Relevant bibliographies by topics / Genomics workflow

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers

Academic literature on the topic 'Genomics workflow'

Author: Grafiati
Published: 4 June 2021
Last updated: 1 February 2022

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Journal articles on the topic "Genomics workflow"

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John, Aji, Kathleen Muenzen, and Kristiina Ausmees. "Evaluation of serverless computing for scalable execution of a joint variant calling workflow." PLOS ONE 16, no. 7 (2021): e0254363. http://dx.doi.org/10.1371/journal.pone.0254363.

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Advances in whole-genome sequencing have greatly reduced the cost and time of obtaining raw genetic information, but the computational requirements of analysis remain a challenge. Serverless computing has emerged as an alternative to using dedicated compute resources, but its utility has not been widely evaluated for standardized genomic workflows. In this study, we define and execute a best-practice joint variant calling workflow using the SWEEP workflow management system. We present an analysis of performance and scalability, and discuss the utility of the serverless paradigm for executing w
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Diamond, Joel. "Genomics Within the Clinical Workflow." Oncology Times 40, no. 18 (2018): 13. http://dx.doi.org/10.1097/01.cot.0000546351.05658.8b.

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Carey, Vincent J., Marcel Ramos, Benjamin J. Stubbs, et al. "Global Alliance for Genomics and Health Meets Bioconductor: Toward Reproducible and Agile Cancer Genomics at Cloud Scale." JCO Clinical Cancer Informatics, no. 4 (September 2020): 472–79. http://dx.doi.org/10.1200/cci.19.00111.

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PURPOSE Institutional efforts toward the democratization of cloud-scale data and analysis methods for cancer genomics are proceeding rapidly. As part of this effort, we bridge two major bioinformatic initiatives: the Global Alliance for Genomics and Health (GA4GH) and Bioconductor. METHODS We describe in detail a use case in pancancer transcriptomics conducted by blending implementations of the GA4GH Workflow Execution Services and Tool Registry Service concepts with the Bioconductor curatedTCGAData and BiocOncoTK packages. RESULTS We carried out the analysis with a formally archived workflow
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Khvorykh, Gennady, Andrey Khrunin, Ivan Filippenkov, Vasily Stavchansky, Lyudmila Dergunova, and Svetlana Limborska. "A Workflow for Selection of Single Nucleotide Polymorphic Markers for Studying of Genetics of Ischemic Stroke Outcomes." Genes 12, no. 3 (2021): 328. http://dx.doi.org/10.3390/genes12030328.

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In this paper we propose a workflow for studying the genetic architecture of ischemic stroke outcomes. It develops further the candidate gene approach. The workflow is based on the animal model of brain ischemia, comparative genomics, human genomic variations, and algorithms of selection of tagging single nucleotide polymorphisms (tagSNPs) in genes which expression was changed after ischemic stroke. The workflow starts from a set of rat genes that changed their expression in response to brain ischemia and results in a set of tagSNPs, which represent other SNPs in the human genes analyzed and i
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Kulchak Rahm, Alanna, Nephi A. Walton, Lynn K. Feldman, et al. "User testing of a diagnostic decision support system with machine-assisted chart review to facilitate clinical genomic diagnosis." BMJ Health & Care Informatics 28, no. 1 (2021): e100331. http://dx.doi.org/10.1136/bmjhci-2021-100331.

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ObjectivesThere is a need in clinical genomics for systems that assist in clinical diagnosis, analysis of genomic information and periodic reanalysis of results, and can use information from the electronic health record to do so. Such systems should be built using the concepts of human-centred design, fit within clinical workflows and provide solutions to priority problems.MethodsWe adapted a commercially available diagnostic decision support system (DDSS) to use extracted findings from a patient record and combine them with genomic variant information in the DDSS interface. Three representati
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Ukmar, G., G. E. M. Melloni, L. Raddrizzani, et al. "PATRI, a Genomics Data Integration Tool for Biomarker Discovery." BioMed Research International 2018 (June 28, 2018): 1–13. http://dx.doi.org/10.1155/2018/2012078.

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The availability of genomic datasets in association with clinical, phenotypic, and drug sensitivity information represents an invaluable source for potential therapeutic applications, supporting the identification of new drug sensitivity biomarkers and pharmacological targets. Drug discovery and precision oncology can largely benefit from the integration of treatment molecular discriminants obtained from cell line models and clinical tumor samples; however this task demands comprehensive analysis approaches for the discovery of underlying data connections. Here we introduce PATRI (Platform for
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Silva, Tiago C., Antonio Colaprico, Catharina Olsen, et al. "TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages." F1000Research 5 (June 29, 2016): 1542. http://dx.doi.org/10.12688/f1000research.8923.1.

