{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,12]],"date-time":"2025-11-12T03:17:28Z","timestamp":1762917448343,"version":"3.37.3"},"reference-count":51,"publisher":"Springer Science and Business Media LLC","issue":"S6","license":[{"start":{"date-parts":[[2013,4,1]],"date-time":"2013-04-01T00:00:00Z","timestamp":1364774400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2013,4]]},"DOI":"10.1186\/1471-2105-14-s6-s1","type":"journal-article","created":{"date-parts":[[2013,4,17]],"date-time":"2013-04-17T11:35:24Z","timestamp":1366198524000},"source":"Crossref","is-referenced-by-count":11,"title":["Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection"],"prefix":"10.1186","volume":"14","author":[{"given":"Elena","family":"Zaslavsky","sequence":"first","affiliation":[]},{"given":"German","family":"Nudelman","sequence":"additional","affiliation":[]},{"given":"Susanna","family":"Marquez","sequence":"additional","affiliation":[]},{"given":"Uri","family":"Hershberg","sequence":"additional","affiliation":[]},{"given":"Boris M","family":"Hartmann","sequence":"additional","affiliation":[]},{"given":"Juilee","family":"Thakar","sequence":"additional","affiliation":[]},{"given":"Stuart C","family":"Sealfon","sequence":"additional","affiliation":[]},{"given":"Steven H","family":"Kleinstein","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2013,4,17]]},"reference":[{"issue":"4","key":"5799_CR1","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1038\/nrmicro1126","volume":"3","author":"R Jenner","year":"2005","unstructured":"Jenner R, Young R: Insights into host responses against pathogens from transcriptional profiling. Nat Rev Microbiol. 2005, 3 (4): 281-294. 10.1038\/nrmicro1126.","journal-title":"Nat Rev Microbiol"},{"issue":"12","key":"5799_CR2","doi-asserted-by":"publisher","first-page":"1215","DOI":"10.1002\/bies.20683","volume":"29","author":"T Ravasi","year":"2007","unstructured":"Ravasi T, Wells C, Hume D: Systems biology of transcription control in macrophages. BioEssays. 2007, 29 (12): 1215-1226. 10.1002\/bies.20683.","journal-title":"BioEssays"},{"issue":"3","key":"5799_CR3","doi-asserted-by":"publisher","first-page":"e1000021","DOI":"10.1371\/journal.pcbi.1000021","volume":"4","author":"SA Ramsey","year":"2008","unstructured":"Ramsey SA, Klemm SL, Zak DE, Kennedy KA, Thorsson V, Li B, Gilchrist M, Gold ES, Johnson CD, Litvak V, Navarro G, Roach JC, Rosenberger CM, Rust AG, Yudkovsky N, Aderem A, Shmulevich I: Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics. PLoS Comput Biol. 2008, 4 (3): e1000021-10.1371\/journal.pcbi.1000021.","journal-title":"PLoS Comput Biol"},{"key":"5799_CR4","doi-asserted-by":"publisher","first-page":"e6","DOI":"10.1371\/journal.ppat.0040006","volume":"4","author":"J Leber","year":"2008","unstructured":"Leber J, Crimmins G, Raghavan S, Meyer-Morse N, Cox J, Portnoy D: Distinct TLR- and NLR-mediated transcriptional responses to an intracellular pathogen. PLoS Pathogens. 2008, 4: e6-10.1371\/journal.ppat.0040006.","journal-title":"PLoS Pathogens"},{"issue":"5950","key":"5799_CR5","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1126\/science.1179050","volume":"326","author":"I Amit","year":"2009","unstructured":"Amit I, Garber M, Chevrier N, Leite AP, Donner Y, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, Smith Z, Deering R, McDonald RC, Cabili M, Bernstein BE, Rinn JL, Meissner A, Root DE, Hacohen N, Regev A: Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses. Science. 2009, 326 (5950): 257-263. 