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Items: 1 to 50 of 149

1.

Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps.

Jansen C, Ramirez RN, El-Ali NC, Gomez-Cabrero D, Tegner J, Merkenschlager M, Conesa A, Mortazavi A.

PLoS Comput Biol. 2019 Nov 4;15(11):e1006555. doi: 10.1371/journal.pcbi.1006555. eCollection 2019 Nov.

2.

Mip6 binds directly to the Mex67 UBA domain to maintain low levels of Msn2/4 stress-dependent mRNAs.

Martín-Expósito M, Gas ME, Mohamad N, Nuño-Cabanes C, Tejada-Colón A, Pascual-García P, de la Fuente L, Chaves-Arquero B, Merran J, Corden J, Conesa A, Pérez-Cañadillas JM, Bravo J, Rodríguez-Navarro S.

EMBO Rep. 2019 Dec 5;20(12):e47964. doi: 10.15252/embr.201947964. Epub 2019 Nov 3.

PMID:
31680439
3.

STATegra, a comprehensive multi-omics dataset of B-cell differentiation in mouse.

Gomez-Cabrero D, Tarazona S, Ferreirós-Vidal I, Ramirez RN, Company C, Schmidt A, Reijmers T, Paul VVS, Marabita F, Rodríguez-Ubreva J, Garcia-Gomez A, Carroll T, Cooper L, Liang Z, Dharmalingam G, van der Kloet F, Harms AC, Balzano-Nogueira L, Lagani V, Tsamardinos I, Lappe M, Maier D, Westerhuis JA, Hankemeier T, Imhof A, Ballestar E, Mortazavi A, Merkenschlager M, Tegner J, Conesa A.

Sci Data. 2019 Oct 31;6(1):256. doi: 10.1038/s41597-019-0202-7.

4.

Making multi-omics data accessible to researchers.

Conesa A, Beck S.

Sci Data. 2019 Oct 31;6(1):251. doi: 10.1038/s41597-019-0258-4. No abstract available.

5.

A Multiomics Study To Unravel the Effects of Developmental Exposure to Endosulfan in Rats: Molecular Explanation for Sex-Dependent Effects.

Tarazona S, Bernabeu E, Carmona H, Gómez-Giménez B, García-Planells J, Leonards PEG, Jung S, Conesa A, Felipo V, Llansola M.

ACS Chem Neurosci. 2019 Oct 16;10(10):4264-4279. doi: 10.1021/acschemneuro.9b00304. Epub 2019 Sep 10.

PMID:
31464424
6.

Differential Modulation of Quorum Sensing Signaling through QslA in Pseudomonas aeruginosa Strains PAO1 and PA14.

Sana TG, Lomas R, Gimenez MR, Laubier A, Soscia C, Chauvet C, Conesa A, Voulhoux R, Ize B, Bleves S.

J Bacteriol. 2019 Oct 4;201(21). pii: e00362-19. doi: 10.1128/JB.00362-19. Print 2019 Nov 1.

PMID:
31405911
7.

Tartrate-resistant acid phosphatase 5b, but not periostin, is useful for assessing Paget's disease of bone.

Guañabens N, Filella X, Florez H, Ruiz-Gaspá S, Conesa A, Peris P, Monegal A, Torres F.

Bone. 2019 Jul;124:132-136. doi: 10.1016/j.bone.2019.04.023. Epub 2019 Apr 30.

PMID:
31051316
8.

Differences in gene expression profiling and biomarkers between histological colorectal carcinoma subsets from the serrated pathway.

García-Solano J, Turpin-Sevilla MDC, García-García F, Carbonell-Muñoz R, Torres-Moreno D, Conesa A, Conesa-Zamora P.

Histopathology. 2019 Oct;75(4):496-507. doi: 10.1111/his.13889. Epub 2019 Aug 2.

PMID:
31025430
9.

Feedforward regulation of Myc coordinates lineage-specific with housekeeping gene expression during B cell progenitor cell differentiation.

Ferreirós-Vidal I, Carroll T, Zhang T, Lagani V, Ramirez RN, Ing-Simmons E, Gómez-Valadés AG, Cooper L, Liang Z, Papoutsoglou G, Dharmalingam G, Guo Y, Tarazona S, Fernandes SJ, Noori P, Silberberg G, Fisher AG, Tsamardinos I, Mortazavi A, Lenhard B, Conesa A, Tegner J, Merkenschlager M, Gomez-Cabrero D.

PLoS Biol. 2019 Apr 12;17(4):e2006506. doi: 10.1371/journal.pbio.2006506. eCollection 2019 Apr.

