HAL collection

All publications related to Genhotel are also available on HAL.

  1. Fang J, Jia J, Makowski M, Xu M, Wang Z, Zhang T, Hoskins JW, Choi J, Han Y, Zhang M, Thomas J, Kovacs M, Collins I, Dzyadyk M, Thompson A, O’Neill M, Das S, Lan Q, Koster R, PanScan Consortium, TRICL Consortium, GenoMEL Consortium, Stolzenberg-Solomon RS, Kraft P, Wolpin BM, Jansen PWTC, Olson S, McGlynn KA, Kanetsky PA, Chatterjee N, Barrett JH, Dunning AM, Taylor JC, Newton-Bishop JA, Bishop DT, Andresson T, Petersen GM, Amos CI, Iles MM, Nathanson KL, Landi MT, Vermeulen M, Brown KM, Amundadottir LT. (2017) Functional characterization of a multi-cancer risk locus on chr5p15.33 reveals regulation of TERT by ZNF148. Nat Commun; 8:15034.
  2. A. Niarakis Computational Systems Biology Approach For The Study Of Rheumatoid Arthritis: From A Molecular Map To A Dynamical Model - CCB 2017 Protein Interaction Networks and Disease, 20 November (2017) - Alte Mensa of the Johannes Gutenberg Universität, Mainz, Germany
  3. A.Niarakis, RA-MAP, 1st Disease Maps Community Meeting, 15-17 February, Lyon (2017)A.Niarakis, Integrative Modelling And Analysis Of Molecular Pathways Involved In Rheumatoid Arthritis, 4th CoLoMoTo Meeting, Paris July 14-17 (2017)
  4. A.Niarakis, Protein-Protein Interactions: Cornerstones Of Cellular Signaling Cascades, In Health And Disease. The Case Of Rheumatoid Arthritis (Ra). Mapping2017-Understanding Protein Interactions: From Molecules To Organisms, 24-26 April, Lyon (2017)
  5. Guerreiro-Cacais AO, Norin U, Gyllenberg A, Berglund R, Beyeen AD; Rheumatoid Arthritis Consortium International (RACI)., Petit-Teixeira E, Cornélis F, Saoudi A, Fournié GJ, Holmdahl R, Alfredsson L, Klareskog L, Jagodic M, Olsson T, Kockum I, Padyukov L. VAV1 regulates experimental autoimmune arthritis and is associated with anti-CCP negative rheumatoid arthritis. Genes Immun. 2017 Jan 5.
  6. Boughrara W, Benzaoui A, Aberkane M, Moghtit FZ, Dorgham S, Lardjam-Hetraf AS, Ouhaibi-Djellouli H, Teixeira EP, Boudjema A. No correlation between MTHFR c.677 C > T, MTHFR c.1298 A > C, and ABCB1 c.3435 C > T polymorphisms and methotrexate therapeutic outcome of rheumatoid arthritis in West Algerian population. Inflamm Res. 2017 Mar 15.
  7. Singh V, Ostaszewski M, Kalliolias GD, Chiocchia G, Olaso R, Petit-Teixeira E, Helikar T, Niarakis A, Computational systems biology approach for the study of Rheumatoid Arthritis: from a molecular map to a dynamical model, Genomics and Computational Biology, 2018, 4 (1): e10050.
  8. Marek Ostaszewski, Stephan Gebel, Inna Kuperstein, Alexander Mazein, Andrei Zinovyev, Ugur Dogrusoz, Jan Hasenauer, Ronan Fleming, Nicolas Le Novere, Piotr Gawron, Thomas Ligon, Anna Niarakis, David Nickerson, Daniel Weindl, Rudi Balling, Emmanuel Barillot, Charles Auffray, Reinhard Schneider. The roadmap for integrated disease maps - the proceedings of the 2nd Disease Maps Community meeting. Brief Bioinform. 2018 Apr 23.
  9. Dahmani CA, Benzaoui A, Amroun H, Mecabih F, Sediki FZ, Zemani-Fodil F, Fodil M, Boughrara W, Mecheti B, Attal N, Mehtar N, Petit-Teixeira E, Boudjema A. Association of the HLA-B27 antigen and the CTLA4 gene CT60/rs3087243 polymorphism with ankylosing spondylitis in Algerian population: a case-control study. Int J Immunogenet. 2018 Jun;45(3):109-117.
  10. Achour Y, Ben Kilani MS, Ben Hamad M, Marzouk S, Mahfoudh N, Bahloul Z, Keskes L, Petit-Teixeira E, Maalej A. Measurement of absolute copy number variation of Glutathione S-Transferase M1 gene by digital droplet PCR and association analysis in Tunisian Rheumatoid Arthritis population. J Clin Lab Anal. 2018 Mar;32(3).
  11. Veyssiere M, Perea J, Michou L, Boland A, Caloustian C, Olaso R, Deleuze JF, Cornelis F, Petit-Teixeira E, Chaudru V. A novel nonsense variant in SUPT20H gene associated with Rheumatoid Arthritis identified by Whole Exome Sequencing of multiplex families. PLOS ONE 14(3): e0213387.DOI : 10.1371/journal.pone.0213387
  12. Ben Kilani MS, Cornélis F, Olaso R, Chaudru V, Petit-Teixeira E. Investigation of candidate gene copy number identifies FCGR3B as a potential biomarker for rheumatoid arthritis. Clin Exp Rheumatol.  Mar 7. PubMed PMID: 30873943.
