implementation of particle swarm optimization algorithm Search Results


miltenyi magnetic cd4 microbeads  (Miltenyi Biotec)
96
Miltenyi Biotec miltenyi magnetic cd4 microbeads
(A) Enrichment of the identified cis -mCpGs in comparison to all tested CpGs in relation to UCSC CpG islands and gene functional regions (annotations from R IlluminaHumanMethylationEPICanno.ilm10b2.hg19 package) and chromatin states modeled for <t>CD4</t> + T cells (annotations from Roadmap Epigenomics Project, sample #E043). Significant enrichment/depletion are shown using upwards/downwards arrows, respectively. (B) Percentage of our identified cis -mCpGs available in the BLUEPRINT study and the comparison between the two studies regarding the direction of effect and significance of association for the top mSNPs are shown on the left . Comparison between the effect sizes found in our study and in BLUEPRINT are shown on the right .
Miltenyi Magnetic Cd4 Microbeads, supplied by Miltenyi Biotec, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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particle swarm optimization implementation  (MathWorks Inc)
97
MathWorks Inc particle swarm optimization implementation
(A) Enrichment of the identified cis -mCpGs in comparison to all tested CpGs in relation to UCSC CpG islands and gene functional regions (annotations from R IlluminaHumanMethylationEPICanno.ilm10b2.hg19 package) and chromatin states modeled for <t>CD4</t> + T cells (annotations from Roadmap Epigenomics Project, sample #E043). Significant enrichment/depletion are shown using upwards/downwards arrows, respectively. (B) Percentage of our identified cis -mCpGs available in the BLUEPRINT study and the comparison between the two studies regarding the direction of effect and significance of association for the top mSNPs are shown on the left . Comparison between the effect sizes found in our study and in BLUEPRINT are shown on the right .
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amigo toolbox  (MathWorks Inc)
96
MathWorks Inc amigo toolbox
(A) Enrichment of the identified cis -mCpGs in comparison to all tested CpGs in relation to UCSC CpG islands and gene functional regions (annotations from R IlluminaHumanMethylationEPICanno.ilm10b2.hg19 package) and chromatin states modeled for <t>CD4</t> + T cells (annotations from Roadmap Epigenomics Project, sample #E043). Significant enrichment/depletion are shown using upwards/downwards arrows, respectively. (B) Percentage of our identified cis -mCpGs available in the BLUEPRINT study and the comparison between the two studies regarding the direction of effect and significance of association for the top mSNPs are shown on the left . Comparison between the effect sizes found in our study and in BLUEPRINT are shown on the right .
Amigo Toolbox, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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spectral methods for partial differential equations  (Verlag GmbH)
90
Verlag GmbH spectral methods for partial differential equations
(A) Enrichment of the identified cis -mCpGs in comparison to all tested CpGs in relation to UCSC CpG islands and gene functional regions (annotations from R IlluminaHumanMethylationEPICanno.ilm10b2.hg19 package) and chromatin states modeled for <t>CD4</t> + T cells (annotations from Roadmap Epigenomics Project, sample #E043). Significant enrichment/depletion are shown using upwards/downwards arrows, respectively. (B) Percentage of our identified cis -mCpGs available in the BLUEPRINT study and the comparison between the two studies regarding the direction of effect and significance of association for the top mSNPs are shown on the left . Comparison between the effect sizes found in our study and in BLUEPRINT are shown on the right .
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ti e inverted microscope  (Nikon)
99
Nikon ti e inverted microscope
(A) Enrichment of the identified cis -mCpGs in comparison to all tested CpGs in relation to UCSC CpG islands and gene functional regions (annotations from R IlluminaHumanMethylationEPICanno.ilm10b2.hg19 package) and chromatin states modeled for <t>CD4</t> + T cells (annotations from Roadmap Epigenomics Project, sample #E043). Significant enrichment/depletion are shown using upwards/downwards arrows, respectively. (B) Percentage of our identified cis -mCpGs available in the BLUEPRINT study and the comparison between the two studies regarding the direction of effect and significance of association for the top mSNPs are shown on the left . Comparison between the effect sizes found in our study and in BLUEPRINT are shown on the right .
