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Items: 1 to 50 of 293

1.

Association of a single nucleotide polymorphism in ubxn6 gene with long term non progression phenotype in hiv-positive individuals.

Díez-Fuertes F, Erick de la Torre-Tarazona H, Calonge E, Pernas M, Bermejo M, García-Pérez J, Álvarez A, Capa L, García-García F, Saumoy M, Riera M, Boland-Auge A, López-Galíndez C, Lathrop M, Dopazo J, Sakuntabhai A, Alcamí J.

Clin Microbiol Infect. 2019 May 31. pii: S1198-743X(19)30274-5. doi: 10.1016/j.cmi.2019.05.015. [Epub ahead of print]

PMID:
31158522
2.

PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources.

Perez-Gil D, Lopez FJ, Dopazo J, Marin-Garcia P, Rendon A, Medina I.

BMC Bioinformatics. 2019 Mar 28;20(1):159. doi: 10.1186/s12859-019-2726-4.

3.

Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models.

Çubuk C, Hidalgo MR, Amadoz A, Rian K, Salavert F, Pujana MA, Mateo F, Herranz C, Carbonell-Caballero J, Dopazo J.

NPJ Syst Biol Appl. 2019 Mar 1;5:7. doi: 10.1038/s41540-019-0087-2. eCollection 2019.

4.

Fibroblast activation and abnormal extracellular matrix remodelling as common hallmarks in three cancer-prone genodermatoses.

Chacón-Solano E, León C, Díaz F, García-García F, García M, Escámez MJ, Guerrero-Aspizua S, Conti CJ, Mencía Á, Martínez-Santamaría L, Llames S, Pévida M, Carbonell-Caballero J, Puig-Butillé JA, Maseda R, Puig S, de Lucas R, Baselga E, Larcher F, Dopazo J, Del Río M.

Br J Dermatol. 2019 Jan 28. doi: 10.1111/bjd.17698. [Epub ahead of print]

PMID:
30693469
5.

Pazopanib for treatment of advanced malignant and dedifferentiated solitary fibrous tumour: a multicentre, single-arm, phase 2 trial.

Martin-Broto J, Stacchiotti S, Lopez-Pousa A, Redondo A, Bernabeu D, de Alava E, Casali PG, Italiano A, Gutierrez A, Moura DS, Peña-Chilet M, Diaz-Martin J, Biscuola M, Taron M, Collini P, Ranchere-Vince D, Garcia Del Muro X, Grignani G, Dumont S, Martinez-Trufero J, Palmerini E, Hindi N, Sebio A, Dopazo J, Dei Tos AP, LeCesne A, Blay JY, Cruz J.

Lancet Oncol. 2019 Jan;20(1):134-144. doi: 10.1016/S1470-2045(18)30676-4. Epub 2018 Dec 18.

PMID:
30578023
6.

The modular network structure of the mutational landscape of Acute Myeloid Leukemia.

Ibáñez M, Carbonell-Caballero J, Such E, García-Alonso L, Liquori A, López-Pavía M, Llop M, Alonso C, Barragán E, Gómez-Seguí I, Neef A, Hervás D, Montesinos P, Sanz G, Sanz MA, Dopazo J, Cervera J.

PLoS One. 2018 Oct 10;13(10):e0202926. doi: 10.1371/journal.pone.0202926. eCollection 2018.

7.

The first complete genomic structure of Butyrivibrio fibrisolvens and its chromid.

Rodríguez Hernáez J, Cerón Cucchi ME, Cravero S, Martinez MC, Gonzalez S, Puebla A, Dopazo J, Farber M, Paniego N, Rivarola M.

Microb Genom. 2018 Oct;4(10). doi: 10.1099/mgen.0.000216. Epub 2018 Sep 14.

8.

Gene Expression Integration into Pathway Modules Reveals a Pan-Cancer Metabolic Landscape.

Cubuk C, Hidalgo MR, Amadoz A, Pujana MA, Mateo F, Herranz C, Carbonell-Caballero J, Dopazo J.

Cancer Res. 2018 Nov 1;78(21):6059-6072. doi: 10.1158/0008-5472.CAN-17-2705. Epub 2018 Aug 22.

PMID:
30135189
9.

Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome.

Hidalgo MR, Amadoz A, Çubuk C, Carbonell-Caballero J, Dopazo J.

Biol Direct. 2018 Aug 22;13(1):16. doi: 10.1186/s13062-018-0219-4.

10.

