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Items: 1 to 50 of 119

1.

DECO: decompose heterogeneous population cohorts for patient stratification and discovery of sample biomarkers using omic data profiling.

Campos-Laborie FJ, Risueño A, Ortiz-Estévez M, Rosón-Burgo B, Droste C, Fontanillo C, Loos R, Sánchez-Santos JM, Trotter MW, De Las Rivas J.

Bioinformatics. 2019 Mar 1. pii: btz148. doi: 10.1093/bioinformatics/btz148. [Epub ahead of print]

PMID:
30824909
2.

APID database: redefining protein-protein interaction experimental evidences and binary interactomes.

Alonso-López D, Campos-Laborie FJ, Gutiérrez MA, Lambourne L, Calderwood MA, Vidal M, De Las Rivas J.

Database (Oxford). 2019 Jan 1;2019. doi: 10.1093/database/baz005.

3.

Survival marker genes of colorectal cancer derived from consistent transcriptomic profiling.

Martinez-Romero J, Bueno-Fortes S, Martín-Merino M, Ramirez de Molina A, De Las Rivas J.

BMC Genomics. 2018 Dec 11;19(Suppl 8):857. doi: 10.1186/s12864-018-5193-9.

4.

Lmo2 expression defines tumor cell identity during T-cell leukemogenesis.

García-Ramírez I, Bhatia S, Rodríguez-Hernández G, González-Herrero I, Walter C, González de Tena-Dávila S, Parvin S, Haas O, Woessmann W, Stanulla M, Schrappe M, Dugas M, Natkunam Y, Orfao A, Domínguez V, Pintado B, Blanco O, Alonso-López D, De Las Rivas J, Martín-Lorenzo A, Jiménez R, García Criado FJ, García Cenador MB, Lossos IS, Vicente-Dueñas C, Borkhardt A, Hauer J, Sánchez-García I.

EMBO J. 2018 Jul 13;37(14). pii: e98783. doi: 10.15252/embj.201798783. Epub 2018 Jun 7.

5.

JAMI: a Java library for molecular interactions and data interoperability.

Sivade Dumousseau M, Koch M, Shrivastava A, Alonso-López D, De Las Rivas J, Del-Toro N, Combe CW, Meldal BHM, Heimbach J, Rappsilber J, Sullivan J, Yehudi Y, Orchard S.

BMC Bioinformatics. 2018 Apr 11;19(1):133. doi: 10.1186/s12859-018-2119-0.

6.

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.

BMC Bioinformatics. 2018 Apr 11;19(1):134. doi: 10.1186/s12859-018-2118-1.

7.

Human Interactomics: Comparative Analysis of Different Protein Interaction Resources and Construction of a Cancer Protein-Drug Bipartite Network.

De Las Rivas J, Alonso-López D, Arroyo MM.

Adv Protein Chem Struct Biol. 2018;111:263-282. doi: 10.1016/bs.apcsb.2017.09.002. Epub 2017 Nov 6.

PMID:
29459035
8.

Bioinformatics in Latin America and SoIBio impact, a tale of spin-off and expansion around genomes and protein structures.

De Las Rivas J, Bonavides-Martínez C, Campos-Laborie FJ.

Brief Bioinform. 2019 Mar 22;20(2):390-397. doi: 10.1093/bib/bbx064. Erratum in: Brief Bioinform. 2017 Nov 1;18(6):1091.

9.

Bioinformatics in Latin America and SoIBio impact, a tale of spin-off and expansion around genomes and protein structures.

De Las Rivas J, Bonavides-Martínez C, Campos-Laborie FJ.

Brief Bioinform. 2017 Nov 1;18(6):1091. doi: 10.1093/bib/bbx114. No abstract available.

10.

Mesenchymal stromal cells (MSC) from JAK2+ myeloproliferative neoplasms differ from normal MSC and contribute to the maintenance of neoplastic hematopoiesis.

