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DNA methylation data by sequencing: experimental approaches and recommendations for tools and pipelines for data analysis

Ieva Rauluseviciute, Finn Drabløs, Morten Beck Rye
2019 Clinical Epigenetics  
present and discuss the most pronounced computational pipelines that can be used to analyze such data.  ...  Increasing numbers of DNA methylation sequencing datasets from human genome are produced using various platforms-from methylated DNA precipitation to the whole genome bisulfite sequencing.  ...  Acknowledgements We want to thank the author of msgbsR Dr. Jimmy Breen and authors of Bicycle Dr. Osvaldo Graña Castro and Dr.  ... 
doi:10.1186/s13148-019-0795-x pmid:31831061 pmcid:PMC6909609 fatcat:khl5mza45nfqhnlx7ozu7qguua

wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data

Marius Wöste, Elsa Leitão, Sandra Laurentino, Bernhard Horsthemke, Sven Rahmann, Christopher Schröder
2020 BMC Bioinformatics  
We developed wg-blimp (whole genome bisulfite sequencing methylation analysis pipeline) as an end-to-end pipeline to ease whole genome bisulfite sequencing data analysis.  ...  Analysing whole genome bisulfite sequencing datasets is a data-intensive task that requires comprehensive and reproducible workflows to generate valid results.  ...  As a result, data-intensive whole genome bisulfite sequencing (WGBS) is required to properly identify all CpG methylation levels.  ... 
doi:10.1186/s12859-020-3470-5 pmid:32357829 fatcat:md67spuwangtfpv7ywyxmyimqq

Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements

Ilektra-Chara Giassa, Panagiotis Alexiou
2021 Biology  
analysis through bisulfite sequencing data.  ...  Advancements in bioinformatics and machine learning approaches are increasingly contributing to the analysis of the regulation mechanisms.  ...  -C.G. and P.A. would like to thank Eva Klimentová for her help with the initial literature research for the bioinformatics tools. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/biology10090896 pmid:34571773 pmcid:PMC8465862 fatcat:5a5osyvzfjhc3jogue42lgrtyy

MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data

Yadollah Shahryary, Rashmi R. Hazarika, Frank Johannes
2020 BMC Genomics  
To offer an efficient analysis solution, we present MethylStar, a fast, stable and flexible pre-processing pipeline for WGBS data.  ...  Whole-Genome Bisulfite Sequencing (WGBS) is a Next Generation Sequencing (NGS) technique for measuring DNA methylation at base resolution.  ...  Acknowledgements We thank Markus List for his suggestion to use a docker container for version control. Authors' contributions FJ, RRH and YS conceptualized the method.  ... 
doi:10.1186/s12864-020-06886-3 pmid:32660416 fatcat:hgs64riav5czfljzdrgpc5zzru

Challenges and Perspectives in the Epigenetics of Climate Change-Induced Forests Decline

Isabel García-García, Belén Méndez-Cea, David Martín-Gálvez, José Ignacio Seco, Francisco Javier Gallego, Juan Carlos Linares
2022 Frontiers in Plant Science  
Huge genome sizes, absence of reference genomes and annotation, and having to analyze huge amounts of data are among these difficulties, which limit the current ability to understand how climate change  ...  As sessile organisms with long generation times, their adaptation to a local changing environment may rely on epigenetic modifications when allele frequencies are not able to shift fast enough.  ...  BIOINFORMATIC TOOLS Bioinformatic pipelines for the analysis of DNA methylation data obtained after bisulfite treatments consist of four main steps: quality check and read trimming, read mapping, methylation  ... 
doi:10.3389/fpls.2021.797958 pmid:35058957 pmcid:PMC8764141 fatcat:kn2vheackzd4tizipbjmar775e

MethylStar: A fast and robust pipeline for high-throughput analysis of bulk or single-cell WGBS data [article]

Yadollah Shahryary Dizaji, Rashmi R. Hazarika, Frank Johannes
2019 bioRxiv   pre-print
To offer an efficient analysis solution for such emerging data, we have developed MethylStar, a fast, stable and flexible computational pipeline.  ...  Summary: Whole-Genome Bisulfite Sequencing (WGBS) is a Next Generation Sequencing (NGS) technique for measuring DNA methylation at base resolution.  ...  pipeline for WGBS data.  ... 
doi:10.1101/2019.12.20.884536 fatcat:g4qkppobabgitdwrbisdljhxvm

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  
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  ...  However, only a few studies have applied WGBS to allopolyploids, which might be due to lack of genomic resources combined with a burdensome data analysis process.  ...  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

msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data

Heesun Kim, Mikang Sim, Nayoung Park, Kisang Kwon, Junyoung Kim, Jaebum Kim
2022
Whole-genome bisulfite sequencing (WGBS) is a powerful method for studying cytosine methylation in a whole genome.  ...  Here we present msPIPE, a pipeline for DNA methylation analyses with WGBS data seamlessly connecting all the required tasks ranging from data pre-processing to multiple downstream DNA methylation analyses  ...  To alleviate these difficulties, several pipelines have been developed to analyze methylation sequencing data [27, [29] [30] [31] [32] .  ... 
doi:10.1186/s12859-022-04925-2 pmid:36123620 pmcid:PMC9487059 fatcat:haqmqk2yenh7lfsajiglnyoixa