Ti E Inverted Microscope, supplied by Nikon, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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elekta axessetm linear accelerator  (Elekta)
86
Elekta elekta axessetm linear accelerator
(A) Enrichment of the identified cis -mCpGs in comparison to all tested CpGs in relation to UCSC CpG islands and gene functional regions (annotations from R IlluminaHumanMethylationEPICanno.ilm10b2.hg19 package) and chromatin states modeled for <t>CD4</t> + T cells (annotations from Roadmap Epigenomics Project, sample #E043). Significant enrichment/depletion are shown using upwards/downwards arrows, respectively. (B) Percentage of our identified cis -mCpGs available in the BLUEPRINT study and the comparison between the two studies regarding the direction of effect and significance of association for the top mSNPs are shown on the left . Comparison between the effect sizes found in our study and in BLUEPRINT are shown on the right .
Elekta Axessetm Linear Accelerator, supplied by Elekta, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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zetaview system  (Particle Metrix)
90
Particle Metrix zetaview system
(A) Enrichment of the identified cis -mCpGs in comparison to all tested CpGs in relation to UCSC CpG islands and gene functional regions (annotations from R IlluminaHumanMethylationEPICanno.ilm10b2.hg19 package) and chromatin states modeled for <t>CD4</t> + T cells (annotations from Roadmap Epigenomics Project, sample #E043). Significant enrichment/depletion are shown using upwards/downwards arrows, respectively. (B) Percentage of our identified cis -mCpGs available in the BLUEPRINT study and the comparison between the two studies regarding the direction of effect and significance of association for the top mSNPs are shown on the left . Comparison between the effect sizes found in our study and in BLUEPRINT are shown on the right .
Zetaview System, supplied by Particle Metrix, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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laser diffraction particle size distribution analyzer la-960v2  (HORIBA Ltd)
90
HORIBA Ltd laser diffraction particle size distribution analyzer la-960v2
(A) Enrichment of the identified cis -mCpGs in comparison to all tested CpGs in relation to UCSC CpG islands and gene functional regions (annotations from R IlluminaHumanMethylationEPICanno.ilm10b2.hg19 package) and chromatin states modeled for <t>CD4</t> + T cells (annotations from Roadmap Epigenomics Project, sample #E043). Significant enrichment/depletion are shown using upwards/downwards arrows, respectively. (B) Percentage of our identified cis -mCpGs available in the BLUEPRINT study and the comparison between the two studies regarding the direction of effect and significance of association for the top mSNPs are shown on the left . Comparison between the effect sizes found in our study and in BLUEPRINT are shown on the right .
Laser Diffraction Particle Size Distribution Analyzer La 960v2, supplied by HORIBA Ltd, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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universal software radio peripheral (usrp) boards  (Ettus Research LLC)
90
Ettus Research LLC universal software radio peripheral (usrp) boards
(A) Enrichment of the identified cis -mCpGs in comparison to all tested CpGs in relation to UCSC CpG islands and gene functional regions (annotations from R IlluminaHumanMethylationEPICanno.ilm10b2.hg19 package) and chromatin states modeled for <t>CD4</t> + T cells (annotations from Roadmap Epigenomics Project, sample #E043). Significant enrichment/depletion are shown using upwards/downwards arrows, respectively. (B) Percentage of our identified cis -mCpGs available in the BLUEPRINT study and the comparison between the two studies regarding the direction of effect and significance of association for the top mSNPs are shown on the left . Comparison between the effect sizes found in our study and in BLUEPRINT are shown on the right .