Ramos TL, Sánchez-Abarca LI, Rosón-Burgo B, Redondo A, Rico A, Preciado S, Ortega R, Rodríguez C, Muntión S, Hernández-Hernández Á, De Las Rivas J, González M, González Porras JR, Del Cañizo C, Sánchez-Guijo F.

PLoS One. 2017 Aug 10;12(8):e0182470. doi: 10.1371/journal.pone.0182470. eCollection 2017.

11.

Infection Exposure Promotes ETV6-RUNX1 Precursor B-cell Leukemia via Impaired H3K4 Demethylases.

Rodríguez-Hernández G, Hauer J, Martín-Lorenzo A, Schäfer D, Bartenhagen C, García-Ramírez I, Auer F, González-Herrero I, Ruiz-Roca L, Gombert M, Okpanyi V, Fischer U, Chen C, Dugas M, Bhatia S, Linka RM, Garcia-Suquia M, Rascón-Trincado MV, Garcia-Sanchez A, Blanco O, García-Cenador MB, García-Criado FJ, Cobaleda C, Alonso-López D, De Las Rivas J, Müschen M, Vicente-Dueñas C, Sánchez-García I, Borkhardt A.

Cancer Res. 2017 Aug 15;77(16):4365-4377. doi: 10.1158/0008-5472.CAN-17-0701. Epub 2017 Jun 19.

12.

Screening and Validation of Novel Biomarkers in Osteoarticular Pathologies by Comprehensive Combination of Protein Array Technologies.

Sierra-Sánchez Á, Garrido-Martín D, Lourido L, González-González M, Díez P, Ruiz-Romero C, Sjöber R, Droste C, De Las Rivas J, Nilsson P, Blanco F, Fuentes M.

J Proteome Res. 2017 May 5;16(5):1890-1899. doi: 10.1021/acs.jproteome.6b00980. Epub 2017 Apr 17.

PMID:
28379711
13.

Ten simple rules for forming a scientific professional society.

Gaëta BA, De Las Rivas J, Horton P, Meysman P, Mulder N, Romano P, Welch L.

PLoS Comput Biol. 2017 Mar 23;13(3):e1005226. doi: 10.1371/journal.pcbi.1005226. eCollection 2017 Mar. No abstract available.

14.

Epidermal Growth Factor Signaling towards Proliferation: Modeling and Logic Inference Using Forward and Backward Search.

Riesco A, Santos-Buitrago B, De Las Rivas J, Knapp M, Santos-García G, Talcott C.

Biomed Res Int. 2017;2017:1809513. doi: 10.1155/2017/1809513. Epub 2017 Jan 16.

15.

Identification of expression patterns in the progression of disease stages by integration of transcriptomic data.

Aibar S, Abaigar M, Campos-Laborie FJ, Sánchez-Santos JM, Hernandez-Rivas JM, De Las Rivas J.

BMC Bioinformatics. 2016 Nov 22;17(Suppl 15):432. doi: 10.1186/s12859-016-1290-4.

16.

Linking amyotrophic lateral sclerosis and spinal muscular atrophy through RNA-transcriptome homeostasis: a genomics perspective.

Gama-Carvalho M, L Garcia-Vaquero M, R Pinto F, Besse F, Weis J, Voigt A, Schulz JB, De Las Rivas J.

J Neurochem. 2017 Apr;141(1):12-30. doi: 10.1111/jnc.13945. Epub 2017 Feb 28. Review.

17.

MicroRNA (miR)-203 and miR-205 expression patterns identify subgroups of prognosis in cutaneous squamous cell carcinoma.

Cañueto J, Cardeñoso-Álvarez E, García-Hernández JL, Galindo-Villardón P, Vicente-Galindo P, Vicente-Villardón JL, Alonso-López D, De Las Rivas J, Valero J, Moyano-Sanz E, Fernández-López E, Mao JH, Castellanos-Martín A, Román-Curto C, Pérez-Losada J.

Br J Dermatol. 2017 Jul;177(1):168-178. doi: 10.1111/bjd.15236. Epub 2017 May 8.

18.

Insights into the human mesenchymal stromal/stem cell identity through integrative transcriptomic profiling.

