{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,16]],"date-time":"2025-07-16T13:20:20Z","timestamp":1752672020945},"reference-count":28,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s12859-017-1731-8","type":"journal-article","created":{"date-parts":[[2017,7,4]],"date-time":"2017-07-04T05:26:41Z","timestamp":1499146001000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters"],"prefix":"10.1186","volume":"18","author":[{"given":"Shailesh","family":"Tripathi","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jason","family":"Lloyd-Price","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andre","family":"Ribeiro","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olli","family":"Yli-Harja","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthias","family":"Dehmer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Frank","family":"Emmert-Streib","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2017,7,4]]},"reference":[{"key":"1731_CR1","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1007\/978-94-015-8054-0_8","volume":"65","author":"SA Kauffman","year":"1992","unstructured":"Kauffman SA. The origins of order: Self-organization and selection in evolution. Underst Origs. 1992; 65:153\u201381.","journal-title":"Underst Origs"},{"key":"1731_CR2","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1038\/nature08454","volume":"461","author":"EE Schadt","year":"2009","unstructured":"Schadt EE. Molecular networks as sensors and drivers of common human diseases. Nature. 2009; 461:218\u201323.","journal-title":"Nature"},{"issue":"4","key":"1731_CR3","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1002\/wsbm.134","volume":"3","author":"F Emmert-Streib","year":"2011","unstructured":"Emmert-Streib F, Glazko GV. Network Biology: A direct approach to study biological function. Wiley Interdiscip Rev Syst Biol Med. 2011; 3(4):379\u201391.","journal-title":"Wiley Interdiscip Rev Syst Biol Med"},{"issue":"24","key":"1731_CR4","doi-asserted-by":"crossref","first-page":"3891","DOI":"10.1016\/j.febslet.2009.11.024","volume":"583","author":"M Vidal","year":"2009","unstructured":"Vidal M. A unifying view of 21st century systems biology. FEBS Lett. 2009; 583(24):3891\u20134.","journal-title":"FEBS Lett"},{"key":"1731_CR5","doi-asserted-by":"crossref","first-page":"8","DOI":"10.3389\/fgene.2012.00008","volume":"3","author":"F Emmert-Streib","year":"2012","unstructured":"Emmert-Streib F, Glazko GV, Altay G, de Matos Simoes R. Statistical inference and reverse engineering of gene regulatory networks from observational expression data. Front Genet. 2012; 3:8.","journal-title":"Front Genet"},{"key":"1731_CR6","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/1471-2105-8-S6-S5","volume":"8","author":"F Markowetz","year":"2007","unstructured":"Markowetz F, Spang R. Inferring cellular networks\u2013a review. BMC Bioinforma. 2007; 8:5.","journal-title":"BMC Bioinforma"},{"key":"1731_CR7","doi-asserted-by":"crossref","first-page":"281","DOI":"10.3389\/fgene.2013.00281","volume":"4","author":"R de Matos Simoes","year":"2013","unstructured":"de Matos Simoes R, Dehmer M, Emmert-Streib F. B-cell lymphoma gene regulatory networks: Biological consistency among inference methods. Front Genet. 2013; 4:281.","journal-title":"Front Genet"},{"issue":"1","key":"1731_CR8","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/1471-2105-7-43","volume":"7","author":"T Van den Bulcke","year":"2006","unstructured":"Van den Bulcke T, Van Leemput K, Naudts B, van Remortel P, Ma H, Verschoren A, De Moor B, Marchal K. Syntren: a generator of synthetic gene expression data for design and analysis of structure learning algorithms. BMC Bioinforma. 