Wasserman Group Wiki
Current Group Members

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Welcome To The Wasserman Lab Website

About Wyeth Wasserman and the Wasserman Lab

Wasserman Lab Open Access Software

The source code for much of the newer Wasserman Lab software is available at GitHub

BiasAway - An open-access tool for generating multiple different sequence backgrounds of comparable nucleotide composition relative to a set of input sequences

CAGEd-oPOSSUM - Motif enrichment analysis from CAGE-derived TSSs.

ConSite - Transcription factor binding site detection using phylogenetic footprinting. Note that this is an older tool which is hosted remotely. You may also be interested in our ORCAtk tool which is maintained locally and performs similar functionality.

The Gene Characterization Index - a bioinformatics method for scoring the extent to which a protein-encoding gene is functionally described

JASPAR - Transcription Factor Binding Profile Database

MeSHOP - Using Medical Subject Heading Overrepresentation Profiles (MeSHOPs), an entity of interest can be robustly summarized, quantitatively identifying associated biomedical terms and suggesting indirect associations

MSCAN - Algorithm that detects clusters of transcription factor binding sites in genomic sequences

NHRscan - A computational predictor of nuclear hormone receptor binding sites

oPOSSUM v3 (2012) A web-based system for the detection of over-represented conserved transcription factor binding sites and binding site combinations in sets of genes or sequences. For the previous version of oPOSSUM see v2 (2008) below.

ORCAtk - Transcription factor binding site detection using phylogenetic footprinting (alternative to ConSite)

PAZAR - An open-access system for the collection and dissemination of regulatory sequence annotation

Phylofoot - Tools for phylogenetic footprinting

TFBS_Visualization - An open-access tool for visualizing and assessing transcription factor topological motif enrichment in ChIP-Seq datasets

TFBS - Perl modules for transcription factor binding site detection and analysis

TFCat - TFCat is a catalog of mouse and human TFs based on a reliable core collection of annotations obtained by expert review of the scientific literature.

TFe - An online encyclopedic collection of well-studied transcription factor proteins in the human, mouse, and rat genomes

TFFM - Transcription Factor Flexible Models (TFFMs) are hidden Markov model (HMM) representations of TFBS motifs. This online tool allows you to generate TFFMs and scan sequences with them.

Project Websites

Pleiades Promoter Project: Genomic Resources Advancing Therapies for Brain Disorders



Retired Software Tools

Expression platform comparison

GeneLynx - A portal to the human genome. This tool was developed to fulfill a need for easily accessible gene information at a particular point in time. Having fulfilled its purpose, this tool has been retired. Current tools are available to provide similar services.

Gene Set Builder - A tool for collation, curation and distribution of sets of genes

GOToolBox - Functional Investigation of Gene Datasets

dbMTN - Multiple Tissue Northern Blot Comparison Tool

NovelFam3000 - A bioinformatics tool created to accelerate characterization of gene families sharing uncharacterized protein domains

oPOSSUM v2 (2008) - Web-based analysis of over-represented transcription factor binding sites

OrthoSeq - Alignment of DNA sequences

RAVEN - Regulatory analysis of Variation in ENhancers

SAGE2Splice - A tool that uses unmapped SAGE tags to predict novel splice junctions in the genome

Ulysses - Protein Interactions Conserved Across Evolution

University of British Columbia
CFRIBC Children\'s Hospital Foundation