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CINECA Framework and APIs for executing federated genomics analyses D4.2

Alvaro Gonzalez, Shubham Kapoor, Kirill Tsukanov
2020 Zenodo  
The chosen framework supports different computing environments, which is a requirement for true federated analysis.  ...  In this deliverable, we gathered the technical requirements based on these use case descriptions and wrote a short design document which explains the requirements and lists the different options for a  ...  Deployment Scenarios for Federated Genomics Analysis 3.3.1. CWL and GA4GH compatible ELIXIR Cloud APIs D4.2 Framework and APIs for executing federated genomics analyses CINECA 3.  ... 
doi:10.5281/zenodo.4609356 fatcat:ax4pdl4ztrdo5adoz4gxguod3q

Gigwa—Genotype investigator for genome-wide analyses

Guilhem Sempéré, Florian Philippe, Alexis Dereeper, Manuel Ruiz, Gautier Sarah, Pierre Larmande
2016 GigaScience  
Findings: Dedicated to 'whole-genome assembly-free' treatments, the Colib'read tools suite uses optimized algorithms for various analyses of NGS datasets, such as variant calling or read set comparisons  ...  Based on the use of a de Bruijn graph and bloom filter, such analyses can be performed in a few hours, using small amounts of memory.  ...  Hence, LORDEC fulfills a need for preprocessing the read data before further analyses can extract biological information from it, as illustrated by the application to genome assembly described below.  ... 
doi:10.1186/s13742-016-0131-8 pmid:27267926 pmcid:PMC4897896 fatcat:2h4hdmtqongejnaky7et5pfafa

A Framework to Analyse and Interpret Mouse Functional Genome by Prioritizing High Impact SNPs [article]

Ahmed Arslan
2020 bioRxiv   pre-print
The essential understanding of disease pathogenesis and enabling genetic findings to be used for developing new therapeutics, is missing in the identifications of genomic loci through whole genome association  ...  By doing so, the method limits data to human interpretation level by prioritizing SNPs that have the potential to mediate a biological phenotype.  ...  DISCUSSION We provided a computational pipeline with two data analyses examples to highlight the importance of linking big SNPs data to biological features in order to interpret the potential consequences  ... 
doi:10.1101/2020.12.18.423378 fatcat:bnlfxcoydnd6xd35z2speo2s7u

Rank-based Bayesian variable selection for genome-wide transcriptomic analyses [article]

Emilie Eliseussen, Thomas Fleischer, Valeria Vitelli
2022 arXiv   pre-print
We use the novel approach to analyse genome-wide RNAseq gene expression data from ovarian cancer patients: several genes that affect cancer development are correctly detected in a completely unsupervised  ...  fashion, showing the usefulness of the method in the context of signature discovery for cancer genomics.  ...  Converting continuous data to rankings and then performing rank-based analyses is a practice that has gained much popularity in statistical genomics [10] .  ... 
arXiv:2107.05072v2 fatcat:3vjza7g7rfdlvik3nqqb5y3fm4

Genome-wide analyses for personality traits identify six genomic loci and show correlations with psychiatric disorders

Min-Tzu Lo, David A Hinds, Joyce Y Tung, Carol Franz, Chun-Chieh Fan, Yunpeng Wang, Olav B Smeland, Andrew Schork, Dominic Holland, Karolina Kauppi, Nilotpal Sanyal, Valentina Escott-Price (+10 others)
2016 Nature Genetics  
Genomes Project reference data.  ...  As part of 23andMe standard practice, individuals whose analyses failed repeatedly were contacted and asked to provide a new sample. 23andMe participant genotype data were imputed using the 1000 Genomes  ...  (dhinds@23andme.com) for more information and to apply for data access. All other data reported in the paper are included in the paper and Supplementary Materials.  ... 
doi:10.1038/ng.3736 pmid:27918536 pmcid:PMC5278898 fatcat:btis7dt32vazzbxmvxih2whea4

