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A (fire)cloud-based DNA methylation data preprocessing and quality control platform
2019
BMC Bioinformatics
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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. harvard.edu/dna-methylation-tools ...
doi:10.1186/s12859-019-2750-4
fatcat:thscp52dmfdbnlv6mb36xcmz2a
EMBnet.journal 19 Suppl. A
2013
EMBnet journal
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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
2021
Frontiers in Cell and Developmental Biology
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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
2019
IEEE Access
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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
2014
Molecular Systems Biology
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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
2018
Genome Biology
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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
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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
2008
Journal of automated methods & management in chemistry (Print)
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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
2011
Epidemiology
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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
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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]
2018
Food Control and Biosecurity
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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
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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
2011
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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
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), 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
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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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