{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T14:16:04Z","timestamp":1761920164183},"reference-count":57,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,28]],"date-time":"2016-10-28T00:00:00Z","timestamp":1477612800000},"content-version":"vor","delay-in-days":139,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Most methods for reconstructing response networks from high throughput data generate static models which cannot distinguish between early and late response stages.<\/jats:p>\n               <jats:p>Results: We present TimePath, a new method that integrates time series and static datasets to reconstruct dynamic models of host response to stimulus. TimePath uses an Integer Programming formulation to select a subset of pathways that, together, explain the observed dynamic responses. Applying TimePath to study human response to HIV-1 led to accurate reconstruction of several known regulatory and signaling pathways and to novel mechanistic insights. We experimentally validated several of TimePaths\u2019 predictions highlighting the usefulness of temporal models.<\/jats:p>\n               <jats:p>Availability and Implementation: Data, Supplementary text and the TimePath software are available from http:\/\/sb.cs.cmu.edu\/timepath<\/jats:p>\n               <jats:p>Contact: \u00a0zivbj@cs.cmu.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw254","type":"journal-article","created":{"date-parts":[[2016,6,15]],"date-time":"2016-06-15T15:43:52Z","timestamp":1466005432000},"page":"i253-i261","source":"Crossref","is-referenced-by-count":15,"title":["Reconstructing the temporal progression of HIV-1 immune response pathways"],"prefix":"10.1093","volume":"32","author":[{"given":"Siddhartha","family":"Jain","sequence":"first","affiliation":[{"name":"1 Computer Science Department, Carnegie Mellon University, Pittsburgh, PA, USA"}]},{"given":"Joel","family":"Arrais","sequence":"additional","affiliation":[{"name":"2 Department of Computer Science, University of Coimbra, Coimbra, Portugal"}]},{"given":"Narasimhan J.","family":"Venkatachari","sequence":"additional","affiliation":[{"name":"3 Department of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, USA"}]},{"given":"Velpandi","family":"Ayyavoo","sequence":"additional","affiliation":[{"name":"3 Department of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, USA"}]},{"given":"Ziv","family":"Bar-Joseph","sequence":"additional","affiliation":[{"name":"4 Computational Biology and Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA, USA"}]}],"member":"286","published-online":{"date-parts":[[2016,6,11]]},"reference":[{"key":"2023020112300579100_btw254-B1","doi-asserted-by":"crossref","DOI":"10.1201\/9780203833445","volume-title":"Molecular Biology of the Cell","author":"Alberts","year":"2007","edition":"5th ed."},{"key":"2023020112300579100_btw254-B2","doi-asserted-by":"crossref","first-page":"R106.","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol"},{"key":"2023020112300579100_btw254-B3","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511804090","volume-title":"Computational Complexity: A Modern Approach.","author":"Arora","year":"2009"},{"key":"2023020112300579100_btw254-B4","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1038\/nrg3244","article-title":"Studying and modelling dynamic biological processes using time-series gene expression data","volume":"13","author":"Bar-Joseph","year":"2012","journal-title":"Nat. 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