{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T07:12:03Z","timestamp":1773213123707,"version":"3.50.1"},"reference-count":40,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2014,12,1]],"date-time":"2014-12-01T00:00:00Z","timestamp":1417392000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2014,12]]},"DOI":"10.1186\/s12859-014-0400-4","type":"journal-article","created":{"date-parts":[[2014,12,13]],"date-time":"2014-12-13T09:55:54Z","timestamp":1418464554000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":37,"title":["Exact reconstruction of gene regulatory networks using compressive sensing"],"prefix":"10.1186","volume":"15","author":[{"given":"Young Hwan","family":"Chang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joe W","family":"Gray","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claire J","family":"Tomlin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2014,12,14]]},"reference":[{"key":"400_CR1","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1093\/bioinformatics\/18.suppl_1.S233","volume":"18","author":"T Ideker","year":"2002","unstructured":"Ideker T, Ozier O, Schwikowski B, Siegel AF: Discovering regulatory and signaling circuits in molecular interaction networks . Bioinfomatics. 2002, 18: 233-240. 10.1093\/bioinformatics\/18.suppl_1.S233.","journal-title":"Bioinfomatics"},{"issue":"1","key":"400_CR2","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1016\/S0962-8924(02)00009-0","volume":"13","author":"HS Wiley","year":"2003","unstructured":"Wiley HS, Shvartsman SY, Lauffenburger DA: Computational modeling of the egf-receptor system: a paradigm for systems biology . Trends Cell Biol. 2003, 13 (1): 43-50. 10.1016\/S0962-8924(02)00009-0.","journal-title":"Trends Cell Biol"},{"issue":"38","key":"400_CR3","first-page":"1","volume":"3","author":"L Ma","year":"2002","unstructured":"Ma L, Iglesiass PA: Quantifying robustness of biochemical network models . BMC Bioinformatics. 2002, 3 (38): 1-13.","journal-title":"BMC Bioinformatics"},{"key":"400_CR4","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1042\/bse0450161","volume":"45","author":"ED Sontag","year":"2008","unstructured":"Sontag ED: Network reconstruction based on steady-state data . Essays Biochem. 2008, 45: 161-176. 10.1042\/BSE0450161.","journal-title":"Essays Biochem"},{"issue":"21","key":"400_CR5","doi-asserted-by":"publisher","first-page":"8340","DOI":"10.1073\/pnas.1200161109","volume":"109","author":"C Zechnera","year":"2012","unstructured":"Zechnera C, Ruessa J, Krenn P, Pelet S, Peter M, Lygeros J, Koeppl H: Moment-based inference predicts bimodality in transient gene expression . Proc Natl Acad Sci U S A. 2012, 109 (21): 8340-8345. 10.1073\/pnas.1200161109.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"400_CR6","first-page":"2755","volume-title":"Proceedings of the American Control Conference (ACC)","author":"MM Zavlanos","year":"2008","unstructured":"Zavlanos MM, Julius AA, Boyd SP, Pappas GJ: Identification of stable genetic networks using convex programming . Proceedings of the American Control Conference (ACC) . 2008, IEEE, Seattle, WA, 2755-2760."},{"key":"400_CR7","doi-asserted-by":"publisher","first-page":"2208","DOI":"10.1109\/CDC.2011.6161460","volume-title":"Proceedings of the IEEE conference on Decision and Control and European Control Conference (CDC-ECC)","author":"NG Cooper","year":"2011","unstructured":"Cooper NG, Belta CA, Julius AA: Genetic regulatory network identification using multivariate monotone functions . Proceedings of the IEEE conference on Decision and Control and European Control Conference (CDC-ECC) . 2011, IEEE, Orlando, FL, 2208-2213."},{"issue":"10","key":"400_CR8","doi-asserted-by":"publisher","first-page":"1365","DOI":"10.1089\/cmb.2008.0109","volume":"15","author":"R Porreca","year":"2008","unstructured":"Porreca R, Drulhe S, de Jong H, Ferrari-Trecate G: Structural identification of piecewise-linear models of genetic regulatory networks . J Comput Biol. 2008, 15 (10): 1365-1380. 10.1089\/cmb.2008.0109.","journal-title":"J Comput Biol"},{"key":"400_CR9","first-page":"486","volume":"9","author":"DD Bernardo","year":"2004","unstructured":"Bernardo DD, Gardner TS, Collins JJ: Robust identification of large genetic networks . Pac Symp Biocomput. 