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Items: 1 to 20 of 23

1.

Heteroaryldihydropyrimidine (HAP) and Sulfamoylbenzamide (SBA) Inhibit Hepatitis B Virus Replication by Different Molecular Mechanisms.

Zhou Z, Hu T, Zhou X, Wildum S, Garcia-Alcalde F, Xu Z, Wu D, Mao Y, Tian X, Zhou Y, Shen F, Zhang Z, Tang G, Najera I, Yang G, Shen HC, Young JA, Qin N.

Sci Rep. 2017 Feb 13;7:42374. doi: 10.1038/srep42374.

2.

Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes.

Petrova OE, Garcia-Alcalde F, Zampaloni C, Sauer K.

Sci Rep. 2017 Jan 24;7:41114. doi: 10.1038/srep41114.

3.

InFusion: Advancing Discovery of Fusion Genes and Chimeric Transcripts from Deep RNA-Sequencing Data.

Okonechnikov K, Imai-Matsushima A, Paul L, Seitz A, Meyer TF, Garcia-Alcalde F.

PLoS One. 2016 Dec 1;11(12):e0167417. doi: 10.1371/journal.pone.0167417. eCollection 2016.

4.

Association study between mannose-binding lectin haplotypes and X gene mutation of hepatitis B virus from treatment naïve patients.

Su C, Lin Y, Mao Q, Wu D, Zhu L, Najera I, Garcia-Alcalde F, Niu J.

Aging (Albany NY). 2016 Nov 7;8(11):2862-2870. doi: 10.18632/aging.101097.

5.

Combinations of Oseltamivir and T-705 Extend the Treatment Window for Highly Pathogenic Influenza A(H5N1) Virus Infection in Mice.

Marathe BM, Wong SS, Vogel P, Garcia-Alcalde F, Webster RG, Webby RJ, Najera I, Govorkova EA.

Sci Rep. 2016 May 25;6:26742. doi: 10.1038/srep26742.

6.

Using NS5B Sequencing for Hepatitis C Virus Genotyping Reveals Discordances with Commercial Platforms.

Chueca N, Rivadulla I, Lovatti R, Reina G, Blanco A, Fernandez-Caballero JA, Cardeñoso L, Rodriguez-Granjer J, Fernandez-Alonso M, Aguilera A, Alvarez M, Galán JC, García F.

PLoS One. 2016 Apr 20;11(4):e0153754. doi: 10.1371/journal.pone.0153754. eCollection 2016.

7.

Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data.

Okonechnikov K, Conesa A, García-Alcalde F.

Bioinformatics. 2016 Jan 15;32(2):292-4. doi: 10.1093/bioinformatics/btv566. Epub 2015 Oct 1.

8.

Helicobacter pylori Infection Causes Characteristic DNA Damage Patterns in Human Cells.

Koeppel M, Garcia-Alcalde F, Glowinski F, Schlaermann P, Meyer TF.

Cell Rep. 2015 Jun 23;11(11):1703-13. doi: 10.1016/j.celrep.2015.05.030. Epub 2015 Jun 11.

9.

CisMiner: genome-wide in-silico cis-regulatory module prediction by fuzzy itemset mining.

Navarro C, Lopez FJ, Cano C, Garcia-Alcalde F, Blanco A.

PLoS One. 2014 Sep 30;9(9):e108065. doi: 10.1371/journal.pone.0108065. eCollection 2014.

10.

Evidence for a crucial role of a host non-coding RNA in influenza A virus replication.

Winterling C, Koch M, Koeppel M, Garcia-Alcalde F, Karlas A, Meyer TF.

RNA Biol. 2014;11(1):66-75. doi: 10.4161/rna.27504. Epub 2013 Dec 20.

11.

Qualimap: evaluating next-generation sequencing alignment data.

García-Alcalde F, Okonechnikov K, Carbonell J, Cruz LM, Götz S, Tarazona S, Dopazo J, Meyer TF, Conesa A.

Bioinformatics. 2012 Oct 15;28(20):2678-9. doi: 10.1093/bioinformatics/bts503. Epub 2012 Aug 22.

PMID:
22914218
12.

Gene network profiling before and after transplantation in alcoholic cirrhosis liver transplant recipients.

Muffak-Granero K, Olmedo C, Garcia-Alcalde F, Comino A, Villegas T, Villar JM, Garrote D, Blanco A, Bueno P, Ferron JA.

Transplant Proc. 2012 Jul-Aug;44(6):1493-5. doi: 10.1016/j.transproceed.2012.05.017.

PMID:
22841193
13.

Genome-wide gene expression analysis in mouse embryonic stem cells.

Sainz J, García-Alcalde F, Blanco A, Concha A.

Int J Dev Biol. 2011;55(10-12):995-1006. doi: 10.1387/ijdb.103123js.

14.

Transdifferentiation of MALME-3M and MCF-7 Cells toward Adipocyte-like Cells is Dependent on Clathrin-mediated Endocytosis.

Carcel-Trullols J, Aguilar-Gallardo C, Garcia-Alcalde F, Pardo-Cea MA, Dopazo J, Conesa A, Simón C.

Springerplus. 2012 Oct 30;1:44. doi: 10.1186/2193-1801-1-44. eCollection 2012.

15.

Genome-wide differential genetic profiling characterizes colorectal cancers with genetic instability and specific routes to HLA class I loss and immune escape.

Bernal M, García-Alcalde F, Concha A, Cano C, Blanco A, Garrido F, Ruiz-Cabello F.

Cancer Immunol Immunother. 2012 Jun;61(6):803-16. doi: 10.1007/s00262-011-1147-7. Epub 2011 Nov 10.

PMID:
22072317
16.

Differential expression in RNA-seq: a matter of depth.

Tarazona S, García-Alcalde F, Dopazo J, Ferrer A, Conesa A.

Genome Res. 2011 Dec;21(12):2213-23. doi: 10.1101/gr.124321.111. Epub 2011 Sep 8.

17.

Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data.

García-Alcalde F, García-López F, Dopazo J, Conesa A.

Bioinformatics. 2011 Jan 1;27(1):137-9. doi: 10.1093/bioinformatics/btq594. Epub 2010 Nov 23.

18.

An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs.

Garcia-Alcalde F, Blanco A, Shepherd AJ.

BMC Bioinformatics. 2010 Nov 8;11:551. doi: 10.1186/1471-2105-11-551.

19.

TNFR1 mRNA expression level and TNFR1 gene polymorphisms are predictive markers for susceptibility to develop invasive pulmonary aspergillosis.

Sainz J, Salas-Alvarado I, López-Fernández E, Olmedo C, Comino A, García F, Blanco A, Gómez-Lopera S, Oyonarte S, Bueno P, Jurado M.

Int J Immunopathol Pharmacol. 2010 Apr-Jun;23(2):423-36.

PMID:
20646338
20.

FISim: a new similarity measure between transcription factor binding sites based on the fuzzy integral.

Garcia F, Lopez FJ, Cano C, Blanco A.

BMC Bioinformatics. 2009 Jul 20;10:224. doi: 10.1186/1471-2105-10-224.

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