10.1126\/science.1179050.","journal-title":"Science"},{"issue":"7","key":"5799_CR6","doi-asserted-by":"publisher","first-page":"1255","DOI":"10.1016\/j.cell.2009.12.018","volume":"139","author":"SD Shapira","year":"2009","unstructured":"Shapira SD, Gat-Viks I, Shum BO, Dricot A, de Grace MM, Wu L, Gupta PB, Hao T, Silver SJ, Root DE, Hill DE, Regev A, Hacohen N: A Physical and Regulatory Map of Host-Influenza Interactions Reveals Pathways in H1N1 Infection. Cell. 2009, 139 (7): 1255-1267. 10.1016\/j.cell.2009.12.018.","journal-title":"Cell"},{"key":"5799_CR7","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1038\/ng1165","volume":"34","author":"E Segal","year":"2003","unstructured":"Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N: Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nature Genetics. 2003, 34: 166-176. 10.1038\/ng1165.","journal-title":"Nature Genetics"},{"key":"5799_CR8","doi-asserted-by":"publisher","first-page":"1337","DOI":"10.1038\/nbt890","volume":"21","author":"Z Bar-Joseph","year":"2003","unstructured":"Bar-Joseph Z, Gerber GK, Lee TI, Rinaldi NJ, Yoo JY, Robert F, Gordon DB, Fraenkel E, Jaakkola TS, Young RA, Gifford DK: Computational discovery of gene modules and regulatory networks. Nat Biotechnol. 2003, 21: 1337-1342. 10.1038\/nbt890.","journal-title":"Nat Biotechnol"},{"key":"5799_CR9","doi-asserted-by":"publisher","first-page":"R37","DOI":"10.1186\/gb-2006-7-5-r37","volume":"7","author":"K Lemmens","year":"2006","unstructured":"Lemmens K, Dhollander T, De Bie T, Monsieurs P, Engelen K, Smets B, Winderickx J, De Moor B, Marchal K: Inferring transcriptional modules from ChIP-chip, motif and microarray data. Genome Biology. 2006, 7: R37-10.1186\/gb-2006-7-5-r37.","journal-title":"Genome Biology"},{"issue":"5","key":"5799_CR10","doi-asserted-by":"publisher","first-page":"R36","DOI":"10.1186\/gb-2006-7-5-r36","volume":"7","author":"R Bonneau","year":"2006","unstructured":"Bonneau R, Reiss DJ, Shannon P, Facciotti M, Hood L, Baliga NS, Thorsson V: The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol. 2006, 7 (5): R36-10.1186\/gb-2006-7-5-r36.","journal-title":"Genome Biol"},{"issue":"2","key":"5799_CR11","doi-asserted-by":"publisher","first-page":"662","DOI":"10.1038\/nprot.2006.106","volume":"1","author":"AA Margolin","year":"2006","unstructured":"Margolin AA, Wang K, Lim WK, Kustagi M, Nemenman I, Califano A: Reverse engineering cellular networks. Nat Protocols. 2006, 1 (2): 662-671. 10.1038\/nprot.2006.106.","journal-title":"Nat Protocols"},{"key":"5799_CR12","doi-asserted-by":"publisher","first-page":"R4","DOI":"10.1186\/gb-2007-8-1-r4","volume":"8","author":"G Chen","year":"2007","unstructured":"Chen G, Jensen ST, Stoeckert CJ: Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biology. 2007, 8: R4-10.1186\/gb-2007-8-1-r4.","journal-title":"Genome Biology"},{"key":"5799_CR13","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1038\/msb4100115","volume":"3","author":"J Ernst","year":"2007","unstructured":"Ernst J, Vainas O, Harbison C, Simon I, Bar-Joseph Z: Reconstructing dynamic regulatory maps. Nature-EMBO Molecular Systems Biology. 2007, 3: 74.","journal-title":"Nature-EMBO Molecular Systems Biology"},{"key":"5799_CR14","doi-asserted-by":"publisher","first-page":"R2","DOI":"10.1186\/gb-2008-9-1-r2","volume":"9","author":"HG Lee","year":"2008","unstructured":"Lee HG, Lee HS, Jeon SH, Chung TH, Lim YS, Huh WK: High-resolution analysis of condition-specific regulatory modules in Saccharomyces cerevisiae. Genome Biology. 2008, 9: R2-10.1186\/gb-2008-9-1-r2.","journal-title":"Genome Biology"},{"key":"5799_CR15","doi-asserted-by":"publisher","first-page":"155+","DOI":"10.1186\/1471-2105-10-155","volume":"10","author":"I Nachman","year":"2009","unstructured":"Nachman I, Regev A: BRNI: Modular analysis of transcriptional regulatory programs. BMC Bioinformatics. 