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Biotechnological advances in sequencing have led to an explosion of publicly available data via large international consortia such as The Cancer Genome Atlas (TCGA), The Encyclopedia of DNA Elements (ENCODE), and The NIH Roadmap Epigenomics Mapping Consortium (Roadmap). These projects have provided unprecedented opportunities to interrogate the epigenome of cultured cancer cell lines as well as normal and tumor tissues with high genomic resolution. The bioconductor project offers more than 1,000 open-source software and statistical packages to analyze high-throughput genomic data. However, mos
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Silva, Tiago C., Antonio Colaprico, Catharina Olsen, et al. "TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages." F1000Research 5 (December 28, 2016): 1542. http://dx.doi.org/10.12688/f1000research.8923.2.

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Biotechnological advances in sequencing have led to an explosion of publicly available data via large international consortia such as The Cancer Genome Atlas (TCGA), The Encyclopedia of DNA Elements (ENCODE), and The NIH Roadmap Epigenomics Mapping Consortium (Roadmap). These projects have provided unprecedented opportunities to interrogate the epigenome of cultured cancer cell lines as well as normal and tumor tissues with high genomic resolution. The Bioconductor project offers more than 1,000 open-source software and statistical packages to analyze high-throughput genomic data. However, mos
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Rossetto, Maurizio, Jia-Yee Samantha Yap, Jedda Lemmon, et al. "A conservation genomics workflow to guide practical management actions." Global Ecology and Conservation 26 (April 2021): e01492. http://dx.doi.org/10.1016/j.gecco.2021.e01492.

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Ahmed, Azza E., Phelelani T. Mpangase, Sumir Panji, et al. "Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience." AAS Open Research 1 (April 18, 2018): 9. http://dx.doi.org/10.12688/aasopenres.12847.1.

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The need for portable and reproducible genomics analysis pipelines is growing globally as well as in Africa, especially with the growth of collaborative projects like the Human Health and Heredity in Africa Consortium (H3Africa). The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for portable, reproducible pipelines adapted to heterogeneous compute environments, and for the nurturing of technical expertise in workflow languages and containerization technologies. To address this need, in 2016 H3ABioNet arranged its first Cloud Computing and Reproducible Workflows Ha
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Dissertations / Theses on the topic "Genomics workflow"

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Puthige, Ashwin Acharya. "Bioflow: A web based workflow management system for design and execution of genomics pipelines." Thesis, Virginia Tech, 2014. http://hdl.handle.net/10919/24809.

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The cost required for the process of sequencing genomes has decreased drastically in the last few years. The knowledge of full genomes has increased the pace of the advancements in the field of functional genomics. Computational genomics, which analyses these sequences, has seen a similar growth. The multitude of sequencing technologies has resulted in various formats for storing the sequences. This has resulted in the creation of many tools for DNA analysis. There are various tools for sorting, indexing, analyzing read groups and other tasks. The analysis of genomics often requires the creati
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Carrión, Collado Abel Antonio. "Management of generic and multi-platform workflows for exploiting heterogeneous environments on e-Science." Doctoral thesis, Universitat Politècnica de València, 2017. http://hdl.handle.net/10251/86179.

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Scientific Workflows (SWFs) are widely used to model applications in e-Science. In this programming model, scientific applications are described as a set of tasks that have dependencies among them. During the last decades, the execution of scientific workflows has been successfully performed in the available computing infrastructures (supercomputers, clusters and grids) using software programs called Workflow Management Systems (WMSs), which orchestrate the workload on top of these computing infrastructures. However, because each computing infrastructure has its own architecture and each scien
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Liu, Yang, Saad M. Khan, Juexin Wang, et al. "PGen: large-scale genomic variations analysis workflow and browser in SoyKB." BIOMED CENTRAL LTD, 2016. http://hdl.handle.net/10150/624651.