2004, 9: 486-497.","journal-title":"Pac Symp Biocomput"},{"key":"400_CR10","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1109\/CDC.2013.6759971","volume-title":"IEEE Conference on Decision and Control (CDC)","author":"G Richard","year":"2013","unstructured":"Richard G, Julius A. A, Belta C: Optimizing regulation functions in gene network identification . IEEE Conference on Decision and Control (CDC) . 2013, IEEE, Firenze, Italy, 745-750."},{"issue":"7","key":"400_CR11","doi-asserted-by":"publisher","first-page":"1670","DOI":"10.1109\/TAC.2008.928114","volume":"53","author":"JM Gon\u00e7alves","year":"2008","unstructured":"Gon\u00e7alves JM, Warnick SC: Necessary and sufficient conditions for dynamical structure reconstruction of lti networks . IEEE Trans Automatic Control. 2008, 53 (7): 1670-1674. 10.1109\/TAC.2008.928114.","journal-title":"IEEE Trans Automatic Control"},{"issue":"12","key":"400_CR12","doi-asserted-by":"publisher","first-page":"1877","DOI":"10.1093\/bioinformatics\/bth173","volume":"20","author":"E Sontag","year":"2004","unstructured":"Sontag E, Kiyatkin A, Kholodenko BN: Inferring dynamics architecture of cellular network using time series of gene expression, protein and metabolite data . Bioinformatics. 2004, 20 (12): 1877-1886. 10.1093\/bioinformatics\/bth173.","journal-title":"Bioinformatics"},{"issue":"5-6","key":"400_CR13","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1016\/j.compbiolchem.2007.08.003","volume":"31","author":"S Han","year":"2007","unstructured":"Han S, Yoon Y, Cho K-H: Inferring biomolecular interaction networks based on convex optimization . Comput Biol Chem. 2007, 31 (5-6): 347-354. 10.1016\/j.compbiolchem.2007.08.003.","journal-title":"Comput Biol Chem"},{"issue":"2","key":"400_CR14","doi-asserted-by":"publisher","first-page":"026103","DOI":"10.1103\/PhysRevE.77.026103","volume":"77","author":"D Napoletani","year":"2008","unstructured":"Napoletani D, Sauer TD: Reconstructing the topology of sparsely connected dynamical networks . Phys Rev E. 2008, 77 (2): 026103-10.1103\/PhysRevE.77.026103.","journal-title":"Phys Rev E"},{"issue":"1","key":"400_CR15","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1016\/j.jtbi.2008.07.026","volume":"255","author":"D Napoletani","year":"2008","unstructured":"Napoletani D, Sauer T, Struppa DC, Petricoin E, Liotta L: Augmented sparse reconstruction of protein signaling networks . J Theor Biol. 2008, 255 (1): 40-52. 10.1016\/j.jtbi.2008.07.026.","journal-title":"J Theor Biol"},{"key":"400_CR16","doi-asserted-by":"publisher","first-page":"1230","DOI":"10.1016\/j.automatica.2011.03.008","volume":"47","author":"Y Yuan","year":"2011","unstructured":"Yuan Y, Stan G-B, Warnick S, Gon\u00e7alves J: Robust dynamical network structure reconstruction . Automatica. 2011, 47: 1230-1235. 10.1016\/j.automatica.2011.03.008.","journal-title":"Automatica"},{"key":"400_CR17","first-page":"1035","volume-title":"IEEE Conference on Decision and Control (CDC)","author":"YH Chang","year":"2012","unstructured":"Chang YH, Tomlin CJ: Data-driven graph reconstruction using compressive sensing . IEEE Conference on Decision and Control (CDC) . 2012, IEEE, Maui, HI, 1035-1040."},{"key":"400_CR18","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1186\/1752-0509-1-51","volume":"1","author":"F Steinke","year":"2007","unstructured":"Steinke F, Seeger M, Tsuda K: Experimental design for efficient identification of gene regulatory networks using sparse bayesian models . BMC Syst Biol. 2007, 1: 51-10.1186\/1752-0509-1-51. doi: 10.1186\/1752-0509-1-51,","journal-title":"BMC Syst Biol"},{"issue":"5629","key":"400_CR19","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1126\/science.1081900","volume":"301","author":"TS Gardner","year":"2003","unstructured":"Gardner TS, di Bernardo D, Lorenz D, Collins JJ: Inferring genetic networks and identifying compound mode of action via expression profiling . Science. 2003, 301 (5629): 102-105. 10.1126\/science.1081900.","journal-title":"Science"},{"key":"400_CR20","doi-asserted-by":"publisher","first-page":"5944","DOI":"10.1073\/pnas.0933416100","volume":"100","author":"J Tegner","year":"2003","unstructured":"Tegner J, Yeung MKS, Hasty J, Collins JJ: Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling . Proc Natl Acad Sci. 2003, 100: 5944-5949. 