geometrical approach to identify differentially expressed genes

Avi Ma'ayan, Kevin S. Hu, Edward Y. Chen, 2014, BMC Bioinformatics.

Connecting omics signatures of diseases, drugs, and mechanisms of actions with iLINCS

Vasileios Stathias, Amar Koleti, Mario Medvedovic, 2019, bioRxiv.

Clustergrammer: web-based heatmap visualization and analysis tool for high-dimensional biological data

Andrew D. Rouillard, Avi Ma'ayan, Adeeb Rahman, 2016 .

Toward stem cell systems biology: from molecules to networks and landscapes.

Avi Ma'ayan, Ben D. MacArthur, Ihor R. Lemischka, 2008, Cold Spring Harbor symposia on quantitative biology.

BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud.

Denis Torre, Avi Ma'ayan, Alexander Lachmann, 2018, Cell systems.

GATE: software for the analysis and visualization of high-dimensional time series expression data

Avi Ma'ayan, Ben D. MacArthur, Ihor Lemischka, 2009, Bioinform..

A blueprint of cell identity

Avi Ma'ayan, Qiaonan Duan, Avi Ma’ayan, 2014, Nature Biotechnology.

SNAVI: Desktop application for analysis and visualization of large-scale signaling networks

Avi Ma'ayan, Tony Flores, Ravi Iyengar, 2009, BMC Systems Biology.

Microdynamics and criticality of adaptive regulatory networks.

Avi Ma'ayan, Rubén J. Sánchez-García, Ben D MacArthur, 2009, Physical review letters.

Cell-specific prediction and application of drug-induced gene expression profiles

Jianying Hu, Joel Dudley, Fei Wang, 2017, PSB.

Predicting opioid dependence from electronic health records with machine learning

Avi Ma'ayan, Nicholas Genes, Zichen Wang, 2019, BioData Mining.

Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases

Avi Ma'ayan, Seth I. Berger, Jeremy M. Posner, 2007, BMC Bioinformatics.

KEA: kinase enrichment analysis

Avi Ma'ayan, Alexander Lachmann, Alexander Lachmann, 2009, Bioinform..

Visualization of the Phosphoproteomic Data from AfCS with the Google Motion Chart Gadget

Avi Ma'ayan, Huilei Xu, Avi Ma’ayan, 2009 .

Inferring the Sign of Kinase-Substrate Interactions by Combining Quantitative Phosphoproteomics with a Literature-Based Mammalian Kinome Network

Avi Ma'ayan, Shan Zhao, Marylens Hernandez, 2010, 2010 IEEE International Conference on BioInformatics and BioEngineering.

The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins

Avi Ma'ayan, Nicolas F. Fernandez, Gregory W. Gundersen, 2016, Database J. Biol. Databases Curation.

L1000FWD: fireworks visualization of drug‐induced transcriptomic signatures

Avi Ma'ayan, Zichen Wang, Alexander Lachmann, 2018, Bioinform..

Elysium: RNA-seq Alignment in the Cloud

Avi Ma'ayan, Alexander Lachmann, Zhuorui Xie, 2018, bioRxiv.

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

Avi Ma'ayan, Alexander Lachmann, Amin R. Mazloom, 2010, Bioinform..

Lists2Networks: Integrated analysis of gene/protein lists

Avi Ma'ayan, Alexander Lachmann, Alexander Lachmann, 2010, BMC Bioinformatics.

Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers

Avi Ma'ayan, Edward Y. Chen, Huilei Xu, 2012, Bioinform..

Genes2WordCloud: a quick way to identify biological themes from gene lists and free text

Avi Ma'ayan, Caroline Baroukh, Ruth Dannenfelser, 2011, Source Code for Biology and Medicine.

PubMedAlertMe - Standalone Windows-based PubMed SDI software application

Avi Ma'ayan, 2008, Comput. Biol. Medicine.

Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets

Andrew D. Rouillard, Avi Ma'ayan, Nicolas F. Fernandez, 2014, Bioinform..

Network Analysis in Systems Biology

Avi Ma'ayan, 2012 .

Mining data and metadata from the gene expression omnibus

Avi Ma'ayan, Zichen Wang, Alexander Lachmann, 2018, Biophysical Reviews.

FAIR LINCS Data and Metadata powered by the CEDAR Framework

Vasileios Stathias, Amar Koleti, Michele Forlin, 2016 .

Large Collection of Diverse Gene Set Search Queries Recapitulate Known Protein-Protein Interactions and Gene-Gene Functional Associations pdf

Avi Ma'ayan, Neil R. Clark, 2016, ArXiv.

Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures

Avi Ma'ayan, Kathleen M. Jagodnik, Zichen Wang, 2018, Bioinform..

Principle Angle Enrichment Analysis (PAEA): Dimensionally reduced multivariate gene set enrichment analysis tool

Avi Ma'ayan, Matthew R. Jones, Zichen Wang, 2015, 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

FAIRshake: toolkit to evaluate the findability, accessibility, interoperability, and reusability of research digital resources

Michel Dumontier, Denis Torre, Avi Ma'ayan, 2019, bioRxiv.

