@article {801,
	title = {Evaluation of a combined detection of SARS-CoV-2 and its variants using real-time allele-specific PCR strategy: an advantage for clinical practice.},
	journal = {Epidemiol Infect},
	volume = {151},
	year = {2023},
	month = {2023 Nov 24},
	pages = {e201},
	abstract = {<p>This study aimed to assess the ability of a real-time reverse transcription polymerase chain reaction (RT-PCR) with multiple targets to detect SARS-CoV-2 and its variants in a single test. Nasopharyngeal specimens were collected from patients in Granada, Spain, between January 2021 and December 2022. Five allele-specific RT-PCR kits were used sequentially, with each kit designed to detect a predominant variant at the time. When the Alpha variant was dominant, the kit included the HV69/70 deletion, E and N genes. When Delta replaced Alpha, the kit incorporated the L452R mutation in addition to E and N genes. When Omicron became dominant, L452R was replaced with the N679K mutation. Before incorporating each variant kit, a comparative analysis was carried out with SARS-CoV-2 whole genome sequencing (WGS). The results demonstrated that RT-PCR with multiple targets can provide rapid and effective detection of SARS-CoV-2 and its variants in a single test. A very high degree of agreement (96.2\%) was obtained between the comparison of RT-PCR and WGS. Allele-specific RT-PCR assays make it easier to implement epidemiological surveillance systems for effective public health decision making.</p>},
	keywords = {Alleles, COVID-19, COVID-19 Testing, Humans, Real-Time Polymerase Chain Reaction, SARS-CoV-2, Sensitivity and Specificity},
	issn = {1469-4409},
	doi = {10.1017/S095026882300184X},
	author = {Chaves-Blanco, Luc{\'\i}a and de Salazar, Adolfo and Fuentes, Ana and Vi{\~n}uela, Laura and Perez-Florido, Javier and Dopazo, Joaquin and Garc{\'\i}a, Federico}
}
@article {441,
	title = {Highly sensitive and ultrafast read mapping for RNA-seq analysis.},
	journal = {DNA Res},
	volume = {23},
	year = {2016},
	month = {2016 Apr},
	pages = {93-100},
	abstract = {<p>As sequencing technologies progress, the amount of data produced grows exponentially, shifting the bottleneck of discovery towards the data analysis phase. In particular, currently available mapping solutions for RNA-seq leave room for improvement in terms of sensitivity and performance, hindering an efficient analysis of transcriptomes by massive sequencing. Here, we present an innovative approach that combines re-engineering, optimization and parallelization. This solution results in a significant increase of mapping sensitivity over a wide range of read lengths and substantial shorter runtimes when compared with current RNA-seq mapping methods available. </p>},
	keywords = {Genomics, High-Throughput Nucleotide Sequencing, Humans, Sensitivity and Specificity, Sequence Analysis, RNA, Transcriptome},
	issn = {1756-1663},
	doi = {10.1093/dnares/dsv039},
	author = {Medina, I and T{\'a}rraga, J and Mart{\'\i}nez, H and Barrachina, S and Castillo, M I and Paschall, J and Salavert-Torres, J and Blanquer-Espert, I and Hern{\'a}ndez-Garc{\'\i}a, V and Quintana-Ort{\'\i}, E S and Dopazo, J}
}
