{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,18]],"date-time":"2025-12-18T13:51:40Z","timestamp":1766065900748},"publisher-location":"Berlin, Heidelberg","reference-count":31,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642038440"},{"type":"electronic","value":"9783642038457"}],"license":[{"start":{"date-parts":[[2009,1,1]],"date-time":"2009-01-01T00:00:00Z","timestamp":1230768000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009]]},"DOI":"10.1007\/978-3-642-03845-7_6","type":"book-chapter","created":{"date-parts":[[2009,8,26]],"date-time":"2009-08-26T02:41:17Z","timestamp":1251254477000},"page":"83-95","source":"Crossref","is-referenced-by-count":4,"title":["A Prize-Collecting Steiner Tree Approach for Transduction Network Inference"],"prefix":"10.1007","author":[{"given":"Marc","family":"Bailly-Bechet","sequence":"first","affiliation":[]},{"given":"Alfredo","family":"Braunstein","sequence":"additional","affiliation":[]},{"given":"Riccardo","family":"Zecchina","sequence":"additional","affiliation":[]}],"member":"297","reference":[{"key":"6_CR1","doi-asserted-by":"crossref","unstructured":"Elston, T.C.: Probing pathways periodically. Sci. Signal\u00a01(42) (2008); pe47","DOI":"10.1126\/scisignal.142pe47"},{"key":"6_CR2","doi-asserted-by":"crossref","unstructured":"Dohlman, H.G., Slessareva, J.E.: Pheromone signaling pathways in yeast. Sci. STKE\u00a02006(364) (December 2006); cm6","DOI":"10.1126\/stke.3642006cm6"},{"key":"6_CR3","first-page":"3","volume":"332","author":"L. Luttrel","year":"2006","unstructured":"Luttrel, L.: Transmembrane signalling by g protein couple receptors. Methods Mol. Biol.\u00a0332, 3\u201349 (2006)","journal-title":"Methods Mol. Biol."},{"issue":"8","key":"6_CR4","doi-asserted-by":"publisher","first-page":"1311","DOI":"10.1016\/j.bbamcr.2007.05.003","volume":"1773","author":"R.E. Chen","year":"2007","unstructured":"Chen, R.E., Thorner, J.: Function and regulation in MAPK signaling pathways: lessons learned from the yeast Saccharomyces cerevisiae. Biochem. Biophys. Acta\u00a01773(8), 1311\u20131340 (2007)","journal-title":"Biochem. Biophys. Acta"},{"issue":"6","key":"6_CR5","doi-asserted-by":"publisher","first-page":"2943","DOI":"10.1016\/S0006-3495(02)75635-X","volume":"82","author":"M. Thattai","year":"2002","unstructured":"Thattai, M., van Oudenaarden, A.: Attenuation of noise in ultrasensitive signaling cascades. Biophys. J.\u00a082(6), 2943\u20132950 (2002)","journal-title":"Biophys. J."},{"issue":"3","key":"6_CR6","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1038\/nrm1838","volume":"7","author":"B.N. Kholodenko","year":"2006","unstructured":"Kholodenko, B.N.: Cell-signalling dynamics in time and space. Nat. Rev. Mol. Cell Biol.\u00a07(3), 165\u2013176 (2006)","journal-title":"Nat. Rev. Mol. Cell Biol."},{"issue":"3","key":"6_CR7","doi-asserted-by":"publisher","first-page":"1000041","DOI":"10.1371\/journal.pcbi.1000041","volume":"4","author":"A.C. Ventura","year":"2008","unstructured":"Ventura, A.C., Sepulchre, J.A., Merajver, S.D.: A hidden feedback in signaling cascades is revealed. PLoS Comput. Biol.\u00a04(3), e1000041 (2008)","journal-title":"PLoS Comput. Biol."},{"issue":"6","key":"6_CR8","doi-asserted-by":"publisher","first-page":"1000099","DOI":"10.1371\/journal.pcbi.1000099","volume":"4","author":"J.W. Locasale","year":"2008","unstructured":"Locasale, J.W., Chakraborty, A.K.: Regulation of signal duration and the statistical dynamics of kinase activation by scaffold proteins. PLoS Comput. Biol.\u00a04(6), e1000099 (2008)","journal-title":"PLoS Comput. Biol."},{"issue":"5869","key":"6_CR9","doi-asserted-by":"publisher","first-page":"1539","DOI":"10.1126\/science.1151153","volume":"319","author":"C.J. Bashor","year":"2008","unstructured":"Bashor, C.J., Helman, N.C., Yan, S., Lim, W.A.: Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics. Science\u00a0319(5869), 1539\u20131543 (2008)","journal-title":"Science"},{"issue":"2","key":"6_CR10","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1089\/cmb.2006.13.133","volume":"13","author":"J. Scott","year":"2006","unstructured":"Scott, J., Ideker, T., Karp, R.M., Sharan, R.: Efficient algorithms for detecting signaling pathways in protein interaction networks. J. Comput. Biol.