The next generation of transcription factor binding site prediction von Mathelier, Anthony, Wasserman, Wyeth W

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Obtaining genetics insights from deep learning via explainable artificial intelligence von Novakovsky, Gherman, Dexter, Nick, Libbrecht, Maxwell W., Wasserman, Wyeth W., Mostafavi, Sara

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Genome-wide prediction of cis-regulatory regions using supervised deep learning methods von Li, Yifeng, Shi, Wenqiang, Wasserman, Wyeth W

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JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles von Castro-Mondragon, Jaime A, Riudavets-Puig, Rafael, Rauluseviciute, Ieva, Berhanu Lemma, Roza, Turchi, Laura, Blanc-Mathieu, Romain, Lucas, Jeremy, Boddie, Paul, Khan, Aziz, Manosalva Pérez, Nicolás, Fornes, Oriol, Leung, Tiffany Y, Aguirre, Alejandro, Hammal, Fayrouz, Schmelter, Daniel, Baranasic, Damir, Ballester, Benoit, Sandelin, Albin, Lenhard, Boris, Vandepoele, Klaas, Wasserman, Wyeth W, Parcy, François, Mathelier, Anthony

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Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters von Li, Yifeng, Chen, Chih-Yu, Wasserman, Wyeth W

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JASPAR 2020: update of the open-access database of transcription factor binding profiles von Fornes, Oriol, Castro-Mondragon, Jaime A, Khan, Aziz, van der Lee, Robin, Zhang, Xi, Richmond, Phillip A, Modi, Bhavi P, Correard, Solenne, Gheorghe, Marius, Baranašić, Damir, Santana-Garcia, Walter, Tan, Ge, Chèneby, Jeanne, Ballester, Benoit, Parcy, François, Sandelin, Albin, Lenhard, Boris, Wasserman, Wyeth W, Mathelier, Anthony

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JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework von Khan, Aziz, Fornes, Oriol, Stigliani, Arnaud, Gheorghe, Marius, Castro-Mondragon, Jaime A, van der Lee, Robin, Bessy, Adrien, Chèneby, Jeanne, Kulkarni, Shubhada R, Tan, Ge, Baranasic, Damir, Arenillas, David J, Sandelin, Albin, Vandepoele, Klaas, Lenhard, Boris, Ballester, Benoît, Wasserman, Wyeth W, Parcy, François, Mathelier, Anthony

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ExplaiNN: interpretable and transparent neural networks for genomics von Novakovsky, Gherman, Fornes, Oriol, Saraswat, Manu, Mostafavi, Sara, Wasserman, Wyeth W

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JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles von Rauluseviciute, Ieva, Riudavets-Puig, Rafael, Blanc-Mathieu, Romain, Castro-Mondragon, Jaime A, Ferenc, Katalin, Kumar, Vipin, Lemma, Roza Berhanu, Lucas, Jérémy, Chèneby, Jeanne, Baranasic, Damir, Khan, Aziz, Fornes, Oriol, Gundersen, Sveinung, Johansen, Morten, Hovig, Eivind, Lenhard, Boris, Sandelin, Albin, Wasserman, Wyeth W, Parcy, François, Mathelier, Anthony

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JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles von Mathelier, Anthony, Fornes, Oriol, Arenillas, David J, Chen, Chih-Yu, Denay, Grégoire, Lee, Jessica, Shi, Wenqiang, Shyr, Casper, Tan, Ge, Worsley-Hunt, Rebecca, Zhang, Allen W, Parcy, François, Lenhard, Boris, Sandelin, Albin, Wasserman, Wyeth W

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JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework von Khan, Aziz, Fornes, Oriol, Stigliani, Arnaud, Gheorghe, Marius, Castro-Mondragon, Jaime A, van der Lee, Robin, Bessy, Adrien, Chèneby, Jeanne, Kulkarni, Shubhada R, Tan, Ge, Baranasic, Damir, Arenillas, David J, Sandelin, Albin, Vandepoele, Klaas, Lenhard, Boris, Ballester, Benoît, Wasserman, Wyeth W, Parcy, François, Mathelier, Anthony

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Identification of altered cis -regulatory elements in human disease von Mathelier, Anthony, Shi, Wenqiang, Wasserman, Wyeth W

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JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles von Mathelier, Anthony, Zhao, Xiaobei, Zhang, Allen W, Parcy, François, Worsley-Hunt, Rebecca, Arenillas, David J, Buchman, Sorana, Chen, Chih-yu, Chou, Alice, Ienasescu, Hans, Lim, Jonathan, Shyr, Casper, Tan, Ge, Zhou, Michelle, Lenhard, Boris, Sandelin, Albin, Wasserman, Wyeth W

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Biologically relevant transfer learning improves transcription factor binding prediction von Novakovsky, Gherman, Saraswat, Manu, Fornes, Oriol, Mostafavi, Sara, Wasserman, Wyeth W.

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Applied bioinformatics for the identification of regulatory elements von Wasserman, Wyeth W, Sandelin, Albin

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

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ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data von Dolzhenko, Egor, Bennett, Mark F., Richmond, Phillip A., Trost, Brett, Chen, Sai, van Vugt, Joke J. F. A., Nguyen, Charlotte, Narzisi, Giuseppe, Gainullin, Vladimir G., Gross, Andrew M., Lajoie, Bryan R., Taft, Ryan J., Wasserman, Wyeth W., Scherer, Stephen W., Veldink, Jan H., Bentley, David R., Yuen, Ryan K. C., Bahlo, Melanie, Eberle, Michael A.

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TFBSshape: a motif database for DNA shape features of transcription factor binding sites von Yang, Lin, Zhou, Tianyin, Dror, Iris, Mathelier, Anthony, Wasserman, Wyeth W, Gordân, Raluca, Rohs, Remo

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oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets von Kwon, Andrew T, Arenillas, David J, Worsley Hunt, Rebecca, Wasserman, Wyeth W

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OnTarget: in silico design of MiniPromoters for targeted delivery of expression von Fornes, Oriol, Av-Shalom, Tamar V, Korecki, Andrea J, Farkas, Rachelle A, Arenillas, David J, Mathelier, Anthony, Simpson, Elizabeth M, Wasserman, Wyeth W

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