{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T07:13:12Z","timestamp":1779347592592,"version":"3.51.4"},"reference-count":58,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2008,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:p>The detection and analysis of steady-state gene expression has become routine. Time-series microarrays are of growing interest to systems biologists for deciphering the dynamic nature and complex regulation of biosystems. Most temporal microarray data only contain a limited number of time points, giving rise to short-time-series data, which imposes challenges for traditional methods of extracting meaningful information. To obtain useful information from the wealth of short-time series data requires addressing the problems that arise due to limited sampling. Current efforts have shown promise in improving the analysis of short time-series microarray data, although challenges remain. This commentary addresses recent advances in methods for short-time series analysis including simplification-based approaches and the integration of multi-source information. Nevertheless, further studies and development of computational methods are needed to provide practical solutions to fully exploit the potential of this data.<\/jats:p>","DOI":"10.1186\/1752-0509-2-58","type":"journal-article","created":{"date-parts":[[2008,7,8]],"date-time":"2008-07-08T06:13:51Z","timestamp":1215497631000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":39,"title":["Short time-series microarray analysis: Methods and challenges"],"prefix":"10.1186","volume":"2","author":[{"given":"Xuewei","family":"Wang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ming","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zheng","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christina","family":"Chan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,7,7]]},"reference":[{"issue":"3","key":"215_CR1","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1016\/S0962-8924(03)00006-0","volume":"13","author":"S Panda","year":"2003","unstructured":"Panda S, Sato TK, Hampton GM, Hogenesch JB: An array of insights: application of DNA chip technology in the study of cell biology. Trends in cell biology. 2003, 13 (3): 151-156.","journal-title":"Trends in cell biology"},{"issue":"13","key":"215_CR2","doi-asserted-by":"publisher","first-page":"4801","DOI":"10.1073\/pnas.0409768102","volume":"102","author":"JP Cobb","year":"2005","unstructured":"Cobb JP, Mindrinos MN, Miller-Graziano C, Calvano SE, Baker HV, Xiao W, Laudanski K, Brownstein BH, Elson CM, Hayden DL, Herndon DN, Lowry SF, Maier RV, Schoenfeld DA, Moldawer LL, Davis RW, Tompkins RG, Baker HV, Bankey P, Billiar T, Brownstein BH, Calvano SE, Camp D, Chaudry I, Cobb JP, Davis RW, Elson CM, Freeman B, Gamelli R, Gibran N, Harbrecht B, Hayden DL, Heagy W, Heimbach D, Herndon DN, Horton J, Hunt J, Laudanski K, Lederer J, Lowry SF, Maier RV, Mannick J, McKinley B, Miller-Graziano C, Mindrinos MN, Minei J, Moldawer LL, Moore E, Moore F, Munford R, Nathens A, O'Keefe G, Purdue G, Rahme L, Remick D, Sailors M, Schoenfeld DA, Shapiro M, Silver G, Smith R, Stephanopoulos G, Stormo G, Tompkins RG, Toner M, Warren S, West M, Wolfe S, Xiao W, Young V: Application of genome-wide expression analysis to human health and disease. Proceedings of the National Academy of Sciences of the United States of America. 2005, 102 (13): 4801-4806.