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Wasserman Group Wiki
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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
(208) 960-4409The 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.7189306957
BiasAwayAn open-access tool for generating multiple different sequence backgrounds of comparable nucleotide composition relative to a set of input sequences 9492302862
5104413886Transcription factor binding profile Bioconductor data package813-213-9800
CAGEd-oPOSSUMMotif enrichment analysis from CAGE-derived TSSs.540-940-9122
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.
403-590-2283Deep 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: 970268380327546793
Gene Characerization IndexA bioinformatics method for scoring the extent to which a protein-encoding gene is functionally described9705266817
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.Ithomiinae
(386) 338-1389Biopython 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 TFBSs(856) 418-6658
MeSHOPUsing Medical Subject Heading Overrepresentation Profiles (MeSHOPs), an entity of interest can be robustly summarized, quantitatively identifying associated biomedical terms and suggesting indirect associations(978) 338-0733
MSCANAlgorithm that detects clusters of transcription factor binding sites in genomic sequences317-675-3330
NHRscanA computational predictor of nuclear hormone receptor binding sites15563547
(605) 274-7896A 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
4407359099An open-access system for the collection and dissemination of regulatory sequence annotation(863) 528-1391
TFBS perl modulesPerl modules for transcription factor binding site detection and analysis713-871-8539
TFBSToolsR/bioconductor package for transcription factor binding site analysis26794315
843-557-7327An 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
pulsatilityAn online encyclopedic collection of well-studied transcription factor proteins in the human, mouse, and rat genomes22458515
(276) 243-9402Transcription 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.5854193907


Project Websites


4106702166


Webinars


9738084228


Retired Software Tools

NameDescriptionPubMed ID
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.(587) 818-0526
dbMTNMultiple Tissue Northern Blot Comparison Tool18629180
Gene Set BuilderA tool for collation, curation and distribution of sets of genes3014126145
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 Datasetshypophrygian
819-938-5126The 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 domains(212) 803-7052
oPOSSUM2Web-based analysis of over-represented transcription factor binding sites17576675
OrthoSeqAlignment of DNA sequences
2024245475Developed 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.(859) 983-0533
4062279454Regulatory analysis of Variation in ENhancers18208319
312-423-6549A tool that uses unmapped SAGE tags to predict novel splice junctions in the genome8329411927
UlyssesProtein Interactions Conserved Across Evolution 16356269

Expression platform comparison


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Mev
(801) 551-1130(352) 641-4491