2009, 10: 155+-10.1186\/1471-2105-10-155.","journal-title":"BMC Bioinformatics"},{"issue":"24","key":"5799_CR16","doi-asserted-by":"publisher","first-page":"3267","DOI":"10.1093\/bioinformatics\/btp588","volume":"25","author":"C Huttenhower","year":"2009","unstructured":"Huttenhower C, Mutungu KT, Indik N, Yang W, Schroeder M, Forman JJ, Troyanskaya OG, Coller HA: Detailing regulatory networks through large scale data integration. Bioinformatics. 2009, 25 (24): 3267-3274. 10.1093\/bioinformatics\/btp588.","journal-title":"Bioinformatics"},{"issue":"19","key":"5799_CR17","doi-asserted-by":"publisher","first-page":"2686","DOI":"10.1093\/bioinformatics\/btr454","volume":"27","author":"Z Li","year":"2011","unstructured":"Li Z, Li P, Krishnan A, Liu J: Large-scale dynamic gene regulatory network inference combining differential equation models with local dynamic Bayesian network analysis. Bioinformatics. 2011, 27 (19): 2686-2691. 10.1093\/bioinformatics\/btr454.","journal-title":"Bioinformatics"},{"issue":"12","key":"5799_CR18","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1038\/nri3109","volume":"11","author":"I Amit","year":"2011","unstructured":"Amit I, Regev A, Hacohen N: Strategies to discover regulatory circuits of the mammalian immune system. Nat Rev Immunol. 2011, 11 (12): 873-880.","journal-title":"Nat Rev Immunol"},{"key":"5799_CR19","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1016\/S0065-2776(09)01204-8","volume":"102","author":"F Petrocca","year":"2009","unstructured":"Petrocca F, Lieberman J: Micromanagers of immune cell fate and function. Adv Immunol. 2009, 102: 227-244.","journal-title":"Adv Immunol"},{"issue":"6","key":"5799_CR20","doi-asserted-by":"publisher","first-page":"e70","DOI":"10.1371\/journal.pcbi.0020070","volume":"2","author":"A Beyer","year":"2006","unstructured":"Beyer A, Workman C, Hollunder J, Radke D, M\u00f6ller U, Wilhelm T, Ideker T: Integrated Assessment and Prediction of Transcription Factor Binding. PLoS Comput Biol. 2006, 2 (6): e70-10.1371\/journal.pcbi.0020070.","journal-title":"PLoS Comput Biol"},{"key":"5799_CR21","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1038\/nature02782","volume":"431","author":"N Luscombe","year":"2004","unstructured":"Luscombe N, Babu M, Yu H, Snyder M, Teichmann S, Gerstein M: Genomic analysis of regulatory network dynamics reveals large topological changes. Nature. 2004, 431: 308-312. 10.1038\/nature02782.","journal-title":"Nature"},{"key":"5799_CR22","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1016\/j.cellimm.2007.01.010","volume":"244","author":"J Tegn\u00e9r","year":"2006","unstructured":"Tegn\u00e9r J, Nilsson R, Bajic V, Bj\u00f6rkegren J, Ravasi T: Systems biology of innate immunity. Cellular Immunology. 2006, 244: 105-109. 10.1016\/j.cellimm.2007.01.010.","journal-title":"Cellular Immunology"},{"key":"5799_CR23","doi-asserted-by":"publisher","first-page":"553","DOI":"10.1038\/ng.375","volume":"41","author":"The FANTOM Consortium and Riken Omics Science Center","year":"2009","unstructured":"The FANTOM Consortium and Riken Omics Science Center: The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet. 2009, 41: 553-562. 10.1038\/ng.375.","journal-title":"Nat Genet"},{"key":"5799_CR24","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1016\/j.virol.2005.09.024","volume":"344","author":"O Haller","year":"2006","unstructured":"Haller O, Kochs G, Weber F: The interferon response circuit: Induction and suppression by pathogenic viruses. Virology. 2006, 344: 119-130. 10.1016\/j.virol.2005.09.024.","journal-title":"Virology"},{"issue":"9","key":"5799_CR25","doi-asserted-by":"publisher","first-page":"3363","DOI":"10.1073\/pnas.0511345103","volume":"103","author":"M Zilliox","year":"2006","unstructured":"Zilliox M, Parmigiani G, Griffin D: Gene expression patterns in dendritic cells infected with measles virus compared with other pathogens. PNAS. 2006, 103 (9): 3363-3368. 