Avi Ma'ayan

According to our database1, Avi Ma'ayan authored at least 48 papers between 2007 and 2019.

Collaborative distances:
  • Dijkstra number2 of five.
  • Erdős number3 of four.



In proceedings 
PhD thesis 



On csauthors.net:


Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures.
Bioinform., 2019

Predicting opioid dependence from electronic health records with machine learning.
BioData Min., 2019

Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition.
PLoS Computational Biology, 2018

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., 2018

eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks.
Nucleic Acids Res., 2018

L1000FWD: fireworks visualization of drug-induced transcriptomic signatures.
Bioinform., 2018

Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning.
Briefings in Bioinformatics, 2018

Cell-specific prediction and application of drug-induced gene expression .
Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

The Art of Connectivity Mapping.
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

Pharos: Collating protein information to shed light on the druggable genome.
Nucleic Acids Res., 2017

Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age.
J. Biomed. Informatics, 2017

Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop.
J. Biomed. Informatics, 2017

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update.
Nucleic Acids Res., 2016

Large Collection of Diverse Gene Set Search Queries Recapitulate Known Protein-Protein Interactions and Gene-Gene Functional Associations.
CoRR, 2016

GEN3VA: aggregation and analysis of gene expression signatures from related studies.
BMC Bioinform., 2016

Drug-induced adverse events prediction with the LINCS L1000 data.
Bioinform., 2016

The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins.
Database, 2016

Reprint of "Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction".
Comput. Biol. Chem., 2015

Dynamics of the discovery process of protein-protein interactions from low content studies.
BMC Syst. Biol., 2015

GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions.
Bioinform., 2015

Principle Angle Enrichment Analysis (PAEA): Dimensionally reduced multivariate gene set enrichment analysis tool.
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

Construction and Validation of a Regulatory Network for Pluripotency and Self-Renewal of Mouse Embryonic Stem Cells.
PLoS Computational Biology, 2014

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures.
Nucleic Acids Res., 2014

The characteristic direction: a geometrical approach to identify differentially expressed genes.
BMC Bioinform., 2014

Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets.
Bioinform., 2014

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool.
BMC Bioinform., 2013

Network2Canvas: network visualization on a canvas with enrichment analysis.
Bioinform., 2013

ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells.
Database, 2013

ChEA2: Gene-Set Libraries from ChIP-X Experiments to Decode the Transcription Regulome.
Proceedings of the Availability, Reliability, and Security in Information Systems and HCI, 2013

Sets2Networks: network inference from repeated observations of sets.
BMC Syst. Biol., 2012

Genes2FANs: connecting genes through functional association networks.
BMC Bioinform., 2012

Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers.
Bioinform., 2012

Connecting clusters of patient to drug responses of cell lines to suggest personalized therapeutics for breast cancer.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012

Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format.
Source Code for Biology and Medicine, 2011

Genes2WordCloud: a quick way to identify biological themes from gene lists and free text.
Source Code for Biology and Medicine, 2011

Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes.
PLoS Computational Biology, 2011

FNV: light-weight flash-based network and pathway viewer.
Bioinform., 2011

Visualization of Patient Samples by Dimensionality Reduction of Genome-Wide Measurements.
Proceedings of the Information Quality in e-Health, 2011

SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells.
BMC Syst. Biol., 2010

Lists2Networks: Integrated analysis of gene/protein lists.
BMC Bioinform., 2010

GATE: software for the analysis and visualization of high-dimensional time series expression data.
Bioinform., 2010

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments.
Bioinform., 2010

Inferring the Sign of Kinase-Substrate Interactions by Combining Quantitative Phosphoproteomics with a Literature-Based Mammalian Kinome Network.
Proceedings of the 10th IEEE International Conference on Bioinformatics and Bioengineering, 2010

SNAVI: Desktop application for analysis and visualization of large-scale signaling networks.
BMC Syst. Biol., 2009

KEA: kinase enrichment analysis.
Bioinform., 2009

PubMedAlertMe - Standalone Windows-based PubMed SDI software application.
Comp. in Bio. and Med., 2008

Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases.
BMC Bioinform., 2007

AVIS: AJAX viewer of interactive signaling networks.
Bioinform., 2007