{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T16:23:12Z","timestamp":1772814192970,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2017,6,23]],"date-time":"2017-06-23T00:00:00Z","timestamp":1498176000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The concept of a \u2018mechanism-based taxonomy of human disease\u2019 is currently replacing the outdated paradigm of diseases classified by clinical appearance. We have tackled the paradigm of mechanism-based patient subgroup identification in the challenging area of research on neurodegenerative diseases.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have developed a knowledge base representing essential pathophysiology mechanisms of neurodegenerative diseases. Together with dedicated algorithms, this knowledge base forms the basis for a \u2018mechanism-enrichment server\u2019 that supports the mechanistic interpretation of multiscale, multimodal clinical data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>NeuroMMSig is available at http:\/\/neurommsig.scai.fraunhofer.de\/<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx399","type":"journal-article","created":{"date-parts":[[2017,6,22]],"date-time":"2017-06-22T11:16:05Z","timestamp":1498130165000},"page":"3679-3681","source":"Crossref","is-referenced-by-count":45,"title":["Multimodal mechanistic signatures for neurodegenerative diseases (NeuroMMSig): a web server for mechanism enrichment"],"prefix":"10.1093","volume":"33","author":[{"given":"Daniel","family":"Domingo-Fern\u00e1ndez","sequence":"first","affiliation":[{"name":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany"},{"name":"Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, Bonn-Aachen International Center for IT, Bonn, Germany"}]},{"given":"Alpha Tom","family":"Kodamullil","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany"},{"name":"Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, Bonn-Aachen International Center for IT, Bonn, Germany"}]},{"given":"Anandhi","family":"Iyappan","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany"},{"name":"Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, Bonn-Aachen International Center for IT, Bonn, Germany"}]},{"given":"Mufassra","family":"Naz","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany"},{"name":"Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, Bonn-Aachen International Center for IT, Bonn, Germany"}]},{"given":"Mohammad Asif","family":"Emon","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany"},{"name":"Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, Bonn-Aachen International Center for IT, Bonn, Germany"}]},{"given":"Tamara","family":"Raschka","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany"},{"name":"Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, Bonn-Aachen International Center for IT, Bonn, Germany"}]},{"given":"Reagon","family":"Karki","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany"},{"name":"Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, Bonn-Aachen International Center for IT, Bonn, Germany"}]},{"given":"Stephan","family":"Springstubbe","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany"}]},{"given":"Christian","family":"Ebeling","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany"}]},{"given":"Martin","family":"Hofmann-Apitius","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany"},{"name":"Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, Bonn-Aachen International Center for IT, Bonn, Germany"}]}],"member":"286","published-online":{"date-parts":[[2017,6,23]]},"reference":[{"key":"2023051308375389200_btx399-B1","doi-asserted-by":"crossref","first-page":"29179","DOI":"10.3390\/ijms161226148","article-title":"Bioinformatics mining and modeling methods for the identification of disease mechanisms in neurodegenerative disorders","volume":"16","author":"Hofmann-Apitius","year":"2015","journal-title":"Int. J. Mol. Sci"},{"key":"2023051308375389200_btx399-B2","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1038\/nrd4537","article-title":"Towards the taxonomy of human disease","volume":"14","author":"Hofmann-Apitius","year":"2015","journal-title":"Nat. Rev. Drug Discov"},{"key":"2023051308375389200_btx399-B3","doi-asserted-by":"crossref","first-page":"1343","DOI":"10.3233\/JAD-151178","article-title":"Towards a pathway inventory of the human brain for modeling disease mechanisms underlying neurodegeneration","volume":"52","author":"Iyappan","year":"2016","journal-title":"J. Alzheimer's Dis"},{"key":"2023051308375389200_btx399-B4","article-title":"Computational modelling approaches on epigenetic factors in neurodegenerative and autoimmune diseases and their mechanistic analysis","volume":"2015","author":"Khanam","year":"2015","journal-title":"J. Immunol. Res"},{"key":"2023051308375389200_btx399-B5","doi-asserted-by":"crossref","first-page":"e1002375","DOI":"10.1371\/journal.pcbi.1002375","article-title":"Ten years of pathway analysis: current approaches and outstanding challenges","volume":"8","author":"Khatri","year":"2012","journal-title":"PLoS Comput Biol"},{"key":"2023051308375389200_btx399-B6","doi-asserted-by":"crossref","first-page":"1329","DOI":"10.1016\/j.jalz.2015.02.006","article-title":"Computable cause-and-effect models of healthy and Alzheimer's disease states and their mechanistic differential analysis","volume":"11","author":"Kodamullil","year":"2015","journal-title":"Alzheimer's Dement"},{"key":"2023051308375389200_btx399-B7","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1093\/bib\/bbv063","article-title":"Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases","volume":"17","author":"Naz","year":"2016","journal-title":"Brief. Bioinf"},{"key":"2023051308375389200_btx399-B8","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2015","journal-title":"Proc. Natl. Acad. Sci"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/22\/3679\/50307271\/bioinformatics_33_22_3679.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/22\/3679\/50307271\/bioinformatics_33_22_3679.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,13]],"date-time":"2023-05-13T08:38:08Z","timestamp":1683967088000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/22\/3679\/3884654"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,6,23]]},"references-count":8,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2017,11,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx399","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,11,15]]},"published":{"date-parts":[[2017,6,23]]}}}