\u00a013(2), 133\u2013144 (2006)","journal-title":"J. Comput. Biol."},{"key":"6_CR11","doi-asserted-by":"crossref","unstructured":"White, A., Ma\u2019yan, A.: Connecting seed lists of mammalian proteins using steiner trees. Nature Precedings (2008)","DOI":"10.1109\/ACSSC.2007.4487185"},{"issue":"5","key":"6_CR12","doi-asserted-by":"publisher","first-page":"683","DOI":"10.1074\/mcp.M400110-MCP200","volume":"4","author":"M.S. Scott","year":"2005","unstructured":"Scott, M.S., Perkins, T., Bunnell, S., Pepin, F., Thomas, D.Y., Hallett, M.: Identifying regulatory subnetworks for a set of genes. Mol. Cell Proteomics\u00a04(5), 683\u2013692 (2005)","journal-title":"Mol. Cell Proteomics"},{"key":"6_CR13","doi-asserted-by":"crossref","unstructured":"Zhao, X.M., Wang, R.S., Chen, L., Aihara, K.: Uncovering signal transduction networks from high-throughput data by integer linear programming. Nucleic Acids Res.\u00a036(9), e48 (2008)","DOI":"10.1093\/nar\/gkn145"},{"issue":"3","key":"6_CR14","doi-asserted-by":"publisher","first-page":"37208","DOI":"10.1103\/PhysRevLett.101.037208","volume":"101","author":"M. Bayati","year":"2008","unstructured":"Bayati, M., Borgs, C., Braunstein, A., Chayes, J., Ramezanpour, A., Zecchina, R.: Statistical mechanics of steiner trees. Phys. Rev. Lett.\u00a0101(3), 037208 (2008)","journal-title":"Phys. Rev. Lett."},{"issue":"5582","key":"6_CR15","doi-asserted-by":"publisher","first-page":"812","DOI":"10.1126\/science.1073287","volume":"297","author":"M. M\u00e9zard","year":"2002","unstructured":"M\u00e9zard, M., Parisi, G., Zecchina, R.: Analytic and algorithmic solution of random satisfiability problems. Science\u00a0297(5582), 812\u2013815 (2002)","journal-title":"Science"},{"issue":"6868","key":"6_CR16","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1038\/415141a","volume":"415","author":"A.C. Gavin","year":"2002","unstructured":"Gavin, A.C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J.M., Michon, A.M., Cruciat, C.M., Remor, M., Hofert, C., Schelder, M., Brajenovic, M., Ruffner, H., Merino, A., Klein, K., Hudak, M., Dickson, D., Rudi, T., Gnau, V., Bauch, A., Bastuck, S., Huhse, B., Leutwein, C., Heurtier, M.A., Copley, R.R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P., Seraphin, B., Kuster, B., Neubauer, G., Superti-Furga, G.: Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature\u00a0415(6868), 141\u2013147 (2002)","journal-title":"Nature"},{"key":"6_CR17","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1186\/1471-2105-6-44","volume":"6","author":"W.C. Chang","year":"2005","unstructured":"Chang, W.C., Li, C.W., Chen, B.S.: Quantitative inference of dynamic regulatory pathways via microarray data. BMC Bioinformatics\u00a06, 44 (2005)","journal-title":"BMC Bioinformatics"},{"key":"6_CR18","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1186\/1471-2105-3-34","volume":"3","author":"M. Steffen","year":"2002","unstructured":"Steffen, M., Petti, A., Aach, J., D\u2019haeseleer, P., Church, G.: Automated modelling of signal transduction networks. BMC Bioinformatics\u00a03, 34 (2002)","journal-title":"BMC Bioinformatics"},{"key":"6_CR19","unstructured":"Johnson, D., Minkoff, M., Phillips, S.: The prize collecting steiner tree problem: theory and practice. In: Proceedings of the eleventh annual ACM-SIAM symposium on Discrete algorithms, Society for Industrial and Applied Mathematics, Philadelphia, PA, USA, pp. 760\u2013769 (2000)"},{"issue":"1-3","key":"6_CR20","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1016\/S0166-218X(03)00380-9","volume":"141","author":"A. Lucena","year":"2004","unstructured":"Lucena, A., Resende, M.G.C.: Strong lower bounds for the prize collecting Steiner problem in graphs. Discrete Applied Mathematics\u00a0141(1-3), 277\u2013294 (2004)","journal-title":"Discrete Applied Mathematics"},{"issue":"12","key":"6_CR21","doi-asserted-by":"publisher","first-page":"125206","DOI":"10.1063\/1.2982805","volume":"49","author":"M. Bayati","year":"2008","unstructured":"Bayati, M., Braunstein, A., Zecchina, R.: A rigorous analysis of the cavity equations for the minimum spanning tree. Journal of Mathematical Physics\u00a049(12), 125206 (2008)","journal-title":"Journal of Mathematical Physics"},{"issue":"1","key":"6_CR22","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1093\/nar\/28.1.289","volume":"28","author":"I. Xenarios","year":"2000","unstructured":"Xenarios, I., Rice, D.W., Salwinski, L., Baron, M.K., Marcotte, E.M., Eisenberg, D.: DIP: the database of interacting proteins. Nucleic Acids Res.