Conesa, Ana; Madrigal, Pedro; Tarazona Campos, Sonia; Gómez Cabrero, David; Cervera, Alejandra; McPherson, Andrew; Wojciech Szczesniak, Michal; Gaffney, Daniel J.; Elo, Laura L.; Zhang, Xuegong; Mortazavi, Ali(BioMed Central, 2016-01)
[EN] RNA-sequencing (RNA-seq) has a wide variety of
applications, but no single analysis pipeline can be
used in all cases. We review all of the major steps in
RNA-seq data analysis, including experimental design,
quality ...
Martorell Marugán, Jordi(Universitat Politècnica de València, 2015-09-04)
[ES] Los avances en tecnologías de secuenciación masiva han dado lugar al desarrollo de la transcriptómica por secuenciación, que permite analizar la expresión de genes e isoformas. El laboratorio de Genómica de la Expresión ...
Villacampa Fernández, Marina(Universitat Politècnica de València, 2019-09-05)
[ES] Las levaduras en un sistema de crecimiento continuo, de alta densidad y con una
concentración de glucosa baja tienen un ciclo robusto de 4-5 horas (ciclo metabólico de la
levadura, o YMC del inglés Yeast Metabolic ...
Tarazona Campos, Sonia; Furió Tarí, Pedro; Turrà, David; Di Pietro, Antonio; Nueda, María José; Ferrer, Alberto; Conesa, Ana(Oxford University Press (OUP), 2015-12-02)
[EN] As the use of RNA-seq has popularized, there is an increasing consciousness of the importance of experimental design, bias removal, accurate quantification and control of false positives for proper data analysis. We ...
Tarazona Campos, Sonia; García-Alcalde, Fernando; Dopazo, Joaquín; Ferrer Riquelme, Alberto José; Conesa, Ana(Cold Spring Harbor Laboratory Press, 2011-09-08)
Next-generation sequencing (NGS) technologies are revolutionizing genome research, and in particular, their application to transcriptomics (RNA-seq) is increasingly being used for gene expression profiling as a replacement ...
Palomar-Abril, V.; Soria-Comes, T.; Tarazona Campos, Sonia; Ureste, M. M.; Giner-Bosch, Vicent; Maiques, I. C. M.(Springer-Verlag, 2020-12)
[EN] Purpose Locally advanced non-small cell lung cancer (LA-NSCLC) is frequently treated with chemoradiotherapy (CRT). Despite the efforts, long-term outcomes are poor, and novel therapies have been introduced to improve ...
Sánchez Gaya, Víctor(Universitat Politècnica de València, 2017-09-05)
[ES] El enfoque multiómico está ganando terreno en el campo de la biología de sistemas, ya
que permite estudiar aspectos complementarios del funcionamiento de un sistema biológico. Sin
embargo, la integración de datos ...
[EN] Pneumocystis species are ascomycete fungi adapted to live inside the lungs of mammals. These ascomycetes show extensive stenoxenism, meaning that each species of Pneumocystis infects a single species of host. Here, ...
[EN] Systems medicine and systems biology have inherent educational challenges. These have largely been addressed either by providing new masters programs or by redesigning undergraduate programs. In contrast, short courses ...
[EN] Multi-omic studies combine measurements at different molecular levels to build comprehensive models of cellular systems. The success of a multi-omic data analysis strategy depends largely on the adoption of adequate ...
[EN] Background: Inflammatory and nutritional indexes are prognostic factors in non-small cell lung cancer (NSCLC). Furthermore, a low grade of chronic inflammation has been described in the older population (inflammaging). ...
Martínez Mira, Carlos(Universitat Politècnica de València, 2015-10-22)
[ES] Los avances en tecnologías de secuenciación masiva permiten obtener datos de expresión génica y también de sus elementos reguladores y productos. Integrar estas medidas multiómicas en un modelo estadístico que explique ...
Laborda Cenjor, Rafael; Bertomeu Cucart, Salvador; Sánchez Domingo, Adrián; Xamaní Monserrat, Pilar; Tarazona Campos, Sonia; Ibañez, J.M.; García Prats, Alberto; García Mari, Ferran(International Organization for Biological and Integrated Control of Noxious Animals and Plants, West Palearctic Regional Section (IOBC-WPRS), 2013)
[EN] We performed a study in nineteen citrus plots representative of the agricultural landscape of
the municipality of Altea (100 km south of Valencia, in eastern Spain) in order to determine the
influence of ecological ...
Bernabeu Gómez, Elena(Universitat Politècnica de València, 2016-07-28)
[EN] In recent years the omics disciplines have made their way across a wider spectrum of
research groups, thus leading to the generation of multi-omics data sets in a great number of
studies. While traditional omics ...
Tomás Riquelme, Blanca(Universitat Politècnica de València, 2019-01-09)
Los avances recientes en las tecnologías de secuenciación nos han brindado una oportunidad sin precedentes para entender mejor el papel de la genómica, epigenética y transcriptómica en la regulación de la expresión génica. ...
Nueda, María José; Tarazona Campos, Sonia; Conesa, Ana(Oxford University Press (OUP): Policy B - Oxford Open Option B, 2014-09-15)
[EN] Motivation: The widespread adoption of RNA-seq to quantitatively
measure gene expression has increased the scope of sequencing
experimental designs to include time-course experiments. maSigPro
is an R package ...
[EN] The increasing availability of multi-omic platforms poses new challenges to data analysis. Joint visualization of multi-omics data is instrumental in better understanding interconnections across molecular layers and ...
[EN] Background: The development of high-throughput omics technologies enabled genome-wide measurements of
the activity of cellular elements and provides the analytical resources for the progress of the Systems ...
García-Alcalde, Fernando; Okonechnikov, Konstantin; Carbonell Caballero, José; Cruz, Luís M.; GOTZ, STEFAN; Tarazona Campos, Sonia; Dopazo, Joaquín; Meyer, Thomas F.; Conesa, Ana(Oxford University Press (OUP): Policy B - Oxford Open Option B, 2012)
Motivation: The sequence alignment/map (SAM) and the binary
alignment/map (BAM) formats have become the standard method of
representation of nucleotide sequence alignments for next-generation
sequencing data. SAM/BAM ...
[EN] Background: The integrative analysis of multiple genomics data often requires that genome coordinates-based
signals have to be associated with proximal genes. The relative location of a genomic region with respect ...