{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,4]],"date-time":"2024-09-04T23:21:10Z","timestamp":1725492070073},"publisher-location":"Berlin, Heidelberg","reference-count":40,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783540730590"},{"type":"electronic","value":"9783540730606"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"DOI":"10.1007\/978-3-540-73060-6_6","type":"book-chapter","created":{"date-parts":[[2007,9,18]],"date-time":"2007-09-18T15:35:17Z","timestamp":1190129717000},"page":"77-95","source":"Crossref","is-referenced-by-count":2,"title":["A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast"],"prefix":"10.1007","author":[{"given":"Mingzhou (Joe)","family":"Song","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Z. Lewis","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"6_CR1","unstructured":"YEAst Search for Transcriptional Regulators And Consensus Tracking (YEASTRACT), January 2006 Last Date of Visit: (September 12, 2006), http:\/\/www.yeastract.com ."},{"issue":"1","key":"6_CR2","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1016\/S0304-3975(02)00425-5","volume":"298","author":"T. Akutsu","year":"2003","unstructured":"Akutsu, T., Kuhara, S., Maruyama, O., Miyano, S.: Identification of genetic networks by strategic gene disruptions and gene overexpressions under a Boolean model. Theoretical Computer Science\u00a0298(1), 235\u2013251 (2003)","journal-title":"Theoretical Computer Science"},{"issue":"5","key":"6_CR3","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1186\/gb-2006-7-5-r36","volume":"7","author":"R. Bonneau","year":"2006","unstructured":"Bonneau, R., Reiss, D.J, Shannon, P., Facciotti, M., Hood, L., Baliga, N.S, Thorsson, V.: The inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biology\u00a07(5), R36 (2006)","journal-title":"Genome Biology"},{"key":"6_CR4","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1016\/S0065-2164(08)70464-7","volume":"44","author":"R. Bothast","year":"1997","unstructured":"Bothast, R., Saha, B.: Ethanol production from agricultural biomass substrate. Adv. App. Microbiol.\u00a044, 261\u2013286 (1997)","journal-title":"Adv. App. Microbiol."},{"issue":"1-3","key":"6_CR5","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1016\/S0014-5793(02)02387-6","volume":"515","author":"F. Devaux","year":"2002","unstructured":"Devaux, F., Carvajal, E., Moye-Rowley, S., Jacq, C.: Genome-wide studies on the nuclear PDR3-controlled response to mitochondrial dysfunction in yeast. FEBS Letters\u00a0515(1-3), 25\u201328 (2002)","journal-title":"FEBS Letters"},{"key":"6_CR6","first-page":"41","volume-title":"Pacific Symposium on Biocomputing","author":"P. D\u2019haeseleer","year":"1999","unstructured":"D\u2019haeseleer, P., Wen, X., Fuhrman, S., Somogyi, R.: Linear modeling of mRNA expression levels during CNS development and injury. In: Pacific Symposium on Biocomputing, pp. 41\u201352. World Scientific Publishing Co, Singapore (1999)"},{"key":"6_CR7","doi-asserted-by":"crossref","unstructured":"Edelstein-Keshet, L.: Mathematical Models in Biology. SIAM (2004)","DOI":"10.1137\/1.9780898719147"},{"key":"6_CR8","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1126\/science.1094068","volume":"303","author":"N. Friedman","year":"2004","unstructured":"Friedman, N.: Inferring cellular networks using probabilistic graphical models. Science\u00a0303, 799\u2013805 (2004)","journal-title":"Science"},{"key":"6_CR9","volume-title":"Matrix Computations","author":"G.H. Golub","year":"1996","unstructured":"Golub, G.H., van Loan, C.F.: Matrix Computations, 3rd edn. The Johns Hopkins University Press, Baltimore, MD (1996)","edition":"3"},{"issue":"12","key":"6_CR10","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1186\/gb-2004-5-12-r95","volume":"5","author":"A.C. Haugen","year":"2004","unstructured":"Haugen, A.C., Kelley, R., Collins, J.B., Tucker, C.J., Deng, C., Afshari, C.A., Brown, J.M., Ideker, T., Van Houten, B.: Integrating phenotypic and expression profiles to map arsenic-response networks. Genome Biology\u00a05(12), R95 (2004)","journal-title":"Genome