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"215_CR3","volume-title":"Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda","author":"US Department of Energy","year":"2006","unstructured":"US Department of Energy : Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda. 2006"},{"issue":"8","key":"215_CR4","doi-asserted-by":"publisher","first-page":"2565","DOI":"10.1128\/JB.187.8.2565-2572.2005","volume":"187","author":"P Salunkhe","year":"2005","unstructured":"Salunkhe P, Topfer T, Buer J, Tummler B: Genome-wide transcriptional profiling of the steady-state response of Pseudomonas aeruginosa to hydrogen peroxide. Journal of bacteriology. 2005, 187 (8): 2565-2572.","journal-title":"Journal of bacteriology"},{"issue":"2","key":"215_CR5","doi-asserted-by":"publisher","first-page":"574","DOI":"10.1104\/pp.106.085886","volume":"142","author":"D Rosso","year":"2006","unstructured":"Rosso D, Ivanov AG, Fu A, Geisler-Lee J, Hendrickson L, Geisler M, Stewart G, Krol M, Hurry V, Rodermel SR, Maxwell DP, Huner NP: IMMUTANS does not act as a stress-induced safety valve in the protection of the photosynthetic apparatus of Arabidopsis during steady-state photosynthesis. Plant physiology. 2006, 142 (2): 574-585.","journal-title":"Plant physiology"},{"issue":"3","key":"215_CR6","doi-asserted-by":"publisher","first-page":"636","DOI":"10.1016\/j.biosystems.2007.02.003","volume":"90","author":"SB Rawool","year":"2007","unstructured":"Rawool SB, Venkatesh KV: Steady state approach to model gene regulatory networks--simulation of microarray experiments. Bio Systems. 2007, 90 (3): 636-655.","journal-title":"Bio Systems"},{"issue":"38","key":"215_CR7","doi-asserted-by":"publisher","first-page":"14027","DOI":"10.1073\/pnas.0603227103","volume":"103","author":"AM Kocabas","year":"2006","unstructured":"Kocabas AM, Crosby J, Ross PJ, Otu HH, Beyhan Z, Can H, Tam WL, Rosa GJ, Halgren RG, Lim B, Fernandez E, Cibelli JB: The transcriptome of human oocytes. Proc Natl Acad Sci U S A. 2006, 103 (38): 14027-14032.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"11","key":"215_CR8","doi-asserted-by":"publisher","first-page":"6866","DOI":"10.1073\/pnas.1031755100","volume":"100","author":"O Laule","year":"2003","unstructured":"Laule O, F\u00fcrholz A, Chang HS, Zhu T, Wang X, Heifetz PB, Gruissem W, Lange M: Crosstalk between cytosolic and plastidial pathways of isoprenoid biosynthesis in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2003, 100 (11): 6866-6871.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"21","key":"215_CR9","doi-asserted-by":"publisher","first-page":"10296","DOI":"10.1158\/0008-5472.CAN-07-2173","volume":"67","author":"SR Setlur","year":"2007","unstructured":"Setlur SR, Royce TE, Sboner A, Mosquera JM, Demichelis F, Hofer MD, Mertz KD, Gerstein M, Rubin MA: Integrative Microarray analysis of pathways dysregulated in metastatic prostate cancer. Cancer Res. 2007, 67 (21): 10296-10303.","journal-title":"Cancer Res"},{"issue":"6","key":"215_CR10","doi-asserted-by":"publisher","first-page":"747","DOI":"10.1007\/s00425-005-1563-z","volume":"221","author":"WD Yong","year":"2005","unstructured":"Yong WD, Link B, O'Malley R, Tewari J, Hunter CT, Lu CA, Li XM, Bleecker AB, Koch KE, McCann MC, McCarty DR, Patterson SE, Reiter WD, Staiger C, Thomas SR, Vermerris W, Carpita NC: Genomics of plant cell wall biogenesis. Planta. 2005, 221 (6): 747-751.","journal-title":"Planta"},{"issue":"1-2","key":"215_CR11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1023\/A:1010603527077","volume":"47","author":"N Carpita","year":"2001","unstructured":"Carpita N, Tierney M, Campbell M: Molecular biology of the plant cell wall: searching for the genes that define structure, architecture and dynamics. Plant Mol Biol. 2001, 47 (1-2): 1-5.","journal-title":"Plant Mol Biol"},{"key":"215_CR12","doi-asserted-by":"publisher","first-page":"S2","DOI":"10.1186\/1471-2105-8-S7-S2","volume":"8 Suppl 7","author":"MG Dozmorov","year":"2007","unstructured":"Dozmorov MG, Kyker KD, Saban R, Shankar N, Baghdayan AS, Centola MB, Hurst RE: Systems biology approach for mapping the response of human urothelial cells to infection by Enterococcus faecalis. BMC bioinformatics. 