A comparison of mechanistic signaling pathway activity analysis methods.

Amadoz A, Hidalgo MR, Çubuk C, Carbonell-Caballero J, Dopazo J.

Brief Bioinform. 2018 Jun 3. doi: 10.1093/bib/bby040. [Epub ahead of print]

PMID:
29868818
11.

The effects of death and post-mortem cold ischemia on human tissue transcriptomes.

Ferreira PG, Muñoz-Aguirre M, Reverter F, Sá Godinho CP, Sousa A, Amadoz A, Sodaei R, Hidalgo MR, Pervouchine D, Carbonell-Caballero J, Nurtdinov R, Breschi A, Amador R, Oliveira P, Çubuk C, Curado J, Aguet F, Oliveira C, Dopazo J, Sammeth M, Ardlie KG, Guigó R.

Nat Commun. 2018 Feb 13;9(1):490. doi: 10.1038/s41467-017-02772-x.

12.

Genomics of the origin and evolution of Citrus.

Wu GA, Terol J, Ibanez V, López-García A, Pérez-Román E, Borredá C, Domingo C, Tadeo FR, Carbonell-Caballero J, Alonso R, Curk F, Du D, Ollitrault P, Roose ML, Dopazo J, Gmitter FG, Rokhsar DS, Talon M.

Nature. 2018 Feb 15;554(7692):311-316. doi: 10.1038/nature25447. Epub 2018 Feb 7.

PMID:
29414943
13.

Graph-theoretical comparison of normal and tumor networks in identifying BRCA genes.

Dopazo J, Erten C.

BMC Syst Biol. 2017 Nov 22;11(1):110. doi: 10.1186/s12918-017-0495-0.

14.

Precision medicine needs pioneering clinical bioinformaticians.

Gómez-López G, Dopazo J, Cigudosa JC, Valencia A, Al-Shahrour F.

Brief Bioinform. 2017 Oct 25. doi: 10.1093/bib/bbx144. [Epub ahead of print]

PMID:
29077790
15.

Reference genome assessment from a population scale perspective: an accurate profile of variability and noise.

Carbonell-Caballero J, Amadoz A, Alonso R, Hidalgo MR, Çubuk C, Conesa D, López-Quílez A, Dopazo J.

Bioinformatics. 2017 Nov 15;33(22):3511-3517. doi: 10.1093/bioinformatics/btx482.

16.

VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy.

Juanes JM, Gallego A, Tárraga J, Chaves FJ, Marín-Garcia P, Medina I, Arnau V, Dopazo J.

BMC Bioinformatics. 2017 Sep 20;18(1):421. doi: 10.1186/s12859-017-1837-z.

17.

The epidemiology of mandibular fractures in Caracas, Venezuela: Incidence and its combination patterns.

Amarista Rojas FJ, Bordoy Soto MA, Cachazo M, Dopazo JR, Vélez H.

Dent Traumatol. 2017 Dec;33(6):427-432. doi: 10.1111/edt.12370. Epub 2017 Sep 28.

PMID:
28887820
18.

Integration of transcriptomic and metabolic data reveals hub transcription factors involved in drought stress response in sunflower (Helianthus annuus L.).

Moschen S, Di Rienzo JA, Higgins J, Tohge T, Watanabe M, González S, Rivarola M, García-García F, Dopazo J, Hopp HE, Hoefgen R, Fernie AR, Paniego N, Fernández P, Heinz RA.

Plant Mol Biol. 2017 Jul;94(4-5):549-564. doi: 10.1007/s11103-017-0625-5. Epub 2017 Jun 21.

PMID:
28639116
19.

HGVA: the Human Genome Variation Archive.

Lopez J, Coll J, Haimel M, Kandasamy S, Tarraga J, Furio-Tari P, Bari W, Bleda M, Rueda A, Gräf S, Rendon A, Dopazo J, Medina I.

Nucleic Acids Res. 2017 Jul 3;45(W1):W189-W194. doi: 10.1093/nar/gkx445.

20.

GGPS1 Mutation and Atypical Femoral Fractures with Bisphosphonates.

Roca-Ayats N, Balcells S, Garcia-Giralt N, Falcó-Mascaró M, Martínez-Gil N, Abril JF, Urreizti R, Dopazo J, Quesada-Gómez JM, Nogués X, Mellibovsky L, Prieto-Alhambra D, Dunford JE, Javaid MK, Russell RG, Grinberg D, Díez-Pérez A.