Biology"},{"key":"6_CR11","doi-asserted-by":"crossref","first-page":"548","DOI":"10.2144\/00293bi01","volume":"29","author":"P. Hegde","year":"2000","unstructured":"Hegde, P., Qi, R., Abernathy, K., Gay, C., Dharap, S., Gaspard, R., Earle-Hughes, J., Snesrud, E., Lee, N., Quackenbush, J.: A concise guide to cdna microarray analysis. BioTechniques\u00a029, 548\u2013562 (2000)","journal-title":"BioTechniques"},{"issue":"2","key":"6_CR12","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1142\/S0219720003000071","volume":"1","author":"S. Imoto","year":"2003","unstructured":"Imoto, S., Kim, S., Goto, T., Aburatani, S., Tashiro, K., Kuhara, S., Miyano, S.: Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network. Journal of Bioinformatics and Computational Biology\u00a01(2), 231\u2013252 (2003)","journal-title":"Journal of Bioinformatics and Computational Biology"},{"issue":"23","key":"6_CR13","doi-asserted-by":"publisher","first-page":"16040","DOI":"10.1074\/jbc.274.23.16040","volume":"274","author":"J. Lee","year":"1999","unstructured":"Lee, J., Godon, C., Lagniel, G., Spector, D., Garin, J., Labarre, J., Toledano, M.B.: Yap1 and Skn7 control two specialized oxidative stress response regulons in yeast. J. Biol. Chem.\u00a0274(23), 16040\u201316046 (1999)","journal-title":"J. Biol. Chem."},{"issue":"5594","key":"6_CR14","doi-asserted-by":"publisher","first-page":"763","DOI":"10.1126\/science.1075090","volume":"298","author":"T.I. Lee","year":"2002","unstructured":"Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerber, G.K., Hannett, N.M., Harbison, C.T., Thompson, C.M., Simon, I., Zeitlinger, J., Jennings, E.G., Murray, H.L., Gordon, D.B., Ren, B., Wyrick, J.J., Tagne, J.B., Volkert, T.L., Fraenkel, E., Gifford, D.K., Young, R.A.: Transcriptional regulatory networks in Saccharomyces cerevisiae. Science\u00a0298(5594), 763\u2013764 (2002)","journal-title":"Science"},{"key":"6_CR15","first-page":"18","volume":"3","author":"S. Liang","year":"1998","unstructured":"Liang, S., Fuhrman, S., Somogyi, R.: REVEAL, a general reverse engineering algorithm for inference of genetic network architectures. Pacific Symposium on Biocomputing\u00a03, 18\u201329 (1998)","journal-title":"Pacific Symposium on Biocomputing"},{"key":"6_CR16","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1007\/s00253-006-0567-3","volume":"73","author":"Z.L. Liu","year":"2006","unstructured":"Liu, Z.L.: Genomic adaptation of ethanologenic yeast to biomass conversion inhibitors. Appl. Microbiol. Biotech.\u00a073, 27\u201336 (2006)","journal-title":"Appl. Microbiol. Biotech."},{"key":"6_CR17","doi-asserted-by":"crossref","unstructured":"Liu, Z.L., Slininger, P.J.: Development of genetically engineered stress tolerant ethanologenic yeasts using integrated functional genomics for effective biomass conversion to ethanol, CAB International, Wallingford, UK, pp. 283\u2013294 (2005)","DOI":"10.1079\/9780851990187.0283"},{"key":"6_CR18","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1002\/9783527611904.ch122","volume-title":"Recent Research Developments in Multidisciplinary Applied Microbiology: Understanding and Exploiting Microbes and Their Interactions-Biological, Physical, Chemical and Engineering Aspects","author":"Z.L. Liu","year":"2006","unstructured":"Liu, Z.L., Slininger, P.J.: Transcriptome dynamics of ethanologenic yeast in response to 5-hydroxymethylfurfural stress related to biomass conversion to ethanol. In: Recent Research Developments in Multidisciplinary Applied Microbiology: Understanding and Exploiting Microbes and Their Interactions-Biological, Physical, Chemical and Engineering Aspects, pp. 679\u2013684. Wiley-VCH, Chichester (2006a)"},{"key":"6_CR19","doi-asserted-by":"crossref","unstructured":"Liu, Z.L., Slininger, P.J.: Universal external RNA controls for microbial gene expression analysis using microarray and qRT-PCR. J. Microbiol. Methods, doi:10.1016\/j.mimet.2006.10.014 (2006b)","DOI":"10.1016\/j.mimet.2006.10.014"},{"key":"6_CR20","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1007\/s10295-004-0148-3","volume":"31","author":"Z.L. Liu","year":"2004","unstructured":"Liu, Z.L., Slininger, P.J., Dien, B.S., Berhow, M.A., Kurtzman, C.P., Gorsich, S.W.: Adaptive response of yeasts to furfural and 5-hydroxymethylfurfural and new chemical evidence for HMF conversion to 2,5-bis-hydroxymethylfuran. J. Ind. Microbiol Biotechnol.