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Browsing by Author "Tarazona Campos, Sonia"

Now showing items 1-20 of 28

A survey of best practices for RNA-seq data analysis

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 ...
Análisis de la expresión alternativa de isoformas en el tiempo mediante datos de RNA-seq

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 ...
Análisis del estado de la cromatina en el ciclo metabólico de la levadura y su integración estadística con el metabolismo y la expresión génica

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 ...
Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package

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 ...
Differential expression in RNA-seq: A matter of depth

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 ...
Dynamic evaluation of neutrophil-to-lymphocyte ratio as prognostic factor in stage III non-small cell lung cancer treated with chemoradiotherapy

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 ...
Estudio del efecto de la exposición a pesticidas en el neurodesarrollo mediante la integración de datos ómicos

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 ...
Estudio metabolómico en ratas con hiperamonemia crónica. Implicaciones en encefalopatía hepática mínima

Rodríguez Hernández, Zulema (Universitat Politècnica de València, 2021-04-21)

[ES] La hiperamonemia resultante de deficiencias hereditarias de las enzimas del ciclo de la urea o de la insuficiencia hepática crónica, ya sea de etiología alcohólica o no alcohólica, da como resultado un aumento de la ...
Evidence of the Red-Queen hypothesis from accelerated rates of evolution of genes involved in biotic interactions in Pneumocystis

Delaye, Luis; Ruiz Ruiz, Susana; Calderon, Enrique; Tarazona Campos, Sonia; Conesa, A.; Moya, Andrés (Oxford University Press, 2018-06)

[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, ...
Guidelines for Developing Successful Short Advanced Courses in Systems Medicine and Systems Biology

Gómez-Cabrero, David; Marabita, Francesco; Tarazona Campos, Sonia; Cano, Isaac; Roca, Josep; Conesa, Ana; Sabatier, Philippe; Tegner, Jesper (Elsevier, 2017-09-27)

[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 ...
Harmonization of quality metrics and power calculation in multi-omic studies

Tarazona Campos, Sonia; Balzano-Nogueira, Leandro; Gómez-Cabrero, David; Schmidt, Andreas; Imhof, Axel; Hankemeier, Thomas; Tegnér, Jesper; Westerhuis, Johan A.; Conesa, Ana (Nature Publishing Group, 2020-06-18)

[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 ...
Impact of Age on Inflammation-Based Scores among Patients Diagnosed with Stage III Non-Small Cell Lung Cancer

Palomar-Abril, Vicente; Soria-Comes, Teresa; Tarazona Campos, Sonia; Martín Ureste, María; Giner-Bosch, Vicent; Maestu-Maiques, Inmaculada Concepción (S. Karger AG, 2020-08)

[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). ...
Implementación de herramientas para el análisis de datos multi-ómicos en una librería de R

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 ...
Influence of ecological infrastructures on the increase of biodiversity and conservation of beneficial arthropods in citrus orchards

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 ...
Integration of multi-omics data to describe link between developmental exposure to pesticides and impaired neurodevelopment

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 ...
Modelos estadísticos para el análisis integrativo de experimentos multi-ómicos

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. ...
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 ...
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 ...