10.1073\/pnas.0511345103.","journal-title":"PNAS"},{"key":"5799_CR26","doi-asserted-by":"publisher","first-page":"2908","DOI":"10.4049\/jimmunol.0903453","volume":"184","author":"E Zaslavsky","year":"2010","unstructured":"Zaslavsky E, Hershberg U, Seto J, Pham AM, Marquez S, Duke JL, Wetmur JG, tenOever BR, Sealfon SC, Kleinstein SH: Antiviral response dictated by choreographed cascade of transcription factors. Journal of Immunology. 2010, 184: 2908-2917. 10.4049\/jimmunol.0903453.","journal-title":"Journal of Immunology"},{"key":"5799_CR27","doi-asserted-by":"publisher","first-page":"651","DOI":"10.1038\/nmeth1068","volume":"4","author":"G Robertson","year":"2007","unstructured":"Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffth OL, He A, Marra M, Snyder M, Jones S: Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nature Methods. 2007, 4: 651-657. 10.1038\/nmeth1068.","journal-title":"Nature Methods"},{"key":"5799_CR28","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1093\/nar\/gkg108","volume":"31","author":"V Matys","year":"2003","unstructured":"Matys V, Fricke E, Ge\u00f6ers R, G\u00f6ssling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, M\u00fcnch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S, Wingender E: TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 2003, 31: 374-378. 10.1093\/nar\/gkg108.","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"5799_CR29","doi-asserted-by":"publisher","first-page":"430","DOI":"10.1093\/bioinformatics\/bti819","volume":"22","author":"T Sauer","year":"2006","unstructured":"Sauer T, Shelest E, Wingender E: Evaluating phylogenetic footprinting for human-rodent comparisons. Bioinformatics. 2006, 22 (4): 430-437. 10.1093\/bioinformatics\/bti819.","journal-title":"Bioinformatics"},{"issue":"2","key":"5799_CR30","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1016\/S0092-8674(04)00304-6","volume":"117","author":"M Beer","year":"2004","unstructured":"Beer M, Tavazoie S: Predicting gene expression from sequence. Cell. 2004, 117 (2): 185-198. 10.1016\/S0092-8674(04)00304-6.","journal-title":"Cell"},{"issue":"21","key":"5799_CR31","doi-asserted-by":"publisher","first-page":"6795","DOI":"10.1093\/nar\/gkn752","volume":"36","author":"M Koudritsky","year":"2008","unstructured":"Koudritsky M, Domany E: Positional distribution of human transcription factor binding sites. Nucleic Acids Res. 2008, 36 (21): 6795-6805. 10.1093\/nar\/gkn752.","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"5799_CR32","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, Markiel A, Ozier O, Baliga N, Wang J, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research. 2003, 13 (11): 2498-2504. 10.1101\/gr.1239303.","journal-title":"Genome Research"},{"issue":"8","key":"5799_CR33","doi-asserted-by":"publisher","first-page":"1040","DOI":"10.1093\/bioinformatics\/btm057","volume":"23","author":"A Barsky","year":"2007","unstructured":"Barsky A, Gardy J, Hancock R, Munzner T: Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation. Bioinformatics. 2007, 23 (8): 1040-1042. 10.1093\/bioinformatics\/btm057.","journal-title":"Bioinformatics"},{"key":"5799_CR34","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1007\/978-1-60761-854-6_24","volume":"674","author":"G Anthony","year":"2010","unstructured":"Anthony G, Lu Y, Bar-Joseph Z: Computational methods for analyzing dynamic regulatory networks. Methods in Molecular Biology. 2010, 674: 419-441. 