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Background: With the advances in next-generation sequencing (NGS) technology and significant reductions in sequencing costs, it is now possible to sequence large collections of germplasm in crops for detecting genome-scale genetic variations and to apply the knowledge towards improvements in traits. To efficiently facilitate large-scale NGS resequencing data analysis of genomic variations, we have developed " PGen", an integrated and optimized workflow using the Extreme Science and Engineering Discovery Environment (XSEDE) high-performance computing (HPC) virtual system, iPlant cloud data stor
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Couse, Madeline Hazel. "A bioinformatic workflow for analyzing whole genomes in rare Mendelian disease." Thesis, University of British Columbia, 2017. http://hdl.handle.net/2429/61332.

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The vast majority of the human genome (~98%) is non-coding. A symphony of non-coding sequences resides in the genome, interacting with genes and the environment to tune gene expression. Functional non-coding sequences include enhancers, silencers, promoters, non-coding RNA and insulators. Variation in these non-coding sequences can cause disease, yet clinical sequencing in patients with rare Mendelian disease currently focuses mostly on variants in the ~2% of the genome that codes for protein. Indeed, variants in protein-coding genes that can explain a phenotype are identified in less tha
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Schlaffner, Christoph Norbert. "Proteogenomics for personalised molecular profiling." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/275137.

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Technological advancements in mass spectrometry allowing quantification of almost complete proteomes make proteomics a key platform for generating unique functional molecular data. Furthermore, the integrative analysis of genomic and proteomic data, termed proteogenomics, has emerged as a new field revealing insights into gene expression regulation, cell signalling, and disease processes. However, the lack of software tools for high-throughput integration and unbiased modification and variant detection hinder efforts for large-scale proteogenomics studies. The main objectives of this work are
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Cantão, Mauricio Egidio. "Abordagem algébrica para seleção de clones ótimos em projetos genomas e metagenomas." Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/95/95131/tde-17092010-123112/.

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Devido à grande diversidade de microrganismos desconhecidos no meio ambiente, 99% deles não podem ser cultivados nos meios de cultura tradicionais dos laboratórios. Para isso, projetos metagenômicos são propostos para estudar comunidades microbianas presentes no meio ambiente, a partir de técnicas moleculares, em especial o seqüenciamento. Dessa forma, para os próximos anos é esperado um acúmulo de seqüências produzidas por esses projetos. As seqüências produzidas pelos projetos genomas e metagenomas apresentam vários desafios para o tratamento, armazenamento e análise, como exemplo: a busca d
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Oluwaseun, Ajayi Olabode. "An evaluation of galaxy and ruffus-scripting workflows system for DNA-seq analysis." University of the Western Cape, 2018. http://hdl.handle.net/11394/6765.

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>Magister Scientiae - MSc<br>Functional genomics determines the biological functions of genes on a global scale by using large volumes of data obtained through techniques including next-generation sequencing (NGS). The application of NGS in biomedical research is gaining in momentum, and with its adoption becoming more widespread, there is an increasing need for access to customizable computational workflows that can simplify, and offer access to, computer intensive analyses of genomic data. In this study, the Galaxy and Ruffus frameworks were designed and implemented with a view to addr
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Voegele, Catherine. "Development of an integrated Information Technology System for management of laboratory data and next-generation sequencing workflows within a cancer genomics research platform." Thesis, Lyon 1, 2015. http://www.theses.fr/2015LYO10095/document.

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L'objectif de mon travail de thèse était de développer des outils bio informatiques permettant d'améliorer la traditionnelle gestion de l'information scientifique au sein d'un grand centre de recherche et en particulier au sein d'une plateforme de génomique. Trois outils ont été développés: un cahier de laboratoire électronique, un système de gestion de l'information de laboratoire pour des applications de génomique dont le séquençage de nouvelle génération, ainsi qu'un système de gestion des échantillons pour de grandes bio-banques. Ce travail a été réalisé en étroite collaboration avec des b
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Weigl, Julia [Verfasser]. "Development of protocols and workflows for a fast gene synthesis and de novo synthesis of viral genomes : Entwicklung von Protokollen und Arbeitsabläufen für eine schnelle Gensynthese und de novo Synthese vitaler Genome / Julia Weigl." Hamburg : Staats- und Universitätsbibliothek Hamburg Carl von Ossietzky, 2018. http://d-nb.info/1223620972/34.

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Witty, Derick. "Implementation of a Laboratory Information Management System To Manage Genomic Samples." Thesis, 2013. http://hdl.handle.net/1805/3521.

