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Items: 1 to 50 of 145

1.

Systems Oncology: Bridging Pancreatic and Castrate Resistant Prostate Cancer.

Fucic A, Aghajanyan A, Culig Z, Le Novere N.

Pathol Oncol Res. 2018 Sep 16. doi: 10.1007/s12253-018-0467-8. [Epub ahead of print] Review.

PMID:
30220022
2.

Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE).

Waltemath D, Bergmann FT, Chaouiya C, Czauderna T, Gleeson P, Goble C, Golebiewski M, Hucka M, Juty N, Krebs O, Le Novère N, Mi H, Moraru II, Myers CJ, Nickerson D, Olivier BG, Rodriguez N, Schreiber F, Smith L, Zhang F, Bonnet E.

Stand Genomic Sci. 2018 Aug 9;13:17. doi: 10.1186/s40793-018-0320-4. eCollection 2018.

3.

Host lipidome analysis during rhinovirus replication in HBECs identifies potential therapeutic targets.

Nguyen A, Guedán A, Mousnier A, Swieboda D, Zhang Q, Horkai D, Le Novere N, Solari R, Wakelam MJO.

J Lipid Res. 2018 Sep;59(9):1671-1684. doi: 10.1194/jlr.M085910. Epub 2018 Jun 26.

PMID:
29946055
4.

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.

5.

Community-driven roadmap for integrated disease maps.

Ostaszewski M, Gebel S, Kuperstein I, Mazein A, Zinovyev A, Dogrusoz U, Hasenauer J, Fleming RMT, Le Novère N, Gawron P, Ligon T, Niarakis A, Nickerson D, Weindl D, Balling R, Barillot E, Auffray C, Schneider R.

Brief Bioinform. 2018 Apr 23. doi: 10.1093/bib/bby024. [Epub ahead of print]

PMID:
29688273
6.

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3).

Bergmann FT, Cooper J, König M, Moraru I, Nickerson D, Le Novère N, Olivier BG, Sahle S, Smith L, Waltemath D.

J Integr Bioinform. 2018 Mar 19;15(1). pii: /j/jib.2018.15.issue-1/jib-2017-0086/jib-2017-0086.xml. doi: 10.1515/jib-2017-0086.

PMID:
29550789
7.

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0.

Cox RS, Madsen C, McLaughlin J, Nguyen T, Roehner N, Bartley B, Bhatia S, Bissell M, Clancy K, Gorochowski T, Grünberg R, Luna A, Le Novère N, Pocock M, Sauro H, Sexton JT, Stan GB, Tabor JJ, Voigt CA, Zundel Z, Myers C, Beal J, Wipat A.

J Integr Bioinform. 2018 Mar 19;15(1). pii: /j/jib.2018.15.issue-1/jib-2017-0074/jib-2017-0074.xml. doi: 10.1515/jib-2017-0074.

8.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.

Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ.

J Integr Bioinform. 2018 Mar 9;15(1). pii: /j/jib.2018.15.issue-1/jib-2017-0081/jib-2017-0081.xml. doi: 10.1515/jib-2017-0081.

PMID:
29522418
9.

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.

10.

BioModels: expanding horizons to include more modelling approaches and formats.

Glont M, Nguyen TVN, Graesslin M, Hälke R, Ali R, Schramm J, Wimalaratne SM, Kothamachu VB, Rodriguez N, Swat MJ, Eils J, Eils R, Laibe C, Malik-Sheriff RS, Chelliah V, Le Novère N, Hermjakob H.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1248-D1253. doi: 10.1093/nar/gkx1023.

11.

PTEN Regulates PI(3,4)P2 Signaling Downstream of Class I PI3K.

Malek M, Kielkowska A, Chessa T, Anderson KE, Barneda D, Pir P, Nakanishi H, Eguchi S, Koizumi A, Sasaki J, Juvin V, Kiselev VY, Niewczas I, Gray A, Valayer A, Spensberger D, Imbert M, Felisbino S, Habuchi T, Beinke S, Cosulich S, Le Novère N, Sasaki T, Clark J, Hawkins PT, Stephens LR.