Roson-Burgo B, Sanchez-Guijo F, Del Cañizo C, De Las Rivas J.

BMC Genomics. 2016 Nov 21;17(1):944.

19.

Path2enet: generation of human pathway-derived networks in an expression specific context.

Droste C, De Las Rivas J.

BMC Genomics. 2016 Oct 25;17(Suppl 8):731.

20.

Evolutionary hallmarks of the human proteome: chasing the age and coregulation of protein-coding genes.

Lopes KP, Campos-Laborie FJ, Vialle RA, Ortega JM, De Las Rivas J.

BMC Genomics. 2016 Oct 25;17(Suppl 8):725.

21.

APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks.

Alonso-López D, Gutiérrez MA, Lopes KP, Prieto C, Santamaría R, De Las Rivas J.

Nucleic Acids Res. 2016 Jul 8;44(W1):W529-35. doi: 10.1093/nar/gkw363. Epub 2016 Apr 30.

22.

Microvesicles from Mesenchymal Stromal Cells Are Involved in HPC-Microenvironment Crosstalk in Myelodysplastic Patients.

Muntión S, Ramos TL, Diez-Campelo M, Rosón B, Sánchez-Abarca LI, Misiewicz-Krzeminska I, Preciado S, Sarasquete ME, de Las Rivas J, González M, Sánchez-Guijo F, Del Cañizo MC.

PLoS One. 2016 Feb 2;11(2):e0146722. doi: 10.1371/journal.pone.0146722. eCollection 2016.

23.

Cystatin D locates in the nucleus at sites of active transcription and modulates gene and protein expression.

Ferrer-Mayorga G, Alvarez-Díaz S, Valle N, De Las Rivas J, Mendes M, Barderas R, Canals F, Tapia O, Casal JI, Lafarga M, Muñoz A.

J Biol Chem. 2015 Oct 30;290(44):26533-48. doi: 10.1074/jbc.M115.660175. Epub 2015 Sep 13.

24.

Integration of Proteomics and Transcriptomics Data Sets for the Analysis of a Lymphoma B-Cell Line in the Context of the Chromosome-Centric Human Proteome Project.

Díez P, Droste C, Dégano RM, González-Muñoz M, Ibarrola N, Pérez-Andrés M, Garin-Muga A, Segura V, Marko-Varga G, LaBaer J, Orfao A, Corrales FJ, De Las Rivas J, Fuentes M.

J Proteome Res. 2015 Sep 4;14(9):3530-40. doi: 10.1021/acs.jproteome.5b00474. Epub 2015 Aug 5.

PMID:
26216070
25.

In Vitro Transcription/Translation System: A Versatile Tool in the Search for Missing Proteins.

Horvatovich P, Végvári Á, Saul J, Park JG, Qiu J, Syring M, Pirrotte P, Petritis K, Tegeler TJ, Aziz M, Fuentes M, Diez P, Gonzalez-Gonzalez M, Ibarrola N, Droste C, De Las Rivas J, Gil C, Clemente F, Hernaez ML, Corrales FJ, Nilsson CL, Berven FS, Bischoff R, Fehniger TE, LaBaer J, Marko-Varga G.

J Proteome Res. 2015 Sep 4;14(9):3441-51. doi: 10.1021/acs.jproteome.5b00486. Epub 2015 Jul 28.

PMID:
26155874
26.

Analyse multiple disease subtypes and build associated gene networks using genome-wide expression profiles.

Aibar S, Fontanillo C, Droste C, Roson-Burgo B, Campos-Laborie FJ, Hernandez-Rivas JM, De Las Rivas J.

BMC Genomics. 2015;16 Suppl 5:S3. doi: 10.1186/1471-2164-16-S5-S3. Epub 2015 May 26.

27.

Deregulation of genes related to iron and mitochondrial metabolism in refractory anemia with ring sideroblasts.

del Rey M, Benito R, Fontanillo C, Campos-Laborie FJ, Janusz K, Velasco-Hernández T, Abáigar M, Hernández M, Cuello R, Borrego D, Martín-Zanca D, De Las Rivas J, Mills KI, Hernández-Rivas JM.