N Engl J Med. 2017 May 4;376(18):1794-1795. doi: 10.1056/NEJMc1612804. No abstract available.

PMID:
28467865
21.

Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes.

Gui H, Schriemer D, Cheng WW, Chauhan RK, Antiňolo G, Berrios C, Bleda M, Brooks AS, Brouwer RW, Burns AJ, Cherny SS, Dopazo J, Eggen BJ, Griseri P, Jalloh B, Le TL, Lui VC, Luzón-Toro B, Matera I, Ngan ES, Pelet A, Ruiz-Ferrer M, Sham PC, Shepherd IT, So MT, Sribudiani Y, Tang CS, van den Hout MC, van der Linde HC, van Ham TJ, van IJcken WF, Verheij JB, Amiel J, Borrego S, Ceccherini I, Chakravarti A, Lyonnet S, Tam PK, Garcia-Barceló MM, Hofstra RM.

Genome Biol. 2017 Mar 8;18(1):48. doi: 10.1186/s13059-017-1174-6.

22.

A new parallel pipeline for DNA methylation analysis of long reads datasets.

Olanda R, Pérez M, Orduña JM, Tárraga J, Dopazo J.

BMC Bioinformatics. 2017 Mar 9;18(1):161. doi: 10.1186/s12859-017-1574-3.

23.

ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data.

Gonzalez S, Clavijo B, Rivarola M, Moreno P, Fernandez P, Dopazo J, Paniego N.

BMC Bioinformatics. 2017 Feb 22;18(1):121. doi: 10.1186/s12859-017-1494-2.

24.

High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes.

Hidalgo MR, Cubuk C, Amadoz A, Salavert F, Carbonell-Caballero J, Dopazo J.

Oncotarget. 2017 Jan 17;8(3):5160-5178. doi: 10.18632/oncotarget.14107.

25.

Genomic expression differences between cutaneous cells from red hair color individuals and black hair color individuals based on bioinformatic analysis.

Puig-Butille JA, Gimenez-Xavier P, Visconti A, Nsengimana J, Garcia-García F, Tell-Marti G, Escamez MJ, Newton-Bishop J, Bataille V, Del Río M, Dopazo J, Falchi M, Puig S.

Oncotarget. 2017 Feb 14;8(7):11589-11599. doi: 10.18632/oncotarget.14140.

26.

The pan-cancer pathological regulatory landscape.

Falco MM, Bleda M, Carbonell-Caballero J, Dopazo J.

Sci Rep. 2016 Dec 21;6:39709. doi: 10.1038/srep39709.

27.

Mutations in TRAPPC11 are associated with a congenital disorder of glycosylation.

Matalonga L, Bravo M, Serra-Peinado C, García-Pelegrí E, Ugarteburu O, Vidal S, Llambrich M, Quintana E, Fuster-Jorge P, Gonzalez-Bravo MN, Beltran S, Dopazo J, Garcia-Garcia F, Foulquier F, Matthijs G, Mills P, Ribes A, Egea G, Briones P, Tort F, Girós M.

Hum Mutat. 2017 Feb;38(2):148-151. doi: 10.1002/humu.23145. Epub 2016 Nov 26.

PMID:
27862579
28.

Dysfunctional mitochondrial fission impairs cell reprogramming.

Prieto J, León M, Ponsoda X, García-García F, Bort R, Serna E, Barneo-Muñoz M, Palau F, Dopazo J, López-García C, Torres J.

Cell Cycle. 2016 Dec;15(23):3240-3250. Epub 2016 Oct 18.

29.

Identification of the Photoreceptor Transcriptional Co-Repressor SAMD11 as Novel Cause of Autosomal Recessive Retinitis Pigmentosa.

Corton M, Avila-Fernández A, Campello L, Sánchez M, Benavides B, López-Molina MI, Fernández-Sánchez L, Sánchez-Alcudia R, da Silva LRJ, Reyes N, Martín-Garrido E, Zurita O, Fernández-San José P, Pérez-Carro R, García-García F, Dopazo J, García-Sandoval B, Cuenca N, Ayuso C.

Sci Rep. 2016 Oct 13;6:35370. doi: 10.1038/srep35370.

30.

Whole exome sequencing of Rett syndrome-like patients reveals the mutational diversity of the clinical phenotype.

Lucariello M, Vidal E, Vidal S, Saez M, Roa L, Huertas D, Pineda M, Dalfó E, Dopazo J, Jurado P, Armstrong J, Esteller M.