  13. Dahmani CA, Benzaoui A, Amroun H, Zemani-Fodil F, Petit-Teixeira E, Boudjema A. Association study of copy number variants in CCL3L1, FCGR3A and FCGR3B genes with risk of ankylosing spondylitis in a West Algerian population. Int J Immunogenet. 2019 Aug 21.
  14. Niarakis A, Giannopoulou E, Syggelos SA, Panagiotopoulos E. Effects of proteasome inhibitors on cytokines, metalloproteinases and their inhibitors and collagen type-I expression in periprosthetic tissues and fibroblasts from loose arthroplasty endoprostheses. Connect Tissue Res. 2019 Nov;60(6):555-570. doi: 10.1080/03008207.2019.1601186. Epub 2019 Apr 25. PMID: 30931650.
  15. 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. Community-driven roadmap for integrated disease maps. Brief Bioinform. 2019 Mar 25;20(2):659-670. doi: 10.1093/bib/bby024. PMID: 29688273; PMCID: PMC6556900.
  16. Ostaszewski M, Mazein A, Gillespie ME, Kuperstein I, Niarakis A, Hermjakob H, Pico AR, Willighagen EL, Evelo CT, Hasenauer J, Schreiber F, Dräger A, Demir E, Wolkenhauer O, Furlong LI, Barillot E, Dopazo J, Orta-Resendiz A, Messina F, Valencia A, Funahashi A, Kitano H, Auffray C, Balling R, Schneider R. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Sci Data. 2020 May 5;7(1):136. doi: 10.1038/s41597-020-0477-8. Erratum in: Sci Data. 2020 Jul 17;7(1):247. PMID:32371892; PMCID: PMC7200764.
  17. Aghamiri SS, Singh V, Naldi A, Helikar T, Soliman S, Niarakis A. Automated inference of Boolean models from molecular interaction maps using CaSQ. Bioinformatics. 2020 Aug 15;36(16):4473-4482. doi:10.1093/bioinformatics/btaa484. PMID: 32403123; PMCID: PMC7575051.
  18. Singh V, Kalliolias GD, Ostaszewski M, Veyssiere M, Pilalis E, Gawron P, Mazein A, Bonnet E, Petit-Teixeira E, Niarakis A. RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis. Database (Oxford). 2020 Jan 1;2020:baaa017. doi: 10.1093/database/baaa017. PMID: 32311035; PMCID: PMC7170216.
  19. Zerrouk N, Miagoux Q, Dispot A, Elati M, Niarakis A. Identification of putative master regulators in rheumatoid arthritis synovial fibroblasts using gene expression data and network inference. Sci Rep. 2020 Oct 1;10(1):16236. doi: 10.1038/s41598-020-73147-4. PMID: 33004899; PMCID: PMC7529794.
  20. Aghakhani S, Zerrouk N, Niarakis A. Metabolic Reprogramming of Fibroblasts as Therapeutic Target in Rheumatoid Arthritis and Cancer: Deciphering Key Mechanisms Using Computational Systems Biology Approaches. Cancers (Basel). 2020 Dec 24;13(1):35. doi: 10.3390/cancers13010035. PMID: 33374292; PMCID: PMC7795338.
  21. 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. 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. Brief Bioinform. 2021 Mar 22;22(2):1848-1859. doi: 10.1093/bib/bbaa046. PMID:32313939; PMCID: PMC7986594.
  22. Dalmasso C, Derbois C, Veyssiere M, Olaso R, Lamacchia C, Alpizar-Rodriguez D, Deleuze JF, Finckh A, Petit-Teixeira E. Identification of biological pathways specific to phases preceding rheumatoid arthritis development through gene expression profiling. Int J Immunogenet. 2021 Jun;48(3):239-249. doi: 10.1111/iji.12528. Epub 2021 Jan 22. PMID: 33480472.
  23. Dräger A, Helikar T, Barberis M, Birtwistle M, Calzone L, Chaouiya C, Hasenauer J, Karr JR, Niarakis A, Rodríguez Martínez M, Saez-Rodriguez J, Thakar J. SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems. Bioinformatics. 2021 Jun 24;37(21):3702–6. doi: 10.1093/bioinformatics/btab229. Epub ahead of print. PMID: 34179955; PMCID:PMC8570808.
  24. Touré V, Flobak Å, Niarakis A, Vercruysse S, Kuiper M. The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling. Brief Bioinform. 2021 Jul 20;22(4):bbaa390. doi: 10.1093/bib/bbaa390. PMID: 33378765; PMCID: PMC8294520.
  25. Niarakis A, Helikar T. A practical guide to mechanistic systems modeling in biology using a logic-based approach. Brief Bioinform. 2021 Jul 20;22(4):bbaa236. doi: 10.1093/bib/bbaa236. PMID: 33064138; PMCID: PMC8293813.
  26. Miagoux Q, Singh V, de Mézquita D, Chaudru V, Elati M, Petit-Teixeira E, Niarakis A. Inference of an Integrative, Executable Network for Rheumatoid Arthritis Combining Data-Driven Machine Learning Approaches and a State-of-the-Art Mechanistic Disease Map. J Pers Med. 2021 Aug 12;11(8):785. doi:10.3390/jpm11080785. PMID: 34442429; PMCID: PMC8400381.
  27. 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, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Willighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D'Eustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R; COVID-19 Disease Map Community. COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol. 2021 Dec;17(12):e10851. doi: 10.15252/msb.202110851. Erratum for: Mol Syst Biol. 2021 Oct;17(10):e10387. PMID: 34939300; PMCID: PMC8696085.