PLoS One. 2015 May 8;10(5):e0126555. doi: 10.1371/journal.pone.0126555. eCollection 2015.

28.

Unraveling heterogeneous susceptibility and the evolution of breast cancer using a systems biology approach.

Castellanos-Martín A, Castillo-Lluva S, Sáez-Freire Mdel M, Blanco-Gómez A, Hontecillas-Prieto L, Patino-Alonso C, Galindo-Villardon P, Pérez Del Villar L, Martín-Seisdedos C, Isidoro-Garcia M, Abad-Hernández MM, Cruz-Hernández JJ, Rodríguez-Sánchez CA, González-Sarmiento R, Alonso-López D, De Las Rivas J, García-Cenador B, García-Criado J, Lee DY, Bowen B, Reindl W, Northen T, Mao JH, Pérez-Losada J.

Genome Biol. 2015 Feb 21;16:40. doi: 10.1186/s13059-015-0599-z.

29.

ColoLipidGene: signature of lipid metabolism-related genes to predict prognosis in stage-II colon cancer patients.

Vargas T, Moreno-Rubio J, Herranz J, Cejas P, Molina S, González-Vallinas M, Mendiola M, Burgos E, Aguayo C, Custodio AB, Machado I, Ramos D, Gironella M, Espinosa-Salinas I, Ramos R, Martín-Hernández R, Risueño A, De Las Rivas J, Reglero G, Yaya R, Fernández-Martos C, Aparicio J, Maurel J, Feliu J, Ramírez de Molina A.

Oncotarget. 2015 Mar 30;6(9):7348-63.

30.

Functional Gene Networks: R/Bioc package to generate and analyse gene networks derived from functional enrichment and clustering.

Aibar S, Fontanillo C, Droste C, De Las Rivas J.

Bioinformatics. 2015 May 15;31(10):1686-8. doi: 10.1093/bioinformatics/btu864. Epub 2015 Jan 18.

31.

A proteome-scale map of the human interactome network.

Rolland T, Taşan M, Charloteaux B, Pevzner SJ, Zhong Q, Sahni N, Yi S, Lemmens I, Fontanillo C, Mosca R, Kamburov A, Ghiassian SD, Yang X, Ghamsari L, Balcha D, Begg BE, Braun P, Brehme M, Broly MP, Carvunis AR, Convery-Zupan D, Corominas R, Coulombe-Huntington J, Dann E, Dreze M, Dricot A, Fan C, Franzosa E, Gebreab F, Gutierrez BJ, Hardy MF, Jin M, Kang S, Kiros R, Lin GN, Luck K, MacWilliams A, Menche J, Murray RR, Palagi A, Poulin MM, Rambout X, Rasla J, Reichert P, Romero V, Ruyssinck E, Sahalie JM, Scholz A, Shah AA, Sharma A, Shen Y, Spirohn K, Tam S, Tejeda AO, Trigg SA, Twizere JC, Vega K, Walsh J, Cusick ME, Xia Y, Barabási AL, Iakoucheva LM, Aloy P, De Las Rivas J, Tavernier J, Calderwood MA, Hill DE, Hao T, Roth FP, Vidal M.

Cell. 2014 Nov 20;159(5):1212-1226. doi: 10.1016/j.cell.2014.10.050.

32.

Transcriptomic portrait of human Mesenchymal Stromal/Stem Cells isolated from bone marrow and placenta.

Roson-Burgo B, Sanchez-Guijo F, Del Cañizo C, De Las Rivas J.

BMC Genomics. 2014 Oct 19;15:910. doi: 10.1186/1471-2164-15-910.

33.

A robust estimation of exon expression to identify alternative spliced genes applied to human tissues and cancer samples.

Risueño A, Roson-Burgo B, Dolnik A, Hernandez-Rivas JM, Bullinger L, De Las Rivas J.

BMC Genomics. 2014 Oct 8;15:879. doi: 10.1186/1471-2164-15-879.

34.

