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A (fire)cloud-based DNA methylation data preprocessing and quality control platform

Divy Kangeyan, Andrew Dunford, Sowmya Iyer, Chip Stewart, Megan Hanna, Gad Getz, Martin J. Aryee
2019 BMC Bioinformatics  
Results: We present a set of preprocessing pipelines for bisulfite sequencing DNA methylation data that include a new R/Bioconductor package, scmeth, for a series of efficient QC analyses of large datasets  ...  Bisulfite sequencing allows base-pair resolution profiling of DNA methylation and has recently been adapted for use in single-cells.  ...  Availability of data and materials Detailed usage instructions and all code is available at http://aryee.mgh.  ... 
doi:10.1186/s12859-019-2750-4 fatcat:thscp52dmfdbnlv6mb36xcmz2a

EMBnet.journal 19 Suppl. A

EMBnet Journal
2013 EMBnet journal  
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  ...  Ivo Gut: High-Throughput DNA Analysis Posters&Beers * Carine Poussin: Translational Systems Biology Understanding the limits of Animals Models as Predictors of Human Biology. transcriptomics using the  ...  Acknowledgements This work was supported by the Cloud Software and D2I Programs of the Finnish Strategic Centre for Science, Technology and Innovation TIVIT and by the Sardinian (Italy) Regional Grant  ... 
doi:10.14806/ej.19.a.689 fatcat:2xs4bsifarfipopojjerizk3ce

Evaluating the Consistency of Gene Methylation in Liver Cancer Using Bisulfite Sequencing Data

Xubin Zheng, Qiong Wu, Haonan Wu, Kwong-Sak Leung, Man-Hon Wong, Xueyan Liu, Lixin Cheng
2021 Frontiers in Cell and Developmental Biology  
Bisulfite sequencing is considered as the gold standard approach for measuring DNA methylation, which acts as a pivotal part in regulating a variety of biological processes without changes in DNA sequences  ...  Next, we discussed the principles and compared different methods for alignment, quality assessment, methylation level scoring, and differentially methylated region identification.  ...  A (fire)cloud-based platform proposed in 2019 by Kangeyan et al. (2019) involved a lot of metrics for quality assessment including Read metrics, CpG Coverage, M-bias, Downsampling saturation curve, CpG  ... 
doi:10.3389/fcell.2021.671302 pmid:33996828 pmcid:PMC8116545 fatcat:v3gqs77lnrb4taabrfiwawtcoq

In Search of Big Medical Data Integration Solutions -A Comprehensive Survey

Houssein Dhayne, Rafiqul Haque, Rima Kilany, Yehia Taher
2019 IEEE Access  
The data-intensive industries have been experiencing a wide variety of challenges in terms of processing, managing, and analysis of data.  ...  Data integration is critically important within the healthcare sector because it enriches data, enhances its value, and more importantly paves a solid foundation for highly efficient and effective healthcare  ...  statistical learning methods make decisions based on a weighted sum of rule firings.  ... 
doi:10.1109/access.2019.2927491 fatcat:6ooixehrznfdnbwghzfeds3mky

Common dysregulation network in the human prefrontal cortex underlies two neurodegenerative diseases

M. Narayanan, J. L. Huynh, K. Wang, X. Yang, S. Yoo, J. McElwee, B. Zhang, C. Zhang, J. R. Lamb, T. Xie, C. Suver, C. Molony (+8 others)
2014 Molecular Systems Biology  
This subnetwork revealed a surprising dichotomy of gained/lost correlations among two inter-connected processes, chromatin organization and neural differentiation, and included DNA methyltransferases,  ...  DNMT1 and DNMT3A, of which we predicted the former but not latter as a key regulator.  ...  Research Program of the NIH (specifically NIAID and NHLBI institutes for MN and AJ, respectively).  ... 
doi:10.15252/msb.20145304 pmid:25080494 pmcid:PMC4299500 fatcat:p4rlbwkmybgebazdokxv5whrbe

Cancer expression quantitative trait loci (eQTLs) can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity

Paul Geeleher, Aritro Nath, Fan Wang, Zhenyu Zhang, Alvaro N. Barbeira, Jessica Fessler, Robert L. Grossman, Cathal Seoighe, R. Stephanie Huang
2018 Genome Biology  
Here, we have demonstrated a method to identify eQTLs affecting expression in cancer cells by modeling the statistical interaction between genotype and tumor purity.  ...  Expression quantitative trait loci (eQTLs) identified using tumor gene expression data could affect gene expression in cancer cells, tumor-associated normal cells, or both.  ...  We acknowledge the Genomics Data Commons (GDC) and the Bionimbus Protected Data Cloud for data acquisition and analysis services and the patients and research groups who generated the TCGA data.  ... 
doi:10.1186/s13059-018-1507-0 pmid:30205839 pmcid:PMC6131897 fatcat:22kd4edgkzhfjhohbntv75boli

New Developments in Science and Technology - 60th Anniversary Special Issue, Beihang University (BUAA)

2012 Science  
science, and failure analysis.  ...  provides cutting-edge research and education in advanced structural and functional materials, nanomaterials, new materials for clean energy, polymers and composites, nonequilibrium fabrication, corrosion  ...  A cloud data center.  ... 
doi:10.1126/science.338.6104.274-c fatcat:iurk5neuwvh2jgbohwevb5dicy

