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Items: 16

1.

Embracing the Dark Side: Computational Approaches to Unveil the Functionality of Genes Lacking Biological Annotation in Drug-Induced Liver Injury.

Souza T, Trairatphisan P, Piñero J, Furlong LI, Saez-Rodriguez J, Kleinjans J, Jennen D.

Front Genet. 2018 Nov 20;9:527. doi: 10.3389/fgene.2018.00527. eCollection 2018.

2.

Adipocyte-secreted BMP8b mediates adrenergic-induced remodeling of the neuro-vascular network in adipose tissue.

Pellegrinelli V, Peirce VJ, Howard L, Virtue S, Türei D, Senzacqua M, Frontini A, Dalley JW, Horton AR, Bidault G, Severi I, Whittle A, Rahmouni K, Saez-Rodriguez J, Cinti S, Davies AM, Vidal-Puig A.

Nat Commun. 2018 Nov 26;9(1):4974. doi: 10.1038/s41467-018-07453-x.

3.

Open Targets Platform: new developments and updates two years on.

Carvalho-Silva D, Pierleoni A, Pignatelli M, Ong C, Fumis L, Karamanis N, Carmona M, Faulconbridge A, Hercules A, McAuley E, Miranda A, Peat G, Spitzer M, Barrett J, Hulcoop DG, Papa E, Koscielny G, Dunham I.

Nucleic Acids Res. 2019 Jan 8;47(D1):D1056-D1065. doi: 10.1093/nar/gky1133.

4.

Transcriptomic and functional network features of lung squamous cell carcinoma through integrative analysis of GEO and TCGA data.

Li Y, Gu J, Xu F, Zhu Q, Ge D, Lu C.

Sci Rep. 2018 Oct 26;8(1):15834. doi: 10.1038/s41598-018-34160-w.

5.

Bioinformatics Analysis Identifies p53 as a Candidate Prognostic Biomarker for Neuropathic Pain.

Gao Y, Sun N, Wang L, Wu Y, Ma L, Hong J, Ren J, Zhu B, Yu L, Yan M.

Front Genet. 2018 Aug 31;9:320. doi: 10.3389/fgene.2018.00320. eCollection 2018.

6.

Exploring the Mechanism of Flavonoids Through Systematic Bioinformatics Analysis.

Qiu T, Wu D, Yang L, Ye H, Wang Q, Cao Z, Tang K.

Front Pharmacol. 2018 Aug 15;9:918. doi: 10.3389/fphar.2018.00918. eCollection 2018.

7.

Reconstructing phosphorylation signalling networks from quantitative phosphoproteomic data.

Invergo BM, Beltrao P.

Essays Biochem. 2018 Oct 26;62(4):525-534. doi: 10.1042/EBC20180019. Print 2018 Oct 26. Review.

8.

Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data.

Alexander-Dann B, Pruteanu LL, Oerton E, Sharma N, Berindan-Neagoe I, Módos D, Bender A.

Mol Omics. 2018 Aug 6;14(4):218-236. doi: 10.1039/c8mo00042e. Review.

9.

Integrative Computational Network Analysis Reveals Site-Specific Mediators of Inflammation in Alzheimer's Disease.

Ravichandran S, Michelucci A, Del Sol A.

Front Physiol. 2018 Mar 2;9:154. doi: 10.3389/fphys.2018.00154. eCollection 2018.

10.

Discriminate the response of Acute Myeloid Leukemia patients to treatment by using proteomics data and Answer Set Programming.

Chebouba L, Miannay B, Boughaci D, Guziolowski C.

BMC Bioinformatics. 2018 Mar 8;19(Suppl 2):59. doi: 10.1186/s12859-018-2034-4.

11.

Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells.

Wirbel J, Cutillas P, Saez-Rodriguez J.

Methods Mol Biol. 2018;1711:103-132. doi: 10.1007/978-1-4939-7493-1_6.

12.

GDSCTools for mining pharmacogenomic interactions in cancer.

Cokelaer T, Chen E, Iorio F, Menden MP, Lightfoot H, Saez-Rodriguez J, Garnett MJ.

Bioinformatics. 2018 Apr 1;34(7):1226-1228. doi: 10.1093/bioinformatics/btx744.

13.

From word models to executable models of signaling networks using automated assembly.

Gyori BM, Bachman JA, Subramanian K, Muhlich JL, Galescu L, Sorger PK.

Mol Syst Biol. 2017 Nov 24;13(11):954. doi: 10.15252/msb.20177651.

14.

DISNOR: a disease network open resource.

Lo Surdo P, Calderone A, Iannuccelli M, Licata L, Peluso D, Castagnoli L, Cesareni G, Perfetto L.

Nucleic Acids Res. 2018 Jan 4;46(D1):D527-D534. doi: 10.1093/nar/gkx876.

15.

Logic Modeling in Quantitative Systems Pharmacology.

Traynard P, Tobalina L, Eduati F, Calzone L, Saez-Rodriguez J.

CPT Pharmacometrics Syst Pharmacol. 2017 Aug;6(8):499-511. doi: 10.1002/psp4.12225. Epub 2017 Jul 29.

16.

Data-driven reverse engineering of signaling pathways using ensembles of dynamic models.

Henriques D, Villaverde AF, Rocha M, Saez-Rodriguez J, Banga JR.

PLoS Comput Biol. 2017 Feb 6;13(2):e1005379. doi: 10.1371/journal.pcbi.1005379. eCollection 2017 Feb.

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