Wyeth W. Wasserman

39 papers B 2Journal 36Unranked 1

Year	Rank	Type	Title / Venue / Authors
2023	J	`jnl`	OnTarget: Nucleic Acids Res. Oriol Fornes, Tamar Vered Av-Shalom, Andrea J. Korecki, Rachelle A. Farkas, David J. Arenillas, Anthony Mathelier, Elizabeth M. Simpson, Wyeth W. Wasserman
2022	J	`jnl`	JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. Nucleic Acids Res. Jaime Abraham Castro-Mondragón, Rafael Riudavets Puig, Ieva Rauluseviciute, Roza Berhanu lemma, Laura Turchi, Romain Blanc-Mathieu, Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol Fornes, Tiffany Y. Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel Schmelter, Damir Baranasic, Benoît Ballester, Albin Sandelin, Boris Lenhard, Klaas Vandepoele, Wyeth W. Wasserman, François Parcy, Anthony Mathelier
2022	J	`jnl`	RevUP: an online scoring system for regulatory variants implicated in rare diseases. Bioinform. Solenne Correard, Brittany Hewitson, Robin van der Lee, Wyeth W. Wasserman
2021	J	`jnl`	Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper. PLoS Comput. Biol. Phillip Andrew Richmond, Alice Mary Kaye, Godfrain Jacques Kounkou, Tamar Vered Av-Shalom, Wyeth W. Wasserman
2020	J	`jnl`	JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. Oriol Fornes, Jaime Abraham Castro-Mondragón, Aziz Khan, Robin van der Lee, Xi Zhang, Phillip Andrew Richmond, Bhavi P. Modi, Solenne Correard, Marius Gheorghe, Damir Baranasic, Walter Santana-Garcia, Ge Tan, Jeanne Chèneby, Benoît Ballester, François Parcy, Albin Sandelin, Boris Lenhard, Wyeth W. Wasserman, Anthony Mathelier
2019	J	`jnl`	Development and user evaluation of a rare disease gene prioritization workflow based on cognitive ergonomics. J. Am. Medical Informatics Assoc. Jessica J. Y. Lee, Clara D. M. van Karnebeek, Wyeth W. Wasserman
2019	J	`jnl`	Gene expression models based on transcription factor binding events confer insight into functional cis-regulatory variants. Bioinform. Wenqiang Shi, Oriol Fornes, Wyeth W. Wasserman
2019	J	`jnl`	TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets. Bioinform. Laura Puente-Santamaria, Wyeth W. Wasserman, Luis del Peso
2018	J	`jnl`	Genome-wide prediction of cis-regulatory regions using supervised deep learning methods. BMC Bioinform. Yifeng Li, Wenqiang Shi, Wyeth W. Wasserman
2018	J	`jnl`	JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. Aziz Khan, 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, Albin Sandelin, Klaas Vandepoele, Boris Lenhard, Benoît Ballester, Wyeth W. Wasserman, François Parcy, Anthony Mathelier
2018	J	`jnl`	JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. Aziz Khan, 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, Albin Sandelin, Klaas Vandepoele, Boris Lenhard, Benoît Ballester, Wyeth W. Wasserman, François Parcy, Anthony Mathelier
2016	J	`jnl`	CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs. Bioinform. David J. Arenillas, Alistair R. R. Forrest, Hideya Kawaji, Timo Lassmann, Wyeth W. Wasserman, Anthony Mathelier
2016	J	`jnl`	Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters. J. Comput. Biol. Yifeng Li, Chih-Yu Chen, Wyeth W. Wasserman
2016	J	`jnl`	Dynamic software design for clinical exome and genome analyses: insights from bioinformaticians, clinical geneticists, and genetic counselors. J. Am. Medical Informatics Assoc. Casper Shyr, Andre Kushniruk, Clara D. M. van Karnebeek, Wyeth W. Wasserman
2016	J	`jnl`	JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 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, Boris Lenhard, Albin Sandelin, Wyeth W. Wasserman
2015	B	`conf`	Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters. RECOMB Yifeng Li, Chih-Yu Chen, Wyeth W. Wasserman
2015	J	`jnl`	The identification of cis-regulatory elements: A review from a machine learning perspective. Biosyst. Yifeng Li, Chih-Yu Chen, Alice Mary Kaye, Wyeth W. Wasserman
2014	J	`jnl`	JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 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, Ge Tan, Michelle Zhou, Boris Lenhard, Albin Sandelin, Wyeth W. Wasserman