2006; 7(1):43. doi: 10.1186\/1471-2105-7-43 .","journal-title":"BMC Bioinforma"},{"issue":"1","key":"1731_CR9","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1111\/j.1749-6632.2008.03756.x","volume":"1158","author":"B Di Camillo","year":"2009","unstructured":"Di Camillo B, Toffolo G, Cobelli C. A gene network simulator to assess reverse engineering algorithms. Ann N Y Acad Sci. 2009; 1158(1):125\u201342. doi: 10.1111\/j.1749-6632.2008.03756.x .","journal-title":"Ann N Y Acad Sci"},{"issue":"2","key":"1731_CR10","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1089\/cmb.2008.08TT","volume":"16","author":"R Castelo","year":"2009","unstructured":"Castelo R, Roverato A. Reverse engineering molecular regulatory networks from microarray data with qp-graphs. J Comput Biol. 2009; 16(2):213\u20137.","journal-title":"J Comput Biol"},{"issue":"1","key":"1731_CR11","doi-asserted-by":"crossref","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(1):37. doi: 10.1186\/1752-0509-1-37 .","journal-title":"BMC Syst Biol"},{"issue":"9","key":"1731_CR12","doi-asserted-by":"crossref","first-page":"1630","DOI":"10.1089\/cmb.2006.13.1630","volume":"13","author":"AS Ribeiro","year":"2006","unstructured":"Ribeiro AS, Zhu R, Kauffman SA. A general modeling strategy for gene regulatory networks with stochastic dynamics. J Comput Biol. 2006; 13(9):1630\u20139.","journal-title":"J Comput Biol"},{"issue":"6","key":"1731_CR13","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1093\/bioinformatics\/btm004","volume":"23","author":"AS Ribeiro","year":"2007","unstructured":"Ribeiro AS, Lloyd-Price J. Sgn sim, a stochastic genetic networks simulator. Bioinformatics. 2007; 23(6):777.","journal-title":"Bioinformatics"},{"issue":"6060","key":"1731_CR14","doi-asserted-by":"crossref","first-page":"1226","DOI":"10.1126\/science.1213847","volume":"334","author":"RD Peng","year":"2011","unstructured":"Peng RD. Reproducible research in computational science. Science. 2011; 334(6060):1226\u20137.","journal-title":"Science"},{"issue":"19","key":"1731_CR15","doi-asserted-by":"crossref","first-page":"2834","DOI":"10.1093\/bioinformatics\/btu384","volume":"30","author":"S Tripathi","year":"2014","unstructured":"Tripathi S, Dehmer M, Emmert-Streib F. NetBioV: An R package for visualizing large network data in biology and medicine. Bioinformatics. 2014; 30(19):2834\u20136.","journal-title":"Bioinformatics"},{"issue":"suppl_1","key":"1731_CR16","first-page":"D637","volume":"36","author":"BJ Breitkreutz","year":"2008","unstructured":"Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, Livstone M, Oughtred R, Lackner DH, B\u00e4hler J, Wood V, Dolinski K, Tyers M. The BioGRID Interaction Database: 2008 update. Nucl Acids Res. 2008; 36(suppl_1):D637\u201340.","journal-title":"Nucl Acids Res"},{"issue":"suppl_1","key":"1731_CR17","doi-asserted-by":"crossref","first-page":"D525","DOI":"10.1093\/nar\/gkp878","volume":"38","author":"B Aranda","year":"2010","unstructured":"Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J, Kerssemakers J, Leroy C, Menden M, Michaut M, Montecchi-Palazzi L, Neuhauser SN, Orchard S, Perreau V, Roechert B, van Eijk K, Hermjakob H. The IntAct molecular interaction database in 2010. Nucl Acids Res. 2010; 38(suppl_1):D525\u201331.","journal-title":"Nucl Acids Res"},{"issue":"D1","key":"1731_CR18","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1093\/nar\/gks1201","volume":"41","author":"H Salgado","year":"2013","unstructured":"Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Mu\u00f1iz-Rascado L, Garc\u00eda-Sotelo JS, Weiss V, Solano-Lira H, Mart\u00ednez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hern\u00e1ndez S, Alquicira-Hern\u00e1ndez K, L\u00f3pez-Fuentes A, Porr\u00f3n-Sotelo L, Huerta AM, Bonavides-Mart\u00ednez C, Balderas-Mart\u00ednez YI, Pannier L, Olvera M, Labastida A, Jim\u00e9nez-Jacinto V, Vega-Alvarado L, del Moral-Ch\u00e1vez V, Hern\u00e1ndez-Alvarez A, Morett E, Collado-Vides J. Regulondb v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res. 2013; 41(D1):203\u201313. doi: 10.1093\/nar\/gks1201 .","journal-title":"Nucleic Acids Res"},{"key":"1731_CR19","doi-asserted-by":"crossref","unstructured":"Wang E. Cancer systems biology. Chapman & Hall\/CRC Mathematical and Computational Biology. 