TFBS: Computational framework for transcription factor binding site analysis. - Boris Lenhard; Wyeth W. Wasserman (Bioinform., 2002)

Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm. - Öjvind Johansson; Wynand Alkema; Wyeth W. Wasserman; Jens Lagergren (ISMB (Supplement of Bioinformatics), 2003)

MSCAN: identification of functional clusters of transcription factor binding sites. - Wynand Alkema; Öjvind Johansson; Jens Lagergren; Wyeth W. Wasserman (Nucleic Acids Res., 2004)

JASPAR: an open-access database for eukaryotic transcription factor binding profiles. - Albin Sandelin; Wynand Alkema; Pär G. Engström; Wyeth W. Wasserman; Boris Lenhard (Nucleic Acids Res., 2004)

ConSite: web-based prediction of regulatory elements using cross-species comparison. - Albin Sandelin; Wyeth W. Wasserman; Boris Lenhard (Nucleic Acids Res., 2004)

The Gene Set Builder: collation, curation, and distribution of sets of genes. - Dimas Yusuf; Jonathan S. Lim; Wyeth W. Wasserman (BMC Bioinform., 2005)

Identification of Over-Represented Combinations of Transcription Factor Binding Sites in Sets of Co-Expressed Genes. - Shao-Shan Huang; Debra L. Fulton; David J. Arenillas; Paul Perco; Shannan J. Ho Sui; James R. Mortimer; Wyeth W. Wasserman (APBC, 2006)

Visualization of complementary systems biology data with parallel heatmaps. - Raf M. Podowski; Brett Miller; Wyeth W. Wasserman (IBM J. Res. Dev., 2006)

A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. - Dominique Vlieghe; Albin Sandelin; Pieter J. De Bleser; Kris Vleminckx; Wyeth W. Wasserman; Frans van Roy; Boris Lenhard (Nucleic Acids Res., 2006)

SAGE2Splice: Unmapped SAGE Tags Reveal Novel Splice Junctions. - Byron Yu-Lin Kuo; Ying Chen; Slavita Bohacec; Öjvind Johansson; Wyeth W. Wasserman; Elizabeth M. Simpson (PLoS Comput. Biol., 2006)

oPOSSUM: integrated tools for analysis of regulatory motif over-representation. - Shannan J. Ho Sui; Debra L. Fulton; David J. Arenillas; Andrew T. Kwon; Wyeth W. Wasserman (Nucleic Acids Res., 2007)

ORegAnno: an open-access community-driven resource for regulatory annotation. - Obi L. Griffith; Stephen B. Montgomery; Bridget Bernier; Bryan Chu; Katayoon Kasaian; Stein Aerts; Shaun Mahony; Monica C. Sleumer; Mikhail Bilenky; Maximilian Haeussler; Malachi Griffith; Steven M. Gallo; et al. (Nucleic Acids Res., 2008)

In Silico Detection of Sequence Variations Modifying Transcriptional Regulation. - Malin C. Andersen; Pär G. Engström; Stuart Lithwick; David J. Arenillas; Per Eriksson; Boris Lenhard; Wyeth W. Wasserman; Jacob Odeberg (PLoS Comput. Biol., 2008)

The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences. - Elodie Portales-Casamar; David J. Arenillas; Jonathan S. Lim; Magdalena I. Swanson; Steven Jiang; Anthony McCallum; Stefan Kirov; Wyeth W. Wasserman (Nucleic Acids Res., 2009)

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. - Elodie Portales-Casamar; Supat Thongjuea; Andrew T. Kwon; David J. Arenillas; Xiaobei Zhao; Eivind Valen; Dimas Yusuf; Boris Lenhard; Wyeth W. Wasserman; Albin Sandelin (Nucleic Acids Res., 2010)

MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model. - Antony Le Béchec; Elodie Portales-Casamar; Guillaume Vetter; Michèle Moes; Pierre-Joachim Zindy; Anne Saumet; David J. Arenillas; Charles Theillet; Wyeth W. Wasserman; Charles-Henri Lecellier; Evelyne Friederich (BMC Bioinform., 2011)

Validation of Skeletal Muscle cis-Regulatory Module Predictions Reveals Nucleotide Composition Bias in Functional Enhancers. - Andrew T. Kwon; Alice Yi Chou; David J. Arenillas; Wyeth W. Wasserman (PLoS Comput. Biol., 2011)

Quantitative biomedical annotation using medical subject heading over-representation profiles (MeSHOPs). - Warren A. Cheung; B. F. Francis Ouellette; Wyeth W. Wasserman (BMC Bioinform., 2012)

The Next Generation of Transcription Factor Binding Site Prediction. - Anthony Mathelier; Wyeth W. Wasserman (PLoS Comput. Biol., 2013)

Usability study of clinical exome analysis software: Top lessons learned and recommendations. - Casper Shyr; André Kushniruk; Wyeth W. Wasserman (J. Biomed. Informatics, 2014)