Mol Cell. 2017 Nov 2;68(3):566-580.e10. doi: 10.1016/j.molcel.2017.09.024. Epub 2017 Oct 19.

12.

Tia1 dependent regulation of mRNA subcellular location and translation controls p53 expression in B cells.

Díaz-Muñoz MD, Kiselev VY, Le Novère N, Curk T, Ule J, Turner M.

Nat Commun. 2017 Sep 13;8(1):530. doi: 10.1038/s41467-017-00454-2.

13.

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.

McMurry JA, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Hériché JK, Hermjakob H, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Rocca-Serra P, Sansone SA, Sariyar M, Snoep JL, Soiland-Reyes S, Stanford NJ, Swainston N, Washington N, Williams AR, Wimalaratne SM, Winfree LM, Wolstencroft K, Goble C, Mungall CJ, Haendel MA, Parkinson H.

PLoS Biol. 2017 Jun 29;15(6):e2001414. doi: 10.1371/journal.pbio.2001414. eCollection 2017 Jun.

14.

Reciprocal regulation of ARPP-16 by PKA and MAST3 kinases provides a cAMP-regulated switch in protein phosphatase 2A inhibition.

Musante V, Li L, Kanyo J, Lam TT, Colangelo CM, Cheng SK, Brody AH, Greengard P, Le Novère N, Nairn AC.

Elife. 2017 Jun 14;6. pii: e24998. doi: 10.7554/eLife.24998.

15.

SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks.

Dalle Pezze P, Le Novère N.

BMC Syst Biol. 2017 Apr 10;11(1):46. doi: 10.1186/s12918-017-0423-3.

16.

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.

Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Le Novère N, Myers C, Nickerson D, Sommer B, Walthemath D.

J Integr Bioinform. 2016 Dec 18;13(3):289. doi: 10.2390/biecoll-jib-2016-289.

17.

The Impact of Mathematical Modeling in Understanding the Mechanisms Underlying Neurodegeneration: Evolving Dimensions and Future Directions.

Lloret-Villas A, Varusai TM, Juty N, Laibe C, Le NovÈre N, Hermjakob H, Chelliah V.

CPT Pharmacometrics Syst Pharmacol. 2017 Feb;6(2):73-86. doi: 10.1002/psp4.12155. Epub 2017 Jan 7. Review.

18.

The promises of quantitative systems pharmacology modelling for drug development.

Knight-Schrijver VR, Chelliah V, Cucurull-Sanchez L, Le Novère N.

Comput Struct Biotechnol J. 2016 Sep 23;14:363-370. eCollection 2016. Review.

19.

The health care and life sciences community profile for dataset descriptions.

Dumontier M, Gray AJG, Marshall MS, Alexiev V, Ansell P, Bader G, Baran J, Bolleman JT, Callahan A, Cruz-Toledo J, Gaudet P, Gombocz EA, Gonzalez-Beltran AN, Groth P, Haendel M, Ito M, Jupp S, Juty N, Katayama T, Kobayashi N, Krishnaswami K, Laibe C, Le Novère N, Lin S, Malone J, Miller M, Mungall CJ, Rietveld L, Wimalaratne SM, Yamaguchi A.

PeerJ. 2016 Aug 16;4:e2331. doi: 10.7717/peerj.2331. eCollection 2016.

20.

The systems biology format converter.

Rodriguez N, Pettit JB, Dalle Pezze P, Li L, Henry A, van Iersel MP, Jalowicki G, Kutmon M, Natarajan KN, Tolnay D, Stefan MI, Evelo CT, Le Novère N.

BMC Bioinformatics. 2016 Apr 5;17:154. doi: 10.1186/s12859-016-1000-2.

21.

The evolution of standards and data management practices in systems biology.

Stanford NJ, Wolstencroft K, Golebiewski M, Kania R, Juty N, Tomlinson C, Owen S, Butcher S, Hermjakob H, Le Novère N, Mueller W, Snoep J, Goble C.

Mol Syst Biol. 2015 Dec 23;11(12):851. doi: 10.15252/msb.20156053. No abstract available.

