@article {1203,
	title = {Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models.},
	journal = {Nucleic acids research},
	year = {2016},
	month = {2016 May 2},
	abstract = {The discovery of actionable targets is crucial for targeted therapies and is also a constituent part of the drug discovery process. The success of an intervention over a target depends critically on its contribution, within the complex network of gene interactions, to the cellular processes responsible for disease progression or therapeutic response. Here we present PathAct, a web server that predicts the effect that interventions over genes (inhibitions or activations that simulate knock-outs, drug treatments or over-expressions) can have over signal transmission within signaling pathways and, ultimately, over the cell functionalities triggered by them. PathAct implements an advanced graphical interface that provides a unique interactive working environment in which the suitability of potentially actionable genes, that could eventually become drug targets for personalized or individualized therapies, can be easily tested. The PathAct tool can be found at: http://pathact.babelomics.org.},
	keywords = {actionable genes, Disease mechanism, drug action mechanism, Drug discovery, pathway analysis, personalized medicine, signalling, therapeutic targets},
	issn = {1362-4962},
	doi = {10.1093/nar/gkw369},
	url = {http://nar.oxfordjournals.org/content/early/2016/05/02/nar.gkw369.full},
	author = {Salavert, Francisco and Hidago, Marta R and Amadoz, Alicia and Cubuk, Cankut and Medina, Ignacio and Crespo, Daniel and Carbonell-Caballero, Jos{\'e} and Joaqu{\'\i}n Dopazo}
}
@article {1182,
	title = {Assessment of Targeted Next-Generation Sequencing as a Tool for the Diagnosis of Charcot-Marie-Tooth Disease and Hereditary Motor Neuropathy.},
	journal = {The Journal of molecular diagnostics : JMD},
	year = {2016},
	month = {2016 Jan 2},
	abstract = {Charcot-Marie-Tooth disease is characterized by broad genetic heterogeneity with >50 known disease-associated genes. Mutations in some of these genes can cause a pure motor form of hereditary motor neuropathy, the genetics of which are poorly characterized. We designed a panel comprising 56 genes associated with Charcot-Marie-Tooth disease/hereditary motor neuropathy. We validated this diagnostic tool by first testing 11 patients with pathological mutations. A cohort of 33 affected subjects was selected for this study. The DNAJB2 c.352+1G>A mutation was detected in two cases; novel changes and/or variants with low frequency (<1\%) were found in 12 cases. There were no candidate variants in 18 cases, and amplification failed for one sample. The DNAJB2 c.352+1G>A mutation was also detected in three additional families. On haplotype analysis, all of the patients from these five families shared the same haplotype; therefore, the DNAJB2 c.352+1G>A mutation may be a founder event. Our gene panel allowed us to perform a very rapid and cost-effective screening of genes involved in Charcot-Marie-Tooth disease/hereditary motor neuropathy. Our diagnostic strategy was robust in terms of both coverage and read depth for all of the genes and patient samples. These findings demonstrate the difficulty in achieving a definitive molecular diagnosis because of the complexity of interpreting new variants and the genetic heterogeneity that is associated with these neuropathies.},
	keywords = {Charcot-Marie-Tooth, CMT, Diagnostic, NGS, Panels, rare diseases, Targeted resequencing},
	issn = {1943-7811},
	doi = {10.1016/j.jmoldx.2015.10.005},
	url = {http://www.sciencedirect.com/science/article/pii/S1525157815002615},
	author = {Lupo, Vincenzo and Garcia-Garcia, Francisco and Sancho, Paula and Tello, Cristina and Garc{\'\i}a-Romero, Mar and Villarreal, Liliana and Alberti, Antonia and Sivera, Rafael and Joaqu{\'\i}n Dopazo and Pascual-Pascual, Samuel I and M{\'a}rquez-Infante, Celedonio and Casasnovas, Carlos and Sevilla, Teresa and Espin{\'o}s, Carmen}
}
@article {1128,
	title = {Assessing the impact of mutations found in next generation sequencing data over human signaling pathways.},
	journal = {Nucleic acids research},
	volume = {43},
	number = {W1},
	year = {2015},
	month = {2015 Apr 16},
	pages = {W270-W275},