Comparative analyses of plastid genomes from fourteen Cornales species: inferences for phylogenetic relationships and genome evolution

Chao-Nan Fu, Hong-Tao Li, Richard Milne, Ting Zhang, Peng-Fei Ma, Jing Yang, De-Zhu Li, Lian-Ming Gao
2017 BMC Genomics  
L-M 2017, 'Comparative analyses of plastid genomes from fourteen Cornales species: inferences for phylogenetic relationships and genome evolution'  ...  Acknowledgements We are grateful to Jun-Bo Yang, Xiang-Qin Yu, Jian-Jun Jin, Gang Yao and Zhi-Rong Zhang for their help with data analysis and laboratory work. We also thank Dr.  ...  Availability of data and materials Sequence data that support the findings of this study have been deposited in GenBank (accession numbers were provided in Table 1 ).  ... 
doi:10.1186/s12864-017-4319-9 pmid:29216844 pmcid:PMC5721659 fatcat:vbxd5iz3gvhgjdcwd7e4t7ijo4

A genome-wide view of mutation rate co-variation using multivariate analyses

Guruprasad Ananda, Francesca Chiaromonte, Kateryna D Makova
2011 Genome Biology  
The software tools developed for our analyses are available through Galaxy, an open-source genomics portal, to facilitate the use of multivariate techniques in future large-scale genomics studies.  ...  , hindering a deeper understanding of mutagenesis and genome dynamics.  ...  Our thanks are also due to the Genome Center at Washington University School of Medicine in St Louis, and the Broad Institute at MIT and Harvard for making available the marmoset and guinea pig genome  ... 
doi:10.1186/gb-2011-12-3-r27 pmid:21426544 pmcid:PMC3129677 fatcat:dk7u7p6a6zaztmcgw6w3mqbg74

GenPipes: an open-source framework for distributed and scalable genomic analyses

Mathieu Bourgey, Rola Dali, Robert Eveleigh, Kuang Chung Chen, Louis Letourneau, Joel Fillon, Marc Michaud, Maxime Caron, Johanna Sandoval, Francois Lefebvre, Gary Leveque, Eloi Mercier (+11 others)
2019 GigaScience  
With the decreasing cost of sequencing and the rapid developments in genomics technologies and protocols, the need for validated bioinformatics software that enables efficient large-scale data processing  ...  Acknowledgements Data analyses were enabled by compute and storage resources provided by Compute Canada and Calcul Qu ébec.  ...  We would also like to acknowledge Romain Gregoire and Tushar Dubey for their contribution to the code and Patricia Goerner-Potvin for her help in planning the report content.  ... 
doi:10.1093/gigascience/giz037 pmid:31185495 pmcid:PMC6559338 fatcat:rqn3brcaazajrhmm2boqynaaee

Importance of genetic drift during Pleistocene divergence as revealed by analyses of genomic variation

L. LACEY KNOWLES, CORINNE L. RICHARDS
2005 Molecular Ecology  
The genomic analyses indicate that drift-induced divergence, despite the lack of long-standing geographic barriers, has significantly contributed to species divergence during the Pleistocene.  ...  Here we present analyses of amplified fragment length polymorphisms (AFLPs) in the montane grasshopper Melanoplus oregonensis to assess the evolutionary significance of past demographic events and associated  ...  The research was funded by a National Science Foundation grant (DEB-04-47224) and a grant from the University of Michigan (Office of the Vice President for Research) to L.L.K.  ... 
doi:10.1111/j.1365-294x.2005.02711.x pmid:16262856 fatcat:ykf7bl6tfrg4pnn2axcqz7th34

Statistical and Computational Challenges in Whole Genome Prediction and Genome-Wide Association Analyses for Plant and Animal Breeding

