{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,7]],"date-time":"2025-05-07T04:57:28Z","timestamp":1746593848299},"publisher-location":"Berlin, Heidelberg","reference-count":39,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783540482932"},{"type":"electronic","value":"9783540485407"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"DOI":"10.1007\/978-3-540-48540-7_13","type":"book-chapter","created":{"date-parts":[[2007,5,15]],"date-time":"2007-05-15T20:28:49Z","timestamp":1179260929000},"page":"150-165","source":"Crossref","is-referenced-by-count":23,"title":["Combinatorial Genetic Regulatory Network Analysis Tools for High Throughput Transcriptomic Data"],"prefix":"10.1007","author":[{"given":"Elissa J.","family":"Chesler","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael A.","family":"Langston","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"13_CR1","unstructured":"Abu-Khzam, F.N., Collins, R.L., Fellows, M.R., Langston, M.A., Suters, W.H., Symons, C.T.: Kernelization algorithms for the vertex cover problem: Theory and experiments. In: Proceedings, Workshop on Algorithm Engineering and Experiments, New Orleans, Louisiana (2004)"},{"key":"13_CR2","doi-asserted-by":"crossref","unstructured":"Abu-Khzam, F.N., Langston, M.A., Shanbhag, P., Symons, C.T.: Scalable parallel algorithms for FPT problems. Algorithmica (accepted for publication, 2006)","DOI":"10.1007\/s00453-006-1214-1"},{"key":"13_CR3","doi-asserted-by":"publisher","first-page":"10101","DOI":"10.1073\/pnas.97.18.10101","volume":"97","author":"O. Alter","year":"2000","unstructured":"Alter, O., Brown, P.O., Botstein, D.: Singular value decomposition for genome-wide expression data processing and modeling. Proceedings of the National Academy of Sciences\u00a097, 10101\u201310106 (2000)","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"13_CR4","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1155\/JBB.2005.172","volume":"2","author":"N.E. Baldwin","year":"2005","unstructured":"Baldwin, N.E., Chesler, E.J., Kirov, S., Langston, M.A., Snoddy, J.R., Williams, R.W., Zhang, B.: Computational, integrative, and comparative methods for the elucidation of genetic coexpression networks. Journal of Biomedicine and Biotechnology\u00a02, 172\u2013180 (2005)","journal-title":"Journal of Biomedicine and Biotechnology"},{"key":"13_CR5","doi-asserted-by":"publisher","first-page":"234","DOI":"10.1002\/(SICI)1097-4695(199908)40:2<234::AID-NEU9>3.0.CO;2-T","volume":"40","author":"M. Bartoli","year":"1999","unstructured":"Bartoli, M., Ternaux, J.P., Forni, C., Portalier, P., Salin, P., Amalric, M., Monneron, A.: Down-regulation of striatin, a neuronal calmodulin-binding protein, impairs rat locomotor activity. Journal of Neurobiology\u00a040, 234\u2013243 (1999)","journal-title":"Journal of Neurobiology"},{"key":"13_CR6","doi-asserted-by":"publisher","first-page":"20257","DOI":"10.1074\/jbc.M312106200","volume":"279","author":"C. Becamel","year":"2004","unstructured":"Becamel, C., Gavarini, S., Chanrion, B., Alonso, G., Galeotti, N., Dumuis, A., Bockaert, J., Marin, P.: The serotonin 5-ht2a and 5-ht2c receptors interact with specific sets of pdz proteins. Journal of Biological Chemistry\u00a0279, 20257\u201320266 (2004)","journal-title":"Journal of Biological Chemistry"},{"key":"13_CR7","unstructured":"Bellaachia, A., Portnoy, D., Chen, Y., Elkahloun, A.G.: E-cast: A data mining algorithm for gene expression data. In: Proceedings, Workshop on