10.

Chitosan nanoparticles enhance the antibacterial activity of the native polymer against bovine mastitis pathogens.

Orellano MS, Isaac P, Breser ML, Bohl LP, Conesa A, Falcone RD, Porporatto C.

Carbohydr Polym. 2019 Jun 1;213:1-9. doi: 10.1016/j.carbpol.2019.02.016. Epub 2019 Feb 21.

PMID:
30879647
11.

Tocilizumab in giant cell arteritis. Observational, open-label multicenter study of 134 patients in clinical practice.

Calderón-Goercke M, Loricera J, Aldasoro V, Castañeda S, Villa I, Humbría A, Moriano C, Romero-Yuste S, Narváez J, Gómez-Arango C, Pérez-Pampín E, Melero R, Becerra-Fernández E, Revenga M, Álvarez-Rivas N, Galisteo C, Sivera F, Olivé-Marqués A, Álvarez Del Buergo M, Marena-Rojas L, Fernández-López C, Navarro F, Raya E, Galindez-Agirregoikoa E, Arca B, Solans-Laqué R, Conesa A, Hidalgo C, Vázquez C, Román-Ivorra JA, Lluch P, Manrique-Arija S, Vela P, De Miguel E, Torres-Martín C, Nieto JC, Ordas-Calvo C, Salgado-Pérez E, Luna-Gomez C, Toyos-Sáenz de Miera FJ, Fernández-Llanio N, García A, Larena C, Palmou-Fontana N, Calvo-Río V, Prieto-Peña D, González-Vela C, Corrales A, Varela-García M, Aurrecoechea E, Dos Santos R, García-Manzanares Á, Ortego N, Fernández S, Ortiz-Sanjuán F, Corteguera M, Hernández JL, González-Gay MÁ, Blanco R.

Semin Arthritis Rheum. 2019 Aug;49(1):126-135. doi: 10.1016/j.semarthrit.2019.01.003. Epub 2019 Jan 5.

PMID:
30655091
12.

Transcriptional profiling of the mutualistic bacterium Vibrio fischeri and an hfq mutant under modeled microgravity.

Duscher AA, Conesa A, Bishop M, Vroom MM, Zubizarreta SD, Foster JS.

NPJ Microgravity. 2018 Dec 18;4:25. doi: 10.1038/s41526-018-0060-1. eCollection 2018.

13.

Elucidating the Role of Chromatin State and Transcription Factors on the Regulation of the Yeast Metabolic Cycle: A Multi-Omic Integrative Approach.

Sánchez-Gaya V, Casaní-Galdón S, Ugidos M, Kuang Z, Mellor J, Conesa A, Tarazona S.

Front Genet. 2018 Nov 30;9:578. doi: 10.3389/fgene.2018.00578. eCollection 2018.

14.

Two histologically colorectal carcinomas subsets from the serrated pathway show different methylome signatures and diagnostic biomarkers.

García-Solano J, Turpin MC, Torres-Moreno D, Huertas-López F, Tuomisto A, Mäkinen MJ, Conesa A, Conesa-Zamora P.

Clin Epigenetics. 2018 Nov 9;10(1):141. doi: 10.1186/s13148-018-0571-3.

15.

Overexpression of the vascular brassinosteroid receptor BRL3 confers drought resistance without penalizing plant growth.

Fàbregas N, Lozano-Elena F, Blasco-Escámez D, Tohge T, Martínez-Andújar C, Albacete A, Osorio S, Bustamante M, Riechmann JL, Nomura T, Yokota T, Conesa A, Alfocea FP, Fernie AR, Caño-Delgado AI.

Nat Commun. 2018 Nov 8;9(1):4680. doi: 10.1038/s41467-018-06861-3.

16.

Changes in the uterine metabolome of the cow during the first 7 days after estrus.

Tríbulo P, Balzano-Nogueira L, Conesa A, Siqueira LG, Hansen PJ.

Mol Reprod Dev. 2019 Jan;86(1):75-87. doi: 10.1002/mrd.23082. Epub 2018 Nov 25.

17.

Short and long-term effectiveness and safety of vedolizumab in inflammatory bowel disease: results from the ENEIDA registry.