10.1007\/978-1-60761-854-6_24.","journal-title":"Methods in Molecular Biology"},{"issue":"14","key":"5799_CR35","doi-asserted-by":"publisher","first-page":"6286","DOI":"10.1073\/pnas.0913357107","volume":"107","author":"D Marbach","year":"2010","unstructured":"Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, Stolovitzky G: Revealing strengths and weaknesses of methods for gene network inference. Proceedings of the National Academy of Sciences. 2010, 107 (14): 6286-6291. 10.1073\/pnas.0913357107.","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"10","key":"5799_CR36","doi-asserted-by":"publisher","first-page":"e13397","DOI":"10.1371\/journal.pone.0013397","volume":"5","author":"A Greenfield","year":"2010","unstructured":"Greenfield A, Madar A, Ostrer H, Bonneau R: DREAM4: Combining Genetic and Dynamic Information to Identify Biological Networks and Dynamical Models. PLoS ONE. 2010, 5 (10): e13397-10.1371\/journal.pone.0013397. [ http:\/\/dx.doi.org\/10.1371%2Fjournal.pone.0013397 ]","journal-title":"PLoS ONE"},{"key":"5799_CR37","doi-asserted-by":"publisher","first-page":"e8121","DOI":"10.1371\/journal.pone.0008121","volume":"5","author":"KY Yip","year":"2010","unstructured":"Yip KY, Alexander RP, Yan KK, Gerstein M: Improved Reconstruction of In Silico Gene Regulatory Networks by Integrating Knockout and Perturbation Data. PLoS ONE. 2010, 5: e8121-10.1371\/journal.pone.0008121.","journal-title":"PLoS ONE"},{"issue":"5543","key":"5799_CR38","doi-asserted-by":"publisher","first-page":"870","DOI":"10.1126\/science.294.5543.870","volume":"294","author":"Q Huang","year":"2001","unstructured":"Huang Q, Liu D, Majewski P, Schulte L, Korn J, Young R, Lander E, Hacohen N: The plasticity of dendritic cell responses to pathogens and their components. Science. 2001, 294 (5543): 870-875. 10.1126\/science.294.5543.870.","journal-title":"Science"},{"issue":"13","key":"5799_CR39","doi-asserted-by":"publisher","first-page":"6295","DOI":"10.1128\/JVI.02381-05","volume":"80","author":"A Fernandez-Sesma","year":"2006","unstructured":"Fernandez-Sesma A, Marukian S, Ebersole BJ, Kaminski D, Park MS, Yuen T, Sealfon SC, Garca-Sastre A, Moran TM: Influenza virus evades innate and adaptive immunity via the NS1 protein. J Virol. 2006, 80 (13): 6295-304. 10.1128\/JVI.02381-05.","journal-title":"J Virol"},{"key":"5799_CR40","doi-asserted-by":"publisher","first-page":"514","DOI":"10.1128\/JVI.01265-06","volume":"81","author":"M Mibayashi","year":"2007","unstructured":"Mibayashi M, Martinez-Sobrido L, Loo Y, Cardenas W, Gale M, Garcia-Sastre A: Inhibition of retinoic acid-inducible gene I-mediated induction of beta interferon by the NS1 protein of influenza A virus. J Virol. 2007, 81: 514-524. 10.1128\/JVI.01265-06.","journal-title":"J Virol"},{"issue":"11","key":"5799_CR41","doi-asserted-by":"publisher","first-page":"6413","DOI":"10.4049\/jimmunol.1001829","volume":"185","author":"AY Wen","year":"2010","unstructured":"Wen AY, Sakamoto KM, Miller LS: The Role of the Transcription Factor CREB in Immune Function. The Journal of Immunology. 2010, 185 (11): 6413-6419. 10.4049\/jimmunol.1001829.","journal-title":"The Journal of Immunology"},{"issue":"3","key":"5799_CR42","first-page":"227","volume":"21","author":"J Wang","year":"2009","unstructured":"Wang J, Lee S, Seto J, Teh CE, Bunting K, Ma L, Shannon MF: The transcription repressor, ZEB1, cooperates with CtBP2 and HDAC1 to suppress IL-2 gene activation in T cells. Nature Immunology. 2009, 21 (3): 227-235.","journal-title":"Nature Immunology"},{"issue":"41","key":"5799_CR43","doi-asserted-by":"publisher","first-page":"16245","DOI":"10.1073\/pnas.0707757104","volume":"104","author":"J Roach","year":"2007","unstructured":"Roach J, Smith K, Strobe K, Nissen S, Haudenschild C, Zhou D, Vasicek T, Held G, Stolovitzky G, Hood L, Aderem A: Transcription factor expression in lipopolysaccharide-activated peripheral-blood-derived mononuclear cells. PNAS. 2007, 104 (41): 16245-16250. 