Data Mining in Bioinformatics, Edmonton, Alberta, Canada (2002)"},{"key":"13_CR8","doi-asserted-by":"crossref","unstructured":"Ben-Dor, A., Bruhn, L., Friedman, N., Nachman, I., Schummer, M., Yakhini, Z.: Tissue classification with gene expression profiles. Journal of Computational Biology, 54\u201364 (2000)","DOI":"10.1145\/332306.332328"},{"issue":"3\/4","key":"13_CR9","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1089\/106652799318274","volume":"6","author":"A. Ben-Dor","year":"1999","unstructured":"Ben-Dor, A., Shamir, R., Yakhini, Z.: Clustering gene expression patterns. Journal of Computational Biology\u00a06(3\/4), 281\u2013297 (1999)","journal-title":"Journal of Computational Biology"},{"key":"13_CR10","volume-title":"Handbook of Combinatorial Optimization, vol. 4","author":"I. Bomze","year":"1999","unstructured":"Bomze, I., Budinich, M., Pardalos, P., Pelillo, M.: The maximum clique problem. In: Du, D.Z., Pardalos, P.M. (eds.) Handbook of Combinatorial Optimization, vol. 4, Kluwer Academic Publishers, Dordrecht (1999)"},{"key":"13_CR11","doi-asserted-by":"publisher","first-page":"1572","DOI":"10.1073\/pnas.0408709102","volume":"102","author":"R.B. Brem","year":"2005","unstructured":"Brem, R.B., Kruglyak, L.: The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proceedings of the National Academy of Sciences\u00a0102, 1572\u20131577 (2005)","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"13_CR12","doi-asserted-by":"publisher","first-page":"752","DOI":"10.1126\/science.1069516","volume":"296","author":"R.B. Brem","year":"2002","unstructured":"Brem, R.B., Yvert, G., Clinton, R., Kruglyak, L.: Genetic dissection of transcriptional regulation in budding yeast. Science\u00a0296, 752\u2013755 (2002)","journal-title":"Science"},{"key":"13_CR13","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1111\/1467-9868.00354","volume":"64","author":"K.W. Broman","year":"2002","unstructured":"Broman, K.W., Speed, T.P.: A model selection approach for the identification of quantitative trait loci in experimental crosses. Journal of the Royal Statistical Society: Series B (Statistical Methodology)\u00a064, 641\u2013656 (2002)","journal-title":"Journal of the Royal Statistical Society: Series B (Statistical Methodology)"},{"key":"13_CR14","doi-asserted-by":"publisher","first-page":"12182","DOI":"10.1073\/pnas.220392197","volume":"97","author":"A.J. Butte","year":"2000","unstructured":"Butte, A.J., Tamayo, P., Slonim, D., Golub, T.R., Kohane, I.S.: Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proceedings of the National Academy of Sciences\u00a097, 12182\u201312186 (2000)","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"13_CR15","doi-asserted-by":"publisher","first-page":"773","DOI":"10.1016\/S0092-8674(00)81736-5","volume":"94","author":"S. Butz","year":"1998","unstructured":"Butz, S., Okamoto, M., Sudhof, T.C.: A tripartite protein complex with the potential to couple synaptic vesicle exocytosis to cell adhesion in brain. Cell\u00a094, 773\u2013782 (1998)","journal-title":"Cell"},{"key":"13_CR16","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1038\/ng1497","volume":"37","author":"L. Bystrykh","year":"2005","unstructured":"Bystrykh, L., Weersing, E., Dontje, B., Sutton, S., Pletcher, M.T., Wiltshire, T., Su, A., Vellenga, E., Wang, J., Manly, K.F., Lu, L., Chesler, E.J., Alberts, R., Jansen, R.C., Williams, R.W., Cooke, M.P., Haan, G.d.: Uncovering regulatory pathways that affect hematopoietic