Chaparro M, Garre A, Ricart E, Iborra M, Mesonero F, Vera I, Riestra S, García-Sánchez V, Luisa De Castro M, Martin-Cardona A, Aldeguer X, Mínguez M, de-Acosta MB, Rivero M, Muñoz F, Andreu M, Bargalló A, González-Muñoza C, Pérez Calle JL, García-Sepulcre MF, Bermejo F, Huguet JM, Cabriada JL, Gutiérrez A, Mañosa M, Villoria A, Carbajo AY, Lorente R, García-López S, Piqueras M, Hinojosa E, Arajol C, Sicilia B, Conesa AM, Sainz E, Almela P, Llaó J, Roncero O, Camo P, Taxonera C, Domselaar MV, Pajares R, Legido J, Madrigal R, Lucendo AJ, Alcaín G, Doménech E, Gisbert JP; GETECCU study group.

Aliment Pharmacol Ther. 2018 Oct;48(8):839-851. doi: 10.1111/apt.14930.

PMID:
30281832
18.

Tumor microenvironment-targeted poly-L-glutamic acid-based combination conjugate for enhanced triple negative breast cancer treatment.

Arroyo-Crespo JJ, Armiñán A, Charbonnier D, Balzano-Nogueira L, Huertas-López F, Martí C, Tarazona S, Forteza J, Conesa A, Vicent MJ.

Biomaterials. 2018 Dec;186:8-21. doi: 10.1016/j.biomaterials.2018.09.023. Epub 2018 Sep 18.

19.

Gene expression profile and molecular pathway datasets resulting from benzo(a)pyrene exposure in the liver and testis of adult tilapia.

Colli-Dula RC, Fang X, Moraga-Amador D, Albornoz-Abud N, Zamora-Bustillos R, Conesa A, Zapata-Perez O, Moreno D, Hernandez-Nuñez E.

Data Brief. 2018 Sep 5;20:1500-1509. doi: 10.1016/j.dib.2018.08.206. eCollection 2018 Oct.

20.

Single-cell RNAseq for the study of isoforms-how is that possible?

Arzalluz-Luque Á, Conesa A.

Genome Biol. 2018 Aug 10;19(1):110. doi: 10.1186/s13059-018-1496-z. Review.

21.

Event Analysis: Using Transcript Events To Improve Estimates of Abundance in RNA-seq Data.

Newman JRB, Concannon P, Tardaguila M, Conesa A, McIntyre LM.

G3 (Bethesda). 2018 Aug 30;8(9):2923-2940. doi: 10.1534/g3.118.200373.

22.

Comparative Metagenomics Provides Insight Into the Ecosystem Functioning of the Shark Bay Stromatolites, Western Australia.

Babilonia J, Conesa A, Casaburi G, Pereira C, Louyakis AS, Reid RP, Foster JS.

Front Microbiol. 2018 Jun 25;9:1359. doi: 10.3389/fmicb.2018.01359. eCollection 2018.

23.

Corrigendum: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification.

Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, Del Risco H, Ferrell M, Mellado M, Macchietto M, Verheggen K, Edelmann M, Ezkurdia I, Vazquez J, Tress M, Mortazavi A, Martens L, Rodriguez-Navarro S, Moreno-Manzano V, Conesa A.

Genome Res. 2018 Jul;28(7):1096. doi: 10.1101/gr.239137.118. No abstract available.

24.

Transcriptome analysis reveals novel insights into the response of low-dose benzo(a)pyrene exposure in male tilapia.

Colli-Dula RC, Fang X, Moraga-Amador D, Albornoz-Abud N, Zamora-Bustillos R, Conesa A, Zapata-Perez O, Moreno D, Hernandez-Nuñez E.

Aquat Toxicol. 2018 Aug;201:162-173. doi: 10.1016/j.aquatox.2018.06.005. Epub 2018 Jun 8.

PMID:
29913432
25.

Evidence of the Red-Queen Hypothesis from Accelerated Rates of Evolution of Genes Involved in Biotic Interactions in Pneumocystis.

Delaye L, Ruiz-Ruiz S, Calderon E, Tarazona S, Conesa A, Moya A.

Genome Biol Evol. 2018 Jun 1;10(6):1596-1606. doi: 10.1093/gbe/evy116.

26.

PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data.

Hernández-de-Diego R, Tarazona S, Martínez-Mira C, Balzano-Nogueira L, Furió-Tarí P, Pappas GJ Jr, Conesa A.

Nucleic Acids Res. 2018 Jul 2;46(W1):W503-W509. doi: 10.1093/nar/gky466.

27.

The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally.

García-Molinero V, García-Martínez J, Reja R, Furió-Tarí P, Antúnez O, Vinayachandran V, Conesa A, Pugh BF, Pérez-Ortín JE, Rodríguez-Navarro S.

