About Us

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Summary of Research Interests

The Ma’ayan Laboratory develops computational and mathematical methods to study the complexity of regulatory networks in mammalian cells. We apply and invent graph-theory algorithms, machine-learning techniques and dynamical modeling methods to study how intracellular regulatory systems function as networks to control cellular processes such as differentiation, de-differentiation, apoptosis and proliferation. We develop novel software systems to help experimental biologists form novel hypotheses from high-throughput data, and theorize about the structure and function of regulatory networks in mammalian systems. Below are some of the software tools we designed and developed recently:

enrichr

Enrichr

Gene-List Enrichment Analysis Tool
An integrative web-based and mobile gene list enrichment analysis tool providing various types of visualization summaries of collective functions of gene lists.
PMID: 27141961

g2e

GEO2Enrichr

Browser Extension for Extracting Differentially Expressed Gene Sets from GEO
A browser extension and web application to extract gene sets from GEO and analyze these lists for common biological functions.
PMID: 25971742

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CREEDS

Crowd Extracted Expression of Differential Signatures
Collections of processed gene, drug and disease signatures from GEO.
PMID: 27667448

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GEN3VA

Gene Expression and Enrichment Vector Analyzer
Aggregates and analyzes gene expression signatures extracted from GEO by the crowd using GEO2Enrichr.
PMID: 27846806

l1000cds2

L1000CDS2

L1000 Characteristic Direction Signature Search Engine
Queries gene expression signatures against the LINCS L1000 to identify and prioritize small molecules that can reverse or mimic the observed input expression pattern.
doi:10.1038/npjsba.2016.15

harmonizome

Harmonizome

Biological Knowledge Engine
Built on top of information about genes and proteins from 114 datasets, the Harmonizome is a knowledge engine for a diverse set of integrated resources.
PMID: 27374120

sep

SEP L1000

Side Effect Prediction Based on L1000 Data
Web portal for searching and browsing predictive small-molecule/ADR connections.
PMID: 27153606

For a complete list of our software tools, databases and datasets please visit our Resources page. We apply these and other computational methods for the analysis of a variety of collaborative projects. The results from our analyses produce concrete suggestions and predictions for further functional experiments. The predictions are tested by our collaborators and our analyses methods are delivered as software tools and databases for the systems biology research community.