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Indiana University-Purdue University Indianapolis (IUPUI)<br>A Laboratory Information Management Systems (LIMS) is designed to manage laboratory processes and data. It has the ability to extend the core functionality of the LIMS through configuration tools and add-on modules to support the implementation of complex laboratory workflows. The purpose of this project is to demonstrate how laboratory data and processes from a complex workflow can be implemented using a LIMS. Genomic samples have become an important part of the drug development process due to advances in molecular testing tec
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Book chapters on the topic "Genomics workflow"

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Díaz, David, Sergio Gálvez, Juan Falgueras, et al. "Intuitive Bioinformatics for Genomics Applications: Omega-Brigid Workflow Framework." In Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living. Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-642-02481-8_164.

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Strozzi, Francesco, Roel Janssen, Ricardo Wurmus, et al. "Scalable Workflows and Reproducible Data Analysis for Genomics." In Methods in Molecular Biology. Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9074-0_24.

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Contaldi, Felice, Elisa Cappetta, and Salvatore Esposito. "Practical Workflow from High-Throughput Genotyping to Genomic Estimated Breeding Values (GEBVs)." In Methods in Molecular Biology. Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-1201-9_9.

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Valadares, Andressa, Maria Emília Walter, and Tainá Raiol. "A Workflow for Predicting MicroRNAs Targets via Accessibility in Flavivirus Genomes." In Advances in Bioinformatics and Computational Biology. Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-030-01722-4_12.

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Ocaña, Kary A. C. S., Daniel de Oliveira, Eduardo Ogasawara, Alberto M. R. Dávila, Alexandre A. B. Lima, and Marta Mattoso. "SciPhy: A Cloud-Based Workflow for Phylogenetic Analysis of Drug Targets in Protozoan Genomes." In Advances in Bioinformatics and Computational Biology. Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-22825-4_9.

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"TCGA Workflow Diagrams." In Collaborative Genomics Projects: A Comprehensive Guide. Elsevier, 2016. http://dx.doi.org/10.1016/b978-0-12-802143-9.00019-1.

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Hall, David, John Miller, Jonathan Arnold, Krzysztof Kochut, Amit Sheth, and Michael Weise. "Using Workflow to Build an Information Management System for a Geographically Distributed Genome Sequencing Initiative." In Genomics of Plants and Fungi. CRC Press, 2003. http://dx.doi.org/10.1201/9780203912249.pt3.

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Zainal-Abidin, Rabiatul-Adawiah, and Zeti-Azura Mohamed-Hussein. "Computational Analysis of Rice Transcriptomic and Genomic Datasets in Search for SNPs Involved in Flavonoid Biosynthesis." In Recent Advances in Rice Research [Working Title]. IntechOpen, 2020. http://dx.doi.org/10.5772/intechopen.94876.

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This chapter describes the computational approach used in analyzing rice transcriptomics and genomics data to identify and annotate potential single nucleotide polymorphism (SNPs) as potential biomarker in the production of flavonoid. SNPs play a role in the accumulation of nutritional components (e.g. antioxidants), and flavonoid is one of them. However, the number of identified SNPs associated with flavonoid nutritional trait is still limited. We develop a knowledge-based bioinformatic workflow to search for specific SNPs and integration analysis on the SNPs and their co-expressed genes to investigate their influence on the gain/loss of functional genes that are involved in the production of flavonoids. Raw files obtained from the functional genomics studies can be analyzed in details to obtain a useful biological insight. Different tools, algorithms and databases are available to analyze the ontology, metabolic and pathway at the molecular level in order to observe the effects of gene and protein expression. The usage of different tools, algorithms and databases allows the integration, interpretation and the inference of analysis to provide better understanding of the biological meaning of the resutls. This chapter illustrates how to select and bring together several software to develop a specific bioinformatic workflow that processes and analyses omics data. The implementation of this bioinformatic workflow revealed the identification of potential flavonoid biosynthetic genes that can be used as guided-gene to screen the single nucleotide polymorphisms (SNPs) in the flavonoid biosynthetic genes from genome and transcriptomics data.
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Yang, Jitao. "Human Knowledge and Expertise Platform for Managing Genomics Projects." In Handbook of Research on the Role of Human Factors in IT Project Management. IGI Global, 2020. http://dx.doi.org/10.4018/978-1-7998-1279-1.ch009.

