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Items: 1 to 20 of 25


Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms.

Mazein A, Ostaszewski M, Kuperstein I, Watterson S, Le Novère N, Lefaudeux D, De Meulder B, Pellet J, Balaur I, Saqi M, Nogueira MM, He F, Parton A, Lemonnier N, Gawron P, Gebel S, Hainaut P, Ollert M, Dogrusoz U, Barillot E, Zinovyev A, Schneider R, Balling R, Auffray C.

NPJ Syst Biol Appl. 2018 Jun 2;4:21. doi: 10.1038/s41540-018-0059-y. eCollection 2018.


New perspectives: systems medicine in cardiovascular disease.

Kramer F, Just S, Zeller T.

BMC Syst Biol. 2018 Apr 25;12(1):57. doi: 10.1186/s12918-018-0579-5.


Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation.

Touré V, Le Novère N, Waltemath D, Wolkenhauer O.

PLoS Comput Biol. 2018 Feb 15;14(2):e1005740. doi: 10.1371/journal.pcbi.1005740. eCollection 2018 Feb. No abstract available.


Is systems pharmacology ready to impact upon therapy development? A study on the cholesterol biosynthesis pathway.

Benson HE, Watterson S, Sharman JL, Mpamhanga CP, Parton A, Southan C, Harmar AJ, Ghazal P.

Br J Pharmacol. 2017 Dec;174(23):4362-4382. doi: 10.1111/bph.14037. Epub 2017 Nov 26.


STON: exploring biological pathways using the SBGN standard and graph databases.

Touré V, Mazein A, Waltemath D, Balaur I, Saqi M, Henkel R, Pellet J, Auffray C.

BMC Bioinformatics. 2016 Dec 5;17(1):494.


Qualitative dynamics semantics for SBGN process description.

Rougny A, Froidevaux C, Calzone L, Paulevé L.

BMC Syst Biol. 2016 Jun 16;10(1):42. doi: 10.1186/s12918-016-0285-0.


An algorithm for automated layout of process description maps drawn in SBGN.

Genc B, Dogrusoz U.

Bioinformatics. 2016 Jan 1;32(1):77-84. doi: 10.1093/bioinformatics/btv516. Epub 2015 Sep 10.


Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways.

King ZA, Dräger A, Ebrahim A, Sonnenschein N, Lewis NE, Palsson BO.

PLoS Comput Biol. 2015 Aug 27;11(8):e1004321. doi: 10.1371/journal.pcbi.1004321. eCollection 2015 Aug.


BioModels: Content, Features, Functionality, and Use.

Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat MJ, Wimalaratne SM, Hermjakob H, Le Novère N, Laibe C, Chelliah V.

CPT Pharmacometrics Syst Pharmacol. 2015 Feb;4(2):e3. doi: 10.1002/psp4.3. Epub 2015 Feb 26.


JSBML 1.0: providing a smorgasbord of options to encode systems biology models.

Rodriguez N, Thomas A, Watanabe L, Vazirabad IY, Kofia V, Gómez HF, Mittag F, Matthes J, Rudolph J, Wrzodek F, Netz E, Diamantikos A, Eichner J, Keller R, Wrzodek C, Fröhlich S, Lewis NE, Myers CJ, Le Novère N, Palsson BØ, Hucka M, Dräger A.

Bioinformatics. 2015 Oct 15;31(20):3383-6. doi: 10.1093/bioinformatics/btv341. Epub 2015 Jun 16.


SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps.

Sari M, Bahceci I, Dogrusoz U, Sumer SO, Aksoy BA, Babur Ö, Demir E.

PLoS One. 2015 Jun 1;10(6):e0128985. doi: 10.1371/journal.pone.0128985. eCollection 2015.


Mimoza: web-based semantic zooming and navigation in metabolic networks.

Zhukova A, Sherman DJ.

BMC Syst Biol. 2015 Feb 26;9:10. doi: 10.1186/s12918-015-0151-5.


An integrated network visualization framework towards metabolic engineering applications.

Noronha A, Vilaça P, Rocha M.

BMC Bioinformatics. 2014 Dec 30;15:420. doi: 10.1186/s12859-014-0420-0.


Improving collaboration by standardization efforts in systems biology.

Dräger A, Palsson BØ.

Front Bioeng Biotechnol. 2014 Dec 8;2:61. doi: 10.3389/fbioe.2014.00061. eCollection 2014. Review.


COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.

Bergmann FT, Adams R, Moodie S, Cooper J, Glont M, Golebiewski M, Hucka M, Laibe C, Miller AK, Nickerson DP, Olivier BG, Rodriguez N, Sauro HM, Scharm M, Soiland-Reyes S, Waltemath D, Yvon F, Le Novère N.

BMC Bioinformatics. 2014 Dec 14;15:369. doi: 10.1186/s12859-014-0369-z.


BioModels: ten-year anniversary.

Chelliah V, Juty N, Ajmera I, Ali R, Dumousseau M, Glont M, Hucka M, Jalowicki G, Keating S, Knight-Schrijver V, Lloret-Villas A, Natarajan KN, Pettit JB, Rodriguez N, Schubert M, Wimalaratne SM, Zhao Y, Hermjakob H, Le Novère N, Laibe C.

Nucleic Acids Res. 2015 Jan;43(Database issue):D542-8. doi: 10.1093/nar/gku1181. Epub 2014 Nov 20.


NetworkViewer: visualizing biochemical reaction networks with embedded rendering of molecular interaction rules.

Cheng HC, Angermann BR, Zhang F, Meier-Schellersheim M.

BMC Syst Biol. 2014 Jun 16;8:70. doi: 10.1186/1752-0509-8-70.


Path2Models: large-scale generation of computational models from biochemical pathway maps.

Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Dräger A, Le Novère N.

BMC Syst Biol. 2013 Nov 1;7:116. doi: 10.1186/1752-0509-7-116.


Using biological pathway data with paxtools.

Demir E, Babur O, Rodchenkov I, Aksoy BA, Fukuda KI, Gross B, Sümer OS, Bader GD, Sander C.

PLoS Comput Biol. 2013;9(9):e1003194. doi: 10.1371/journal.pcbi.1003194. Epub 2013 Sep 19.

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