{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:03Z","timestamp":1772138043957,"version":"3.50.1"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2021,2,22]],"date-time":"2021-02-22T00:00:00Z","timestamp":1613952000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012390","name":"SystemsX.ch","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012390","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012390","name":"Swiss Initiative in Systems Biology","doi-asserted-by":"publisher","award":["RTD 2013\/152"],"award-info":[{"award-number":["RTD 2013\/152"]}],"id":[{"id":"10.13039\/501100012390","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"name":"ERC Synergy","award":["609883"],"award-info":[{"award-number":["609883"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Cancer is one of the most prevalent diseases in the world. Tumors arise due to important genes changing their activity, e.g. when inhibited or over-expressed. But these gene perturbations are difficult to observe directly. Molecular profiles of tumors can provide indirect evidence of gene perturbations. However, inferring perturbation profiles from molecular alterations is challenging due to error-prone molecular measurements and incomplete coverage of all possible molecular causes of gene perturbations.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We have developed a novel mathematical method to analyze cancer driver genes and their patient-specific perturbation profiles. We combine genetic aberrations with gene expression data in a causal network derived across patients to infer unobserved perturbations. We show that our method can predict perturbations in simulations, CRISPR perturbation screens and breast cancer samples from The Cancer Genome Atlas.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The method is available as the R-package nempi at https:\/\/github.com\/cbg-ethz\/nempi and http:\/\/bioconductor.org\/packages\/nempi.<\/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\/btab113","type":"journal-article","created":{"date-parts":[[2021,2,18]],"date-time":"2021-02-18T16:06:31Z","timestamp":1613664391000},"page":"2441-2449","source":"Crossref","is-referenced-by-count":1,"title":["Inferring perturbation profiles of cancer samples"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6986-0813","authenticated-orcid":false,"given":"Martin","family":"Pirkl","sequence":"first","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Zurich , Basel 4058, Switzerland"},{"name":"Swiss Institute of Bioinformatics , Basel 4058, Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0573-6119","authenticated-orcid":false,"given":"Niko","family":"Beerenwinkel","sequence":"additional","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Zurich , Basel 4058, Switzerland"},{"name":"Swiss Institute of Bioinformatics , Basel 4058, Switzerland"}]}],"member":"286","published-online":{"date-parts":[[2021,2,22]]},"reference":[{"key":"2023051609134871700_btab113-B1","doi-asserted-by":"crossref","first-page":"1867","DOI":"10.1016\/j.cell.2016.11.048","article-title":"A multiplexed single-cell crispr screening platform enables systematic dissection of the unfolded protein response","volume":"167","author":"Adamson","year":"2016","journal-title":"Cell"},{"key":"2023051609134871700_btab113-B2","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1038\/nbt.2284","article-title":"Combinatorial drug therapy for cancer in the post-genomic era","volume":"30","author":"Al-Lazikani","year":"2012","journal-title":"Nat. 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