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Genomics has been used to more accurately support the realization of scientific research, personalized healthcare, and precision medicine. Professional knowledge and expertise are required to process the genomics project and laboratory workflows which include project enrollment, project and sample tracking, sample warehousing, nucleic acid extraction, library construction, concentration and peak map detection, pooling, sequencing, etc. Therefore, the digitizing management of projects and laboratory workflows is very important to support the handling of tens of thousands of samples in parallel. This chapter implements the human knowledge and expertise to a project and laboratory management platform, which can integrated manage the complex genomics projects, the laboratory workflows, the sequencing instruments, the analysis pipelines, and the genetic interpretation service. The platform can automate routine tasks, facilitate communication, optimize business procedures and workflows, process tens of thousands of samples parallelly, and increase the business efficiency.
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Ugur Sezerman, Osman, Ege Ulgen, Nogayhan Seymen, and Ilknur Melis Durasi. "Bioinformatics Workflows for Genomic Variant Discovery, Interpretation and Prioritization." In Bioinformatics Tools for Detection and Clinical Interpretation of Genomic Variations. IntechOpen, 2019. http://dx.doi.org/10.5772/intechopen.85524.

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Conference papers on the topic "Genomics workflow"

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Pellegrino, Renata, Michael Benway, Paulina Kocjan, et al. "Abstract 5353: High-throughput automation of the 10x Genomics® Chromium™ workflow for linked-read whole exome sequencing and a targeted lynch syndrome panel." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-5353.

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Pireddu, Luca, Simone Leo, and Gianluigi Zanetti. "MapReducing a genomic sequencing workflow." In the second international workshop. ACM Press, 2011. http://dx.doi.org/10.1145/1996092.1996106.

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Potamias, George, Lefteris Koumakis, Alexandros Kanterakis, et al. "Knowledge Discovery Scientific Workflows in Clinico-Genomics." In 19th IEEE International Conference on Tools with Artificial Intelligence(ICTAI 2007). IEEE, 2007. http://dx.doi.org/10.1109/ictai.2007.32.

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Kanwal, Sehrish, Andrew Lonie, and Richard O. Sinnott. "Digital reproducibility requirements of computational genomic workflows." In 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2017. http://dx.doi.org/10.1109/bibm.2017.8217887.

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Banerjee, Subho S., Arjun P. Athreya, Liudmila S. Mainzer, et al. "Efficient and Scalable Workflows for Genomic Analyses." In HPDC'16: The 25th International Symposium on High-Performance Parallel and Distributed Computing. ACM, 2016. http://dx.doi.org/10.1145/2912152.2912156.

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Yang-Turner, Fan, Lawrence Gripper, Jeremy Swann, et al. "An Open-Source Azure Solution for Scalable Genomics Workflows." In 2018 IEEE World Congress on Services (SERVICES). IEEE, 2018. http://dx.doi.org/10.1109/services.2018.00033.

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Rodriguez, Benjamin, Hok-Hei Tam, David Frankhouser, et al. "A scalable, flexible workflow for MethylCap-seq data analysis." In 2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS). IEEE, 2011. http://dx.doi.org/10.1109/gensips.2011.6169426.

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Terra, Rafael, Micaella Coelho, Lucas Cruz, et al. "Gerência e Análises de Workflows aplicados a Redes Filogenéticas de Genomas de Dengue no Brasil." In Brazilian e-Science Workshop. Sociedade Brasileira de Computação, 2021. http://dx.doi.org/10.5753/bresci.2021.15788.

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Processos evolutivos e dispersão de genomas de Dengue no Brasil são relevantes na direção do impacto e vigilância endemo-epidêmico e social de arboviroses emergentes. Árvores e redes filogenéticas permitem exibir eventos evolutivos e reticulados em vírus originados pela alta diversidade e taxa de mutação de recombinação homóloga frequente. Apresentamos um workflow científico paralelo e distribuído para redes filogenéticas desenhado para trabalhar com a diversidade de ferramentas e recursos em experimentos da biologia computacional e acoplados a ambientes de computação de alto desempenho. Apres
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Fowler, Jerry, F. Anthony San Lucas, Smruthy Sivakumar, Aditya Deshpande, Humam Kadara, and Paul A. Scheet. "Abstract 2594: Optimizing the replication of cancer genomics workflows: case studies." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-2594.

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Choudhury, Olivia, Nicholas L. Hazekamp, Douglas Thain, and Scott Emrich. "Accelerating Comparative Genomics Workflows in a Distributed Environment with Optimized Data Partitioning." In 2014 14th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid). IEEE, 2014. http://dx.doi.org/10.1109/ccgrid.2014.79.

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