2014	J	`jnl`	NAR Breakthrough Article: TFBSshape: a motif database for DNA shape features of transcription factor binding sites. Nucleic Acids Res. Lin Yang, Tianyin Zhou, Iris Dror, Anthony Mathelier, Wyeth W. Wasserman, Raluca Gordân, Remo Rohs
2014	J	`jnl`	Usability study of clinical exome analysis software: Top lessons learned and recommendations. J. Biomed. Informatics Casper Shyr, Andre Kushniruk, Wyeth W. Wasserman
2013	J	`jnl`	The Next Generation of Transcription Factor Binding Site Prediction. PLoS Comput. Biol. Anthony Mathelier, Wyeth W. Wasserman
2012	J	`jnl`	Quantitative biomedical annotation using medical subject heading over-representation profiles (MeSHOPs). BMC Bioinform. Warren A. Cheung, B. F. Francis Ouellette, Wyeth W. Wasserman
2011	J	`jnl`	MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model. BMC Bioinform. 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
2011	J	`jnl`	Validation of Skeletal Muscle PLoS Comput. Biol. Andrew T. Kwon, Alice Yi Chou, David J. Arenillas, Wyeth W. Wasserman
2010	J	`jnl`	JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res. Elodie Portales-Casamar, Supat Thongjuea, Andrew T. Kwon, David J. Arenillas, Xiaobei Zhao, Eivind Valen, Dimas Yusuf, Boris Lenhard, Wyeth W. Wasserman, Albin Sandelin
2009	J	`jnl`	The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences. Nucleic Acids Res. Elodie Portales-Casamar, David J. Arenillas, Jonathan S. Lim, Magdalena I. Swanson, Steven Jiang, Anthony McCallum, Stefan Kirov, Wyeth W. Wasserman
2008	J	`jnl`	In Silico Detection of Sequence Variations Modifying Transcriptional Regulation. PLoS Comput. Biol. Malin C. Andersen, Pär G. Engström, Stuart Lithwick, David J. Arenillas, Per Eriksson, Boris Lenhard, Wyeth W. Wasserman, Jacob Odeberg
2008	J	`jnl`	ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res. 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, Belinda Giardine, Bart Hooghe, Peter Van Loo, Enrique Blanco, Amy Ticoll, Stuart Lithwick, Elodie Portales-Casamar, Ian J. Donaldson, Gordon Robertson, Claes Wadelius, Pieter J. De Bleser, Dominique Vlieghe, Marc S. Halfon, Wyeth W. Wasserman, Ross C. Hardison, Casey M. Bergman, Steven J. M. Jones
2007	J	`jnl`	oPOSSUM: integrated tools for analysis of regulatory motif over-representation. Nucleic Acids Res. Shannan J. Ho Sui, Debra L. Fulton, David J. Arenillas, Andrew T. Kwon, Wyeth W. Wasserman
2006	J	`jnl`	A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Res. Dominique Vlieghe, Albin Sandelin, Pieter J. De Bleser, Kris Vleminckx, Wyeth W. Wasserman, Frans van Roy, Boris Lenhard
2006	B	`conf`	Identification of Over-Represented Combinations of Transcription Factor Binding Sites in Sets of Co-Expressed Genes. APBC Shao-Shan Huang, Debra L. Fulton, David J. Arenillas, Paul Perco, Shannan J. Ho Sui, James R. Mortimer, Wyeth W. Wasserman
2006	J	`jnl`	SAGE2Splice: Unmapped SAGE Tags Reveal Novel Splice Junctions. PLoS Comput. Biol. Byron Yu-Lin Kuo, Ying Chen, Slavita Bohacec, Öjvind Johansson, Wyeth W. Wasserman, Elizabeth M. Simpson
2006	J	`jnl`	Visualization of complementary systems biology data with parallel heatmaps. IBM J. Res. Dev. Raf M. Podowski, Brett Miller, Wyeth W. Wasserman
2005	J	`jnl`	The Gene Set Builder: collation, curation, and distribution of sets of genes. BMC Bioinform. Dimas Yusuf, Jonathan S. Lim, Wyeth W. Wasserman
2004	J	`jnl`	ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res. Albin Sandelin, Wyeth W. Wasserman, Boris Lenhard
2004	J	`jnl`	JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. Albin Sandelin, Wynand Alkema, Pär G. Engström, Wyeth W. Wasserman, Boris Lenhard
2004	J	`jnl`	MSCAN: identification of functional clusters of transcription factor binding sites. Nucleic Acids Res. Wynand Alkema, Öjvind Johansson, Jens Lagergren, Wyeth W. Wasserman
2003	—	`conf`	Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm. ISMB (Supplement of Bioinformatics) Öjvind Johansson, Wynand Alkema, Wyeth W. Wasserman, Jens Lagergren
2002	J	`jnl`	TFBS: Computational framework for transcription factor binding site analysis. Bioinform. Boris Lenhard, Wyeth W. Wasserman