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2006 1
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Page 1
UPMaBoSS: A Novel Framework for Dynamic Cell Population Modeling.
Stoll G, Naldi A, Noël V, Viara E, Barillot E, Kroemer G, Thieffry D, Calzone L. Stoll G, et al. Among authors: naldi a. Front Mol Biosci. 2022 Mar 2;9:800152. doi: 10.3389/fmolb.2022.800152. eCollection 2022. Front Mol Biosci. 2022. PMID: 35309516 Free PMC article. Review.
SBML Level 3: an extensible format for the exchange and reuse of biological models.
Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, Naldi A, Olivier BG, Sahle S, Schaff JC, Smith LP, Swat MJ, Thieffry D, Watanabe L, Wilkinson DJ, Blinov ML, Begley K, Faeder JR, Gómez HF, Hamm TM, Inagaki Y, Liebermeister W, Lister AL, Lucio D, Mjolsness E, Proctor CJ, Raman K, Rodriguez N, Shaffer CA, Shapiro BE, Stelling J, Swainston N, Tanimura N, Wagner J, Meier-Schellersheim M, Sauro HM, Palsson B, Bolouri H, Kitano H, Funahashi A, Hermjakob H, Doyle JC, Hucka M; SBML Level 3 Community members. Keating SM, et al. Among authors: naldi a. Mol Syst Biol. 2020 Aug;16(8):e9110. doi: 10.15252/msb.20199110. Mol Syst Biol. 2020. PMID: 32845085 Free PMC article. Review.
Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.
Niarakis A, Kuiper M, Ostaszewski M, Malik Sheriff RS, Casals-Casas C, Thieffry D, Freeman TC, Thomas P, Touré V, Noël V, Stoll G, Saez-Rodriguez J, Naldi A, Oshurko E, Xenarios I, Soliman S, Chaouiya C, Helikar T, Calzone L. Niarakis A, et al. Among authors: naldi a. Brief Bioinform. 2021 Mar 22;22(2):1848-1859. doi: 10.1093/bib/bbaa046. Brief Bioinform. 2021. PMID: 32313939 Free PMC article. Review.
Dynamical Boolean Modeling of Immunogenic Cell Death.
Checcoli A, Pol JG, Naldi A, Noel V, Barillot E, Kroemer G, Thieffry D, Calzone L, Stoll G. Checcoli A, et al. Among authors: naldi a. Front Physiol. 2020 Nov 12;11:590479. doi: 10.3389/fphys.2020.590479. eCollection 2020. Front Physiol. 2020. PMID: 33281620 Free PMC article.
GOATOOLS: A Python library for Gene Ontology analyses.
Klopfenstein DV, Zhang L, Pedersen BS, Ramírez F, Warwick Vesztrocy A, Naldi A, Mungall CJ, Yunes JM, Botvinnik O, Weigel M, Dampier W, Dessimoz C, Flick P, Tang H. Klopfenstein DV, et al. Among authors: naldi a. Sci Rep. 2018 Jul 18;8(1):10872. doi: 10.1038/s41598-018-28948-z. Sci Rep. 2018. PMID: 30022098 Free PMC article.
BioSimulators: a central registry of simulation engines and services for recommending specific tools.
Shaikh B, Smith LP, Vasilescu D, Marupilla G, Wilson M, Agmon E, Agnew H, Andrews SS, Anwar A, Beber ME, Bergmann FT, Brooks D, Brusch L, Calzone L, Choi K, Cooper J, Detloff J, Drawert B, Dumontier M, Ermentrout GB, Faeder JR, Freiburger AP, Fröhlich F, Funahashi A, Garny A, Gennari JH, Gleeson P, Goelzer A, Haiman Z, Hasenauer J, Hellerstein JL, Hermjakob H, Hoops S, Ison JC, Jahn D, Jakubowski HV, Jordan R, Kalaš M, König M, Liebermeister W, Sheriff RSM, Mandal S, McDougal R, Medley JK, Mendes P, Müller R, Myers CJ, Naldi A, Nguyen TVN, Nickerson DP, Olivier BG, Patoliya D, Paulevé L, Petzold LR, Priya A, Rampadarath AK, Rohwer JM, Saglam AS, Singh D, Sinha A, Snoep J, Sorby H, Spangler R, Starruß J, Thomas PJ, van Niekerk D, Weindl D, Zhang F, Zhukova A, Goldberg AP, Schaff JC, Blinov ML, Sauro HM, Moraru II, Karr JR. Shaikh B, et al. Among authors: naldi a. Nucleic Acids Res. 2022 Jul 5;50(W1):W108-W114. doi: 10.1093/nar/gkac331. Nucleic Acids Res. 2022. PMID: 35524558 Free PMC article.
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.
Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Senff Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Mo… See abstract for full author list ➔ Ostaszewski M, et al. Among authors: naldi a. Mol Syst Biol. 2021 Oct;17(10):e10387. doi: 10.15252/msb.202110387. Mol Syst Biol. 2021. PMID: 34664389 Free PMC article.
PTPN13 induces cell junction stabilization and inhibits mammary tumor invasiveness.
Hamyeh M, Bernex F, Larive RM, Naldi A, Urbach S, Simony-Lafontaine J, Puech C, Bakhache W, Solassol J, Coopman PJ, Hendriks WJAJ, Freiss G. Hamyeh M, et al. Among authors: naldi a. Theranostics. 2020 Jan 1;10(3):1016-1032. doi: 10.7150/thno.38537. eCollection 2020. Theranostics. 2020. PMID: 31938048 Free PMC article.
MaBoSS 2.0: an environment for stochastic Boolean modeling.
Stoll G, Caron B, Viara E, Dugourd A, Zinovyev A, Naldi A, Kroemer G, Barillot E, Calzone L. Stoll G, et al. Among authors: naldi a. Bioinformatics. 2017 Jul 15;33(14):2226-2228. doi: 10.1093/bioinformatics/btx123. Bioinformatics. 2017. PMID: 28881959
40 results