Hum Genet. 2016 Dec;135(12):1343-1354. Epub 2016 Aug 19.

31.

Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq).

Lagarde J, Uszczynska-Ratajczak B, Santoyo-Lopez J, Gonzalez JM, Tapanari E, Mudge JM, Steward CA, Wilming L, Tanzer A, Howald C, Chrast J, Vela-Boza A, Rueda A, Lopez-Domingo FJ, Dopazo J, Reymond A, Guigó R, Harrow J.

Nat Commun. 2016 Aug 17;7:12339. doi: 10.1038/ncomms12339.

32.

Integrated gene set analysis for microRNA studies.

Garcia-Garcia F, Panadero J, Dopazo J, Montaner D.

Bioinformatics. 2016 Sep 15;32(18):2809-16. doi: 10.1093/bioinformatics/btw334. Epub 2016 Jun 20.

33.

Web-based network analysis and visualization using CellMaps.

Salavert F, García-Alonso L, Sánchez R, Alonso R, Bleda M, Medina I, Dopazo J.

Bioinformatics. 2016 Oct 1;32(19):3041-3. doi: 10.1093/bioinformatics/btw332. Epub 2016 Jun 13.

34.

Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models.

Salavert F, Hidago MR, Amadoz A, Çubuk C, Medina I, Crespo D, Carbonell-Caballero J, Dopazo J.

Nucleic Acids Res. 2016 Jul 8;44(W1):W212-6. doi: 10.1093/nar/gkw369. Epub 2016 May 2.

35.

The transcriptomics of an experimentally evolved plant-virus interaction.

Hillung J, García-García F, Dopazo J, Cuevas JM, Elena SF.

Sci Rep. 2016 Apr 26;6:24901. doi: 10.1038/srep24901.

36.

Improving the management of Inherited Retinal Dystrophies by targeted sequencing of a population-specific gene panel.

Bravo-Gil N, Méndez-Vidal C, Romero-Pérez L, González-del Pozo M, Rodríguez-de la Rúa E, Dopazo J, Borrego S, Antiñolo G.

Sci Rep. 2016 Apr 1;6:23910. doi: 10.1038/srep23910.

37.

Chronic subordination stress selectively downregulates the insulin signaling pathway in liver and skeletal muscle but not in adipose tissue of male mice.

Sanghez V, Cubuk C, Sebastián-Leon P, Carobbio S, Dopazo J, Vidal-Puig A, Bartolomucci A.

Stress. 2016;19(2):214-24. doi: 10.3109/10253890.2016.1151491. Epub 2016 Mar 7.

38.

HPG pore: an efficient and scalable framework for nanopore sequencing data.

Tarraga J, Gallego A, Arnau V, Medina I, Dopazo J.

BMC Bioinformatics. 2016 Feb 27;17:107. doi: 10.1186/s12859-016-0966-0.

39.

Progress in pharmacogenetics: consortiums and new strategies.

Maroñas O, Latorre A, Dopazo J, Pirmohamed M, Rodríguez-Antona C, Siest G, Carracedo Á, LLerena A.

Drug Metab Pers Ther. 2016 Mar;31(1):17-23. doi: 10.1515/dmpt-2015-0039. Review.

40.

Transcriptional repressor DREAM regulates trigeminal noxious perception.

Benedet T, Gonzalez P, Oliveros JC, Dopazo JM, Ghimire K, Palczewska M, Mellstrom B, Naranjo JR.

J Neurochem. 2017 May;141(4):544-552. doi: 10.1111/jnc.13584. Epub 2017 Feb 21.

41.

The Mutational Landscape of Acute Promyelocytic Leukemia Reveals an Interacting Network of Co-Occurrences and Recurrent Mutations.

Ibáñez M, Carbonell-Caballero J, García-Alonso L, Such E, Jiménez-Almazán J, Vidal E, Barragán E, López-Pavía M, LLop M, Martín I, Gómez-Seguí I, Montesinos P, Sanz MA, Dopazo J, Cervera J.

PLoS One. 2016 Feb 17;11(2):e0148346. doi: 10.1371/journal.pone.0148346. eCollection 2016.

42.

Serum metabolomic profiling facilitates the non-invasive identification of metabolic biomarkers associated with the onset and progression of non-small cell lung cancer.

Puchades-Carrasco L, Jantus-Lewintre E, Pérez-Rambla C, García-García F, Lucas R, Calabuig S, Blasco A, Dopazo J, Camps C, Pineda-Lucena A.