2007, 8 Suppl 7: S2-","journal-title":"BMC bioinformatics"},{"key":"215_CR13","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1038\/msb4100112","volume":"3","author":"SD Hooper","year":"2007","unstructured":"Hooper SD, Boue S, Krause R, Jensen LJ, Mason CE, Ghanim M, White KP, Furlong EE, Bork P: Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis. Mol Syst Biol. 2007, 3: 72-","journal-title":"Mol Syst Biol"},{"issue":"5","key":"215_CR14","doi-asserted-by":"publisher","first-page":"889","DOI":"10.1242\/dev.00302","volume":"130","author":"LR Baugh","year":"2003","unstructured":"Baugh LR, Hill AA, Slonim DK, Brown EL, Hunter CP: Composition and dynamics of the Caenorhabditis elegans early embryonic transcriptome. Development (Cambridge, England). 2003, 130 (5): 889-900.","journal-title":"Development (Cambridge, England)"},{"key":"215_CR15","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1146\/annurev.bioeng.9.060906.151904","volume":"9","author":"IP Androulakis","year":"2007","unstructured":"Androulakis IP, Yang E, Almon RR: Analysis of time-series gene expression data: Methods, challenges, and opportunities. Annual Review of Biomedical Engineering. 2007, 9: 205-228.","journal-title":"Annual Review of Biomedical Engineering"},{"issue":"3","key":"215_CR16","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1038\/nchembio767","volume":"2","author":"KL Hsu","year":"2006","unstructured":"Hsu KL, Pilobello KT, Mahal LK: Analyzing the dynamic bacterial glycome with a lectin microarray approach. Nature chemical biology. 2006, 2 (3): 153-157.","journal-title":"Nature chemical biology"},{"issue":"5641","key":"215_CR17","doi-asserted-by":"publisher","first-page":"1874","DOI":"10.1126\/science.1087694","volume":"301","author":"HH McAdams","year":"2003","unstructured":"McAdams HH, Shapiro L: A bacterial cell-cycle regulatory network operating in time and space. Science. 2003, 301 (5641): 1874-1877.","journal-title":"Science"},{"key":"215_CR18","doi-asserted-by":"publisher","first-page":"358","DOI":"10.1186\/1471-2105-8-358","volume":"8","author":"H Lan","year":"2007","unstructured":"Lan H, Carson R, Provart NJ, Bonner AJ: Combining classifiers to predict gene function in Arabidopsis thaliana using large-scale gene expression measurements. BMC bioinformatics. 2007, 8: 358-","journal-title":"BMC bioinformatics"},{"issue":"1","key":"215_CR19","doi-asserted-by":"publisher","first-page":"71","DOI":"10.2134\/agronj2003.0071","volume":"95","author":"SM Welch","year":"2003","unstructured":"Welch SM, Roe JL, Dong ZS: A genetic neural network model of flowering time control in Arabidopsis thaliana. Agron J. 2003, 95 (1): 71-81.","journal-title":"Agron J"},{"issue":"3","key":"215_CR20","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1016\/j.jtbi.2004.11.038","volume":"234","author":"JC Locke","year":"2005","unstructured":"Locke JC, Millar AJ, Turner MS: Modelling genetic networks with noisy and varied experimental data: the circadian clock in Arabidopsis thaliana. Journal of theoretical biology. 2005, 234 (3): 383-393.","journal-title":"Journal of theoretical biology"},{"issue":"16","key":"215_CR21","doi-asserted-by":"publisher","first-page":"2493","DOI":"10.1093\/bioinformatics\/bth283","volume":"20","author":"Z Bar-Joseph","year":"2004","unstructured":"Bar-Joseph Z: Analyzing time series gene expression data. Bioinformatics (Oxford, England). 