Abstracts of Papers Presented at the 2008 Pittsburgh Conference

Peter B. Stockwell
2008 Journal of automated methods & management in chemistry (Print)  
systems for detection and inspection of food quality, safety, sanitation, and security.  ...  The major challenge will be how to deal with the huge amount of data generated in a short period of time and turning it into information relevant to the problem at hand.  ...  Research Centre at Hyderabad for providing the analytical support to pursue this work, and they are also grateful to colleagues who helped them in this work.  ... 
doi:10.1155/2008/502953 pmid:19365566 pmcid:PMC2665694 fatcat:cwx4g3nawzewreu7iz6vldtj2m

Latent Immunological Effects of Gestational Exposure to Heptachlor Epoxide

Dean Baker, Haiou Yang, Ulrike Luderer, Sastry Gollapudi
2011 Epidemiology  
The second uses generalized additive Poisson regression models, controlling for long-term trend, seasonality, and day of the week to determine the daily excess mortality related to temperature and the  ...  Methods: We established time-series Poisson regression models based on cause-specific mortality and age stratified mortality in Stockholm County, 1990 -2002, adjusting for time trends and potential confounders  ...  Methods: We used baseline data (2000 -2003) from the Heinz Nixdorf Recall-Study, a population-based cohort of 4814 participants living in 3 cities in Germany.  ... 
doi:10.1097/01.ede.0000392128.65234.11 fatcat:dft32xujtzchzcnldns7ppf6iq

ACNP 58th Annual Meeting: Panels, Mini-Panels and Study Groups

2019 Neuropsychopharmacology  
The kinetics of dynorphin signal activation, duration and spread were characterized in striatum using a combination of photorelease, sensor imaging and electrophysiology.  ...  Methods: Photoactivatable or "caged" dynorphin derivatives were synthesized and evaluated at heterologously expressed receptors using a functional secreted alkaline phosphatase assay in HEK293 cells and  ...  DNAm GrimAge estimates were calculated from beta values after quality control procedures, using the validated methylation age calculator.  ... 
doi:10.1038/s41386-019-0544-z pmid:31801977 pmcid:PMC6957922 fatcat:hjyvf7fcpbf2fhxit6rlhsvg2y

Detection of Irradiated Food and Evaluation of the Given Dose by Electron Spin Resonance, Thermoluminescence, and Gas Chromatographic/Mass Spectrometric Analysis [chapter]

Maria C. D'Oca, Antonio Bartolotta
2018 Food Control and Biosecurity  
Acknowledgments This work was supported by national funds through the Pluriannual Program (PEst-OE/AGR/U10276/2014), financed by FCT-Fundação para a Ciência e a Tecnologia (FCT).  ...  Acknowledgments The authors thank the Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (Process no.  ...  Used to control access to areas; it can replace password control to data systems. • DNA recognition uses genetic profiling, also called genetic fingerprinting, to isolate and identify the repetitive DNA  ... 
doi:10.1016/b978-0-12-811445-2.00010-6 fatcat:flc2mqpiwrhn3cmrmnbkgwgfxe

Abstracts of papers presented at the 1994 Pittsburgh Conference

1994 Journal of Automatic Chemistry  
However, it is also important to master these new instruments, to understand the data flow and transformations that yield measurements and control our systems.  ...  HI 96740 Powerful and elegant analytical methods and instruments are used daily in industry, hospitals, R & D laboratories and process control systems.  ...  A variety of applications of the SL methodology were presented, from real-time environmental monitoring, petroleum process control, DNA sequencing applications to human health protection (DNA adduct detection  ... 
doi:10.1155/s146392469400009x pmid:18924983 pmcid:PMC2548030 fatcat:pfs356duznffzid6c3qa52pcwe

Epigenetic information in the cell : a potential avenue for biocompatible computing

Thomas Hentrich
As a computation and storage layer chromatin offers a high degree of plasticity to integrate (environmental) signals into DNA-based regulation and allows information propagation according to epigenetic  ...  From the perspective of Living Computers, I address the question of information encoding by biomolecules and draw on principles of epigenetics to devise a model for an RNA interference-based equivalent  ...  As one of the most popular, versatile and cloud-ready platforms, the Galaxy framework integrates a variety of tools, which enable experimentalists without programming expertise to easily retrieve and query  ... 
doi:10.14288/1.0052107 fatcat:v4jgomluwvhk5i23qoobkzywfq

Engineering, Technology & Applied Science Research (ETASR), Vol. 11, No. 3, pp. 7069-7290

2021 Zenodo  
), and has been awarded a DOAJ seal.  ...  ISSN: 1792-8036 and 2241-4487.  ...  We also thank the NED University of Engineering and Technology for providing us the platform to carry out this work. ACKNOWLEDGMENT The work presented in this paper was supported by  ... 
doi:10.5281/zenodo.5136285 fatcat:2beknqdb3bcq7fqfav6btil6ci

Poster Session II

2015 Neuropsychopharmacology  
RNA was sequenced using the Illumina HiSeq platform (425 million 50 base reads).  ...  There was no significant effect of demographic and clinical variables on methylation levels. Conclusions: DNA methylation is altered in two distinct regions of SLC1A2 promoter of BD patients.  ...  The imaging data was preprocessed following standard procedures and analyzed with CONN toolbox (MIT, Cambridge).  ... 
doi:10.1038/npp.2015.326 pmid:26632287 pmcid:PMC4672311 fatcat:ib64i5qmzngvxcpn5hznkcagie
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