stem cell function using \u2019genetical genomics\u2019. Nature Genetics\u00a037, 225\u2013232 (2005)","journal-title":"Nature Genetics"},{"key":"13_CR17","doi-asserted-by":"crossref","unstructured":"Chandran, L.S., Grandoni, F.: Refined memorisation for vertex cover. In: Proceedings, International Workshop on Parameterized and Exact Computation (IWPEC) (2004)","DOI":"10.1007\/978-3-540-28639-4_6"},{"key":"13_CR18","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1038\/ng1518","volume":"37","author":"E.J. Chesler","year":"2005","unstructured":"Chesler, E.J., Lu, L., Shou, S., Qu, Y., Gu, J., Wang, J., Hsu, H.C., Mountz, J.D., Baldwin, N.E., Langston, M.A., Hogenesch, J.B., Threadgill, D.W., Manly, K.F., Williams, R.W.: Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nature Genetics\u00a037, 233\u2013242 (2005)","journal-title":"Nature Genetics"},{"key":"13_CR19","doi-asserted-by":"publisher","first-page":"486","DOI":"10.1038\/nn0504-485","volume":"7","author":"E.J. Chesler","year":"2004","unstructured":"Chesler, E.J., Lu, L., Wang, J., Williams, R.W., Manly, K.F.: Webqtl: Rapid exploratory analysis of gene expression and genetic networks for brain and behavior. Nature Neuroscience\u00a07, 486\u2013486 (2004)","journal-title":"Nature Neuroscience"},{"key":"13_CR20","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1385\/NI:1:4:343","volume":"1","author":"E.J. Chesler","year":"2003","unstructured":"Chesler, E.J., Wang, J., Lu, L., Qu, Y., Manly, K.F., Williams, R.W.: Genetic correlates of gene expression in recombinant inbred strains: a relational model system to explore neurobehavioral phenotypes. Neuroinformatics\u00a01, 343\u2013357 (2003)","journal-title":"Neuroinformatics"},{"key":"13_CR21","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1016\/S0074-7742(04)60003-1","volume":"60","author":"E.J. Chesler","year":"2004","unstructured":"Chesler, E.J., Williams, R.W.: Brain gene expression: Genomics and genetics. International Review of Neurobiology\u00a060, 59\u201395 (2004)","journal-title":"International Review of Neurobiology"},{"key":"13_CR22","doi-asserted-by":"publisher","first-page":"1133","DOI":"10.1038\/ng1104-1133","volume":"36","author":"G.A. Churchill","year":"2004","unstructured":"Churchill, G.A., Airey, D.C., Allayee, H., Angel, J.M., Attie, A.D., Beatty, J., Beavis, W.D., Belknap, J.K., Bennett, B., Berrettini, W., Bleich, A., Bogue, M., Broman, K.W., Buck, K.J., Buckler, E., Burmeister, M., Chesler, E.J., Cheverud, J.M., Clapcote, S., Cook, M.N., Cox, R.D., Crabbe, J.C., Crusio, W.E., Darvasi, A., Deschepper, C.F., Doerge, R.W., Farber, C.R., Forejt, J., Gaile, D., Garlow, S.J., Geiger, H., Gershenfeld, H., Gordon, T., Gu, J., Gu, W., Haan, G.d., Hayes, N.L., Heller, C., Himmelbauer, H., Hitzemann, R., Hunter, K., Hsu, H.C., Iraqi, F.A., Ivandic, B., Jacob, H.J., Jansen, R.C., Jepsen, K.J., Johnson, D.K., Johnson, T.E., Kempermann, G., Kendziorski, C., Kotb, M., Kooy, R.F., Llamas, B., Lammert, F., Lassalle, J.M., Lowenstein, P.R., Lu, A.L.L., Manly, K.F., Marcucio, R., Matthews, D., Medrano, J.F., Miller, D.R., Mittleman, G., Mock, B.A., Mogil, J.S., Montagutelli, X., Morahan, G., Morris, D.G., Mott, R., Nadeau, J.H., Nagase, H., Nowakowski, R.S., O\u2019Hara, B.F., Osadchuk, A.V., Page, G.P., Paigen, A., Paigen, K., Palmer, A.A., Pan, H.J., Peltonen-Palotie, L., Peirce, J., Pomp, D., Pravenec, M., Prows, D.R., Qi, Z., Reeves, R.H., Roder, J., Rosen, G.D., Schadt, E.E., Schalkwyk, L.C., Seltzer, Z., Shimomura, K., Shou, S., Sillanpaa, M.J., Siracusa, L.D., Snoeck, H.W., Spearow, J.L., Svenson, K., Tarantino, L.M., Threadgill, D., Toth, L.A., Valdar, W., Villena, F.P.d., Warden, C., Whatley, S., Williams, R.W., Wiltshire, T., Yi, N., Zhang, D., Zhang, M., Zou, F.: The collaborative cross, a community resource for the genetic analysis of complex traits. Nature Genetics\u00a036, 1133\u20131137 (2004)","journal-title":"Nature Genetics"},{"key":"13_CR23","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1038\/nrg703","volume":"3","author":"R.W. Doerge","year":"2002","unstructured":"Doerge, R.W.: Mapping and analysis of quantitative trait loci in experimental populations. Nature Reviews Genetics\u00a03, 43\u201352 (2002)","journal-title":"Nature Reviews Genetics"},{"key":"13_CR24","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4612-0515-9","volume-title":"Parameterized Complexity","author":"R.G. Downey","year":"1999","unstructured":"Downey, R.G., Fellows, M.R.: Parameterized Complexity. Springer, Heidelberg (1999)"},{"key":"13_CR25","doi-asserted-by":"publisher","first-page":"410","DOI":"10.1007\/s004530010050","volume":"29","author":"U. Feige","year":"2001","unstructured":"Feige, U., Peleg, D., Kortsarz, G.: The dense k-subgraph problem. Algorithmica\u00a029, 410\u2013421 (2001)","journal-title":"Algorithmica"},{"key":"13_CR26","doi-asserted-by":"publisher","first-page":"3021","DOI":"10.1093\/bioinformatics\/bth354","volume":"20","author":"M. Girolami","year":"2004","unstructured":"Girolami, M., Breitling, R.: Biologically valid linear factor models of gene expression. Bioinformatics\u00a020, 3021\u20133033 (2004)","journal-title":"Bioinformatics"},{"issue":"1-3","key":"13_CR27","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1007\/BF02614317","volume":"79","author":"P. Hansen","year":"1997","unstructured":"Hansen, P., Jaumard, B.: Cluster analysis and mathematical programming. Mathematical Programming\u00a079(1-3), 191\u2013215 (1997)","journal-title":"Mathematical Programming"},{"key":"13_CR28","doi-asserted-by":"crossref","unstructured":"Hartuv, E., Schmitt, A., Lange, J., Meier-Ewert, S., Lehrachs, H., Shamir, R.: An algorithm for clustering cDNAs for gene expression analysis. In: Proceedings, RECOMB, Lyon, France (1999)","DOI":"10.1145\/299432.299483"},{"key":"13_CR29","doi-asserted-by":"publisher","first-page":"1106","DOI":"10.1101\/gr.9.11.1106","volume":"9","author":"L.J. Heyer","year":"1999","unstructured":"Heyer, L.J., Kruglyak, S., Yooseph, S.: Exploring expression data: Identification and analysis of coexpressed genes. Genome Research\u00a09, 1106\u20131115 (1999)","journal-title":"Genome Research"},{"key":"13_CR30","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1038\/ng1522","volume":"37","author":"N. Hubner","year":"2005","unstructured":"Hubner, N., Wallace, C.A., Zimdahl, H., Petretto, E., Schulz, H., Maciver, F., Mueller, M., Hummel, O., Monti, J., Zidek, V., Musilova, A., Kren, V., Causton, H., Game, L., Born, G., Schmidt, S., Muller, A., Cook, S.A., Kurtz, T.W., Whittaker, J., Pravenec, M., Aitman, T.J.: Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nature Genetics\u00a037, 243\u2013253 (2005)","journal-title":"Nature Genetics"},{"key":"13_CR31","volume-title":"Methods of Microarray Data Analysis IV","author":"M.A. Langston","year":"2005","unstructured":"Langston, M.A., Lan, L., Peng, X., Baldwin, N.E., Symons, C.T., Zhang, B., Snoddy, J.R.: A combinatorial