{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T18:02:14Z","timestamp":1774375334742,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2018,6,20]],"date-time":"2018-06-20T00:00:00Z","timestamp":1529452800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Federal Ministry of Education and Research of Germany"},{"DOI":"10.13039\/501100002347","name":"BMBF","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"name":"ZiSS-Trans","award":["02NUK047E"],"award-info":[{"award-number":["02NUK047E"]}]},{"name":"ColoSys and MapTorNet","award":["031A426A"],"award-info":[{"award-number":["031A426A"]}]},{"DOI":"10.13039\/501100017268","name":"Berlin Institute of Health","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100017268","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Intracellular signalling is realized by complex signalling networks, which are almost impossible to understand without network models, especially if feedbacks are involved. Modular Response Analysis (MRA) is a convenient modelling method to study signalling networks in various contexts.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We developed the software package STASNet (STeady-STate Analysis of Signalling Networks) that provides an augmented and extended version of MRA suited to model signalling networks from incomplete perturbation schemes and multi-perturbation data. Using data from the Dialogue on Reverse Engineering Assessment and Methods challenge, we show that predictions from STASNet models are among the top-performing methods. We applied the method to study the effect of SHP2, a protein that has been implicated in resistance to targeted therapy in colon cancer, using a novel dataset from the colon cancer cell line Widr and a SHP2-depleted derivative. We find that SHP2 is required for mitogen-activated protein kinase signalling, whereas AKT signalling only partially depends on SHP2.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>An R-package is available at https:\/\/github.com\/molsysbio\/STASNet.<\/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\/bty473","type":"journal-article","created":{"date-parts":[[2018,6,13]],"date-time":"2018-06-13T07:13:21Z","timestamp":1528874001000},"page":"4079-4086","source":"Crossref","is-referenced-by-count":31,"title":["Modelling signalling networks from perturbation data"],"prefix":"10.1093","volume":"34","author":[{"given":"Mathurin","family":"Dorel","sequence":"first","affiliation":[{"name":"Institute of Pathology, Charit\u00e9 Universit\u00e4tsmedizin, Berlin, Germany"},{"name":"IRI Life Sciences, Humboldt University of Berlin, Berlin, Germany"},{"name":"Berlin Institute of Health, Berlin, Germany"}]},{"given":"Bertram","family":"Klinger","sequence":"additional","affiliation":[{"name":"Institute of Pathology, Charit\u00e9 Universit\u00e4tsmedizin, Berlin, Germany"},{"name":"IRI Life Sciences, Humboldt University of Berlin, Berlin, Germany"}]},{"given":"Torsten","family":"Gross","sequence":"additional","affiliation":[{"name":"Institute of Pathology, Charit\u00e9 Universit\u00e4tsmedizin, Berlin, Germany"},{"name":"IRI Life Sciences, Humboldt University of Berlin, Berlin, Germany"}]},{"given":"Anja","family":"Sieber","sequence":"additional","affiliation":[{"name":"Institute of Pathology, Charit\u00e9 Universit\u00e4tsmedizin, Berlin, Germany"},{"name":"IRI Life Sciences, Humboldt University of Berlin, Berlin, Germany"}]},{"given":"Anirudh","family":"Prahallad","sequence":"additional","affiliation":[{"name":"Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, CX, Amsterdam, The Netherlands"}]},{"given":"Evert","family":"Bosdriesz","sequence":"additional","affiliation":[{"name":"Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, CX, Amsterdam, The Netherlands"}]},{"given":"Lodewyk F A","family":"Wessels","sequence":"additional","affiliation":[{"name":"Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, CX, Amsterdam, The Netherlands"}]},{"given":"Nils","family":"Bl\u00fcthgen","sequence":"additional","affiliation":[{"name":"Institute of Pathology, Charit\u00e9 Universit\u00e4tsmedizin, Berlin, Germany"},{"name":"IRI Life Sciences, Humboldt University of Berlin, Berlin, Germany"},{"name":"Berlin Institute of Health, Berlin, Germany"}]}],"member":"286","published-online":{"date-parts":[[2018,6,19]]},"reference":[{"key":"2023012712293675200_bty473-B1","doi-asserted-by":"crossref","first-page":"596","DOI":"10.1038\/nature09454","article-title":"Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant melanoma","volume":"467","author":"Bollag","year":"2010","journal-title":"Nature"},{"key":"2023012712293675200_bty473-B2","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/msb.2010.108","article-title":"A comprehensive map of the mTOR signaling network","volume":"6","author":"Caron","year":"2010","journal-title":"Mol. 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