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RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses

M. Rubio-Camarillo, G. Gomez-Lopez, J. M. Fernandez, A. Valencia, D. G. Pisano
2013 Bioinformatics  
Motivation: RUbioSeq has been developed to facilitate the primary and secondary analysis of re-sequencing projects by providing an integrated software suite of parallelized pipelines to detect exome variants  ...  (single-nucleotide variants and copy number variations) and to perform bisulfite-seq analyses automatically.  ...  INTRODUCTION Primary and secondary data analyses of next-generation sequencing studies (NGS) consist of a set of successive stages that are repetitively and routinely executed using a wide collection of  ... 
doi:10.1093/bioinformatics/btt203 pmid:23630175 pmcid:PMC3694642 fatcat:fneoupjbfzdijcbvljl4nxmpei

RUbioSeq+: A multiplatform application that executes parallelized pipelines to analyse next-generation sequencing data

Miriam Rubio-Camarillo, Hugo López-Fernández, Gonzalo Gómez-López, Ángel Carro, José María Fernández, Coral Fustero Torre, Florentino Fdez-Riverola, Daniel Glez-Peña
2017 Computer Methods and Programs in Biomedicine  
Results: Here, we present RUbioSeq+, an updated and extended version of RUbioSeq (ref), a multiplatform application that incorporates a suite of automated and parallelized workflows to analyse NGS data  ...  and Objective: To facilitate routine analysis and to improve the reproducibility of the results, next-generation sequencing (NGS) analysis requires intuitive, efficient and integrated data processing pipelines  ...  Acknowledgements We are thankful to CNIO's Translational Bioinformatics Unit staff for their assistance in beta testing and for their useful suggestions. We also thank O. Graña, E.  ... 
doi:10.1016/j.cmpb.2016.10.008 pmid:27886717 fatcat:dtoon7uu3bc7zbmgvbaqrmwiui

VarGenius executes cohort-level DNA-seq variant calling and annotation and allows to manage the resulting data through a PostgreSQL database

F. Musacchia, TUDP, A. Ciolfi, M. Mutarelli, A. Bruselles, R. Castello, M. Pinelli, S. Basu, S. Banfi, G. Casari, M. Tartaglia, V. Nigro
2018 BMC Bioinformatics  
Several open source tools are available to build a generic variant calling pipeline, but a tool able to simultaneously execute multiple analyses, organize, and categorize the samples is still missing.  ...  Results: Here we describe VarGenius, a Linux based command line software able to execute customizable pipelines for the analysis of multiple targeted resequencing data using parallel computing.  ...  Acknowledgements The authors acknowledge the valuable feedback from Annalaura Torella that is responsible for the sequencing of the data used for testing VarGenius.  ... 
doi:10.1186/s12859-018-2532-4 fatcat:ekmp2inhr5an7dwdav7lpisuri

Pancreas Cancer Precision Treatment Using Avatar Mice from a Bioinformatics Perspective

Javier Perales-Patón, Elena Piñeiro-Yañez, Héctor Tejero, Pedro P. López-Casas, Manuel Hidalgo, Gonzalo Gómez-López, Fátima Al-Shahrour
2017 Public Health Genomics  
Therefore, there is an urgent need to improve the arsenal of anti-PDAC drugs for an effective treatment of these patients.  ...  This aggressiveness is related to the genomic complexity and heterogeneity of PDAC, but also to the absence of an effective screening for the detection of early-stage tumors and a lack of efficient therapeutic  ...  Disclosure Statement The authors declare that they have no relevant or material financial interests that relate to the research described in this paper.  ... 
doi:10.1159/000479812 pmid:28858862 fatcat:jfcizhlx6bbivo4utyujpqrgta

ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw

Stefan Milosavljevic, Tony Kuo, Samuele Decarli, Lucas Mohn, Jun Sese, Kentaro K. Shimizu, Rie Shimizu-Inatsugi, Mark D. Robinson
2021 BMC Genomics  
ARPEGGIO utilizes an updated read classification algorithm (EAGLE-RC), to tackle the challenge of sequence similarity amongst parental genomes.  ...  With the improvement of high-throughput methods, such as whole genome bisulfite sequencing (WGBS), an opportunity opened to further understand the role of DNA methylation at a larger scale and higher resolution  ...  Hatakeyama for sequencing and data handling; the URPP Evolution in Action program for the opportunity to present ARPEGGIO; the Robinson and Shimizu group members for the feedback during different stages  ... 
doi:10.1186/s12864-021-07845-2 pmid:34273949 pmcid:PMC8285871 fatcat:53zyggo6dnh7tirk3gqpaususu