AVIS: AJAX viewer of interactive signaling networks

Ravi Iyengar, Avi Ma'ayan, Seth I. Berger, 2007, Bioinform..

Faculty Opinions recommendation of Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens.

Avi Ma'ayan, Avi Ma’ayan, 2019, Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature.

Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses

Kathleen M Jagodnik, Denis Torre, Avi Ma'ayan, 2018, Scientific Data.

Sets2Networks: network inference from repeated observations of sets

Avi Ma'ayan, Ruth Dannenfelser, Christopher M. Tan, 2012, BMC Systems Biology.

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.

Ravi Iyengar, Vasileios Stathias, Amar Koleti, 2017, Cell systems.

EnrichrBot: Twitter bot tracking tweets about human genes

Kathleen M Jagodnik, Avi Ma'ayan, Daniel J B Clarke, 2020, Bioinform..

Introduction to Statistical Methods to Analyze Large Data Sets: Principal Components Analysis

Avi Ma'ayan, Neil R Clark, Avi Ma’ayan, 2011, Science Signaling.

Connecting clusters of patient to drug responses of cell lines to suggest personalized therapeutics for breast cancer

Avi Ma'ayan, Simon Gordonov, 2012, 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops.

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

Andrew D. Rouillard, Avi Ma'ayan, Matthew R. Jones, 2016, Nucleic Acids Res..

Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data

Vasileios Stathias, Amar Koleti, Raymond Terryn, 2017, Nucleic Acids Res..

Reprint of "Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction"

Andrew D. Rouillard, Avi Ma'ayan, Zichen Wang, 2015, Comput. Biol. Chem..

Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes

Ravi Iyengar, Avi Ma'ayan, Timothy Cardozo, 2011, PLoS Comput. Biol..

The Art of Connectivity Mapping

Avi Ma'ayan, 2018, BCB.

Dynamics of the discovery process of protein-protein interactions from low content studies

Avi Ma'ayan, Neil R. Clark, Zichen Wang, 2015, BMC Systems Biology.

Construction and Validation of a Regulatory Network for Pluripotency and Self-Renewal of Mouse Embryonic Stem Cells

Avi Ma'ayan, Ihor Lemischka, Huilei Xu, 2014, PLoS Comput. Biol..

Connecting Seed Lists of Mammalian Proteins Using Steiner Trees

Avi Ma'ayan, Amelia G. White, 2008 .

Genes2Networks web interface

Avi Ma'ayan, Seth I. Berger, Jeremy M Posner, 2011 .

piNET: a versatile web platform for downstream analysis and visualization of proteomics data

Cathy H. Wu, Mario Medvedovic, Avi Ma'ayan, 2019, bioRxiv.

Intracellular Regulatory Networks are close to Monotone Systems

Avi Ma'ayan, Eduardo D. Sontag, Ravi Iyengar, 2007 .

GEN3VA: aggregation and analysis of gene expression signatures from related studies

Avner Schlessinger, Avi Ma'ayan, Kathleen M. Jagodnik, 2016, BMC Bioinformatics.

Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop

Ruben Verborgh, Michel Dumontier, Lucila Ohno-Machado, 2017, J. Biomed. Informatics.

Faculty Opinions recommendation of Deep learning: new computational modelling techniques for genomics.

Avi Ma'ayan, Zichen Wang, Avi Ma’ayan, 2019, Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature.

ChEA2: Gene-Set Libraries from ChIP-X Experiments to Decode the Transcription Regulome

Avi Ma'ayan, Christopher M. Tan, Edward Y. Chen, 2013, CD-ARES.

SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells

Avi Ma'ayan, Ihor Lemischka, Huilei Xu, 2010, BMC Systems Biology.

FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources.

Daniel J Cooper, Kathleen M Jagodnik, Denis Torre, 2019, Cell systems.

Connectivity Mapping: Methods and Applications

Avi Ma'ayan, Kathleen M. Jagodnik, Alexander Lachmann, 2019, Annual Review of Biomedical Data Science.

The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins

Andrew D. Rouillard, Avi Ma'ayan, Nicolas F. Fernandez, 2016, Database J. Biol. Databases Curation.

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

Avi Ma'ayan, Zichen Wang, Christopher M. Tan, 2013, BMC Bioinformatics.

Cycles and Dynamics on Evolving Signed Digraphs

Avi Ma'ayan, Ben D. MacArthur, Rubén J. Sánchez-García, 2009 .

ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells

Avi Ma'ayan, Caroline Baroukh, Ruth Dannenfelser, 2013, Database J. Biol. Databases Curation.

Genes2Networks: Connecting Lists of Proteins by Using Background Literature-based Mammalian Networks

Avi Ma'ayan, Seth I. Berger, Jeremy I. Posner, 2007 .

