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Table representation of search results timeline featuring number of search results per year.

Year Number of Results
2006 1
2009 1
2010 1
2012 3
2013 2
2014 2
2015 3
2016 1
2017 5
2018 6
2019 3
2020 6
2021 1
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35 results
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Page 1
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.
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 article. Review.
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.
Automated inference of Boolean models from molecular interaction maps using CaSQ.
Aghamiri SS, Singh V, Naldi A, Helikar T, Soliman S, Niarakis A. Aghamiri SS, et al. Among authors: naldi a. Bioinformatics. 2020 Aug 15;36(16):4473-4482. doi: 10.1093/bioinformatics/btaa484. Bioinformatics. 2020. PMID: 32403123 Free PMC article.
Network Reconstruction and Significant Pathway Extraction Using Phosphoproteomic Data from Cancer Cells.
Buffard M, Naldi A, Radulescu O, Coopman PJ, Larive RM, Freiss G. Buffard M, et al. Among authors: naldi a. Proteomics. 2019 Nov;19(21-22):e1800450. doi: 10.1002/pmic.201800450. Epub 2019 Oct 3. Proteomics. 2019. PMID: 31472481
Contribution of ROS and metabolic status to neonatal and adult CD8+ T cell activation.
Sánchez-Villanueva JA, Rodríguez-Jorge O, Ramírez-Pliego O, Rosas Salgado G, Abou-Jaoudé W, Hernandez C, Naldi A, Thieffry D, Santana MA. Sánchez-Villanueva JA, et al. Among authors: naldi a. PLoS One. 2019 Dec 16;14(12):e0226388. doi: 10.1371/journal.pone.0226388. eCollection 2019. PLoS One. 2019. PMID: 31841528 Free PMC article.
Computational Verification of Large Logical Models-Application to the Prediction of T Cell Response to Checkpoint Inhibitors.
Hernandez C, Thomas-Chollier M, Naldi A, Thieffry D. Hernandez C, et al. Among authors: naldi a. Front Physiol. 2020 Sep 30;11:558606. doi: 10.3389/fphys.2020.558606. eCollection 2020. Front Physiol. 2020. PMID: 33101049 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.
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. 2020 Apr 21:bbaa046. doi: 10.1093/bib/bbaa046. Online ahead of print. Brief Bioinform. 2020. PMID: 32313939
System analysis of cross-talk between nuclear receptors reveals an opposite regulation of the cell cycle by LXR and FXR in human HepaRG liver cells.
Wigger L, Casals-Casas C, Baruchet M, Trang KB, Pradervand S, Naldi A, Desvergne B. Wigger L, et al. Among authors: naldi a. PLoS One. 2019 Aug 22;14(8):e0220894. doi: 10.1371/journal.pone.0220894. eCollection 2019. PLoS One. 2019. PMID: 31437187 Free PMC article.
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