2010.","DOI":"10.1201\/9781439811863"},{"issue":"9","key":"1731_CR20","doi-asserted-by":"crossref","first-page":"1876","DOI":"10.1021\/jp993732q","volume":"104","author":"MA Gibson","year":"2000","unstructured":"Gibson MA, Bruck J. Efficient exact stochastic simulation of chemical systems with many species and many channels. J Phys Chem A. 2000; 104(9):1876\u201389. doi: 10.1021\/jp993732q .","journal-title":"J Phys Chem A"},{"key":"1731_CR21","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1126\/science.286.5439.509","volume":"206","author":"AL Barab\u00e1si","year":"1999","unstructured":"Barab\u00e1si AL, Albert R. Emergence of scaling in random networks. Science. 1999; 206:509\u201312.","journal-title":"Science"},{"issue":"3","key":"1731_CR22","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0033624","volume":"7","author":"R de Matos Simoes","year":"2012","unstructured":"de Matos Simoes R, Emmert-Streib F. Bagging statistical network inference from large-scale gene expression data. PLOS ONE. 2012; 7(3):1\u201311. doi: 10.1371\/journal.pone.0033624 .","journal-title":"PLOS ONE"},{"issue":"1","key":"1731_CR23","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1186\/1752-0509-4-132","volume":"4","author":"G Altay","year":"2010","unstructured":"Altay G, Emmert-Streib F. Inferring the conservative causal core of gene regulatory networks. BMC Syst Biol. 2010; 4(1):132. doi: 10.1186\/1752-0509-4-132 .","journal-title":"BMC Syst Biol"},{"issue":"D1","key":"1731_CR24","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1093\/nar\/gkv1156","volume":"44","author":"S Gama-Castro","year":"2016","unstructured":"Gama-Castro S, Salgado H, Santos-Zavaleta A, Ledezma-Tejeida D, Muniz-Rascado L, Garc\u00eda-Sotelo JS, Alquicira-Hern\u00e1ndez K, Mart\u00ednez-Flores I, Pannier L, Castro-Mondrag\u00f3n JA, Medina-Rivera A, Solano-Lira H, Bonavides-Mart\u00ednez C, P\u00e9rez-Rueda E, Alquicira-Hern\u00e1ndez S, Porr\u00f3n-Sotelo L, L\u00f3pez-Fuentes A, Hern\u00e1ndez-Koutoucheva A, Moral-Ch\u00e1vez VD, Rinaldi F, Collado-Vides J. Regulondb version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond. Nucleic Acids Res. 2016; 44(D1):133. doi: 10.1093\/nar\/gkv1156 .","journal-title":"Nucleic Acids Res"},{"key":"1731_CR25","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1093\/bioinformatics\/btg1069","volume":"19","author":"P Mendes","year":"2003","unstructured":"Mendes P, Sha W, Ye K. Artificial gene networks for objective comparison of analysis algorithms. Bioinformatics. 2003; 19:122\u20139.","journal-title":"Bioinformatics"},{"key":"1731_CR26","doi-asserted-by":"crossref","unstructured":"Hache H, Wierling C, Lehrach H, Herwig R. Genge: systematic generation of gene regulatory networks. Bioinformatics. 2009; 25(9):1205\u20137. doi: 10.1093\/bioinformatics\/btp115 . http:\/\/bioinformatics.oxfordjournals.org\/content\/25\/9\/1205.full.pdf+html .","DOI":"10.1093\/bioinformatics\/btp115"},{"issue":"6","key":"1731_CR27","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1093\/bioinformatics\/btp068","volume":"25","author":"BM Haynes BC","year":"2009","unstructured":"Haynes BC BM. Benchmarking regulatory network reconstruction with grendel. Bioinformatics. 2009; 25(6):801\u20137.","journal-title":"Bioinformatics"},{"key":"1731_CR28","doi-asserted-by":"crossref","unstructured":"Roy S, Werner-Washburne M, Lane T. A system for generating transcription regulatory networks with combinatorial control of transcription. Bioinformatics. 2008; 24(10):1318\u201320. doi: 10.1093\/bioinformatics\/btn126 . http:\/\/bioinformatics.oxfordjournals.org\/content\/24\/10\/1318.full.pdf+html .","DOI":"10.1093\/bioinformatics\/btn126"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1731-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,28]],"date-time":"2019-09-28T07:10:34Z","timestamp":1569654634000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1731-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,7,4]]},"references-count":28,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["1731"],"URL":"https:\/\/doi.org\/10.1186\/s12859-017-1731-8","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,7,4]]},"article-number":"325"}}