{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,1,19]],"date-time":"2025-01-19T22:10:09Z","timestamp":1737324609609,"version":"3.33.0"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: When analyzing expression experiments, researchers are often interested in identifying the set of biological processes that are up-or down-regulated under the experimental condition studied. Current approaches, including clustering expression profiles and averaging the expression profiles of genes known to participate in specific processes, fail to provide an accurate estimate of the activity levels of many biological processes.<\/jats:p><jats:p>Results: We introduce a probabilistic continuous hidden process Model (CHPM) for time series expression data. CHPM can simultaneously determine the most probable assignment of genes to processes and the level of activation of these processes over time. To estimate model parameters, CHPM uses multiple time series datasets and incorporates prior biological knowledge. Applying CHPM to yeast expression data, we show that our algorithm produces more accurate functional assignments for genes compared to other expression analysis methods. The inferred process activity levels can be used to study the relationships between biological processes. We also report new biological experiments confirming some of the process activity levels predicted by CHPM.<\/jats:p><jats:p>Availability: A Java implementation is available at http:\\\\www.cs.cmu.edu\\~yanxins\\chpm<\/jats:p><jats:p>Contact: zivbj@cs.cmu.edu<\/jats:p><jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm218","type":"journal-article","created":{"date-parts":[[2007,7,23]],"date-time":"2007-07-23T16:13:46Z","timestamp":1185207226000},"page":"i459-i467","source":"Crossref","is-referenced-by-count":10,"title":["Continuous hidden process model for time series expression experiments"],"prefix":"10.1093","volume":"23","author":[{"given":"Yanxin","family":"Shi","sequence":"first","affiliation":[{"name":"1 School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA and 2Department of Molecular Biology, Hebrew University Medical School, Jerusalem, 91120, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Klustein","sequence":"additional","affiliation":[{"name":"1 School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA and 2Department of Molecular Biology, Hebrew University Medical School, Jerusalem, 91120, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Itamar","family":"Simon","sequence":"additional","affiliation":[{"name":"1 School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA and 2Department of Molecular Biology, Hebrew University Medical School, Jerusalem, 91120, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tom","family":"Mitchell","sequence":"additional","affiliation":[{"name":"1 School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA and 2Department of Molecular Biology, Hebrew University Medical School, Jerusalem, 91120, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ziv","family":"Bar-Joseph","sequence":"additional","affiliation":[{"name":"1 School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA and 2Department of Molecular Biology, Hebrew University Medical School, Jerusalem, 91120, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2007,7,1]]},"reference":[{"key":"2023062708514016200_B1","doi-asserted-by":"crossref","first-page":"10101","DOI":"10.1073\/pnas.97.18.10101","article-title":"Singular value decomposition for genome-wide expression data processing and modeling","volume":"97","author":"Alter","year":"2000","journal-title":"PNAS"},{"key":"2023062708514016200_B2","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1093\/bioinformatics\/btk048","article-title":"Hierarchical multi-label prediction of gene function","volume":"22","author":"Barutcuoglu","year":"2006","journal-title":"Bioinformatics"},{"journal-title":"LIBSVM: A Library for Support Vector Machines","year":"2001","author":"Chang","key":"2023062708514016200_B3"},{"key":"2023062708514016200_B4","first-page":"93","article-title":"Biclustering of expression data","author":"Cheng","year":"2000","journal-title":"Proceeding of ISMB"},{"key":"2023062708514016200_B5","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1137\/0806023","article-title":"An interior trust region approach for nonlinear minimization subject to bounds","volume":"6","author":"Coleman","year":"1996","journal-title":"SIAM J. 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