22.

Mathematical Models of Pluripotent Stem Cells: At the Dawn of Predictive Regenerative Medicine.

Pir P, Le Novère N.

Methods Mol Biol. 2016;1386:331-50. doi: 10.1007/978-1-4939-3283-2_15. Review.

PMID:
26677190
23.

Enabling surface dependent diffusion in spatial simulations using Smoldyn.

Seeliger C, Le Novère N.

BMC Res Notes. 2015 Dec 8;8:752. doi: 10.1186/s13104-015-1723-6.

24.

SBOL Visual: A Graphical Language for Genetic Designs.

Quinn JY, Cox RS 3rd, Adler A, Beal J, Bhatia S, Cai Y, Chen J, Clancy K, Galdzicki M, Hillson NJ, Le Novère N, Maheshwari AJ, McLaughlin JA, Myers CJ, P U, Pocock M, Rodriguez C, Soldatova L, Stan GB, Swainston N, Wipat A, Sauro HM.

PLoS Biol. 2015 Dec 3;13(12):e1002310. doi: 10.1371/journal.pbio.1002310. eCollection 2015 Dec.

25.

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.

Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ.

J Integr Bioinform. 2015 Sep 4;12(2):271. doi: 10.2390/biecoll-jib-2015-271.

26.

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.

Chaouiya C, Keating SM, Berenguier D, Naldi A, Thieffry D, van Iersel MP, Le Novère N, Helikar T.

J Integr Bioinform. 2015 Sep 4;12(2):270. doi: 10.2390/biecoll-jib-2015-270.

PMID:
26528568
27.

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2.

Mi H, Schreiber F, Moodie S, Czauderna T, Demir E, Haw R, Luna A, Le Novère N, Sorokin A, Villéger A.

J Integr Bioinform. 2015 Sep 4;12(2):265. doi: 10.2390/biecoll-jib-2015-265.

PMID:
26528563
28.

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.

Sorokin A, Le Novère N, Luna A, Czauderna T, Demir E, Haw R, Mi H, Moodie S, Schreiber F, Villéger A.

J Integr Bioinform. 2015 Sep 4;12(2):264. doi: 10.2390/biecoll-jib-2015-264.

PMID:
26528562
29.

Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3.

Moodie S, Le Novère N, Demir E, Mi H, Villéger A.

J Integr Bioinform. 2015 Sep 4;12(2):263. doi: 10.2390/biecoll-jib-2015-263.

PMID:
26528561
30.

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

Bergmann FT, Cooper J, Le Novère N, Nickerson D, Waltemath D.

J Integr Bioinform. 2015 Sep 4;12(2):262. doi: 10.2390/biecoll-jib-2015-262.

PMID:
26528560
31.

COMBINE Archive Specification Version 1.

Bergmann FT, Rodriguez N, Le Novère N.

J Integr Bioinform. 2015 Sep 4;12(2):261. doi: 10.2390/biecoll-jib-2015-261.

PMID:
26528559
32.

Specifications of Standards in Systems and Synthetic Biology.

Schreiber F, Bader GD, Golebiewski M, Hucka M, Kormeier B, Le Novère N, Myers C, Nickerson D, Sommer B, Waltemath D, Weise S.

J Integr Bioinform. 2015 Sep 4;12(2):258. doi: 10.2390/biecoll-jib-2015-258.

33.

Do genome-scale models need exact solvers or clearer standards?

Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, Hyduke D, Jamshidi N, Lee SY, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Nielsen LK, Nogales J, Noronha A, Pal C, Palsson BO, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I.

Mol Syst Biol. 2015 Oct 14;11(10):831. doi: 10.15252/msb.20156157. No abstract available.

34.

Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop.

Kiselev VY, Juvin V, Malek M, Luscombe N, Hawkins P, Le Novère N, Stephens L.

Nucleic Acids Res. 2015 Nov 16;43(20):9663-79. doi: 10.1093/nar/gkv1015. Epub 2015 Oct 12.

35.

Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development.