\u00a031, 345\u2013352 (2004)","journal-title":"J. Ind. Microbiol Biotechnol."},{"key":"6_CR21","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1385\/ABAB:121:1-3:0451","volume":"121-124","author":"Z.L. Liu","year":"2005","unstructured":"Liu, Z.L., Slininger, P.J., Gorsich, S.W.: Enhanced biotransformation of furfural and 5-hydroxy methylfurfural by newly developed ethanologenic yeast strains. Appl. Biochem. Biotechnol.\u00a0121-124, 451\u2013460 (2005)","journal-title":"Appl. Biochem. Biotechnol."},{"issue":"5","key":"6_CR22","doi-asserted-by":"publisher","first-page":"1860","DOI":"10.1128\/MCB.25.5.1860-1868.2005","volume":"25","author":"A. Lucau-Danila","year":"2005","unstructured":"Lucau-Danila, A., Lelandais, G., Kozovska, Z., Tanty, V., Delaveau, T., Devaux, F., Jacq, C.: Early expression of yeast genes affected by chemical stress. Mol. Cell Biol.\u00a025(5), 1860\u20131868 (2005)","journal-title":"Mol Cell Biol."},{"key":"6_CR23","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1016\/S0961-9534(01)00061-7","volume":"22","author":"C. Luo","year":"2002","unstructured":"Luo, C., Brink, D., Blanch, H.: Identification of potential fermentation inhibitors in conversion of hybrid poplar hydrolyzate to ethanol. Biomass Bioenergy\u00a022, 125\u2013138 (2002)","journal-title":"Biomass Bioenergy"},{"key":"6_CR24","doi-asserted-by":"publisher","first-page":"386","DOI":"10.1016\/S0141-0229(02)00310-1","volume":"32","author":"C. Martin","year":"2003","unstructured":"Martin, C., Jonsson, L.: Comparison of the resistance of industrial and laboratory strains of Saccharomyces and Zygosaccharomyces to lignocellulose-derived fermentation inhibitors. Enzy. Micro. Technol.\u00a032, 386\u2013395 (2003)","journal-title":"Enzy. Micro. Technol."},{"key":"6_CR25","doi-asserted-by":"publisher","first-page":"216","DOI":"10.1002\/jez.10187","volume":"294","author":"E. Meir","year":"2002","unstructured":"Meir, E., Munro, E.M., Odell, G.M., von Dassow, G.: Ingeneue: A versatile tool for reconstituting genetic networks, with examples from the segment polarity network. Journal of Experimental Zoology\u00a0294, 216\u2013251 (2002)","journal-title":"Journal of Experimental Zoology"},{"key":"6_CR26","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1093\/bioinformatics\/18.suppl_1.S241","volume":"18","author":"I.M. Ong","year":"2002","unstructured":"Ong, I.M., Glasner, J.D., Page, D.: Modelling regulatory pathways in E. coli from time series expression profiles. Bioinformatics\u00a018, S241\u2013S248 (July 2002)","journal-title":"Bioinformatics"},{"key":"6_CR27","doi-asserted-by":"publisher","first-page":"4021","DOI":"10.1093\/bioinformatics\/bti664","volume":"21","author":"R. Pal","year":"2005","unstructured":"Pal, R., Ivanov, I., Datta, A., Bittner, M.L., Dougherty, E.R.: Generating Boolean networks with a prescribed attractor structure. Bioinformatics\u00a021, 4021\u20134025 (November 2005)","journal-title":"Bioinformatics"},{"key":"6_CR28","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1002\/(SICI)1097-0290(19990220)62:4<447::AID-BIT7>3.0.CO;2-0","volume":"62","author":"E. Palmqvist","year":"1999","unstructured":"Palmqvist, E., Almeida, J., Hahn-H\u00e4gerdal, B.: Influence of furfural on anaerobic glycolytic kinetics of Saccharomyces cerevisiae in batch culture. Biotechnol. Bioeng.\u00a062, 447\u2013454 (1999)","journal-title":"Biotechnol. Bioeng."},{"key":"6_CR29","unstructured":"R Development Core Team.: R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria (2006), http:\/\/www.R-project.org ISBN 3-900051-07-0"},{"key":"6_CR30","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1007\/s10295-003-0049-x","volume":"30","author":"B. Saha","year":"2003","unstructured":"Saha, B.: Hemicellulose bioconversion. Journal of Industrial Microbiology and Biotechnology\u00a030, 279\u2013291 (2003)","journal-title":"Journal of Industrial Microbiology and Biotechnology"},{"issue":"1467","key":"6_CR31","doi-asserted-by":"publisher","first-page":"483","DOI":"10.1098\/rstb.2005.1806","volume":"361","author":"T. Schlitt","year":"2006","unstructured":"Schlitt, T., Brazma, A.: Modelling in molecular biology: describing transcription regulatory networks at different scales. Philosophical Transactions of the Royal Society B: Biological Sciences\u00a0361(1467), 483\u2013494 (2006)","journal-title":"Philosophical Transactions of the Royal Society B: Biological Sciences"},{"key":"6_CR32","doi-asserted-by":"publisher","first-page":"3091","DOI":"10.1093\/nar\/18.10.3091","volume":"18","author":"M.E. Schmitt","year":"1990","unstructured":"Schmitt, M.E., Brown, T.A., Trumpower, B.L.: A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucl. Acid Res.