10.1073\/pnas.0933416100.","journal-title":"Proc Natl Acad Sci"},{"issue":"6833","key":"400_CR21","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/35075138","volume":"411","author":"H Jeong","year":"2001","unstructured":"Jeong H, Mason SP, Barabasi A-L, Oltvai ZN: Lethality and centrality in protein networks . Nature. 2001, 411 (6833): 41-42. 10.1038\/35075138.","journal-title":"Nature"},{"issue":"5594","key":"400_CR22","doi-asserted-by":"publisher","first-page":"824","DOI":"10.1126\/science.298.5594.824","volume":"298","author":"R Milo","year":"2002","unstructured":"Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U: Network motifs: Simple building blocks of complex networks . Science. 2002, 298 (5594): 824-827. 10.1126\/science.298.5594.824.","journal-title":"Science"},{"issue":"42","key":"400_CR23","doi-asserted-by":"publisher","first-page":"17263","DOI":"10.1073\/pnas.1109435108","volume":"108","author":"Z Burda","year":"2011","unstructured":"Burda Z, Krzywicki A, Martin OC, Zagorski M: Motifs emerge from function in model gene regulatory networks . Proc Natl Acad Sci. 2011, 108 (42): 17263-17268. 10.1073\/pnas.1109435108.","journal-title":"Proc Natl Acad Sci"},{"key":"400_CR24","first-page":"2334","volume-title":"IEEE Conference on Decision and Control (CDC)","author":"W Pan","year":"2012","unstructured":"Pan W, Yuan Y, Gon\u00e7alves J, Stan G-B: Reconstruction of arbitrary biochemical reaction networks: A compressive sensing approach . IEEE Conference on Decision and Control (CDC) . 2012, IEEE, Maui, HI, 2334-2339."},{"key":"400_CR25","first-page":"11","volume":"2013","author":"A Noor","year":"2013","unstructured":"Noor A, Serpedin E, Nounou M, Nounou H: Reverse engineering sparse gene regulatory networks using cubature kalman filter and compressed sensing . Adv Bioinformatics. 2013, 2013: 11-doi:10.1155\/2013\/205763,","journal-title":"Adv Bioinformatics"},{"issue":"3","key":"400_CR26","doi-asserted-by":"publisher","first-page":"e90781","DOI":"10.1371\/journal.pone.0090781","volume":"9","author":"A Emad","year":"2014","unstructured":"Emad A, Milenkovic O: CaSPIAN: A causal compressive sensing algorithm for discovering directed interactions in gene networks . PLoS ONE. 2014, 9 (3): e90781-10.1371\/journal.pone.0090781. doi:10.1371\/journal.pone.0090781,","journal-title":"PLoS ONE"},{"key":"400_CR27","first-page":"021021","volume":"1","author":"W-X Wang","year":"2011","unstructured":"Wang W-X, Lai Y-C, Grebogi C, Ye J: Network reconstruction based on evolutionary-game data via compressive sensing . Phys Rev X. 2011, 1: 021021-","journal-title":"Phys Rev X"},{"key":"400_CR28","doi-asserted-by":"publisher","first-page":"969","DOI":"10.1088\/0266-5611\/23\/3\/008","volume":"23","author":"E Cand\u00e8s","year":"2006","unstructured":"Cand\u00e8s E, Romberg J: Sparsity and incoherence in compressive sampling . Inverse Probl. 2006, 23: 969-985. 10.1088\/0266-5611\/23\/3\/008.","journal-title":"Inverse Probl"},{"key":"400_CR29","first-page":"4129","volume-title":"Proceedings of the American Control Conference (ACC)","author":"YH Chang","year":"2011","unstructured":"Chang YH, Gray J, Tomlin CJ: Optimization-based inference for temporally evolving boolean networks with applications in biology . Proceedings of the American Control Conference (ACC) . 2011, IEEE, San Francisco, CA, 4129-4134."},{"issue":"12","key":"400_CR30","doi-asserted-by":"publisher","first-page":"1307","DOI":"10.1089\/cmb.2012.0190","volume":"19","author":"YH Chang","year":"2012","unstructured":"Chang YH, Gray J, Tomlin CJ: Optimization-based inference for temporally evolving networks with applications in biology . J Comput Biol. 2012, 19 (12): 1307-1323. 10.1089\/cmb.2012.0190.","journal-title":"J Comput Biol"},{"issue":"7","key":"400_CR31","doi-asserted-by":"publisher","first-page":"2829","DOI":"10.1109\/TIT.2008.924688","volume":"54","author":"EJ Cand\u00e8s","year":"2008","unstructured":"Cand\u00e8s EJ, Randall PA: Highly robust error correction by convex programming . IEEE Trans Inf Theory. 2008, 54 (7): 2829-2840. 