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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

NameDescriptionPubMed ID
ABC4DEThe ABC4DE web-interface allows for the analysis of sets of variants within a region of interest. For a given variant, the tool reports: 1) if it falls within a predicted regulatory region; 2) the predicted role for that region (promoter/enhancer); and 3) if the variant will alter a potential TFBSs.
ASB data setASB data set contains 10,765 ASB events retrieved from 45 ENCODE ChIP-Seq data sets.27492288
BiasAwayAn open-access tool for generating multiple different sequence backgrounds of comparable nucleotide composition relative to a set of input sequences 24927817
Bioconductor data package for JASPARTranscription factor binding profile Bioconductor data package26531826
CAGEd-oPOSSUMMotif enrichment analysis from CAGE-derived TSSs.27334471
cis-reg-predOpen-access tool for the segmentation of the human genome. The tool uses a supervised machine learning approach to segment the human genome using experimental data in the same spirit as Segway and ChromHMM.
ConSiteTranscription 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.15215389
DECRESDeep learning for identifying cis-regulatory elements and other applications.
Deep Learning Package in Python Based on The Deep Learning Tutorials and TheanoThis deep learning package is an extension of the Deep Learning Tutorials (www.deeplearning.net/tutorial/).
DNAshapedTFBSPython module allowing for the construction and application of machine learning classifiers combining TFFM/PSSM + DNA shape features for improving the predictions of TFBSs in ChIP-seq data-sets. Highlighted by PMID: 2768418527546793
Gene Characerization IndexA bioinformatics method for scoring the extent to which a protein-encoding gene is functionally described18213364
IEMBaseOnline inborn errors of metabolism knowledgebase and diagnosis support system.
IndelImpactOpen-access software for the computation of the impact of insertions and deletions on transcription factor binding sites.
JASPARThe 2016 version of the JASPAR database was publicly released on November 2016 and greatly expands the number of transcription factor binding profiles from 2014. Additionally, transcription factor flexible models (TFFMs) have been provided for 130 of the transcription factors. The structural annotation of the TF DNA binding domains (DBDs) has been changed to follow a published hierarchical structural classification and a new web tool has been included to infer JASPAR TF binding profiles recognized by a given TF protein sequence. Finally, A Ruby API module has been created to accompany the existing Perl and Biopython APIs and R/Bioconductor data package.26531826
JASPAR Biopython moduleBiopython package to access and use JASPAR binding profiles.26531826
JASPAR BioRuby gemRuby gems for parsing, searching, and comparing JASPAR motifs; Based on Bio.motifs module in Biopython.26531826
MANTASNV impact on TFBSs25903198
MeSHOPUsing Medical Subject Heading Overrepresentation Profiles (MeSHOPs), an entity of interest can be robustly summarized, quantitatively identifying associated biomedical terms and suggesting indirect associations23017167
MSCANAlgorithm that detects clusters of transcription factor binding sites in genomic sequences15215379
NHRscanA computational predictor of nuclear hormone receptor binding sites15563547
oPOSSUM3A web-based system for the detection of over-represented conserved transcription factor binding sites and binding site combinations in sets of genes or sequences22973536
ORCAtkTranscription factor binding site detection using phylogenetic footprinting (alternative to ConSite)18971253
PAZARAn open-access system for the collection and dissemination of regulatory sequence annotation17916232
TFBS perl modulesPerl modules for transcription factor binding site detection and analysis26531826
TFBSToolsR/bioconductor package for transcription factor binding site analysis26794315
TFBS_VisualizationAn open-access tool for visualizing and assessing transcription factor topological motif enrichment in ChIP-Seq datasets.
TFCatTFCat is a catalog of mouse and human TFs based on a reliable core collection of annotations obtained by expert review of the scientific literature19284633
TFeAn online encyclopedic collection of well-studied transcription factor proteins in the human, mouse, and rat genomes22458515
TFFMTranscription 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.24039567


Project Websites


Pleiades Promoter Project: Genomic Resources Advancing Therapies for Brain Disorders


Webinars


JASPAR-BioPython / MANTA


Retired Software Tools

NameDescriptionPubMed ID
dbMTNMultiple Tissue Northern Blot Comparison Tool18629180
Gene Set BuilderA tool for collation, curation and distribution of sets of genes16371163
GeneLynxA 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.11731507
GOToolBoxFunctional Investigation of Gene Datasets15575967
JASPAR 2014The 2014 version of the JASPAR database was publicly released on November 2013 with the incorporation of new and updated transcription factor binding profiles. Beyond the transcription factor binding profiles, we provide the ChIP-seq derived sequences that have been used to construct the profiles.24194598
NovelFam3000A bioinformatics tool created to accelerate characterization of gene families sharing uncharacterized protein domains16533400
oPOSSUM2Web-based analysis of over-represented transcription factor binding sites17576675
OrthoSeqAlignment of DNA sequences
PFONDDeveloped by the Wasserman Laboratory at UBC, PFOND is a web-based service to promote the sharing of information about research, treatment, and resources for rare genetic disorders.23920006
RAVENRegulatory analysis of Variation in ENhancers18208319
SAGE2SpliceA tool that uses unmapped SAGE tags to predict novel splice junctions in the genome16683015
UlyssesProtein Interactions Conserved Across Evolution 16356269

Expression platform comparison


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University of British Columbia
CFRIBC Children\'s Hospital Foundation