Robert J. Tempelman
2015 Journal of Agricultural Biological and Environmental Statistics  
Whole genome prediction (WGP) modeling and genome-wide association (GWA) analyses are big data issues in agricultural quantitative genetics.  ...  We focus primarily on mixed model and hierarchical Bayesian analyses which have been most commonly pursued by animal and plant breeders for WGP thus far.  ...  large scale BLUP-based genetic/genomic evaluations (Fragomeni et al. 2015 ) within a GBLUP modeling framework.  ... 
doi:10.1007/s13253-015-0225-2 fatcat:pcqlugugdfd3tlfmwsrf35775u

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses

M. J. Fullwood, C.-L. Wei, E. T. Liu, Y. Ruan
2009 Genome Research  
With its versatile and powerful nature for DNA analysis, the PET sequencing strategy has a bright future ahead.  ...  PET protocols have been developed for the analyses of transcriptomes, transcription factor binding sites, epigenetic sites such as histone modification sites, and genome structures.  ...  Acknowledgments The authors are supported by A*STAR of Singapore. In addition, M.J.F. is supported by A*STAR National Science Scholarships. Y.R and C.  ... 
doi:10.1101/gr.074906.107 pmid:19339662 pmcid:PMC3807531 fatcat:7dnsrn5kjzgr3jk63byne6ng64

Project MinE: study design and pilot analyses of a large-scale whole-genome sequencing study in amyotrophic lateral sclerosis

2018 European Journal of Human Genetics  
We use the whole-genome sequence data to explore the implications of poor geographical matching of cases and controls in a sequence-based disease study and to investigate how ancestry-matched, externally  ...  We have therefore begun Project MinE, an international collaboration that seeks to analyze whole-genome sequence data of at least 15 000 ALS patients and 7500 controls.  ...  Acknowledgements Research leading to these results has received funding from the European Community's Health Seventh Framework Programme (FP7/2007(FP7/ -2013  ... 
doi:10.1038/s41431-018-0177-4 pmid:29955173 pmcid:PMC6138692 fatcat:bc3aaaoty5bincswyye3pzk7ha

SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations

Alexis Dereeper, Felix Homa, Gwendoline Andres, Guilhem Sempere, Gautier Sarah, Yann Hueber, Jean-François Dufayard, Manuel Ruiz
2015 Nucleic Acids Research  
a reliable genotyping data matrix for further analyses.  ...  Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3  ...  We are grateful to people that interact regularly for the improvements of the system.  ... 
doi:10.1093/nar/gkv351 pmid:26040700 pmcid:PMC4489301 fatcat:bwzcwxw53jgjbfqykr7rvgsf7m

Predictive Genomic Analyses Inform the Basis for Vitamin Metabolism and Provisioning in Bacteria-Arthropod Endosymbioses

Laura R. Serbus, Brian Rodriguez Garcia, Zinat Sharmin, A. J. M. Zehadee Momtaz, Steen Christensen
2017 G3: Genes, Genomes, Genetics  
The requirement of vitamins for core metabolic processes creates a unique set of pressures for arthropods subsisting on nutrient-limited diets.  ...  Adaptation of this workflow to analysis of other organisms and metabolic pathways will provide new routes for considering the molecular basis for symbiosis on a comprehensive scale.  ...  In this age of "big data," discussion of consensus analytical formats will facilitate broader molecular understanding of host-microbe interactions.  ... 
doi:10.1534/g3.117.042184 pmid:28455417 pmcid:PMC5473766 fatcat:2zgx7am52fd5nbcjieee3ud72q

Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni

Simone Hoegg, Jeffrey L Boore, Jennifer V Kuehl, Axel Meyer
2007 BMC Genomics  
Comparative analyses with data from other teleost fish such as zebrafish, two species of pufferfish, stickleback and medaka were performed.  ...  Since this diversity could be based on regulatory changes, we chose to study the coding as well as putative regulatory regions of their Hox clusters within a comparative genomic framework.  ...  Department of Energy Joint Genome Institute.  ... 
doi:10.1186/1471-2164-8-317 pmid:17845724 pmcid:PMC2080641 fatcat:4orekinl2nhq7augbgothx5h64
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