Precision medicine needs pioneering clinical bioinformaticians

Gonzalo Gómez-López, Joaquín Dopazo, Juan C. Cigudosa, Alfonso Valencia, Fátima Al-Shahrour
2017 Briefings in Bioinformatics  
Success in precision medicine depends on accessing high-quality genetic and molecular data from large, well-annotated patient cohorts that couple biological samples to comprehensive clinical data, which  ...  From such a scenario emerges the need for a new professional profile, an expert bioinformatician with training in clinical areas who can make sense of multi-omics data to improve therapeutic interventions  ...  A.V. to BSC-IRB-CRG Program in Computational Biology and Award Severo Ochoa, SEV 2015-0493.  ... 
doi:10.1093/bib/bbx144 pmid:29077790 fatcat:qvbvzunnavfcnjd7w5dqu3qp2m

Monitoring of clonal evolution of acute myeloid leukemia identifies the leukemia subtype, clinical outcome and potential new drug targets for post-remission strategies or relapse

Esther Onecha, Inmaculada Rapado, María Luz Morales, Gonzalo Carreño-Tarragona, Pilar Martinez-Sanchez, Xabier Gutierrez, José María Sáchez Pina, María Linares, Miguel Gallardo, Joaquín Martinez-López, Rosa Ayala
2020 Haematologica  
We undertook a perspective study using next-generation sequencing (NGS) of clinical follow-up samples (n=91) from 23 patients with AML with therapeutic failure to cytarabine plus idarubicin or fludarabine  ...  New therapeutic targets, either by an approved drug or within clinical trials, were not identified in any of the cases of refractoriness (0/10); however, 8 potential new targets were found in 5 relapsed  ...  RUbioSeq+: A multiplatform application that executes parallelized pipelines to analyse next-generation sequencing data. Comput Methods Programs Biomed. 2017;138:73-81. 21.  ... 
doi:10.3324/haematol.2020.254623 pmid:32732356 pmcid:PMC8409047 fatcat:vfeozyvgundhrgddttvryuy2xi

In vivo phosphoproteomics reveals kinase activity profiles that predict treatment outcome in triple-negative breast cancer

Ivana Zagorac, Sara Fernandez-Gaitero, Renske Penning, Harm Post, Maria J. Bueno, Silvana Mouron, Luis Manso, Manuel M. Morente, Soledad Alonso, Violeta Serra, Javier Muñoz, Gonzalo Gómez-López (+13 others)
2018 Nature Communications  
up to 9.5-fold higher relapse risk.  ...  Here, we use high-throughput phosphoproteomics to build a functional TNBC taxonomy.  ...  CRIS Cancer Foundation contributed to this study with a generous donation.  ... 
doi:10.1038/s41467-018-05742-z pmid:30158526 fatcat:swyp7hboa5gf3nf44kuhuq52cq

ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw

Stefan Milosavljevic, Tony Kuo, Samuele Decarli, Lucas Mohn, Jun Sese, Kentaro K Shimizu, Rie Shimizu-Inatsugi, Mark D Robinson
2021
ARPEGGIO utilizes an updated read classification algorithm (EAGLE-RC), to tackle the challenge of sequence similarity amongst parental genomes.  ...  With the improvement of high-throughput methods, such as whole genome bisulfite sequencing (WGBS), an opportunity opened to further understand the role of DNA methylation at a larger scale and higher resolution  ...  Hatakeyama for sequencing and data handling; the URPP Evolution in Action program for the opportunity to present ARPEGGIO; the Robinson and Shimizu group members for the feedback during different stages  ... 
doi:10.5167/uzh-205983 fatcat:7o4da5v2x5e6didunln4mpbr2u

Bioinformatics from genetic variants to methylation

Christopher Schröder, Technische Universität Dortmund, Technische Universität Dortmund
2019
This critical quality measure represents the proportion of redundant data that in most cases needs to be removed from any further analysis.  ...  An important example of such a mechanism is DNA methylation, a process in which methyl groups are added to DNA without altering the sequence itself.  ...  Even for a single data set and parallel execution, the calculation can take days on suitable server hardware.  ... 
doi:10.17877/de290r-19925 fatcat:7coi5ijotbefreblq6v5siyl2a