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PRADA: pipeline for RNA sequencing data analysis

Wandaliz Torres-García, Siyuan Zheng, Andrey Sivachenko, Rahulsimham Vegesna, Qianghu Wang, Rong Yao, Michael F. Berger, John N. Weinstein, Gad Getz, Roel G.W. Verhaak
2014 Computer applications in the biosciences : CABIOS  
For that purpose, we have developed PRADA (Pipeline for RNA-Sequencing Data Analysis), a flexible, modular and highly scalable software platform that provides many different types of information available  ...  by multifaceted analysis starting from raw paired-end RNA-seq data: gene expression levels, quality metrics, detection of unsupervised and supervised fusion transcripts, detection of intragenic fusion  ...  For that purpose, we have developed PRADA (Pipeline for RNA-Sequencing Data Analysis).  ... 
doi:10.1093/bioinformatics/btu169 pmid:24695405 pmcid:PMC4103589 fatcat:b5ew4ulldrfolnjnfeeybgmsja

D6.1 - Literature mining and preprocessing

Tiziana Sanavia, Lorenzo Dall'Olio, Íñigo Prada-Luengo, Anders Krogh, Gastone Castellani
2021 Zenodo  
The software is available for the entire consortium in the GenoMed4all GitLab repository and will be made publicly available at a later stage in the project.  ...  Different algorithms are used for DNA and RNA sequences.  ...  Figure 3 3 shows the main steps that will be considered for preprocessing the data, considering both what was already done for the preprocessed data and the upcoming DNA and RNA sequencing data.  ... 
doi:10.5281/zenodo.5862467 fatcat:kvjrlnindrfrra5kgu2hfidd7u

To Be or Not to Be: Circular RNAs or mRNAs From Circular DNAs?

Leire Iparraguirre, Iñigo Prada-Luengo, Birgitte Regenberg, David Otaegui
2019 Frontiers in Genetics  
While some protocols remove linear RNA prior to sequencing, many have characterized circRNAs by sorting through total RNA sequencing data without excluding the possibility that some linear RNA can provide  ...  CircRNAs are mainly recorded by RNA-Seq and computational methods focused on the detection of back-splicing junction sequences considered the diagnostic feature of circRNAs.  ...  It has been demonstrated that with a good sequencing depth and quality and a carefully data-analysis, true circRNAs can be detected from total RNA sequencing , however, in this second approach, a later  ... 
doi:10.3389/fgene.2019.00940 pmid:31681407 pmcid:PMC6797608 fatcat:4gjyp3ravnhgzorjtmhmsthrpi

Circular DNA elements of chromosomal origin are common in healthy human somatic tissue

Henrik Devitt Møller, Marghoob Mohiyuddin, Iñigo Prada-Luengo, M. Reza Sailani, Jens Frey Halling, Peter Plomgaard, Lasse Maretty, Anders Johannes Hansen, Michael P. Snyder, Henriette Pilegaard, Hugo Y. K. Lam, Birgitte Regenberg
2018 Nature Communications  
Here, we purify and sequence eccDNAs from muscle and blood samples from 16 healthy men, detecting~100,000 unique eccDNA types from 16 million nuclei.  ...  index labels Uniquely mapped eccDNA pipeline for Circle-Seq data.  ...  Data availability. Sequence data from Circle-Seq and RNA-Seq experiments have been deposited in the Sequence Read Archive. BioSample accession IDs for DNA Circle-Seq: SAMN08054900 to SAMN08054941.  ... 
doi:10.1038/s41467-018-03369-8 pmid:29540679 pmcid:PMC5852086 fatcat:rdr35fdtbrbcznxzijf7hfndli

Mediterranean versus Red sea corals facing climate change, a transcriptome analysis

Keren Maor-Landaw, Hiba Waldman Ben-Asher, Sarit Karako-Lampert, Mali Salmon-Divon, Fiorella Prada, Erik Caroselli, Stefano Goffredo, Giuseppe Falini, Zvy Dubinsky, Oren Levy
2017 Scientific Reports  
To date there are no available genomic nor transcriptomic data available on Mediterranean corals, including on B. europaea 17 , whereas an ESTs library was previously constructed for S. pistillata 18 .  ...  Here we used transcriptome analysis to study the effect of long-term gradual temperature increase (annual rate), combined with lowered pH values, on a sub-tropical Red Sea coral, Stylophora pistillata,  ...  The CASAVA 1.8.2 version of the Illumina pipeline was used to process raw data for both format conversion and de-multiplexing.  ... 
doi:10.1038/srep42405 pmid:28181588 pmcid:PMC5299404 fatcat:b4wsgxb7nve3dlghhg5pegekle