\u00a028(1), 289\u2013291 (2000)","journal-title":"Nucleic Acids Res."},{"issue":"Database issue","key":"6_CR23","doi-asserted-by":"publisher","first-page":"436","DOI":"10.1093\/nar\/gkj003","volume":"34","author":"U. G\u00fcldener","year":"2006","unstructured":"G\u00fcldener, U., Oesterheld, M., Pagel, P., Ruepp, A., Mewes, H.W., St\u00fcmpflen: Mpact: the MIPS protein interaction resource on yeast. Nucleic Acids Res.\u00a034(Database issue), D436\u2013D441 (2006)","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"6_CR24","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1038\/nbt924","volume":"22","author":"J.S. Bader","year":"2004","unstructured":"Bader, J.S., Chaudhuri, A., Rothberg, J.M., Chant, J.: Gaining confidence in high-throughput protein interaction networks. Nat. Biotechnol.\u00a022(1), 78\u201385 (2004)","journal-title":"Nat. Biotechnol."},{"key":"6_CR25","doi-asserted-by":"publisher","first-page":"360","DOI":"10.1186\/1471-2105-7-360","volume":"7","author":"S. Suthram","year":"2006","unstructured":"Suthram, S., Shlomi, T., Ruppin, E., Sharan, R., Ideker, T.: A direct comparison of protein interaction confidence assignment schemes. BMC Bioinformatics\u00a07, 360 (2006)","journal-title":"BMC Bioinformatics"},{"issue":"5454","key":"6_CR26","doi-asserted-by":"publisher","first-page":"873","DOI":"10.1126\/science.287.5454.873","volume":"287","author":"C.J. Roberts","year":"2000","unstructured":"Roberts, C.J., Nelson, B., Marton, M.J., Stoughton, R., Meyer, M.R., Bennett, H.A., He, Y.D., Dai, H., Walker, W.L., Hughes, T.R., Tyers, M., Boone, C., Friend, S.H.: Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science\u00a0287(5454), 873\u2013880 (2000)","journal-title":"Science"},{"key":"6_CR27","unstructured":"The Gene Ontology Consortium: Gene ontology: tool for the unification of biology. Nat. Genet. 25, 25\u201329 (2000)"},{"issue":"3","key":"6_CR28","doi-asserted-by":"publisher","first-page":"719","DOI":"10.1083\/jcb.151.3.719","volume":"151","author":"M.G. Heiman","year":"2000","unstructured":"Heiman, M.G., Walter, P.: Prm1p, a pheromone-regulated multispanning membrane protein, facilitates plasma membrane fusion during yeast mating. J. Cell Biol.\u00a0151(3), 719\u2013730 (2000)","journal-title":"J. Cell Biol."},{"issue":"2","key":"6_CR29","doi-asserted-by":"publisher","first-page":"547","DOI":"10.1091\/mbc.E06-09-0776","volume":"18","author":"P.S. Aguilar","year":"2007","unstructured":"Aguilar, P.S., Engel, A., Walter, P.: The plasma membrane proteins prm1 and fig1 ascertain fidelity of membrane fusion during yeast mating. Mol. Biol. Cell\u00a018(2), 547\u2013556 (2007)","journal-title":"Mol. Biol. Cell"},{"issue":"1","key":"6_CR30","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1016\/j.tig.2005.10.001","volume":"22","author":"L. Despons","year":"2006","unstructured":"Despons, L., Wirth, B., Louis, V.L., Potier, S., Souciet, J.L.: An evolutionary scenario for one of the largest yeast gene families. Trends Genet.\u00a022(1), 10\u201315 (2006)","journal-title":"Trends Genet."},{"issue":"1","key":"6_CR31","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1073\/pnas.0805923106","volume":"106","author":"M. Weigt","year":"2009","unstructured":"Weigt, M., White, R.A., Szurmant, H., Hoch, J.A., Hwa, T.: Identification of direct residue contacts in protein-protein interaction by message passing. Proc. Natl. Acad. Sci. U S A\u00a0106(1), 67\u201372 (2009)","journal-title":"Proc. Natl. Acad. Sci. U S A"}],"container-title":["Lecture Notes in Computer Science","Computational Methods in Systems Biology"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-03845-7_6","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,22]],"date-time":"2019-05-22T01:12:01Z","timestamp":1558487521000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-03845-7_6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009]]},"ISBN":["9783642038440","9783642038457"],"references-count":31,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-03845-7_6","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2009]]}}}