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Browsing by Author "Tarazona Campos, Sonia"

Now showing items 21-34 of 34

MultiBaC: A strategy to remove batch effects between different omic data types

Ugidos, Manuel; Tarazona Campos, Sonia; Prats-Montalbán, José Manuel; Ferrer, Alberto; Conesa, Ana (SAGE Publications, 2020-10)

[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 ...
Network and Systems Medicine Approach against COVID-19

Rodríguez Martínez, Eduardo (Universitat Politècnica de València, 2021-10-07)

[ES] El estudio de diferentes redes basadas en la COVID-19 puede proporcionar un enfoque sistemático para explorar los repositorios de medicamentos al tiempo que se tienen en cuenta otros factores multidimensionales que ...
Next maSigPro: updating maSigPro Bioconductor package for RNA-seq time series

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 ...
PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data

Hernandez-De Diego, Rafael; Tarazona Campos, Sonia; Martínez-Mira, Carlos; Balzano-Nogueira, Leandro; Furió-Tarí, Pedro; Conesa, A.; Pappas, G. (Oxford University Press, 2018)

[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 ...
Pathway network inference from gene expression data

Ponzoni, Ignacio; Nueda, Maria José; Tarazona Campos, Sonia; GOTZ, STEFAN; Montaner, David; Dussaut, Julieta Sol; Dopazo, Joaquín; Conesa, Ana (BioMed Central, 2014-03-13)

[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 ...
Qualimap: evaluating next generation sequencing alignment data

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 ...
RGmatch: matching genomic regions to proximal genes in omics data integration

Furió Tarí, Pedro; Conesa, Ana; Tarazona Campos, Sonia (BioMed Central, 2016)

[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 ...
Role of chromatin modifying enzymes and histone acetylation in the regulation of the yeast metabolic cycle

Onofriychuk, Anastasiya (Universitat Politècnica de València, 2019-09-05)

[EN] The yeast metabolic cycle (YMC) is a phenomenon that occurs in the baking yeast Saccharomyces cerevisiae. The YMC is produced at low glucose levels with a continuous feeding of the culture, and it is characterized ...
spongeScan: A web for detecting microRNA binding elements in lncRNA sequences

Furió-Tarí, Pedro; Tarazona Campos, Sonia; Gabaldón, Toni; Enright, Anton J.; Conesa, Ana (Oxford University Press (OUP), 2016-05)

[EN] Non-coding RNA transcripts such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are important genetic regulators. However, the functions of many of these transcripts are still not clearly understood. Recently, ...
Statistical methods for transcriptomics: From microarrays to RNA-seq

Tarazona Campos, Sonia (Universitat Politècnica de València, 2015-03-30)

La transcriptómica estudia el nivel de expresión de los genes en distintas condiciones experimentales para tratar de identificar los genes asociados a un fenotipo dado así como las relaciones de regulación entre distintos ...
Transcriptome modulation during host shift is driven by secondary metabolites in desert Drosophila

De Panis, Diego N.; Padró, Julián; Furió Tarí, Pedro; Tarazona Campos, Sonia; Milla Carmona, Pablo S.; Soto, Ignacio M.; Dopazo, Hernán; Conesa, Ana; Hasson, Esteban (Wiley, 2016-09)

[EN] High-throughput transcriptome studies are breaking new ground to investigate the responses that organisms deploy in alternative environments. Nevertheless, much remains to be understood about the genetic basis of ...
Tumor microenvironment-targeted poly-L-glutamic acid-based combination conjugate for enhanced triple negative breast cancer treatment

Arroyo-Crespo, Juan J.; Armiñán, Ana; Charbonnier, David; Balzano-Nogueira, Leandro; Huertas-López, Francisco; Martí, Cristina; Tarazona Campos, Sonia; Forteza, Jerónimo; Conesa, A.; Vicent Docon, Maria Jesus (Elsevier, 2018-12)

[EN] The intrinsic characteristics of the tumor microenvironment (TME), including acidic pH and overexpression of hydrolytic enzymes, offer an exciting opportunity for the rational design of TME-drug delivery systems (DDS). ...
Undisclosed, unmet and neglected challenges in multi-omics studies

Tarazona, Sonia; Arzalluz-Luque, Ángeles; Conesa, Ana (Nature Publishing Group, 2021-06-21)

[EN] Multi-omics approaches have become a reality in both large genomics projects and small laboratories. However, the multi-omics research community still faces a number of issues that have either not been sufficiently ...
Variable Selection for Multifactorial Genomic Data

Tarazona Campos, Sonia; PRADO-LÓPEZ, Sonia; Dopazo, Joaquín; Ferrer Riquelme, Alberto José; CONESA, A. (Elsevier, 2012-01-15)

[EN] Dimension reduction techniques are used to explore genomic data. Due to the large number of variables (genes) included in this kind of studies, variable selection methods are needed to identify the most responsive genes ...