Drug resistance analysis by next generation sequencing in Leishmania

Philippe Leprohon, Christopher Fernandez-Prada, Élodie Gazanion, Rubens Monte-Neto, Marc Ouellette
2015 International Journal for Parasitology: Drugs and Drug Resistance  
This review summarizes the most recent highlights that whole genome sequencing brought to our understanding of Leishmania drug resistance and likely new directions.  ...  A B S T R A C T The use of next generation sequencing has the power to expedite the identification of drug resistance determinants and biomarkers and was applied successfully to drug resistance studies  ...  Acknowledgments This work was supported by a Canadian Institutes for Health Research grant to MO. MO holds the Canada Research Chair in Antimicrobial Resistance.  ... 
doi:10.1016/j.ijpddr.2014.09.005 pmid:25941624 pmcid:PMC4412915 fatcat:tvp22t2qc5bv5e2etjlhxcme74

Sensitive detection of circular DNAs at single-nucleotide resolution using guided realignment of partially aligned reads

Iñigo Prada-Luengo, Anders Krogh, Lasse Maretty, Birgitte Regenberg
2019 BMC Bioinformatics  
We compared Circle-Map to similar up-to-date methods for circular DNA and RNA detection and we demonstrate how the approach implemented in Circle-Map dramatically increases sensitivity for detection of  ...  data.  ...  The funding bodies did not play any role in the design, data collection, analysis, interpretation and writing of any of data presented in this study.  ... 
doi:10.1186/s12859-019-3160-3 pmid:31830908 pmcid:PMC6909605 fatcat:rewfcw637ngzvlkxd6zhgpzyny

Versatile workflow for cell type resolved transcriptional and epigenetic profiles from cryopreserved human lung [article]

Maria Llamazares Prada, Elisa Espinet, Vedrana Mijosek, Uwe Schwartz, Sebastian M. Waszak, Pavlo Lutsik, Raluca Tamas, Mandy Richter, Annika Behrendt, Stephanie Pohl, Naja Benz, Thomas Muley (+14 others)
2020 biorxiv/medrxiv   pre-print
In addition, we obtained high-quality single-cell RNA sequencing data of cells isolated from cryopreserved human lung, demonstrating that cryopreservation empowers single-cell approaches.  ...  Importantly, using RNA sequencing (RNA-seq) and Illumina EPIC Array, we show that genome-wide gene expression and DNA methylation signatures are preserved upon cryopreservation, emphasizing the suitability  ...  We acknowledge excellent sequencing service and helpful discussions from the Genomics Core Facility (EMBL) for RNA-Seq and from Genomics Core facility (DKFZ) for EPIC Array DNA methylation service.  ... 
doi:10.1101/2020.04.01.018861 fatcat:c2spymxltjebtbjy3x5kvajx3u

Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2 [article]

Katherine Laiton-Donato, Carlos Franco-Munoz, Diego Alejandro Alvarez-Diaz, Hector Ruiz-Moreno, Jose Usme-Ciro, Diego Prada, Jhonnatan Reales, Sheryll Corchuelo, Maria Herrera-sepulveda, Julian Naizaque, Gerardo Santamaria, Jorge Rivera (+9 others)
2021 medRxiv   pre-print
Further studies in vitro biological assays and epidemiologic analysis will allow evaluating the public health impact of B.1.621 variant.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Data deposition SARS-CoV  ...  We thank Rotary International and Charlie Rut Castro for equipment's donation. Finally, we thank red RENATA and Universidad Industrial de Santander for the workstation bioinformatic support.  ... 
doi:10.1101/2021.05.08.21256619 fatcat:raredp7dtrdsbd6swl2r3bezce

Exploring bacteria diversity in commercialized table olive biofilms by metataxonomic and compositional data analysis

Antonio Benítez-Cabello, Verónica Romero-Gil, Eduardo Medina-Pradas, Antonio Garrido-Fernández, Francisco Noé Arroyo-López
2020 Scientific Reports  
From these, 41 OTUs with a proportion of sequences ≥ 0.01% were studied by compositional data analysis.  ...  Compositional data analysis allowed discriminating between lye treated and natural olive samples, as well as between olives packaged in glass, PET and plastic bags.  ...  The V3 and V4 region of the 16S ribosomal RNA gene was amplified 21 following the 16S rDNA Gene Metagenomic Sequencing Library Preparation Illumina protocol (Part #1504423 Rev. A).  ... 
doi:10.1038/s41598-020-68305-7 pmid:32647238 fatcat:zfhbpixcrbgplca5qpjmskhhiy