2004, 20 (16): 2493-2503.","journal-title":"Bioinformatics (Oxford, England)"},{"key":"215_CR22","doi-asserted-by":"publisher","first-page":"S3","DOI":"10.1186\/1471-2105-8-S2-S3","volume":"8 Suppl 2","author":"R Opgen-Rhein","year":"2007","unstructured":"Opgen-Rhein R, Strimmer K: Learning causal networks from systems biology time course data: an effective model selection procedure for the vector autoregressive process. BMC bioinformatics. 2007, 8 Suppl 2: S3-","journal-title":"BMC bioinformatics"},{"key":"215_CR23","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1186\/1752-0509-1-37","volume":"1","author":"R Opgen-Rhein","year":"2007","unstructured":"Opgen-Rhein R, Strimmer K: From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data. Bmc Syst Biol. 2007, 1: 37-","journal-title":"Bmc Syst Biol"},{"key":"215_CR24","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1186\/1471-2105-7-191","volume":"7","author":"J Ernst","year":"2006","unstructured":"Ernst J, Bar-Joseph Z: STEM: a tool for the analysis of short time series gene expression data. BMC bioinformatics. 2006, 7: 191-","journal-title":"BMC bioinformatics"},{"issue":"9","key":"215_CR25","doi-asserted-by":"publisher","first-page":"1081","DOI":"10.1038\/nm1460","volume":"12","author":"M Ding","year":"2006","unstructured":"Ding M, Cui SY, Li CJ, Jothy S, Haase V, Steer BM, Marsden PA, Pippin J, Shankland S, Rastaldi MP, Cohen CD, Kretzler M, Quaggin SE: Loss of the tumor suppressor Vhlh leads to upregulation of Cxcr4 and rapidly progressive glomerulonephritis in mice. Nat Med. 2006, 12 (9): 1081-1087.","journal-title":"Nat Med"},{"issue":"2","key":"215_CR26","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1038\/nm0202-143","volume":"8","author":"MV Karpuj","year":"2002","unstructured":"Karpuj MV, Becher MW, Springer JE, Chabas D, Youssef S, Pedotti R, Mitchell D, Steinman L: Prolonged survival and decreased abnormal movements in transgenic model of Huntington disease, with administration of the transglutaminase inhibitor cystamine. Nat Med. 2002, 8 (2): 143-149.","journal-title":"Nat Med"},{"issue":"1","key":"215_CR27","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1109\/MSP.2007.273062","volume":"24","author":"U Braga-Neto","year":"2007","unstructured":"Braga-Neto U: Fads and fallacies in the name of small-sample microarray classification. Ieee Signal Proc Mag. 2007, 24 (1): 91-99.","journal-title":"Ieee Signal Proc Mag"},{"key":"215_CR28","doi-asserted-by":"publisher","first-page":"I159","DOI":"10.1093\/bioinformatics\/bti1022","volume":"21","author":"J Ernst","year":"2005","unstructured":"Ernst J, Nau GJ, Bar-Joseph Z: Clustering short time series gene expression data. Bioinformatics (Oxford, England). 2005, 21: I159-I168.","journal-title":"Bioinformatics (Oxford, England)"},{"key":"215_CR29","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1186\/1471-2105-8-10","volume":"8","author":"E Yang","year":"2007","unstructured":"Yang E, Maguire T, Yarmush ML, Berthiaume F, Androulakis IP: Bioinformatics analysis of the early inflammatory response in a rat thermal injury model. BMC bioinformatics. 2007, 8: 10-","journal-title":"BMC bioinformatics"},{"issue":"7-8","key":"215_CR30","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1016\/j.ijmedinf.2005.03.014","volume":"74","author":"L Sacchi","year":"2005","unstructured":"Sacchi L, Bellazzi R, Larizza C, Magni P, Curk T, Petrovic U, Zupan B: TA-clustering: Cluster analysis of gene expression profiles through Temporal Abstractions. Int J Med Inform. 