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ORCIDWyeth W. Wasserman
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- affiliation: University of British Columbia, Vancouver, BC, Canada
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2020 – today
- 2023
[j36]Oriol Fornes
, Tamar Vered Av-Shalom, Andrea J. Korecki, Rachelle A. Farkas, David J. Arenillas, Anthony Mathelier, Elizabeth M. Simpson, Wyeth W. Wasserman:
OnTarget: in silico design of MiniPromoters for targeted delivery of expression. Nucleic Acids Res. 51(W1): 379-386 (2023)- 2022
- [j35]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:
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 50(D1): 165-173 (2022) - 2021
- [j34]Phillip Andrew Richmond, Alice Mary Kaye, Godfrain Jacques Kounkou, Tamar Vered Av-Shalom, Wyeth W. Wasserman:
Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper. PLoS Comput. Biol. 17(3) (2021) - 2020
- [j33]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:
JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 48(Database-Issue): D87-D92 (2020)
2010 – 2019
- 2019
- [j32]Wenqiang Shi, Oriol Fornes, Wyeth W. Wasserman:
Gene expression models based on transcription factor binding events confer insight into functional cis-regulatory variants. Bioinform. 35(15): 2610-2617 (2019) - [j31]Laura Puente-Santamaria, Wyeth W. Wasserman, Luis del Peso:
TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets. Bioinform. 35(24): 5339-5340 (2019) - [j30]Jessica J. Y. Lee, Clara D. M. van Karnebeek, Wyeth W. Wasserman:
Development and user evaluation of a rare disease gene prioritization workflow based on cognitive ergonomics. J. Am. Medical Informatics Assoc. 26(2): 124-133 (2019) - 2018
- [j29]Yifeng Li, Wenqiang Shi, Wyeth W. Wasserman:
Genome-wide prediction of cis-regulatory regions using supervised deep learning methods. BMC Bioinform. 19(1): 202:1-202:14 (2018) - [j28]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:
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. 46(Database-Issue): D1284 (2018) - [j27]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:
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. 46(Database-Issue): D260-D266 (2018) - 2016
- [j26]David J. Arenillas, Alistair R. R. Forrest, Hideya Kawaji, Timo Lassmann, Wyeth W. Wasserman, Anthony Mathelier:
CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs. Bioinform. 32(18): 2858-2860 (2016) - [j25]Casper Shyr, André Kushniruk, Clara D. M. van Karnebeek, Wyeth W. Wasserman:
Dynamic software design for clinical exome and genome analyses: insights from bioinformaticians, clinical geneticists, and genetic counselors. J. Am. Medical Informatics Assoc. 23(2): 257-268 (2016) - [j24]Yifeng Li, Chih-Yu Chen, Wyeth W. Wasserman:
Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters. J. Comput. Biol. 23(5): 322-336 (2016) - [j23]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:
JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 44(Database-Issue): 110-115 (2016) - 2015
- [j22]Yifeng Li, Chih-Yu Chen, Alice Mary Kaye, Wyeth W. Wasserman:
The identification of cis-regulatory elements: A review from a machine learning perspective. Biosyst. 138: 6-17 (2015) - [c3]Yifeng Li, Chih-Yu Chen, Wyeth W. Wasserman:
Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters. RECOMB 2015: 205-217 - 2014
- [j21]Casper Shyr, André Kushniruk, Wyeth W. Wasserman:
Usability study of clinical exome analysis software: Top lessons learned and recommendations. J. Biomed. Informatics 51: 129-136 (2014) - [j20]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:
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 42(Database-Issue): 142-147 (2014) - [j19]Lin Yang, Tianyin Zhou, Iris Dror, Anthony Mathelier, Wyeth W. Wasserman, Raluca Gordân, Remo Rohs:
NAR Breakthrough Article: TFBSshape: a motif database for DNA shape features of transcription factor binding sites. Nucleic Acids Res. 42(Database-Issue): 148-155 (2014) - [j18]The 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, Masayoshi Itoh, Robin Andersson, Christopher J. Mungall, Terrence F. Meehan, Sebastian Schmeier, Nicolas Bertin, Mette Jørgensen, Emmanuel Dimont, Erik Arner, Christian Schmidl, Ulf Schaefer, Yulia A. Medvedeva, Charles Plessy, Morana Vitezic, Jessica Severin, Colin A. M. Semple, Yuri Ishizu, Robert S. Young, Margherita Francescatto, Intikhab Alam, Davide Albanese, Gabriel M. Altschuler, Takahiro Arakawa, John A. C. Archer, Peter Arner, Magda Babina, Sarah Rennie, Piotr J. Balwierz, Anthony G. Beckhouse, Swati Pradhan-Bhatt, Judith A. Blake, Antje Blumenthal, Beatrice Bodega, Alessandro Bonetti, James Briggs, Frank Brombacher, A. Maxwell Burroughs, Andrea Califano, Carlo V. Cannistraci, Daniel Carbajo, Yun Chen, Marco Chierici, Yari Ciani, Hans Clevers, Emiliano Dalla, Carrie A. Davis, Michael Detmar, Alexander D. Diehl, Taeko Dohi, Finn Drabløs, Albert S. B. Edge, Matthias Edinger, Karl Ekwall, Mitsuhiro Endoh, Hideki Enomoto, Michela Fagiolini, Lynsey Fairbairn, Hai Fang, Mary C. Farach-Carson, Geoffrey J. Faulkner, Alexander V. Favorov, Malcolm E. Fisher, Martin C. Frith, Rie Fujita, Shiro Fukuda, Cesare Furlanello, Masaaki Furuno, Jun-ichi Furusawa, Teunis B. Geijtenbeek, Andrew P. Gibson, Thomas R. Gingeras, Daniel Goldowitz, Julian Gough, Sven Guhl, Reto Guler, Stefano Gustincich, Thomas J. Ha, Masahide Hamaguchi, Mitsuko Hara, Matthias Harbers, Jayson Harshbarger, Akira Hasegawa, Yuki Hasegawa, Takehiro Hashimoto, Meenhard Herlyn, Kelly J. Hitchens, Shannan J. Ho Sui, Oliver M. Hofmann, Ilka Hoof, Fumi Hori, Lukasz Huminiecki, Kei Iida, Tomokatsu Ikawa, Boris R. Jankovic, Hui Jia, Anagha Joshi, Giuseppe Jurman, Bogumil Kaczkowski, Chieko Kai, Kaoru Kaida, Ai Kaiho, Kazuhiro Kajiyama, Mutsumi Kanamori-Katayama, Artem S. Kasianov, Takeya Kasukawa, Shintaro Katayama, Sachi Kato, Shuji Kawaguchi, Hiroshi Kawamoto, Yuki I. Kawamura, Tsugumi Kawashima, Judith S. Kempfle, Tony J. Kenna, Juha Kere, Levon M. Khachigian, Toshio Kitamura, S. Peter Klinken, Alan J. Knox, Miki Kojima, Soichi Kojima, Naoto Kondo, Haruhiko Koseki, Shigeo Koyasu, Sarah Krampitz, Atsutaka Kubosaki, Andrew T. Kwon, Jeroen F. J. Laros, Weonju Lee, Andreas Lennartsson, Kang Li, Berit Lilje, Leonard Lipovich, Alan Mackay-Sim, Ri-ichiroh Manabe, Jessica Cara Mar, Benoit Marchand, Anthony Mathelier, Niklas Mejhert, Alison M. Meynert, Yosuke Mizuno, David A. de Lima Morais, Hiromasa Morikawa, Mitsuru Morimoto, Kazuyo Moro, Efthymios Motakis, Hozumi Motohashi, Christine Mummery, Mitsuyoshi Murata, Sayaka Nagao-Sato, Yutaka Nakachi, Fumio Nakahara, Toshiyuki Nakamura, Yukio Nakamura, Kenichi Nakazato, Erik van Nimwegen, Noriko Ninomiya, Hiromi Nishiyori, Shohei Noma, Tadasuke Nozaki, Soichi Ogishima, Naganari Ohkura, Hiroko Ohmiya, Hiroshi Ohno, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Yasushi Okazaki, Valerio Orlando, Dmitry A. Ovchinnikov, Arnab Pain, Robert Passier, Margaret Patrikakis, Helena Persson, Silvano Piazza, James G. D. Prendergast, Owen J. L. Rackham, Jordan A. Ramilowski, Mamoon Rashid, Timothy Ravasi, Patrizia Rizzu, Marco Roncador, Sugata Roy, Morten B. Rye, Eri Saijyo, Antti Sajantila, Akiko Saka, Shimon Sakaguchi, Mizuho Sakai, Hiroki Sato, Hironori Sato, Suzana Savvi, Alka Saxena, Claudio Schneider, Erik A. Schultes, Gundula G. Schulze-Tanzil, Anita Schwegmann, Thierry Sengstag, Guojun Sheng, Hisashi Shimoji, Yishai Shimoni, Jay W. Shin, Christophe Simon, Daisuke Sugiyama, Takaaki Sugiyama, Masanori Suzuki, Naoko Suzuki, Rolf K. Swoboda, Peter A. C. 't Hoen, Michihira Tagami, Naoko Takahashi, Jun Takai, Hiroshi Tanaka, Hideki Tatsukawa, Zuotian Tatum, Mark Thompson, Hiroo Toyoda, Tetsuro Toyoda, Eivind Valen, Marc van de Wetering, Linda M. van den Berg, Roberto Verardo, Dipti Vijayan, Ilya E. Vorontsov, Wyeth W. Wasserman, Shoko Watanabe, Christine A. Wells, Louise N. Winteringham, Ernst Wolvetang, Emily J. Wood, Yoko Yamaguchi, Masayuki Yamamoto, Misako Yoneda, Yohei Yonekura, Shigehiro Yoshida, Susan E. Zabierowski, Peter G. Zhang, Xiaobei Zhao, Silvia Zucchelli, Kim M. Summers, Harukazu Suzuki, Carsten O. Daub, Jun Kawai, Peter Heutink, Winston Hide, Tom C. Freeman, Boris Lenhard, Vladimir B. Bajic, Martin S. Taylor, Vsevolod J. Makeev, Albin Sandelin, David A. Hume, Piero Carninci, Yoshihide Hayashizaki:
A promoter-level mammalian expression atlas. Nat. 507(7493): 462-470 (2014) - 2013
- [j17]Anthony Mathelier, Wyeth W. Wasserman:
The Next Generation of Transcription Factor Binding Site Prediction. PLoS Comput. Biol. 9(9) (2013) - 2012
- [j16]Warren A. Cheung, B. F. Francis Ouellette, Wyeth W. Wasserman:
Quantitative biomedical annotation using medical subject heading over-representation profiles (MeSHOPs). BMC Bioinform. 13: 249 (2012) - 2011
- [j15]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:
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. 12: 67 (2011) - [j14]Andrew T. Kwon, Alice Yi Chou, David J. Arenillas, Wyeth W. Wasserman:
Validation of Skeletal Muscle cis-Regulatory Module Predictions Reveals Nucleotide Composition Bias in Functional Enhancers. PLoS Comput. Biol. 7(12) (2011) - 2010
- [j13]Elodie Portales-Casamar, Supat Thongjuea, Andrew T. Kwon, David J. Arenillas, Xiaobei Zhao, Eivind Valen, Dimas Yusuf, Boris Lenhard, Wyeth W. Wasserman, Albin Sandelin:
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res. 38(Database-Issue): 105-110 (2010)
2000 – 2009
- 2009
- [j12]Elodie Portales-Casamar, David J. Arenillas, Jonathan S. Lim, Magdalena I. Swanson, Steven Jiang, Anthony McCallum, Stefan Kirov, Wyeth W. Wasserman:
The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences. Nucleic Acids Res. 37(Database-Issue): 54-60 (2009) - 2008
- [j11]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:
ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res. 36(Database-Issue): 107-113 (2008) - [j10]Malin C. Andersen, Pär G. Engström, Stuart Lithwick, David J. Arenillas, Per Eriksson, Boris Lenhard, Wyeth W. Wasserman, Jacob Odeberg:
In Silico Detection of Sequence Variations Modifying Transcriptional Regulation. PLoS Comput. Biol. 4(1) (2008) - 2007
- [j9]Shannan J. Ho Sui, Debra L. Fulton, David J. Arenillas, Andrew T. Kwon, Wyeth W. Wasserman:
oPOSSUM: integrated tools for analysis of regulatory motif over-representation. Nucleic Acids Res. 35(Web-Server-Issue): 245-252 (2007) - 2006
- [j8]Raf M. Podowski, Brett Miller, Wyeth W. Wasserman:
Visualization of complementary systems biology data with parallel heatmaps. IBM J. Res. Dev. 50(6): 575-582 (2006) - [j7]Dominique Vlieghe, Albin Sandelin, Pieter J. De Bleser, Kris Vleminckx, Wyeth W. Wasserman, Frans van Roy, Boris Lenhard:
A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Res. 34(Database-Issue): 95-97 (2006) - [j6]Byron Yu-Lin Kuo, Ying Chen, Slavita Bohacec, Öjvind Johansson, Wyeth W. Wasserman, Elizabeth M. Simpson:
SAGE2Splice: Unmapped SAGE Tags Reveal Novel Splice Junctions. PLoS Comput. Biol. 2(4) (2006) - [c2]Shao-Shan Huang, Debra L. Fulton, David J. Arenillas, Paul Perco, Shannan J. Ho Sui, James R. Mortimer, Wyeth W. Wasserman:
Identification of Over-Represented Combinations of Transcription Factor Binding Sites in Sets of Co-Expressed Genes. APBC 2006: 247-256 - 2005
- [j5]Dimas Yusuf, Jonathan S. Lim, Wyeth W. Wasserman:
The Gene Set Builder: collation, curation, and distribution of sets of genes. BMC Bioinform. 6: 305 (2005) - 2004
- [j4]Albin Sandelin, Wynand Alkema, Pär G. Engström, Wyeth W. Wasserman, Boris Lenhard:
JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 32(Database-Issue): 91-94 (2004) - [j3]Wynand Alkema, Öjvind Johansson, Jens Lagergren, Wyeth W. Wasserman:
MSCAN: identification of functional clusters of transcription factor binding sites. Nucleic Acids Res. 32(Web-Server-Issue): 195-198 (2004) - [j2]Albin Sandelin, Wyeth W. Wasserman, Boris Lenhard:
ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res. 32(Web-Server-Issue): 249-252 (2004) - 2003
- [c1]Öjvind Johansson, Wynand Alkema, Wyeth W. Wasserman, Jens Lagergren:
Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm. ISMB (Supplement of Bioinformatics) 2003: 169-176 - 2002
- [j1]Boris Lenhard, Wyeth W. Wasserman:
TFBS: Computational framework for transcription factor binding site analysis. Bioinform. 18(8): 1135-1136 (2002)
Coauthor Index
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