10.1073\/pnas.0707757104.","journal-title":"PNAS"},{"issue":"17","key":"5799_CR44","doi-asserted-by":"publisher","first-page":"9522","DOI":"10.1128\/JVI.77.17.9522-9532.2003","volume":"77","author":"MS Park","year":"2003","unstructured":"Park MS, Garcia-Sastre A, Cros JF, Basler CF, Palese P: Newcastle disease virus V protein is a determinant of host range restriction. J Virol. 2003, 77 (17): 9522-9532. 10.1128\/JVI.77.17.9522-9532.2003.","journal-title":"J Virol"},{"issue":"7","key":"5799_CR45","doi-asserted-by":"publisher","first-page":"1126","DOI":"10.1086\/368381","volume":"187","author":"CB L\u00f3pez","year":"2003","unstructured":"L\u00f3pez CB, Garca-Sastre A, Williams BRG, Moran TM: Type I Interferon Induction Pathway, but Not Released Interferon, Participates in the Maturation of Dendritic Cells Induced by Negative-Strand RNA Viruses. Journal of Infectious Diseases. 2003, 187 (7): 1126-1136. 10.1086\/368381.","journal-title":"Journal of Infectious Diseases"},{"issue":"13","key":"5799_CR46","doi-asserted-by":"publisher","first-page":"1547","DOI":"10.1093\/bioinformatics\/btn224","volume":"24","author":"P Du","year":"2008","unstructured":"Du P, Kibbe WA, Lin SM: lumi: a pipeline for processing Illumina microarray. Bioinformatics. 2008, 24 (13): 1547-1548. 10.1093\/bioinformatics\/btn224.","journal-title":"Bioinformatics"},{"issue":"10","key":"5799_CR47","doi-asserted-by":"publisher","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","volume":"5","author":"RC Gentleman","year":"2004","unstructured":"Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5 (10): R80-10.1186\/gb-2004-5-10-r80.","journal-title":"Genome Biol"},{"key":"5799_CR48","doi-asserted-by":"publisher","first-page":"D501","DOI":"10.1093\/nar\/gki025","volume":"33","author":"K Pruitt","year":"2005","unstructured":"Pruitt K, Tatusova T, Maglott D: NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005, 33: D501-504. 10.1093\/nar\/gki476.","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"5799_CR49","doi-asserted-by":"publisher","first-page":"708","DOI":"10.1101\/gr.1933104","volume":"14","author":"M Blanchette","year":"2004","unstructured":"Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W: Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004, 14 (4): 708-715. 10.1101\/gr.1933104.","journal-title":"Genome Res"},{"key":"5799_CR50","volume-title":"RepeatMasker Open-3.0","author":"A Smit","year":"1996","unstructured":"Smit A, Hubley R, Green P: RepeatMasker Open-3.0. 1996, [ http:\/\/www.repeatmasker.org ]"},{"issue":"13","key":"5799_CR51","doi-asserted-by":"publisher","first-page":"3576","DOI":"10.1093\/nar\/gkg585","volume":"31","author":"A Kel","year":"2003","unstructured":"Kel A, G\u00f6ssling E, Reuter I, Cheremushkin E, Kel-Margoulis O, Wingender E: MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res. 2003, 31 (13): 3576-3579. 10.1093\/nar\/gkg585.","journal-title":"Nucleic Acids Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-S6-S1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-14-S6-S1\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-S6-S1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,7,25]],"date-time":"2020-07-25T14:29:31Z","timestamp":1595687371000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-14-S6-S1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,4]]},"references-count":51,"journal-issue":{"issue":"S6","published-print":{"date-parts":[[2013,4]]}},"alternative-id":["5799"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-14-s6-s1","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2013,4]]},"article-number":"S1"}}