Transcriptomic profile induced in bone marrow mesenchymal stromal cells after interaction with multiple myeloma cells: implications in myeloma progression and myeloma bone disease.

Garcia-Gomez A, De Las Rivas J, Ocio EM, Díaz-Rodríguez E, Montero JC, Martín M, Blanco JF, Sanchez-Guijo FM, Pandiella A, San Miguel JF, Garayoa M.

Oncotarget. 2014 Sep 30;5(18):8284-305.

35.

TET2 overexpression in chronic lymphocytic leukemia is unrelated to the presence of TET2 variations.

Hernández-Sánchez M, Rodríguez AE, Kohlmann A, Benito R, García JL, Risueño A, Fermiñán E, De Las Rivas J, González M, Hernández-Rivas JM.

Biomed Res Int. 2014;2014:814294. doi: 10.1155/2014/814294. Epub 2014 Feb 18.

36.

Identification of a characteristic copy number alteration profile by high-resolution single nucleotide polymorphism arrays associated with metastatic sporadic colorectal cancer.

González-González M, Fontanillo C, Abad MM, Gutiérrez ML, Mota I, Bengoechea O, Santos-Briz Á, Blanco O, Fonseca E, Ciudad J, Fuentes M, De Las Rivas J, Alcazar JA, García J, Muñoz-Bellvis L, Orfao A, Sayagués JM.

Cancer. 2014 Jul 1;120(13):1948-59. doi: 10.1002/cncr.28681. Epub 2014 Mar 25.

37.

miRNA cargo within exosome-like vesicle transfer influences metastatic bone colonization.

Valencia K, Luis-Ravelo D, Bovy N, Antón I, Martínez-Canarias S, Zandueta C, Ormazábal C, Struman I, Tabruyn S, Rebmann V, De Las Rivas J, Guruceaga E, Bandrés E, Lecanda F.

Mol Oncol. 2014 May;8(3):689-703. doi: 10.1016/j.molonc.2014.01.012. Epub 2014 Feb 6.

38.

Transcriptome analysis in prenatal IGF1-deficient mice identifies molecular pathways and target genes involved in distal lung differentiation.

Pais RS, Moreno-Barriuso N, Hernández-Porras I, López IP, De Las Rivas J, Pichel JG.

PLoS One. 2013 Dec 31;8(12):e83028. doi: 10.1371/journal.pone.0083028. eCollection 2013.

39.

RHOB influences lung adenocarcinoma metastasis and resistance in a host-sensitive manner.

Luis-Ravelo D, Antón I, Zandueta C, Valencia K, Pajares MJ, Agorreta J, Montuenga L, Vicent S, Wistuba II, De Las Rivas J, Lecanda F.

Mol Oncol. 2014 Mar;8(2):196-206. doi: 10.1016/j.molonc.2013.11.001. Epub 2013 Nov 12.

40.

A gene signature of bone metastatic colonization sensitizes for tumor-induced osteolysis and predicts survival in lung cancer.

Luis-Ravelo D, Antón I, Zandueta C, Valencia K, Ormazábal C, Martínez-Canarias S, Guruceaga E, Perurena N, Vicent S, De Las Rivas J, Lecanda F.

Oncogene. 2014 Oct 23;33(43):5090-9. doi: 10.1038/onc.2013.440. Epub 2013 Oct 28.

PMID:
24166494
41.

Best practices in bioinformatics training for life scientists.

Via A, Blicher T, Bongcam-Rudloff E, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, Fernandes PL, van Gelder C, Jacob J, Jimenez RC, Loveland J, Moran F, Mulder N, Nyrönen T, Rother K, Schneider MV, Attwood TK.

Brief Bioinform. 2013 Sep;14(5):528-37. doi: 10.1093/bib/bbt043. Epub 2013 Jun 25.

42.

iAnn: an event sharing platform for the life sciences.