2005, 74 (7-8): 505-517.","journal-title":"Int J Med Inform"},{"issue":"8","key":"215_CR31","doi-asserted-by":"publisher","first-page":"e148","DOI":"10.1371\/journal.pcbi.0030148","volume":"3","author":"GK Gerber","year":"2007","unstructured":"Gerber GK, Dowell RD, Jaakkola TS, Gifford DK: Automated discovery of functional generality of human gene expression programs. PLoS Comput Biol. 2007, 3 (8): e148-","journal-title":"PLoS Comput Biol"},{"issue":"1","key":"215_CR32","doi-asserted-by":"publisher","first-page":"454","DOI":"10.1186\/1471-2105-8-454","volume":"8","author":"H Redestig","year":"2007","unstructured":"Redestig H, Weicht D, Selbig J, Hannah MA: Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana. BMC bioinformatics. 2007, 8 (1): 454-","journal-title":"BMC bioinformatics"},{"key":"215_CR33","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1186\/1471-2105-8-253","volume":"8","author":"J Kim","year":"2007","unstructured":"Kim J, Kim JH: Difference-based clustering of short time-course microarray data with replicates. BMC bioinformatics. 2007, 8: 253-","journal-title":"BMC bioinformatics"},{"issue":"2","key":"215_CR34","doi-asserted-by":"publisher","first-page":"442","DOI":"10.1214\/07-AOAS118","volume":"1","author":"H Wu","year":"2007","unstructured":"Wu H, Yuan M, Kaech S, Halloran M: A Statistical Analysis of Memory CD8 T Cell Differentiation: An Application of a Hierarchical State Space Model to a Short Time Course Microarray Experiment. Annals of Applied Statistics. 2007, 1 (2): 442-458.","journal-title":"Annals of Applied Statistics"},{"key":"215_CR35","volume-title":"Bmc Bioinformatics","author":"B Di Camillo","year":"2005","unstructured":"Di Camillo B, Sanchez-Cabo F, Toffolo G, Nair SK, Trajanoski Z, Cobelli C: A quantization method based on threshold optimization for microarray short time series. Bmc Bioinformatics. 2005, 6:"},{"issue":"7","key":"215_CR36","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1016\/j.bbaexp.2006.06.003","volume":"1759","author":"R Breitling","year":"2006","unstructured":"Breitling R: Biological microarray interpretation: the rules of engagement. Biochimica et biophysica acta. 2006, 1759 (7): 319-327.","journal-title":"Biochimica et biophysica acta"},{"issue":"5805","key":"215_CR37","doi-asserted-by":"publisher","first-page":"1595","DOI":"10.1126\/science.1133141","volume":"314","author":"ML Dequeant","year":"2006","unstructured":"Dequeant ML, Glynn E, Gaudenz K, Wahl M, Chen J, Mushegian A, Pourquie O: A complex oscillating network of signaling genes underlies the mouse segmentation clock. Science. 2006, 314 (5805): 1595-1598.","journal-title":"Science"},{"issue":"43","key":"215_CR38","doi-asserted-by":"publisher","first-page":"15545","DOI":"10.1073\/pnas.0506580102","volume":"102","author":"A Subramanian","year":"2005","unstructured":"Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP: Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005, 102 (43): 15545-15550.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"10","key":"215_CR39","doi-asserted-by":"publisher","first-page":"1090","DOI":"10.1038\/ng1434","volume":"36","author":"E Segal","year":"2004","unstructured":"Segal E, Friedman N, Koller D, Regev A: A module map showing conditional activity of expression modules in cancer. Nat Genet. 2004, 36 (10): 1090-1098.","journal-title":"Nat Genet"},{"key":"215_CR40","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1186\/1752-0509-1-21","volume":"1","author":"Z Li","year":"2007","unstructured":"Li Z, Srivastava S, Yang X, Mittal S, Norton P, Resau J, Haab B, Chan C: A hierarchical approach employing metabolic and gene expression profiles to identify the pathways that confer cytotoxicity in HepG2 cells. Bmc Syst Biol. 2007, 1: 21-","journal-title":"Bmc Syst Biol"},{"key":"215_CR41","doi-asserted-by":"publisher","first-page":"364","DOI":"10.1186\/1471-2164-8-364","volume":"8","author":"S Srivastava","year":"2007","unstructured":"Srivastava S, Li Z, Yang X, Yedwabnick M, Shaw S, Chan C: Identification of genes that regulate multiple cellular processes\/responses in the context of lipotoxicity to hepatoma cells. Bmc Genomics. 