Epigenetics Chromatin. 2018 Mar 29;11(1):13. doi: 10.1186/s13072-018-0184-2.

28.

Chitosan and cloxacillin combination improve antibiotic efficacy against different lifestyle of coagulase-negative Staphylococcus isolates from chronic bovine mastitis.

Breser ML, Felipe V, Bohl LP, Orellano MS, Isaac P, Conesa A, Rivero VE, Correa SG, Bianco ID, Porporatto C.

Sci Rep. 2018 Mar 23;8(1):5081. doi: 10.1038/s41598-018-23521-0.

29.

SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification.

Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, Del Risco H, Ferrell M, Mellado M, Macchietto M, Verheggen K, Edelmann M, Ezkurdia I, Vazquez J, Tress M, Mortazavi A, Martens L, Rodriguez-Navarro S, Moreno-Manzano V, Conesa A.

Genome Res. 2018 Feb 9. doi: 10.1101/gr.222976.117. [Epub ahead of print] Erratum in: Genome Res. 2018 Jul;28(7):1096.

30.

Guidelines for Developing Successful Short Advanced Courses in Systems Medicine and Systems Biology.

Gomez-Cabrero D, Marabita F, Tarazona S, Cano I, Roca J, Conesa A, Sabatier P, Tegnér J.

Cell Syst. 2017 Dec 27;5(6):654. doi: 10.1016/j.cels.2017.12.010. No abstract available.

31.

GRAM-CNN: a deep learning approach with local context for named entity recognition in biomedical text.

Zhu Q, Li X, Conesa A, Pereira C.

Bioinformatics. 2018 May 1;34(9):1547-1554. doi: 10.1093/bioinformatics/btx815.

32.

Growth of Chlamydia pneumoniae Is Enhanced in Cells with Impaired Mitochondrial Function.

Käding N, Kaufhold I, Müller C, Szaszák M, Shima K, Weinmaier T, Lomas R, Conesa A, Schmitt-Kopplin P, Rattei T, Rupp J.

Front Cell Infect Microbiol. 2017 Dec 5;7:499. doi: 10.3389/fcimb.2017.00499. eCollection 2017.

33.

A benchmarking of workflows for detecting differential splicing and differential expression at isoform level in human RNA-seq studies.

Merino GA, Conesa A, Fernández EA.

Brief Bioinform. 2019 Mar 22;20(2):471-481. doi: 10.1093/bib/bbx122.

PMID:
29040385
34.

Disease-specific biases in alternative splicing and tissue-specific dysregulation revealed by multitissue profiling of lymphocyte gene expression in type 1 diabetes.

Newman JRB, Conesa A, Mika M, New FN, Onengut-Gumuscu S, Atkinson MA, Rich SS, McIntyre LM, Concannon P.

Genome Res. 2017 Nov;27(11):1807-1815. doi: 10.1101/gr.217984.116. Epub 2017 Oct 12.

35.

Identification and visualization of differential isoform expression in RNA-seq time series.

Nueda MJ, Martorell-Marugan J, Martí C, Tarazona S, Conesa A.

Bioinformatics. 2018 Feb 1;34(3):524-526. doi: 10.1093/bioinformatics/btx578.

36.

The eBioKit, a stand-alone educational platform for bioinformatics.

Hernández-de-Diego R, de Villiers EP, Klingström T, Gourlé H, Conesa A, Bongcam-Rudloff E.

PLoS Comput Biol. 2017 Sep 14;13(9):e1005616. doi: 10.1371/journal.pcbi.1005616. eCollection 2017 Sep.

37.

Guidelines for Developing Successful Short Advanced Courses in Systems Medicine and Systems Biology.

Gomez-Cabrero D, Marabita F, Tarazona S, Cano I, Roca J, Conesa A, Sabatier P, Tegnér J.

Cell Syst. 2017 Sep 27;5(3):168-175. doi: 10.1016/j.cels.2017.05.013. Epub 2017 Aug 23. Erratum in: Cell Syst. 2017 Dec 27;5(6):654.

38.

Commensal coagulase-negative Staphylococcus from the udder of healthy cows inhibits biofilm formation of mastitis-related pathogens.

Isaac P, Bohl LP, Breser ML, Orellano MS, Conesa A, Ferrero MA, Porporatto C.

Vet Microbiol. 2017 Aug;207:259-266. doi: 10.1016/j.vetmic.2017.05.025. Epub 2017 Jun 27.

PMID:
28757033
39.

Dynamic Gene Regulatory Networks of Human Myeloid Differentiation.

