About Us

The Ma’ayan Laboratory develops computational and mathematical methods to study the complexity of regulatory networks in mammalian cells. We apply machine learning and other statistical mining techniques to study how intracellular regulatory systems function as networks to control cellular processes such as differentiation, dedifferentiation, apoptosis and proliferation. We develop software systems to help experimental biologists form novel hypotheses from high-throughput data, while aiming to better understand the structure and function of regulatory networks in mammalian cellular and multi-cellular systems.

Below are some of the resources we designed and developed recently:

BioJupies

Automated Generation of Interactive Notebooks for RNA-seq Data Analysis in the Cloud
Web server that enables automated creation, storage, and deployment of Jupyter Notebooks containing RNA-seq data analyses.
bioRxiv 352476

Drug Gene Budger

Ranking Drugs to Modulate a Specific Gene Based on Transcriptomic Signatures
Web-based and mobile application to prioritize small molecules that are predicted to maximally influence the expression of the target gene of interest.
PMID: 30169739

eXpression2Kinases Web

Linking Expression Signatures to Upstream Cell Signaling Networks
Computationally predicts involvement of upstream cell signaling pathways, given a signature of differentially expressed genes.
PMID: 29800326

ARCHS4

All RNA-seq and CHIP-seq Signature Search Space
Provides access to gene counts from HiSeq 2000 and HiSeq 2500 platforms for human and mouse experiments from GEO and SRA.
PMID: 29636450

Datasets2Tools

Repository and Search Engine for Bioinformatics Datasets, Tools and Canned Analyses
Repository indexing 31,473 canned bioinformatics analyses applied to 6,431 datasets.
PMID: 29485625

L1000FWD

Large-scale Visualization of Drug-induced Transcriptomic Signatures
L1000 fireworks display (L1000FWD) is a web application that provides interactive visualization of over 16,000 drug and small-molecule induced gene expression signatures.
PMID: 29420694

Clustergrammer

Web-based Heatmap Visualization and Analysis Tool for High-Dimensional Biological Data
Clustergrammer is a visualization library built using D3.js that enables intuitive interaction with high-dimensional data.
PMID: 28994825

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.
PMID: 28413689

harmonizome

Harmonizome

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

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

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.