2007, 8: 364-","journal-title":"Bmc Genomics"},{"issue":"1","key":"215_CR42","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1021\/bp070120b","volume":"24","author":"Z Li","year":"2008","unstructured":"Li Z, Srivastava S, Findlan R, Chan C: Using Dynamic Gene Module Map Analysis To Identify Targets That Modulate Free Fatty Acid Induced Cytotoxicity. Biotechnology Progress. 2008, 24 (1): 29-37.","journal-title":"Biotechnology Progress"},{"key":"215_CR43","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1007\/11732990_5","volume":"3909","author":"L Wang","year":"2006","unstructured":"Wang L, Ramoni M, Sebastiani P: Clustering short gene expression profiles. Lect Notes Comput Sc. 2006, 3909: 60-68.","journal-title":"Lect Notes Comput Sc"},{"issue":"1","key":"215_CR44","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1109\/TNB.2008.2000149","volume":"7","author":"Z Wang","year":"2008","unstructured":"Wang Z, Yang F, Ho DW, Swift S, Tucker A, Liu X: Stochastic dynamic modeling of short gene expression time-series data. IEEE transactions on nanobioscience. 2008, 7 (1): 44-55.","journal-title":"IEEE transactions on nanobioscience"},{"key":"215_CR45","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1038\/msb4100115","volume":"3","author":"J Ernst","year":"2007","unstructured":"Ernst J, Vainas O, Harbison CT, Simon I, Bar-Joseph Z: Reconstructing dynamic regulatory maps. Mol Syst Biol. 2007, 3: 74-","journal-title":"Mol Syst Biol"},{"key":"215_CR46","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1186\/1471-2164-8-304","volume":"8","author":"A Chawade","year":"2007","unstructured":"Chawade A, Brautigam M, Lindlof A, Olsson O, Olsson B: Putative cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors. Bmc Genomics. 2007, 8: 304-","journal-title":"Bmc Genomics"},{"issue":"1","key":"215_CR47","doi-asserted-by":"publisher","first-page":"312","DOI":"10.1104\/pp.106.090431","volume":"143","author":"CJ Baxter","year":"2007","unstructured":"Baxter CJ, Redestig H, Schauer N, Repsilber D, Patil KR, Nielsen J, Selbig J, Liu J, Fernie AR, Sweetlove LJ: The metabolic response of heterotrophic Arabidopsis cells to oxidative stress. Plant physiology. 2007, 143 (1): 312-325.","journal-title":"Plant physiology"},{"key":"215_CR48","first-page":"93","volume-title":"Concepts in Plant Metabolomics","author":"MI Klapa","year":"2007","unstructured":"H. Kanani, B. Dutta, J. Quackenbush, Klapa MI: Time-Series Integrated Metabolomic and Transcriptional Profiling Analyses . Concepts in Plant Metabolomics. Edited by: Basil J. Nikolau, Wurtele ES. 2007, 93-110. Springer Netherlands"},{"issue":"8","key":"215_CR49","doi-asserted-by":"publisher","first-page":"2370","DOI":"10.1105\/tpc.107.052811","volume":"19","author":"T Ruttink","year":"2007","unstructured":"Ruttink T, Arend M, Morreel K, Storme V, Rombauts S, Fromm J, Bhalerao RP, Boerjan W, Rohde A: A molecular timetable for apical bud formation and dormancy induction in poplar. The Plant cell. 2007, 19 (8): 2370-2390.","journal-title":"The Plant cell"},{"issue":"4","key":"215_CR50","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1093\/bib\/bbl036","volume":"7","author":"A Ng","year":"2006","unstructured":"Ng A, Bursteinas B, Gao QO, Mollison E, Zvelebil M: Resources for integrative systems biology: from data through databases to networks and dynamic system models. Brief Bioinform. 