Jimenez RC, Albar JP, Bhak J, Blatter MC, Blicher T, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, van Driel MA, Dunn MJ, Fernandes PL, van Gelder CW, Hermjakob H, Ioannidis V, Judge DP, Kahlem P, Korpelainen E, Kraus HJ, Loveland J, Mayer C, McDowall J, Moran F, Mulder N, Nyronen T, Rother K, Salazar GA, Schneider R, Via A, Villaveces JM, Yu P, Schneider MV, Attwood TK, Corpas M.

Bioinformatics. 2013 Aug 1;29(15):1919-21. doi: 10.1093/bioinformatics/btt306. Epub 2013 Jun 5.

43.

Molecular characterization of chronic lymphocytic leukemia patients with a high number of losses in 13q14.

Rodríguez AE, Hernández JÁ, Benito R, Gutiérrez NC, García JL, Hernández-Sánchez M, Risueño A, Sarasquete ME, Fermiñán E, Fisac R, de Coca AG, Martín-Núñez G, de Las Heras N, Recio I, Gutiérrez O, De Las Rivas J, González M, Hernández-Rivas JM.

PLoS One. 2012;7(11):e48485. doi: 10.1371/journal.pone.0048485. Epub 2012 Nov 13.

44.

Combined analysis of genome-wide expression and copy number profiles to identify key altered genomic regions in cancer.

Fontanillo C, Aibar S, Sanchez-Santos JM, De Las Rivas J.

BMC Genomics. 2012;13 Suppl 5:S5. doi: 10.1186/1471-2164-13-S5-S5. Epub 2012 Oct 19.

45.

Genome-wide profiling of methylation identifies novel targets with aberrant hypermethylation and reduced expression in low-risk myelodysplastic syndromes.

del Rey M, O'Hagan K, Dellett M, Aibar S, Colyer HA, Alonso ME, Díez-Campelo M, Armstrong RN, Sharpe DJ, Gutiérrez NC, García JL, De Las Rivas J, Mills KI, Hernández-Rivas JM.

Leukemia. 2013 Mar;27(3):610-8. doi: 10.1038/leu.2012.253. Epub 2012 Aug 31.

PMID:
22936014
46.

Prognostic Impact of del(17p) and del(22q) as assessed by interphase FISH in sporadic colorectal carcinomas.

González-González M, Muñoz-Bellvis L, Mackintosh C, Fontanillo C, Gutiérrez ML, Abad MM, Bengoechea O, Teodosio C, Fonseca E, Fuentes M, De Las Rivas J, Orfao A, Sayagués JM.

PLoS One. 2012;7(8):e42683. doi: 10.1371/journal.pone.0042683. Epub 2012 Aug 17.

47.

Protein-protein interaction networks: unraveling the wiring of molecular machines within the cell.

De Las Rivas J, Fontanillo C.

Brief Funct Genomics. 2012 Nov;11(6):489-96. doi: 10.1093/bfgp/els036. Epub 2012 Aug 20.

48.

A novel molecular mechanism involved in multiple myeloma development revealed by targeting MafB to haematopoietic progenitors.

Vicente-Dueñas C, Romero-Camarero I, González-Herrero I, Alonso-Escudero E, Abollo-Jiménez F, Jiang X, Gutierrez NC, Orfao A, Marín N, Villar LM, Criado MC, Pintado B, Flores T, Alonso-López D, De Las Rivas J, Jiménez R, Criado FJ, Cenador MB, Lossos IS, Cobaleda C, Sánchez-García I.

EMBO J. 2012 Sep 12;31(18):3704-17. doi: 10.1038/emboj.2012.227. Epub 2012 Aug 17.

49.

Protein interactions: mapping interactome networks to support drug target discovery and selection.

De Las Rivas J, Prieto C.

Methods Mol Biol. 2012;910:279-96. doi: 10.1007/978-1-61779-965-5_12. Review.

PMID:
22821600
50.

Integrating literature-constrained and data-driven inference of signalling networks.

Eduati F, De Las Rivas J, Di Camillo B, Toffolo G, Saez-Rodriguez J.

Bioinformatics. 2012 Sep 15;28(18):2311-7. doi: 10.1093/bioinformatics/bts363. Epub 2012 Jun 25.

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