OUP accepted manuscript

2016 Nucleic Acids Research  
ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data and manual curations.  ...  ChimerSeq module is designed to archive the fusion candidates from deep sequencing data.  ...  ChimerSeq collected fusion transcripts identified by computational analysis of transcriptome sequencing data including RNA-Seq and EST sequences.  ... 
doi:10.1093/nar/gkw1083 pmid:27899563 pmcid:PMC5210563 fatcat:6sn2jqqdo5cuzhwkxvtk4tww6i

In situ substrate-formed biofilms using IDODS mimic supragingival tooth-formed biofilms

Inmaculada Tomás, Isabel Prada-López, Victor Quintas, Maria José Carreira, Áurea Simón-Soro, Alejandro Mira, Carlos Balsa-Castro
2018 Journal of Oral Microbiology  
In test 2, the microscopic analysis was repeated only on the SF-biofilm samples, and the volunteers were allowed to brush their teeth.  ...  In test 1, 15 volunteers wore two hemi-splints carrying six discs of human enamel, glass, and hydroxyapatite for 2 days, and were instructed to not perform any oral hygiene measure.  ...  Acknowledgments The authors declare that all other data supporting the findings of this study are available within the paper and its supplementary information files.  ... 
doi:10.1080/20002297.2018.1495975 pmid:30181819 pmcid:PMC6116702 fatcat:rlth7fho5vdbhgekkxdu3pznja

Pipeliner: A Nextflow-Based Framework for the Definition of Sequencing Data Processing Pipelines

Anthony Federico, Tanya Karagiannis, Kritika Karri, Dileep Kishore, Yusuke Koga, Joshua D. Campbell, Stefano Monti
2019 Frontiers in Genetics  
We have used Pipeliner to create several pipelines for sequencing data processing including bulk RNA-sequencing (RNA-seq), single-cell RNA-seq, as well as digital gene expression data.  ...  The Pipeliner framework provides an out-of-the-box solution for processing various types of sequencing data.  ...  Di Tommaso for his assistance with Nextflow-related inquiries and A. Gower for his advice for improving and testing Pipeliner.  ... 
doi:10.3389/fgene.2019.00614 pmid:31316552 pmcid:PMC6609566 fatcat:pu7zj263tncifknlxiip4dwdqy

Whole-Transcriptome Analysis in Peripheral Blood Mononuclear Cells from Patients with Lipid-Specific Oligoclonal IgM Band Characterization Reveals Two Circular RNAs and Two Linear RNAs as Biomarkers of Highly Active Disease

Leire Iparraguirre, Danel Olaverri, Telmo Blasco, Lucía Sepúlveda, Tamara Castillo-Triviño, Mercedes Espiño, Lucienne Costa-Frossard, Álvaro Prada, Luisa María Villar, David Otaegui, Maider Muñoz-Culla
2020 Biomedicines  
The biomarker potential of the candidates was evaluated by ROC curve analysis.  ...  Microarray (miRNA and snoRNA) and RNA-seq (circular and linear RNAs) were used to perform the profiling study in the discovery cohort and candidates were validated by RT-qPCR in the whole cohort.  ...  The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.  ... 
doi:10.3390/biomedicines8120540 pmid:33255923 fatcat:vlhvws5mmnd7nps6iachlswfcq

Metagenomic Analysis of Biocide-Treated Neotropical Oil Reservoir Water Unveils Microdiversity of Thermophile Tepidiphilus

Katherine Bedoya, Jhorman Niño, Julia Acero, Ronald Jaimes-Prada, Felipe Cabarcas, Juan F. Alzate
2021 Frontiers in Microbiology  
In the present work, high throughput sequencing techniques were applied to analyze the microbial community from the injected and produced water in a neotropical hyper-thermophile oil reservoir located  ...  Phylogenomic analysis of the injection water dominant Tepidiphilus positioned it as an independent branch outside T. succinatimandens and T. thermophilus lineage.  ...  cytidylyltransferase, and Superfamily II DNA RNA helicases.  ... 
doi:10.3389/fmicb.2021.741555 pmid:34790180 pmcid:PMC8591294 fatcat:3icjranonncyxjolptip37zhcu
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