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. - Anthony Mathelier; Xiaobei Zhao; Allen W. Zhang; François Parcy; Rebecca Worsley-Hunt; David J. Arenillas; Sorana Buchman; Chih-Yu Chen; Alice Yi Chou; Hans Ienasescu; Jonathan S. Lim; Casper Shyr; et al. (Nucleic Acids Res., 2014)

NAR Breakthrough Article: TFBSshape: a motif database for DNA shape features of transcription factor binding sites. - Lin Yang; Tianyin Zhou; Iris Dror; Anthony Mathelier; Wyeth W. Wasserman; Raluca Gordân; Remo Rohs (Nucleic Acids Res., 2014)

A promoter-level mammalian expression atlas. - Fantom Consortium; RIKEN PMII; RIKEN CLST (DGT); Alistair R. R. Forrest; Hideya Kawaji; Michael Rehli; J. Kenneth Baillie; Michiel J. L. de Hoon; Vanja Haberle; Timo Lassmann; Ivan V. Kulakovskiy; Marina Lizio; et al. (Nat., 2014)

The identification of cis-regulatory elements: A review from a machine learning perspective. - Yifeng Li 001; Chih-Yu Chen; Alice Mary Kaye; Wyeth W. Wasserman (Biosyst., 2015)

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs. - David J. Arenillas; Alistair R. R. Forrest; Hideya Kawaji; Timo Lassmann; Wyeth W. Wasserman; Anthony Mathelier (Bioinform., 2016)

Dynamic software design for clinical exome and genome analyses: insights from bioinformaticians, clinical geneticists, and genetic counselors. - Casper Shyr; André Kushniruk; Clara D. M. van Karnebeek; Wyeth W. Wasserman (J. Am. Medical Informatics Assoc., 2016)

Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters. - Yifeng Li 001; Chih-Yu Chen; Wyeth W. Wasserman (J. Comput. Biol., 2016)

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. - Anthony Mathelier; Oriol Fornes; David J. Arenillas; Chih-Yu Chen; Grégoire Denay; Jessica J. Y. Lee; Wenqiang Shi; Casper Shyr; Ge Tan; Rebecca Worsley-Hunt; Allen W. Zhang; François Parcy; et al. (Nucleic Acids Res., 2016)

Genome-wide prediction of cis-regulatory regions using supervised deep learning methods. - Yifeng Li 001; Wenqiang Shi; Wyeth W. Wasserman (BMC Bioinform., 2018)

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. - Aziz Khan 001; Oriol Fornes; Arnaud Stigliani; Marius Gheorghe; Jaime Abraham Castro-Mondragón; Robin van der Lee; Adrien Bessy; Jeanne Chèneby; Shubhada R. Kulkarni; Ge Tan; Damir Baranasic; David J. Arenillas; et al. (Nucleic Acids Res., 2018)

TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets. - Laura Puente-Santamaria; Wyeth W. Wasserman; Luis del Peso (Bioinform., 2019)

Gene expression models based on transcription factor binding events confer insight into functional cis-regulatory variants. - Wenqiang Shi; Oriol Fornes; Wyeth W. Wasserman (Bioinform., 2019)

Development and user evaluation of a rare disease gene prioritization workflow based on cognitive ergonomics. - Jessica J. Y. Lee; Clara D. M. van Karnebeek; Wyeth W. Wasserman (J. Am. Medical Informatics Assoc., 2019)

JASPAR 2020: update of the open-access database of transcription factor binding profiles. - Oriol Fornes; Jaime Abraham Castro-Mondragón; Aziz Khan 001; Robin van der Lee; Xi Zhang; Phillip Andrew Richmond; Bhavi P. Modi; Solenne Correard; Marius Gheorghe; Damir Baranasic; Walter Santana-Garcia; Ge Tan; et al. (Nucleic Acids Res., 2020)

Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper. - Phillip Andrew Richmond; Alice Mary Kaye; Godfrain Jacques Kounkou; Tamar Vered Av-Shalom; Wyeth W. Wasserman (PLoS Comput. Biol., 2021)

RevUP: an online scoring system for regulatory variants implicated in rare diseases. - Solenne Correard; Brittany Hewitson; Robin van der Lee; Wyeth W. Wasserman (Bioinform., 2022)

JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. - Jaime Abraham Castro-Mondragón; Rafael Riudavets Puig; Ieva Rauluseviciute; Roza Berhanu lemma; Laura Turchi; Romain Blanc-Mathieu; Jeremy Lucas; Paul Boddie; Aziz Khan 001; Nicolás Manosalva Pérez; Oriol Fornes; Tiffany Y. Leung; et al. (Nucleic Acids Res., 2022)

OnTarget: in silico design of MiniPromoters for targeted delivery of expression. - Oriol Fornes; Tamar Vered Av-Shalom; Andrea J. Korecki; Rachelle A. Farkas; David J. Arenillas; Anthony Mathelier; Elizabeth M. Simpson; Wyeth W. Wasserman (Nucleic Acids Res., 2023)