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CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination.
Perfetto L, Acencio ML, Bradley G, Cesareni G, Del Toro N, Fazekas D, Hermjakob H, Korcsmaros T, Kuiper M, Lægreid A, Lo Surdo P, Lovering RC, Orchard S, Porras P, Thomas PD, Touré V, Zobolas J, Licata L. Perfetto L, et al. Among authors: lovering rc. Bioinformatics. 2019 Oct 1;35(19):3779-3785. doi: 10.1093/bioinformatics/btz132. Bioinformatics. 2019. PMID: 30793173 Free PMC article.
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.
Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, del-Toro N, Duesbury M, Dumousseau M, Galeota E, Hinz U, Iannuccelli M, Jagannathan S, Jimenez R, Khadake J, Lagreid A, Licata L, Lovering RC, Meldal B, Melidoni AN, Milagros M, Peluso D, Perfetto L, Porras P, Raghunath A, Ricard-Blum S, Roechert B, Stutz A, Tognolli M, van Roey K, Cesareni G, Hermjakob H. Orchard S, et al. Among authors: lovering rc. Nucleic Acids Res. 2014 Jan;42(Database issue):D358-63. doi: 10.1093/nar/gkt1115. Epub 2013 Nov 13. Nucleic Acids Res. 2014. PMID: 24234451 Free PMC article.
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.
Sivade Dumousseau M, Alonso-López D, Ammari M, Bradley G, Campbell NH, Ceol A, Cesareni G, Combe C, De Las Rivas J, Del-Toro N, Heimbach J, Hermjakob H, Jurisica I, Koch M, Licata L, Lovering RC, Lynn DJ, Meldal BHM, Micklem G, Panni S, Porras P, Ricard-Blum S, Roechert B, Salwinski L, Shrivastava A, Sullivan J, Thierry-Mieg N, Yehudi Y, Van Roey K, Orchard S. Sivade Dumousseau M, et al. Among authors: lovering rc. BMC Bioinformatics. 2018 Apr 11;19(1):134. doi: 10.1186/s12859-018-2118-1. BMC Bioinformatics. 2018. PMID: 29642841 Free PMC article.
Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.
IMEx Consortium Curators; Del-Toro N, Duesbury M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Piñero J, Kotlyar M, Pastrello C, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, Orchard S, Porras P. IMEx Consortium Curators, et al. Nat Commun. 2019 Jan 2;10(1):10. doi: 10.1038/s41467-018-07709-6. Nat Commun. 2019. PMID: 30602777 Free PMC article.
Non-coding RNA regulatory networks.
Panni S, Lovering RC, Porras P, Orchard S. Panni S, et al. Among authors: lovering rc. Biochim Biophys Acta Gene Regul Mech. 2020 Jun;1863(6):194417. doi: 10.1016/j.bbagrm.2019.194417. Epub 2019 Sep 4. Biochim Biophys Acta Gene Regul Mech. 2020. PMID: 31493559 Review.
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST).
Touré V, Vercruysse S, Acencio ML, Lovering RC, Orchard S, Bradley G, Casals-Casas C, Chaouiya C, Del-Toro N, Flobak Å, Gaudet P, Hermjakob H, Hoyt CT, Licata L, Lægreid A, Mungall CJ, Niknejad A, Panni S, Perfetto L, Porras P, Pratt D, Saez-Rodriguez J, Thieffry D, Thomas PD, Türei D, Kuiper M. Touré V, et al. Among authors: lovering rc. Bioinformatics. 2021 Apr 5;36(24):5712-5718. doi: 10.1093/bioinformatics/btaa622. Bioinformatics. 2021. PMID: 32637990 Free PMC article.
A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets.
Breuza L, Arighi CN, Argoud-Puy G, Casals-Casas C, Estreicher A, Famiglietti ML, Georghiou G, Gos A, Gruaz-Gumowski N, Hinz U, Hyka-Nouspikel N, Kramarz B, Lovering RC, Lussi Y, Magrane M, Masson P, Perfetto L, Poux S, Rodriguez-Lopez M, Stoeckert C, Sundaram S, Wang LS, Wu E, Orchard S; IMEx Consortium, UniProt Consortium. Breuza L, et al. Among authors: lovering rc. J Alzheimers Dis. 2020;77(1):257-273. doi: 10.3233/JAD-200206. J Alzheimers Dis. 2020. PMID: 32716361 Free PMC article.
Towards a unified open access dataset of molecular interactions.
Porras P, Barrera E, Bridge A, Del-Toro N, Cesareni G, Duesbury M, Hermjakob H, Iannuccelli M, Jurisica I, Kotlyar M, Licata L, Lovering RC, Lynn DJ, Meldal B, Nanduri B, Paneerselvam K, Panni S, Pastrello C, Pellegrini M, Perfetto L, Rahimzadeh N, Ratan P, Ricard-Blum S, Salwinski L, Shirodkar G, Shrivastava A, Orchard S. Porras P, et al. Among authors: lovering rc. Nat Commun. 2020 Dec 1;11(1):6144. doi: 10.1038/s41467-020-19942-z. Nat Commun. 2020. PMID: 33262342 Free PMC article. Review.
Gene Ontology representation for transcription factor functions.
Gaudet P, Logie C, Lovering RC, Kuiper M, Lægreid A, Thomas PD. Gaudet P, et al. Among authors: lovering rc. Biochim Biophys Acta Gene Regul Mech. 2021 Nov-Dec;1864(11-12):194752. doi: 10.1016/j.bbagrm.2021.194752. Epub 2021 Aug 28. Biochim Biophys Acta Gene Regul Mech. 2021. PMID: 34461313 Free article.
122 results