Swat MJ, Moodie S, Wimalaratne SM, Kristensen NR, Lavielle M, Mari A, Magni P, Smith MK, Bizzotto R, Pasotti L, Mezzalana E, Comets E, Sarr C, Terranova N, Blaudez E, Chan P, Chard J, Chatel K, Chenel M, Edwards D, Franklin C, Giorgino T, Glont M, Girard P, Grenon P, Harling K, Hooker AC, Kaye R, Keizer R, Kloft C, Kok JN, Kokash N, Laibe C, Laveille C, Lestini G, Mentré F, Munafo A, Nordgren R, Nyberg HB, Parra-Guillen ZP, Plan E, Ribba B, Smith G, Trocóniz IF, Yvon F, Milligan PA, Harnisch L, Karlsson M, Hermjakob H, Le Novère N.

CPT Pharmacometrics Syst Pharmacol. 2015 Jun;4(6):316-9. doi: 10.1002/psp4.57. Epub 2015 Jun 15.

36.

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.

37.

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.

38.

Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative.

Hucka M, Nickerson DP, Bader GD, Bergmann FT, Cooper J, Demir E, Garny A, Golebiewski M, Myers CJ, Schreiber F, Waltemath D, Le Novère N.

Front Bioeng Biotechnol. 2015 Feb 24;3:19. doi: 10.3389/fbioe.2015.00019. eCollection 2015. Review.

39.

Quantitative and logic modelling of molecular and gene networks.

Le Novère N.

Nat Rev Genet. 2015 Mar;16(3):146-58. doi: 10.1038/nrg3885. Epub 2015 Feb 3. Review.

40.

SPARQL-enabled identifier conversion with Identifiers.org.

Wimalaratne SM, Bolleman J, Juty N, Katayama T, Dumontier M, Redaschi N, Le Novère N, Hermjakob H, Laibe C.

Bioinformatics. 2015 Jun 1;31(11):1875-7. doi: 10.1093/bioinformatics/btv064. Epub 2015 Jan 31.

41.

Ligand-dependent opening of the multiple AMPA receptor conductance states: a concerted model.

Dutta-Roy R, Rosenmund C, Edelstein SJ, Le Novère N.

PLoS One. 2015 Jan 28;10(1):e0116616. doi: 10.1371/journal.pone.0116616. eCollection 2015.

42.

Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions.

Lai M, Brun D, Edelstein SJ, Le Novère N.

PLoS Comput Biol. 2015 Jan 22;11(1):e1004063. doi: 10.1371/journal.pcbi.1004063. eCollection 2015 Jan.

43.

Finding our way through phenotypes.

Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P.

PLoS Biol. 2015 Jan 6;13(1):e1002033. doi: 10.1371/journal.pbio.1002033. eCollection 2015 Jan.

44.

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.

45.

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.

46.

BioModels linked dataset.

Wimalaratne SM, Grenon P, Hermjakob H, Le Novère N, Laibe C.

BMC Syst Biol. 2014 Aug 15;8:91. doi: 10.1186/s12918-014-0091-5.

47.

The EBI RDF platform: linked open data for the life sciences.

Jupp S, Malone J, Bolleman J, Brandizi M, Davies M, Garcia L, Gaulton A, Gehant S, Laibe C, Redaschi N, Wimalaratne SM, Martin M, Le Novère N, Parkinson H, Birney E, Jenkinson AM.

Bioinformatics. 2014 May 1;30(9):1338-9. doi: 10.1093/bioinformatics/btt765. Epub 2014 Jan 11.

48.

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.

Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, Gonçalves E, Dorier J, Page M, Monteiro PT, von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry D, Le Novère N, Saez-Rodriguez J, Helikar T.

BMC Syst Biol. 2013 Dec 10;7:135. doi: 10.1186/1752-0509-7-135.

49.

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.

50.

Integration of biochemical and electrical signaling-multiscale model of the medium spiny neuron of the striatum.

Mattioni M, Le Novère N.

PLoS One. 2013 Jul 3;8(7):e66811. doi: 10.1371/journal.pone.0066811. Print 2013.

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