Ramirez RN, El-Ali NC, Mager MA, Wyman D, Conesa A, Mortazavi A.

Cell Syst. 2017 Apr 26;4(4):416-429.e3. doi: 10.1016/j.cels.2017.03.005. Epub 2017 Mar 29.

40.

RGmatch: matching genomic regions to proximal genes in omics data integration.

Furió-Tarí P, Conesa A, Tarazona S.

BMC Bioinformatics. 2016 Nov 22;17(Suppl 15):427. doi: 10.1186/s12859-016-1293-1.

41.

Identification of miRNA from Bouteloua gracilis, a drought tolerant grass, by deep sequencing and their in silico analysis.

Ordóñez-Baquera PL, González-Rodríguez E, Aguado-Santacruz GA, Rascón-Cruz Q, Conesa A, Moreno-Brito V, Echavarria R, Dominguez-Viveros J.

Comput Biol Chem. 2017 Feb;66:26-35. doi: 10.1016/j.compbiolchem.2016.11.001. Epub 2016 Nov 9.

PMID:
27871001
42.

Erratum to: Making sense of big data in health research: towards an EU action plan.

Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar HJ, Guo YK, Gut IG, Hanbury A, Hanif S, Hilgers RD, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, Lanfear J, Lengauer T, Maes E, Meert T, Müller W, Nickel D, Oledzki P, Pedersen B, Petkovic M, Pliakos K, Rattray M, I Màs JR, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LA, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaíno JA, Wubbe JP, Zanetti G.

Genome Med. 2016 Nov 7;8(1):118. No abstract available.

43.

Erratum to: A survey of best practices for RNA-seq data analysis.

Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A.

Genome Biol. 2016 Aug 26;17(1):181. No abstract available.

44.

Transcriptome modulation during host shift is driven by secondary metabolites in desert Drosophila.

De Panis DN, Padró J, Furió-Tarí P, Tarazona S, Milla Carmona PS, Soto IM, Dopazo H, Conesa A, Hasson E.

Mol Ecol. 2016 Sep;25(18):4534-50. doi: 10.1111/mec.13785. Epub 2016 Sep 6.

PMID:
27483442
45.

Roundtable on the Prevention of Eating Disorders: The Catalan public policy initiative.

Sánchez-Carracedo D, Carretero C, Conesa A.

Eat Behav. 2017 Apr;25:15-17. doi: 10.1016/j.eatbeh.2016.07.001. Epub 2016 Jul 12.

PMID:
27443799
46.

Making sense of big data in health research: Towards an EU action plan.

Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar HJ, Guo YK, Gut IG, Hanbury A, Hanif S, Hilgers RD, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, Lanfear J, Lengauer T, Maes E, Meert T, Müller W, Nickel D, Oledzki P, Pedersen B, Petkovic M, Pliakos K, Rattray M, I Màs JR, Schneider R, Sengstag T, Serra-Picamal X, Spek W, Vaas LA, van Batenburg O, Vandelaer M, Varnai P, Villoslada P, Vizcaíno JA, Wubbe JP, Zanetti G.

Genome Med. 2016 Jun 23;8(1):71. doi: 10.1186/s13073-016-0323-y. Erratum in: Genome Med. 2016 Nov 7;8(1):118.

47.

Separating common from distinctive variation.

van der Kloet FM, Sebastián-León P, Conesa A, Smilde AK, Westerhuis JA.

BMC Bioinformatics. 2016 Jun 6;17 Suppl 5:195. doi: 10.1186/s12859-016-1037-2.

48.

spongeScan: A web for detecting microRNA binding elements in lncRNA sequences.

Furió-Tarí P, Tarazona S, Gabaldón T, Enright AJ, Conesa A.

Nucleic Acids Res. 2016 Jul 8;44(W1):W176-80. doi: 10.1093/nar/gkw443. Epub 2016 May 19.

49.

Liquid chromatography coupled to tandem and high resolution mass spectrometry for the characterisation of ofloxacin transformation products after titanium dioxide photocatalysis.

Jimenez-Villarin J, Serra-Clusellas A, Martínez C, Conesa A, Garcia-Montaño J, Moyano E.

J Chromatogr A. 2016 Apr 22;1443:201-10. doi: 10.1016/j.chroma.2016.03.063. Epub 2016 Mar 23.

PMID:
27025791
50.

A survey of best practices for RNA-seq data analysis.

Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A.

Genome Biol. 2016 Jan 26;17:13. doi: 10.1186/s13059-016-0881-8. Review. Erratum in: Genome Biol. 2016;17(1):181.

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