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Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv

Farah Zaib Khan, Stian Soiland-Reyes, Richard O. Sinnott, Andrew Lonie, Carole Goble, Michael R. Crusoe
2018 Zenodo  
We demonstrate the utility of this approach through a practical implementation of CWLProv and evaluation using real-life genomic workflows developed by independent groups.  ...  Computationally driven data-intensive experiments using workflows enable Automation, Scaling, Adaption and Provenance support (ASAP).  ...  We would also like to thank Brad Chapman, Christopher Ball and Lon Blauvelt for the work ows used in the evaluation and their prompt replies to our enquiries.  ... 
doi:10.5281/zenodo.1966881 fatcat:gnpjnqu6pzdtfe7d4nzvi2r44a

Analysis of fungal genomes reveals commonalities of intron gain or loss and functions in intron-poor species

Chun Shen Lim, Brooke N Weinstein, Scott W Roy, Chris M Brown, Aida Ouangraoua
2021 Molecular biology and evolution  
Here we have used recently available fungal genomes to address a variety of questions related to intron evolution.  ...  Previous evolutionary reconstructions have concluded that early eukaryotic ancestors including both the last common ancestor of eukaryotes and of all fungi had intron-rich genomes.  ...  MATERIALS AND METHODS Genome sequences and annotations We retrieved 633 fungal genomes (FASTA and GTF files) from the Ensembl Fungi release 34 (Zerbino et al. 2018 ).  ... 
doi:10.1093/molbev/msab094 pmid:33772558 pmcid:PMC8476143 fatcat:jrgx5ozej5c6bo3e5qsmqzgcp4

EMBnet.journal 19 Suppl. A

EMBnet Journal
2013 EMBnet journal  
Leif Andersson: How domestic animal genomics can teach human medicine and medicine and evolutionary biology "down stream " bioinformatics analysis in order to meet the demands of the scientific community  ...  Michele Morgante: Structural variation and the plant pan genomes Infectious Diseases. identification from high-throughput sequencing data by joint Bayesian family calling. arrangement, DNA Methylation  ...  Oversight of the MAVEN project is provided by Genome Prairie and Dr. Reno Pontarollo.  ... 
doi:10.14806/ej.19.a.689 fatcat:2xs4bsifarfipopojjerizk3ce

Rapport d'activités IFB 2019-2020 [article]

Claudine Médigue, Suzanne Lauriou, Angela Saenz, Jacques Van Helden, IFB Teams
2021 Zenodo  
genomic surveillance.  ...  data-producing infrastructures) from 16 research organizations and 160 persons, totaling 40 FTE of involvement in the 4 work packages and 5 thematic implementation studies.  ...  IFB is involved in several work packages of the project: expert network, training, research data management toolkit, use cases, and demonstrators.  ... 
doi:10.5281/zenodo.5324333 fatcat:py5xp6q7ungkdevdqx25zxfwmq

Tests of Robustness in Peer Review

Jeremy Leipzig, Jane Greenberg, Gail Rosen, Xiaohua; Hu, Karthik Ram, Erjia Yan
2021 Zenodo  
Three high-impact genomics publications with open data, but no source code, were selected, refactored, and distributed to active study participants who acted as quasi-e [...]  ...  Purpose: The purpose of this dissertation is to investigate the feasibility of using tests of robustness in peer review.  ...  Acknowledgments I am deeply indebted to my wife Mary Ellen McCarty for her support and sacrifices during this long journey. My mother Pat Ward was also a great help to me.  ... 
doi:10.5281/zenodo.6403281 fatcat:q4pq3fnchzat7jvzl2lnhpyopi

PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks

Jianan Lin, Yuping Zhang, Wayne N. Frankel, Zhengqing Ouyang, Dina Schneidman-Duhovny
2019 PLoS Computational Biology  
In this study, we propose the Protein-RNA Association Strength (PRAS), which integrates the intensities and positions of the binding peaks of RBPs for functional mRNA targets prediction.  ...  We illustrate the superiority of PRAS over existing approaches on predicting the functional targets of two related but divergent CELF (CUGBP, ELAV-like factor) RBPs in mouse brain and muscle.  ...  To reformat the annotation file, PRAS takes use of gtfToGenePred, a toolkit from the UCSC Genome Browser [36] .  ... 
doi:10.1371/journal.pcbi.1007227 pmid:31425505 pmcid:PMC6716675 fatcat:evvagihknvfnnfddpsvh6vf2ii

Expanding the flexibility of genome editing approaches for population control of the malaria mosquito

Nace Kranjc, Andrea Crisanti, Tony Nolan
Discovery and adaptation of CRISPR-Cas systems for genome editing have allowed us to gain an efficient and yet simple tool for genetic manipulation in various fields of molecular biology and biotechnology  ...  genome Anopheles gambiae.  ...  Acknowledgements Acknowledgments: We would like to thank Alistair Miles for sharing the code for plotting transcripts with us and to Silke Fuchs and John Mumford for their comments.  ... 
doi:10.25560/96597 fatcat:hgc4fqjovncwfl2rwt7xq7vvnq

The developemnt of computational approaches for systems genetics and alternative polyadenylation studies and their application in studying genetic predisposition to alcohol related phenotypes [article]

Ryan Lusk
Richard Radcliffe for providing your expertise in genetics and also for the thoughtful and engaging questions posed to me during my committee meetings. And finally thank you to Dr. Peter Anderson.  ...  Boris Tabakoff for lending your expertise on alcohol and the genetics of alcohol and acting as a "grandmentor" to me during my PhD.  ...  Beyond science, and as anyone who has collaborated with Laura can attest, she is a joy to work with.  ... 
doi:10.25677/qz8w-5332 fatcat:vvrl7cuhejbofk4a7suf4z35p4

Algorithms and tools for the analysis of high throughput DNA sequencing data

Marcel Martin, Technische Universität Dortmund, Technische Universität Dortmund
e easy-to-use cutadapt tool is introduced. It contains additional features that make pre-processing of adapter-contaminated reads simple, and is in use by many other researchers.  ...  We show how to use only linear space while still keeping track of all information necessary to correctly locate and remove adapter sequences.  ...  A few publications on flowgrambased alignment already exist, but none clearly separates the two processes of sequence editing and flowgram under-and overcalling.  ... 
doi:10.17877/de290r-439 fatcat:iqmxipdcdrhodf7ei5vumxm3ci

A Single-Cell Immune Map of Normal and Cancerous Breast Reveals an Expansion of Phenotypic States Driven by the Tumor Microenvironment

Ambrose James Carr
This dissertation describes an experiment comprising scRNA-seq of over 47,000 immune cells collected from primary breast carcinomas, matched normal breast tissue, peripheral blood, and using these computational  ...  It combines SEQC with a clustering and normalization method, BISCUIT, and approaches to examine phenotypic diversity and gene variation.  ...  To address this, we constructed a custom annotation by starting with the current GENCODE genome and GTF file and removing all feature annotations that are not theoretically detectable by InDrop (Figure  ... 
doi:10.7916/d88d1c85 fatcat:bdnpxfqpcnfc3b3xpcqzkrwjxy