2006, 7 (4): 318-330.","journal-title":"Brief Bioinform"},{"issue":"6","key":"215_CR51","doi-asserted-by":"publisher","first-page":"755","DOI":"10.1093\/bioinformatics\/btl676","volume":"23","author":"Y Shi","year":"2007","unstructured":"Shi Y, Mitchell T, Bar-Joseph Z: Inferring pairwise regulatory relationships from multiple time series datasets. Bioinformatics (Oxford, England). 2007, 23 (6): 755-763.","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"4","key":"215_CR52","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1038\/ng1201-365","volume":"29","author":"A Brazma","year":"2001","unstructured":"Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FCP, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M: Minimum information about a microarray experiment (MIAME) - toward standards for microarray data. Nat Genet. 2001, 29 (4): 365-371.","journal-title":"Nat Genet"},{"issue":"8","key":"215_CR53","doi-asserted-by":"publisher","first-page":"887","DOI":"10.1038\/nbt1329","volume":"25","author":"CF Taylor","year":"2007","unstructured":"Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK, Jones AR, Zhu WM, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJR, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping PP, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR, Hermjakob H: The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol. 2007, 25 (8): 887-893.","journal-title":"Nat Biotechnol"},{"issue":"3","key":"215_CR54","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1007\/s11306-007-0070-6","volume":"3","author":"O Fiehn","year":"2007","unstructured":"Fiehn O, Robertson D, Griffin J, van der Werf M, Nikolau B, Morrison N, Sumner LW, Goodacre R, Hardy NW, Taylor C, Fostel J, Kristal B, Kaddurah-Daouk R, Mendes P, van Ommen B, Lindon JC, Sansone SA: The metabolomics standards initiative (MSI). Metabolomics. 2007, 3 (3): 175-178.","journal-title":"Metabolomics"},{"issue":"8","key":"215_CR55","doi-asserted-by":"publisher","first-page":"894","DOI":"10.1038\/nbt1324","volume":"25","author":"S Orchard","year":"2007","unstructured":"Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stumpflen V, Ceol A, Chatr-Aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, De Las Rivas J, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H: The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol. 2007, 25 (8): 894-898.","journal-title":"Nat Biotechnol"},{"key":"215_CR56","unstructured":"Gene Expression Omnibus., http:\/\/www.ncbi.nlm.nih.gov\/geo\/"},{"key":"215_CR57","unstructured":"ArrayExpress., http:\/\/www.ebi.ac.uk\/microarray-as\/ae\/"},{"issue":"7","key":"215_CR58","doi-asserted-by":"publisher","first-page":"932","DOI":"10.1093\/bioinformatics\/btm639","volume":"24","author":"O Hirose","year":"2008","unstructured":"Hirose O, Yoshida R, Imoto S, Yamaguchi R, Higuchi T, Charnock-Jones DS, Print C, Miyano S: Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models. Bioinformatics. 2008, 24 (7): 932-942.","journal-title":"Bioinformatics"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-2-58.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T10:29:09Z","timestamp":1630492149000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-2-58"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,7,7]]},"references-count":58,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["215"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-2-58","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,7,7]]},"assertion":[{"value":"13 February 2008","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 July 2008","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 July 2008","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"58"}}