[EN] Patients with liver cirrhosis may develop covert or minimal hepatic encephalopathy (MHE). Hyperammonemia (HA) and peripheral inflammation play synergistic roles in inducing the cognitive and motor alterations in MHE. ...
[EN] T-cell receptor (TCR) analysis is relevant for the study of immune system diseases. The expression of TCRs is usually measured with targeted sequencing approaches where TCR genes are selectively amplified. However, ...
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 ...
[EN] Alternative splicing (AS) is a highly-regulated post-transcriptional mechanism known to modulate isoform expression within genes and contribute to cell-type identity. However, the extent to which alternative isoforms ...
Nueda, María J.; Ferrer Riquelme, Alberto José; Conesa, Ana(Oxford University Press (OUP): Policy B - Oxford Open Option A, 2011-11-14)
Transcriptomic profiling experiments that aim to the identification of responsive genes in specific biological
conditions are commonly set up under defined experimental designs that try to assess the effects
of factors ...
[EN] Understanding the cause of sex disparities in COVID-19 outcomes is a major challenge. We investigate sex hormone levels and their association with outcomes in COVID-19 patients, stratified by sex and age. This ...
Conesa, Ana; Götz, Stefan; Garcia-Gomez, Juan M; Terol, Javier; Talón, Manuel; Robles Viejo, Montserrat(Oxford University Press, 2005-09-15)
[EN] We present here Blast2GO (B2G), a research tool designed with the main purpose of enabling Gene Ontology (GO) based data mining on sequence data for which no GO annotation is yet available. B2G joints in one application ...
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 ...
[EN] Leaf abscission is a common response of plants to drought stress. Some species, such as citrus, have evolved a specific
behaviour in this respect, keeping their leaves attached to the plant body during water stress ...
[EN] The Yeast Metabolic Cycle (YMC) is a model system in which levels of around 60% of the yeast transcripts cycle over time. The spatial and temporal resolution provided by the YMC has revealed that changes in the yeast ...
[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 ...
GOTZ, STEFAN; García Gómez, Juan Miguel; Terol, Javier; Williams, Tim D.; Nagaraj, Shivashankar H.; Nueda, María José; Robles Viejo, Monserrat; Talón, Manuel; Dopazo, Joaquín; Conesa, Ana(Oxford University Press, 2008)
[EN] Functional genomics technologies have been widely adopted in the biological research of both model and non-model species. An efficient functional annotation of DNA or protein sequences is a major requirement for the ...
[EN] Diversity of omic technologies has expanded in the last years together with the number of omic data integration strategies. However, multiomic data generation is costly, and many research groups cannot afford research ...
Ugidos, Manuel; Nueda, María José; Prats-Montalbán, José Manuel; Ferrer, Alberto; Conesa, Ana; Tarazona, Sonia(Oxford University Press, 2022-04-28)
[EN] Motivation: Batch effects in omics datasets are usually a source of technical noise that masks the biological signal and hampers data analysis. Batch effect removal has been widely addressed for individual omics ...
Pérez-Benavente, Beatriz; Fathinajafabadi, Alihamze; de la Fuente, Lorena; Gandía, Carolina; Martínez-Férriz, Arantxa; Pardo-Sánchez, José Miguel; Milian-Medina, Lara; Conesa, Ana; Romero, Octavio A.; Carretero, Julián; Matthiesen, Rune; Jariel-Encontre, Isabelle; Piechaczyk, Marc; Farràs, Rosa(BioMed Central Ltd., 2022-12-09)
[EN] Background: JUNB transcription factor contributes to the formation of the ubiquitous transcriptional complex AP-1 involved in the control of many physiological and disease-associated functions. The roles of JUNB in ...
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] PaintOmics is a web server for the integrative analysis and visualisation of multi-omics datasets using biological pathway maps. PaintOmics 4 has several notable updates that improve and extend analyses. Three pathway ...
[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 ...