Faculty Opinions recommendation of Regularized Programming with the BOSQUE Language.

Avi Ma'ayan, Avi Ma’ayan, 2019, Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature.

GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions

Andrew D. Rouillard, Avi Ma'ayan, Matthew R. Jones, 2015, Bioinform..

Drug-induced adverse events prediction with the LINCS L1000 data

Avi Ma'ayan, Zichen Wang, Neil R. Clark, 2016, Bioinform..

Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age

Benjamin S. Glicksberg, Joel Dudley, Li Li, 2017, J. Biomed. Informatics.

Pathways of Toxicity.

Thomas Hartung, Roded Sharan, Melvin E Andersen, 2014, ALTEX.

eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks

Denis Torre, Avi Ma'ayan, Zichen Wang, 2018, Nucleic Acids Res..

Pharos: Collating protein information to shed light on the druggable genome

Rajarshi Guha, Tudor I. Oprea, Larry A. Sklar, 2016, Nucleic Acids Res..

Network Pharmacology to Aid the Drug Discovery Process

Avi Ma'ayan, Ruth Dannenfelser, Huilei Xu, 2012 .

Massive mining of publicly available RNA-seq data from human and mouse

Kathleen M Jagodnik, Denis Torre, Avi Ma'ayan, 2017, Nature Communications.

BioJupies: Automated Generation of Interactive Notebooks for RNA-seq Data Analysis in the Cloud

Denis Torre, Avi Ma'ayan, Alexander Lachmann, 2018, bioRxiv.

Appyters: Turning Jupyter Notebooks into data-driven web apps

Avi Ma'ayan, Kathleen M. Jagodnik, Minji Jeon, 2021, Patterns.

Mutation in SHOC2 promotes aberrant protein N-myristoylation and underlies Noonan-like syndrome with loose anagen hair

Ravi Iyengar, Avi Ma'ayan, Wendy Schackwitz, 2009, Nature Genetics.

Systems approach to explore components and interactions in the presynapse

Ravi Iyengar, Avi Ma'ayan, Rong Wang, 2009, Proteomics.

Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain

Avi Ma'ayan, Christopher Y. Park, Robert B Darnell, 2016, eLife.

Systems pharmacology meets predictive, preventive, personalized and participatory medicine.

Avi Ma'ayan, Sherry L Jenkins, Sherry L. Jenkins, 2013, Pharmacogenomics.

Introduction to Statistical Methods for Analyzing Large Data Sets: Gene-Set Enrichment Analysis

Avi Ma'ayan, Neil R Clark, Avi Ma’ayan, 2011, Science Signaling.

LINCS Data Portal 2.0: next generation access point for perturbation-response signatures

Vasileios Stathias, Amar Koleti, Raymond Terryn, 2019, Nucleic Acids Res..

Lean Big Data integration in systems biology and systems pharmacology.

Avi Ma'ayan, Zichen Wang, Andrew D Rouillard, 2014, Trends in pharmacological sciences.

Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.

Avi Ma'ayan, Yuji Kajiwara, Christopher S. Poultney, 2013, American journal of human genetics.

Regulation of embryonic and induced pluripotency by aurora kinase-p53 signaling.

Ruiying Zhao, Avi Ma'ayan, Julian Gingold, 2012, Cell stem cell.

Integration of protein phosphorylation, acetylation, and methylation data sets to outline lung cancer signaling networks

Avi Ma'ayan, Travis Wheeler, Alexander Lachmann, 2018, Science Signaling.

Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration

Avi Ma'ayan, Zichen Wang, Alexander Lachmann, 2016, Nature Neuroscience.

Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd

Andrew D. Rouillard, Avi Ma'ayan, Kathleen M. Jagodnik, 2016, Nature Communications.

Systems approach identifies HIPK2 as a critical regulator of kidney fibrosis

Avi Ma'ayan, Nan Chen, Amin R. Mazloom, 2012, Nature Medicine.

Unexplored therapeutic opportunities in the human genome

Anton Simeonov, Christian von Mering, Tudor I. Oprea, 2018, Nature Reviews Drug Discovery.

Sox2 in the dermal papilla niche controls hair growth by fine-tuning BMP signaling in differentiating hair shaft progenitors.

Avi Ma'ayan, Amin R. Mazloom, Xiaoqiang Cai, 2012, Developmental cell.

Ordered cyclic motifs contribute to dynamic stability in biological and engineered networks

Ravi Iyengar, Avi Ma'ayan, Gustavo Stolovitzky, 2008, Proceedings of the National Academy of Sciences.

An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study

Avi Ma'ayan, Zichen Wang, Apostolos Zaravinos, 2016, F1000Research.

Unexplored therapeutic opportunities in the human genome

Anton Simeonov, Christian von Mering, Tudor I. Oprea, 2018, Nature Reviews Drug Discovery.

Far away from the lamppost

Avi Ma'ayan, Stephan Schürer, Michael T. McManus, 2018, PLoS biology.