Oncotarget. 2016 Mar 15;7(11):12904-16. doi: 10.18632/oncotarget.7354.

43.

Stress-induced activation of brown adipose tissue prevents obesity in conditions of low adaptive thermogenesis.

Razzoli M, Frontini A, Gurney A, Mondini E, Cubuk C, Katz LS, Cero C, Bolan PJ, Dopazo J, Vidal-Puig A, Cinti S, Bartolomucci A.

Mol Metab. 2015 Nov 11;5(1):19-33. doi: 10.1016/j.molmet.2015.10.005. eCollection 2016 Jan.

44.

Human DNA methylomes of neurodegenerative diseases show common epigenomic patterns.

Sanchez-Mut JV, Heyn H, Vidal E, Moran S, Sayols S, Delgado-Morales R, Schultz MD, Ansoleaga B, Garcia-Esparcia P, Pons-Espinal M, de Lagran MM, Dopazo J, Rabano A, Avila J, Dierssen M, Lott I, Ferrer I, Ecker JR, Esteller M.

Transl Psychiatry. 2016 Jan 19;6:e718. doi: 10.1038/tp.2015.214.

45.

Screening of CD96 and ASXL1 in 11 patients with Opitz C or Bohring-Opitz syndromes.

Urreizti R, Roca-Ayats N, Trepat J, Garcia-Garcia F, Aleman A, Orteschi D, Marangi G, Neri G, Opitz JM, Dopazo J, Cormand B, Vilageliu L, Balcells S, Grinberg D.

Am J Med Genet A. 2016 Jan;170A(1):24-31. doi: 10.1002/ajmg.a.37418. Epub 2015 Oct 7.

PMID:
26768331
46.

267 Spanish Exomes Reveal Population-Specific Differences in Disease-Related Genetic Variation.

Dopazo J, Amadoz A, Bleda M, Garcia-Alonso L, Alemán A, García-García F, Rodriguez JA, Daub JT, Muntané G, Rueda A, Vela-Boza A, López-Domingo FJ, Florido JP, Arce P, Ruiz-Ferrer M, Méndez-Vidal C, Arnold TE, Spleiss O, Alvarez-Tejado M, Navarro A, Bhattacharya SS, Borrego S, Santoyo-López J, Antiñolo G.

Mol Biol Evol. 2016 May;33(5):1205-18. doi: 10.1093/molbev/msw005. Epub 2016 Jan 13.

47.

Differential Features between Chronic Skin Inflammatory Diseases Revealed in Skin-Humanized Psoriasis and Atopic Dermatitis Mouse Models.

Carretero M, Guerrero-Aspizua S, Illera N, Galvez V, Navarro M, García-García F, Dopazo J, Jorcano JL, Larcher F, del Rio M.

J Invest Dermatol. 2016 Jan;136(1):136-45. doi: 10.1038/JID.2015.362.

48.

Assessment of Targeted Next-Generation Sequencing as a Tool for the Diagnosis of Charcot-Marie-Tooth Disease and Hereditary Motor Neuropathy.

Lupo V, García-García F, Sancho P, Tello C, García-Romero M, Villarreal L, Alberti A, Sivera R, Dopazo J, Pascual-Pascual SI, Márquez-Infante C, Casasnovas C, Sevilla T, Espinós C.

J Mol Diagn. 2016 Mar;18(2):225-34. doi: 10.1016/j.jmoldx.2015.10.005. Epub 2016 Jan 2.

PMID:
26752306
49.

Highly sensitive and ultrafast read mapping for RNA-seq analysis.

Medina I, Tárraga J, Martínez H, Barrachina S, Castillo MI, Paschall J, Salavert-Torres J, Blanquer-Espert I, Hernández-García V, Quintana-Ortí ES, Dopazo J.

DNA Res. 2016 Apr;23(2):93-100. doi: 10.1093/dnares/dsv039. Epub 2016 Jan 5.

50.

Identification of epistatic interactions through genome-wide association studies in sporadic medullary and juvenile papillary thyroid carcinomas.

Luzón-Toro B, Bleda M, Navarro E, García-Alonso L, Ruiz-Ferrer M, Medina I, Martín-Sánchez M, Gonzalez CY, Fernández RM, Torroglosa A, Antiñolo G, Dopazo J, Borrego S.

BMC Med Genomics. 2015 Dec 21;8:83. doi: 10.1186/s12920-015-0160-7.

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