	abstract = {Modern sequencing technologies produce increasingly detailed data on genomic variation. However, conventional methods for relating either individual variants or mutated genes to phenotypes present known limitations given the complex, multigenic nature of many diseases or traits. Here we present PATHiVar, a web-based tool that integrates genomic variation data with gene expression tissue information. PATHiVar constitutes a new generation of genomic data analysis methods that allow studying variants found in next generation sequencing experiment in the context of signaling pathways. Simple Boolean models of pathways provide detailed descriptions of the impact of mutations in cell functionality so as, recurrences in functionality failures can easily be related to diseases, even if they are produced by mutations in different genes. Patterns of changes in signal transmission circuits, often unpredictable from individual genes mutated, correspond to patterns of affected functionalities that can be related to complex traits such as disease progression, drug response, etc. PATHiVar is available at: http://pathivar.babelomics.org.},
	keywords = {NGS, pathways, signalling, Systems biology},
	issn = {1362-4962},
	doi = {10.1093/nar/gkv349},
	url = {http://nar.oxfordjournals.org/content/43/W1/W270},
	author = {Hernansaiz-Ballesteros, Rosa D and Salavert, Francisco and Sebasti{\'a}n-Leon, Patricia and Alem{\'a}n, Alejandro and Medina, Ignacio and Joaqu{\'\i}n Dopazo}
}
@article {1076,
	title = {Acceleration of short and long DNA read mapping without loss of accuracy using suffix array.},
	journal = {Bioinformatics (Oxford, England)},
	volume = {30},
	year = {2014},
	month = {2014 Aug 20},
	pages = {3396-3398},
	abstract = {HPG Aligner applies suffix arrays for DNA read mapping. This implementation produces a highly sensitive and extremely fast mapping of DNA reads that scales up almost linearly with read length. The approach presented here is faster (over 20x for long reads) and more sensitive (over 98\% in a wide range of read lengths) than the current, state-of-the-art mappers. HPG Aligner is not only an optimal alternative for current sequencers but also the only solution available to cope with longer reads and growing throughputs produced by forthcoming sequencing technologies.},
	keywords = {NGS, short read mapping. HPC. suffix arrays},
	issn = {1367-4811},
	doi = {10.1093/bioinformatics/btu553},
	url = {http://bioinformatics.oxfordjournals.org/content/early/2014/08/19/bioinformatics.btu553.long},
	author = {T{\'a}rraga, Joaqu{\'\i}n and Arnau, Vicente and Martinez, Hector and Moreno, Raul and Cazorla, Diego and Salavert-Torres, Jos{\'e} and Blanquer-Espert, Ignacio and Joaqu{\'\i}n Dopazo and Medina, Ignacio}
}
@article {21919703,
	title = {Assessing Differential Expression Measurements by Highly Parallel Pyrosequencing and DNA Microarrays: A Comparative Study.},
	journal = {Omics : a journal of integrative biology},
	year = {2013},
	month = {2011 Sep 15},
	abstract = {<p>Abstract To explore the feasibility of pyrosequencing for quantitative differential gene expression analysis we have performed a comparative study of the results of the sequencing experiments to those obtained by a conventional DNA microarray platform. A conclusion from our analysis is that, over a threshold of 35 normalized reads per gene, the measurements of gene expression display a good correlation with the references. The observed concordance between pyrosequencing and DNA microarray platforms beyond the threshold was of 0.8, measured as a Pearson{\textquoteright}s correlation coefficient. In differential gene expression the initial aim is the quantification the differences among transcripts when comparing experimental conditions. Thus, even in a scenario of low coverage the concordance in the measurements is quite acceptable. On the other hand, the comparatively longer read size obtained by pyrosequencing allows detecting unconventional splicing forms.</p>},
	doi = {10.1089/omi.2011.0065},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545353/},
	author = {Ari{\~n}o, Joaqu{\'\i}n and Casamayor, Antonio and P{\'e}rez, Juli{\'a}n Perez and Pedrola, Laia and Alvarez-Tejado, Miguel and Marb{\`a}, Martina and Santoyo, Javier and Joaqu{\'\i}n Dopazo}
}