approach to the analysis of differential gene expression data: The use of graph algorithms for disease prediction and screening. In: Shoemaker, J.S., Lin, S.M. (eds.) Methods of Microarray Data Analysis IV, Springer, Heidelberg (2005)"},{"key":"13_CR32","doi-asserted-by":"crossref","unstructured":"Langston, M.A., Perkins, A.D., Saxton, A.M., Scharff, J.A., Voy, B.H.: Innovative computational methods for transcriptomic data analysis. In: Proceedings, ACM Symposium on Applied Computing, Dijon, France (accepted for publication, 2006)","DOI":"10.1145\/1141277.1141319"},{"key":"13_CR33","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1093\/hmg\/ddi267","volume":"14","author":"J. Li","year":"2005","unstructured":"Li, J., Burmeister, M.: Genetical genomics: Combining genetics with gene expression analysis. Human Molecular Genetics\u00a014, 163\u2013169 (2005)","journal-title":"Human Molecular Genetics"},{"key":"13_CR34","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1007\/s003359900997","volume":"10","author":"K.F. Manly","year":"1999","unstructured":"Manly, K.F., Olson, J.M.: Overview of qtl mapping software and introduction to map manager qt. Mammalian Genome\u00a010, 327\u2013334 (1999)","journal-title":"Mammalian Genome"},{"key":"13_CR35","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/1471-2156-5-7","volume":"5","author":"J.L. Peirce","year":"2004","unstructured":"Peirce, J.L., Lu, L., Gu, J., Silver, L.M., Williams, R.W.: A new set of bxd recombinant inbred lines from advanced intercross populations in mice. BMC Genetics\u00a05, 7 (2004)","journal-title":"BMC Genetics"},{"key":"13_CR36","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1038\/nature01434","volume":"422","author":"E.E. Schadt","year":"2003","unstructured":"Schadt, E.E., Monks, S.A., Drake, T.A., Lusis, A.J., Che, N., Colinayo, V., Ruff, T.G., Milligan, S.B., Lamb, J.R., Cavet, G., Linsley, P.S., Mao, M., Stoughton, R.B., Friend, S.H.: Genetics of gene expression surveyed in maize, mouse and man. Nature\u00a0422, 297\u2013302 (2003)","journal-title":"Nature"},{"key":"13_CR37","first-page":"502","volume":"32","author":"D.K. Slonim","year":"2002","unstructured":"Slonim, D.K.: From patterns to pathways: gene expression data analysis comes of age. Nature\u00a032, 502\u2013508 (2002)","journal-title":"Nature"},{"key":"13_CR38","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1002\/bies.20170","volume":"27","author":"A. Wagner","year":"2005","unstructured":"Wagner, A.: Distributed robustness versus redundancy as causes of mutational robustness. Bioessays\u00a027, 176\u2013188 (2005)","journal-title":"Bioessays"},{"key":"13_CR39","unstructured":"Zhang, Y., Abu-Khzam, F.N., Baldwin, N.E., Chesler, E.J., Langston, M.A., Samatova, N.F.: Genome-scale computational approaches to memory-intensive applications in systems biology. In: Proceedings, Supercomputing, Seattle, Washington (2005)"}],"container-title":["Lecture Notes in Computer Science","Systems Biology and Regulatory Genomics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-540-48540-7_13.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,19]],"date-time":"2020-11-19T04:47:23Z","timestamp":1605761243000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-540-48540-7_13"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[null]]},"ISBN":["9783540482932","9783540485407"],"references-count":39,"URL":"https:\/\/doi.org\/10.1007\/978-3-540-48540-7_13","relation":{},"subject":[]}}