\u00a018, 3091\u20133092 (1990)","journal-title":"Nucl. Acid Res."},{"key":"6_CR33","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1093\/bioinformatics\/18.2.261","volume":"18","author":"I. Shmulevich","year":"2002","unstructured":"Shmulevich, I., Dougherty, E.R., Kim, S., Zhang, W.: Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics\u00a018, 261\u2013274 (2002)","journal-title":"Bioinformatics"},{"key":"6_CR34","doi-asserted-by":"publisher","first-page":"701","DOI":"10.1007\/s002530000328","volume":"53","author":"M. Taherzadeh","year":"2000","unstructured":"Taherzadeh, M., Gustafsson, L., Niklasson, C.: Physiological effects of 5-Hydroxymethylfurfural on Saccharomyces cerevisiae. App. Microbiol. Biotechnol.\u00a053, 701\u2013708 (2000)","journal-title":"App. Microbiol. Biotechnol."},{"key":"6_CR35","doi-asserted-by":"crossref","unstructured":"Takahashi, K.: Multi-algorithm and multi-timescale cell biology simulation. PhD thesis, Keio University, Fujisawa, Japan (2004)","DOI":"10.1093\/bioinformatics\/btg442"},{"key":"6_CR36","doi-asserted-by":"publisher","first-page":"1783","DOI":"10.1016\/j.febslet.2005.01.072","volume":"579","author":"K. Takahashi","year":"2005","unstructured":"Takahashi, K., Arjunan, S.N.V., Tomita, M.: Space in systems biology of signaling pathways \u2013 towards intracellular molecular crowding in silico. FEBS Letters\u00a0579, 1783\u20131788 (2005)","journal-title":"FEBS Letters"},{"key":"6_CR37","doi-asserted-by":"publisher","first-page":"446","DOI":"10.1093\/nar\/gkj013","volume":"34","author":"M.C. Teixeira","year":"2006","unstructured":"Teixeira, M.C., Monteiro, P., Jain, P., Tenreiro, S., Fernandes, A.R., Mira, N.P., Alenquer, M., Freitas, A.T., Oliveira, A.L., S\u00e1-Correia, I.: The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucl. Acids Res.\u00a034, D446\u2013451 (2006)","journal-title":"Nucl. Acids Res."},{"issue":"1","key":"6_CR38","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1093\/bioinformatics\/15.1.72","volume":"15","author":"M. Tomita","year":"1999","unstructured":"Tomita, M., Hashimoto, K., Takahashi, K., Shimizu, T.S., Matsuzaki, Y., Miyoshi, F., Saito, K., Tanida, S., Yugi, K., Venter, J.C., Hutchison III, C.A.: E-CELL: software environment for whole-cell simulation. Bioinformatics\u00a015(1), 72\u201384 (1999)","journal-title":"Bioinformatics"},{"key":"6_CR39","volume-title":"Stochastic Processes in Physics and Chemistry","author":"N. Kampen van","year":"1997","unstructured":"van Kampen, N.: Stochastic Processes in Physics and Chemistry. Elsevier, Amsterdam (1997)"},{"key":"6_CR40","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1002\/bit.10188","volume":"78","author":"C.F. Wahbom","year":"2002","unstructured":"Wahbom, C.F., Hahn-H\u00e4gerdal, B.: Furfural, 5-hydroxymethylfurfrual, and acetone act as external electron acceptors during anaerobic fermentation of xylose in recombinant Saccharomyces cerevisiae. Biotechnol. Bioeng.\u00a078, 172\u2013178 (2002)","journal-title":"Biotechnol. Bioeng."}],"container-title":["Lecture Notes in Computer Science","Systems Biology and Computational Proteomics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-540-73060-6_6.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,4,27]],"date-time":"2021-04-27T09:58:47Z","timestamp":1619517527000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-540-73060-6_6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[null]]},"ISBN":["9783540730590","9783540730606"],"references-count":40,"URL":"https:\/\/doi.org\/10.1007\/978-3-540-73060-6_6","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[]}}