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Evaluating Methods for the Prediction of Cell Type-Specific Enhancers in the Mammalian Cortex.

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Title: Evaluating Methods for the Prediction of Cell Type-Specific Enhancers in the Mammalian Cortex.
Authors: Johansen NJ; Allen Institute for Brain Science, Seattle, WA 98109.; These authors contributed equally., Kempynck N; VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium.; These authors contributed equally., Zemke NR; Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093., Somasundaram S; Allen Institute for Brain Science, Seattle, WA 98109., De Winter S; VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium., Hooper M; Allen Institute for Brain Science, Seattle, WA 98109., Dwivedi D; Allen Institute for Brain Science, Seattle, WA 98109., Lohia R; Physiology Department and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada., Wehbe F; Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada., Li B; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China., Abaffyová D; VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium., Armand EJ; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093., De Man J; VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium., Eksi EC; VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium., Hecker N; VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium., Hulselmans G; VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium., Konstantakos V; VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium., Mauduit D; VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium., Mich JK; Allen Institute for Brain Science, Seattle, WA 98109., Partel G; VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium., Daigle TL; Allen Institute for Brain Science, Seattle, WA 98109., Levi BP; Allen Institute for Brain Science, Seattle, WA 98109., Zhang K; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China., Tanaka Y; Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada., Gillis J; Physiology Department and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada., Ting JT; Allen Institute for Brain Science, Seattle, WA 98109.; Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195., Ben-Simon Y; Allen Institute for Brain Science, Seattle, WA 98109., Miller J; Allen Institute for Brain Science, Seattle, WA 98109., Ecker JR; Salk Institute for Biological Studies, La Jolla, CA 92037., Ren B; Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093., Aerts S; VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium., Lein ES; Allen Institute for Brain Science, Seattle, WA 98109., Tasic B; Allen Institute for Brain Science, Seattle, WA 98109., Bakken TE; Allen Institute for Brain Science, Seattle, WA 98109.; Lead contact.
Source: BioRxiv : the preprint server for biology [bioRxiv] 2025 Mar 25. Date of Electronic Publication: 2025 Mar 25.
Publication Type: Journal Article; Preprint
Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE
Database: MEDLINE Ultimate
FullText Text:
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  Data: Evaluating Methods for the Prediction of Cell Type-Specific Enhancers in the Mammalian Cortex.
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  Data: <searchLink fieldCode="AU" term="%22Johansen+NJ%22">Johansen NJ</searchLink>; Allen Institute for Brain Science, Seattle, WA 98109.; These authors contributed equally.<br /><searchLink fieldCode="AU" term="%22Kempynck+N%22">Kempynck N</searchLink>; VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium.; These authors contributed equally.<br /><searchLink fieldCode="AU" term="%22Zemke+NR%22">Zemke NR</searchLink>; Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093.<br /><searchLink fieldCode="AU" term="%22Somasundaram+S%22">Somasundaram S</searchLink>; Allen Institute for Brain Science, Seattle, WA 98109.<br /><searchLink fieldCode="AU" term="%22De+Winter+S%22">De Winter S</searchLink>; VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium.<br /><searchLink fieldCode="AU" term="%22Hooper+M%22">Hooper M</searchLink>; Allen Institute for Brain Science, Seattle, WA 98109.<br /><searchLink fieldCode="AU" term="%22Dwivedi+D%22">Dwivedi D</searchLink>; Allen Institute for Brain Science, Seattle, WA 98109.<br /><searchLink fieldCode="AU" term="%22Lohia+R%22">Lohia R</searchLink>; Physiology Department and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.<br /><searchLink fieldCode="AU" term="%22Wehbe+F%22">Wehbe F</searchLink>; Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada.<br /><searchLink fieldCode="AU" term="%22Li+B%22">Li B</searchLink>; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.<br /><searchLink fieldCode="AU" term="%22Abaffyová+D%22">Abaffyová D</searchLink>; VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium.<br /><searchLink fieldCode="AU" term="%22Armand+EJ%22">Armand EJ</searchLink>; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093.<br /><searchLink fieldCode="AU" term="%22De+Man+J%22">De Man J</searchLink>; VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium.<br /><searchLink fieldCode="AU" term="%22Eksi+EC%22">Eksi EC</searchLink>; VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium.<br /><searchLink fieldCode="AU" term="%22Hecker+N%22">Hecker N</searchLink>; VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium.<br /><searchLink fieldCode="AU" term="%22Hulselmans+G%22">Hulselmans G</searchLink>; VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium.<br /><searchLink fieldCode="AU" term="%22Konstantakos+V%22">Konstantakos V</searchLink>; VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium.<br /><searchLink fieldCode="AU" term="%22Mauduit+D%22">Mauduit D</searchLink>; VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium.<br /><searchLink fieldCode="AU" term="%22Mich+JK%22">Mich JK</searchLink>; Allen Institute for Brain Science, Seattle, WA 98109.<br /><searchLink fieldCode="AU" term="%22Partel+G%22">Partel G</searchLink>; VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium.<br /><searchLink fieldCode="AU" term="%22Daigle+TL%22">Daigle TL</searchLink>; Allen Institute for Brain Science, Seattle, WA 98109.<br /><searchLink fieldCode="AU" term="%22Levi+BP%22">Levi BP</searchLink>; Allen Institute for Brain Science, Seattle, WA 98109.<br /><searchLink fieldCode="AU" term="%22Zhang+K%22">Zhang K</searchLink>; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.<br /><searchLink fieldCode="AU" term="%22Tanaka+Y%22">Tanaka Y</searchLink>; Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada.<br /><searchLink fieldCode="AU" term="%22Gillis+J%22">Gillis J</searchLink>; Physiology Department and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.<br /><searchLink fieldCode="AU" term="%22Ting+JT%22">Ting JT</searchLink>; Allen Institute for Brain Science, Seattle, WA 98109.; Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195.<br /><searchLink fieldCode="AU" term="%22Ben-Simon+Y%22">Ben-Simon Y</searchLink>; Allen Institute for Brain Science, Seattle, WA 98109.<br /><searchLink fieldCode="AU" term="%22Miller+J%22">Miller J</searchLink>; Allen Institute for Brain Science, Seattle, WA 98109.<br /><searchLink fieldCode="AU" term="%22Ecker+JR%22">Ecker JR</searchLink>; Salk Institute for Biological Studies, La Jolla, CA 92037.<br /><searchLink fieldCode="AU" term="%22Ren+B%22">Ren B</searchLink>; Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093.<br /><searchLink fieldCode="AU" term="%22Aerts+S%22">Aerts S</searchLink>; VIB Center for AI & Computational Biology, VIB-KU Leuven Center for Brain and Disease Research & KU Leuven Department of Human Genetics, Leuven, Belgium.<br /><searchLink fieldCode="AU" term="%22Lein+ES%22">Lein ES</searchLink>; Allen Institute for Brain Science, Seattle, WA 98109.<br /><searchLink fieldCode="AU" term="%22Tasic+B%22">Tasic B</searchLink>; Allen Institute for Brain Science, Seattle, WA 98109.<br /><searchLink fieldCode="AU" term="%22Bakken+TE%22">Bakken TE</searchLink>; Allen Institute for Brain Science, Seattle, WA 98109.; Lead contact.
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