Metaproteogenomic Profiling of Chemosynthetic Microbial Biofilms Reveals Metabolic Flexibility During Colonization of a Shallow-Water Gas Vent

Sushmita Patwardhan, Francesco Smedile, Donato Giovannelli, Costantino Vetriani
2021 Frontiers in Microbiology  
In this study, we took a metaproteogenomic approach to identify the metabolic potential and in situ expression of central metabolic pathways at two stages of biofilm maturation.  ...  Tor Caldara is a shallow-water gas vent located in the Mediterranean Sea, with active venting of CO2 and H2S.  ...  ACKNOWLEDGMENTS We thank the crew of the R/V Antares for their support during the sampling operations, and Satyajit Rajapurkar for help and guidance with the bioinformatics analyses.  ... 
doi:10.3389/fmicb.2021.638300 pmid:33889140 pmcid:PMC8056087 fatcat:yy6s4yqu2nbgpag4anp3mftxgy

33rd Annual Meeting & Pre-Conference Programs of the Society for Immunotherapy of Cancer (SITC 2018)

2018 Journal for ImmunoTherapy of Cancer  
Special thanks also to J Jabbari and the Australian Genome Research Facility for making the single cell sequencing possible.  ...  the many families who contribute to kConFab. kConFab is supported by a grant from NBCF, and previously NHMRC, the Queensland Cancer Fund, the Cancer Councils of New South Wales, Victoria, Tasmania and  ...  An integrative analytic pipeline was used to analyze gene expression data including pathway analysis and deconvolution.  ... 
doi:10.1186/s40425-018-0423-x pmid:30400822 pmcid:PMC6220479 fatcat:vnbdtqcvqrfdtlsgirjycjot6e

Abstracts

2021 Basic & Clinical Pharmacology & Toxicology  
Conclusion: Emergency nursing model can play a significant role in emergency of critically ill patients.  ...  Objective: The study was to investigate the application of emergency nursing model in emergency treatment in critically ill patients.  ...  Sequencing data were subjected to bioinformatics analysis using SOAPfuse algorithm. A MDA-MB-231 specific fusion gene was uncovered and its function in breast cancer cells progression was identified.  ... 
doi:10.1111/bcpt.13588 pmid:34041856 fatcat:wobg4mjgunfilgvzqsj5l4an7m

Temperature as a predictor of fouling and diarrhea in slaughter pigs

Dan Børge Jensen, Anders Ringgaard Kristensen
2016 Livestock Science  
The day is organized with poster walks and a series of oral presentations and is a great opportunity to practice your research communication skills.  ...  We strive to have a friendly and collaborative environment where you can receive feedback on your research projects from fellow PhD students and supervisors from a wide range of scientific areas.  ...  Using Reduced Representation Bisulfite Sequencing, we aim to analyze the DNA methylation pattern of pure mesenchymal stem cell populations, to determine if the different ART procedures alter the epigenetic  ... 
doi:10.1016/j.livsci.2015.11.007 fatcat:ltydg4mewrbezjydijjhyfw4uu

9th World Congress on Developmental Origins of Health and Disease

2015 Journal of Developmental Origins of Health and Disease  
to their growth.  ...  A research from the references of the selected studies was added.  ...  Data were analyzed by Studentʼs t-test.  ... 
doi:10.1017/s2040174415007801 fatcat:dug7cc75cjfrvl7vst6sn2f27a

Genome-wide Prediction of Regulators Shaping Chromatin State and Gene Expression

Anne Ilse Kraemer
2022
adaptations of cells, tissues and organs to internal and external perturbations.  ...  Epigenetic mechanisms leading to changes in chromatin structure, accessibility for recruitment of transcriptional complexes, and interaction of enhancers and promoters all contribute to acute and chronic  ...  Our algorithm runs as a fully automated pipeline on a dedicated web-server and is designed to process raw data coming directly from the sequencing facilities.  ... 
doi:10.5451/unibas-ep88532 fatcat:n6i6a4jbsffmpoydn723zpwsh4

Endogenous retroviruses drive transcriptional innovation in human cancer

Babaian Artem
2019
To address this hypothesis, I developed a computational tool called 'LIONS' to analyze RNA-sequencing data for TE-initiated transcripts.  ...  data.  ...  The objective of Chapter 2 was to develop a bioinformatic tool to detect and quantify TEderived promoters genome wide.  ... 
doi:10.14288/1.0380699 fatcat:6oqne7n4sjb57gdsgpiw2tb4de