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Computational methodologies that propose pathway\/mechanism communities and reveal respective relationships can be of great value as they can help expedite the process of identifying how perturbations in a single pathway can affect other pathways.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present a random-walks-based methodology called PathWalks, where a walker crosses a pathway-to-pathway network under the guidance of a disease-related map. The latter is a gene network that we construct by integrating multi-source information regarding a specific disease. The most frequent trajectories highlight communities of pathways that are expected to be strongly related to the disease under study.<\/jats:p>\n                    <jats:p>We apply the PathWalks methodology on Alzheimer's disease and idiopathic pulmonary fibrosis and establish that it can highlight pathways that are also identified by other pathway analysis tools as well as are backed through bibliographic references. More importantly, PathWalks produces additional new pathways that are functionally connected with those already established, giving insight for further experimentation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>https:\/\/github.com\/vagkaratzas\/PathWalks.<\/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\/btaa291","type":"journal-article","created":{"date-parts":[[2020,4,27]],"date-time":"2020-04-27T07:09:23Z","timestamp":1587971363000},"page":"4070-4079","source":"Crossref","is-referenced-by-count":4,"title":["PathWalks: identifying pathway communities using a disease-related map of integrated information"],"prefix":"10.1093","volume":"36","author":[{"given":"Evangelos","family":"Karatzas","sequence":"first","affiliation":[{"name":"Department of Informatics and Telecommunications , University of Athens, Athens 15703, Greece"}]},{"given":"Margarita","family":"Zachariou","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics , The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus"},{"name":"The Cyprus School of Molecular Medicine , The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus"}]},{"given":"Marilena M","family":"Bourdakou","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics , The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus"},{"name":"Department of Medicine , Laboratory of Pharmacology, Democritus University of Thrace, Komotini, Greece"}]},{"given":"George","family":"Minadakis","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics , The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus"},{"name":"The Cyprus School of Molecular Medicine , The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus"}]},{"given":"Anastasis","family":"Oulas","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics , The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus"},{"name":"The Cyprus School of Molecular Medicine , The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus"}]},{"given":"George","family":"Kolios","sequence":"additional","affiliation":[{"name":"Department of Medicine , Laboratory of Pharmacology, Democritus University of Thrace, Komotini, Greece"}]},{"given":"Alex","family":"Delis","sequence":"additional","affiliation":[{"name":"Department of Informatics and Telecommunications , University of Athens, Athens 15703, Greece"}]},{"given":"George M","family":"Spyrou","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics , The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus"},{"name":"The Cyprus School of Molecular Medicine , The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus"}]}],"member":"286","published-online":{"date-parts":[[2020,5,5]]},"reference":[{"key":"2023062312040236400_btaa291-B1","doi-asserted-by":"crossref","first-page":"204","DOI":"10.3390\/cells9010204","article-title":"The role of Ca2+ signaling in aging and neurodegeneration: insights from Caenorhabditis elegans models","volume":"9","author":"Alvarez","year":"2020","journal-title":"Cells"},{"key":"2023062312040236400_btaa291-B2","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1016\/j.jalz.2016.12.006","article-title":"Calcium hypothesis of Alzheimer\u2019s disease and brain aging: a framework for integrating new evidence into a comprehensive theory of pathogenesis","volume":"13","year":"2017","journal-title":"Alzheimers Dement"},{"key":"2023062312040236400_btaa291-B3","doi-asserted-by":"crossref","first-page":"D789","DOI":"10.1093\/nar\/gku1205","article-title":"OMIM. org: Online Mendelian Inheritance in Man (OMIM\u00ae), an online catalog of human genes and genetic disorders","volume":"43","author":"Amberger","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023062312040236400_btaa291-B4","doi-asserted-by":"crossref","first-page":"262","DOI":"10.3109\/10799893.2010.489227","article-title":"Expression analysis of Akt and MAPK signaling pathways in lung tissue of patients with idiopathic pulmonary fibrosis (IPF)","volume":"30","author":"Antoniou","year":"2010","journal-title":"J. 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