10.1109\/TIT.2008.924688.","journal-title":"IEEE Trans Inf Theory"},{"key":"400_CR32","doi-asserted-by":"crossref","unstructured":"Hennessy BT, Lu Y, Gonzalez-Angulo AM, Carey MS, Myhre S, Ju Z, Davies MA, Liu W, Coombes K, Meric-Bernstam F, Bedrosian I, McGahren M, Agarwal R, Zhang F, Overgaard J, Alsner J, Neve RM, Kuo W-L, Gray JW, Borresen-Dale A-L, Mills GB: A technical assessment of the utility of reverse phase protein arrays for the study of the functional proteome in non-microdissected human breast cancers. Clinical Proteomics, 6(4):129\u2013151.","DOI":"10.1007\/s12014-010-9055-y"},{"key":"400_CR33","volume-title":"Compressed sensing (Or: the equation Ax = b, revisited), Mahler Lecture Series","author":"T Tao","year":"2009","unstructured":"Tao T: Compressed sensing (Or: the equation Ax = b, revisited), Mahler Lecture Series . 2009, University of California, Los Angeles"},{"issue":"2","key":"400_CR34","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1109\/MSP.2007.914731","volume":"25","author":"E Cand\u00e8s","year":"2008","unstructured":"Cand\u00e8s E, Wakin M: An introduction to compressive sampling . IEEE Signal Process Mag. 2008, 25 (2): 21-30. 10.1109\/MSP.2007.914731.","journal-title":"IEEE Signal Process Mag"},{"key":"400_CR35","doi-asserted-by":"publisher","first-page":"489","DOI":"10.1109\/TIT.2005.862083","volume":"52","author":"EJ Cand\u00e8s","year":"2004","unstructured":"Cand\u00e8s EJ, Romberg JK, Tao T: Robust uncertainty principles: exact signal reconstruction from highly incomplete frequency information . IEEE Trans Inf Theory. 2004, 52: 489-509. 10.1109\/TIT.2005.862083.","journal-title":"IEEE Trans Inf Theory"},{"issue":"9","key":"400_CR36","doi-asserted-by":"publisher","first-page":"6163","DOI":"10.1073\/pnas.092576199","volume":"99","author":"MKS Yeung","year":"2002","unstructured":"Yeung MKS, Tegner J, Collins JJ: Reverse engineering gene networks using singular value decomposition and robust regression . Proc Natl Acad Sci. 2002, 99 (9): 6163-6168. 10.1073\/pnas.092576199.","journal-title":"Proc Natl Acad Sci"},{"issue":"6","key":"400_CR37","doi-asserted-by":"publisher","first-page":"805","DOI":"10.1089\/10665270050514945","volume":"7","author":"T Ideker","year":"2000","unstructured":"Ideker T, Thorsson V, Siegel AF, Hood LE: Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data . J Comput Biol. 2000, 7 (6): 805-817. 10.1089\/10665270050514945.","journal-title":"J Comput Biol"},{"key":"400_CR38","volume-title":"Understanding the network topology underlying addiction to HER. Integrative Cancer Biology Program (ICBP) Retreat (Days of Science, the Sequel)","author":"M Moasser","year":"2012","unstructured":"Moasser M: Understanding the network topology underlying addiction to HER. Integrative Cancer Biology Program (ICBP) Retreat (Days of Science, the Sequel) . 2012, Waverly Club, SoutheastWaverly Drive, Portland"},{"issue":"6","key":"400_CR39","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1016\/j.tem.2008.04.001","volume":"19","author":"J Brognard","year":"2008","unstructured":"Brognard J, Newton AC: Phlipping the switch on akt and protein kinase c signaling . Trends Endocrinol Metab. 2008, 19 (6): 223-30. 10.1016\/j.tem.2008.04.001.","journal-title":"Trends Endocrinol Metab"},{"issue":"1","key":"400_CR40","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1016\/j.molcel.2005.03.008","volume":"18","author":"T Gao","year":"2005","unstructured":"Gao T, Furnari F, Newton AC: Phlpp: a phosphatase that directly dephosphorylates akt, promotes apoptosis, and suppresses tumor growth . Mol Cell. 2005, 18 (1): 13-24. 10.1016\/j.molcel.2005.03.008.","journal-title":"Mol Cell"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-014-0400-4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0400-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0400-4","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-014-0400-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T03:01:17Z","timestamp":1630551677000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-014-0400-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,12]]},"references-count":40,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2014,12]]}},"alternative-id":["400"],"URL":"https:\/\/doi.org\/10.1186\/s12859-014-0400-4","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/004242","asserted-by":"object"}]},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,12]]},"assertion":[{"value":"18 April 2014","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 November 2014","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 December 2014","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"400"}}