{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T17:53:10Z","timestamp":1770832390995,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Time series expression experiments are an increasingly popular method for studying a wide range of biological systems. Here we developed an algorithm that can infer the local network of gene\u2013gene interactions surrounding a gene of interest. This is achieved by a perturbation of the gene of interest and subsequently measuring the gene expression profiles at multiple time points. We applied this algorithm to computer simulated data and to experimental data on a nine gene network in Escherichia coli.<\/jats:p>\n               <jats:p>Results: In this paper we show that it is possible to recover the gene regulatory network from a time series data of gene expression following a perturbation to the cell. We show this both on simulated data and on a nine gene subnetwork part of the DNA-damage response pathway (SOS pathway) in the bacteria E. coli.<\/jats:p>\n               <jats:p>Contact: \u00a0dibernardo@tigem.it<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl003","type":"journal-article","created":{"date-parts":[[2006,1,18]],"date-time":"2006-01-18T03:13:59Z","timestamp":1137554039000},"page":"815-822","source":"Crossref","is-referenced-by-count":304,"title":["Inference of gene regulatory networks and compound mode of action from time course gene expression profiles"],"prefix":"10.1093","volume":"22","author":[{"given":"Mukesh","family":"Bansal","sequence":"first","affiliation":[{"name":"Telethon Institute of Genetics and Medicine 1 \u00a0 1 \u00a0 \u00a0 Via P. Castellino 111, 80131 Naples, Italy"},{"name":"European School of Molecular Medicine (SEMM) 2 \u00a0 2 \u00a0 \u00a0 Naples, Italy"}]},{"given":"Giusy Della","family":"Gatta","sequence":"additional","affiliation":[{"name":"Telethon Institute of Genetics and Medicine 1 \u00a0 1 \u00a0 \u00a0 Via P. Castellino 111, 80131 Naples, Italy"},{"name":"Seconda Universita degli Studi di Napoli 3 \u00a0 3 \u00a0 \u00a0 Naples, Italy"}]},{"given":"Diego","family":"di Bernardo","sequence":"additional","affiliation":[{"name":"Telethon Institute of Genetics and Medicine 1 \u00a0 1 \u00a0 \u00a0 Via P. 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