Universal Software Radio Peripheral (Usrp) Boards, supplied by Ettus Research LLC, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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efab® electrochemical fabrication process  (Microfabrica Inc)
90
Microfabrica Inc efab® electrochemical fabrication process
(A) Enrichment of the identified cis -mCpGs in comparison to all tested CpGs in relation to UCSC CpG islands and gene functional regions (annotations from R IlluminaHumanMethylationEPICanno.ilm10b2.hg19 package) and chromatin states modeled for <t>CD4</t> + T cells (annotations from Roadmap Epigenomics Project, sample #E043). Significant enrichment/depletion are shown using upwards/downwards arrows, respectively. (B) Percentage of our identified cis -mCpGs available in the BLUEPRINT study and the comparison between the two studies regarding the direction of effect and significance of association for the top mSNPs are shown on the left . Comparison between the effect sizes found in our study and in BLUEPRINT are shown on the right .
Efab® Electrochemical Fabrication Process, supplied by Microfabrica Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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the esxi hypervisor infrastructure  (VMware Inc)
90
VMware Inc the esxi hypervisor infrastructure
(A) Enrichment of the identified cis -mCpGs in comparison to all tested CpGs in relation to UCSC CpG islands and gene functional regions (annotations from R IlluminaHumanMethylationEPICanno.ilm10b2.hg19 package) and chromatin states modeled for <t>CD4</t> + T cells (annotations from Roadmap Epigenomics Project, sample #E043). Significant enrichment/depletion are shown using upwards/downwards arrows, respectively. (B) Percentage of our identified cis -mCpGs available in the BLUEPRINT study and the comparison between the two studies regarding the direction of effect and significance of association for the top mSNPs are shown on the left . Comparison between the effect sizes found in our study and in BLUEPRINT are shown on the right .
The Esxi Hypervisor Infrastructure, supplied by VMware Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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partial differential equation model  (COMSOL Inc)
90
COMSOL Inc partial differential equation model
(A) Enrichment of the identified cis -mCpGs in comparison to all tested CpGs in relation to UCSC CpG islands and gene functional regions (annotations from R IlluminaHumanMethylationEPICanno.ilm10b2.hg19 package) and chromatin states modeled for <t>CD4</t> + T cells (annotations from Roadmap Epigenomics Project, sample #E043). Significant enrichment/depletion are shown using upwards/downwards arrows, respectively. (B) Percentage of our identified cis -mCpGs available in the BLUEPRINT study and the comparison between the two studies regarding the direction of effect and significance of association for the top mSNPs are shown on the left . Comparison between the effect sizes found in our study and in BLUEPRINT are shown on the right .
Partial Differential Equation Model, supplied by COMSOL Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


(A) Enrichment of the identified cis -mCpGs in comparison to all tested CpGs in relation to UCSC CpG islands and gene functional regions (annotations from R IlluminaHumanMethylationEPICanno.ilm10b2.hg19 package) and chromatin states modeled for CD4 + T cells (annotations from Roadmap Epigenomics Project, sample #E043). Significant enrichment/depletion are shown using upwards/downwards arrows, respectively. (B) Percentage of our identified cis -mCpGs available in the BLUEPRINT study and the comparison between the two studies regarding the direction of effect and significance of association for the top mSNPs are shown on the left . Comparison between the effect sizes found in our study and in BLUEPRINT are shown on the right .

Journal: bioRxiv

Article Title: Impact of genetic susceptibility to multiple sclerosis on the T cell epigenome: proximal and distal effects

doi: 10.1101/2020.07.11.198721

Figure Lengend Snippet: (A) Enrichment of the identified cis -mCpGs in comparison to all tested CpGs in relation to UCSC CpG islands and gene functional regions (annotations from R IlluminaHumanMethylationEPICanno.ilm10b2.hg19 package) and chromatin states modeled for CD4 + T cells (annotations from Roadmap Epigenomics Project, sample #E043). Significant enrichment/depletion are shown using upwards/downwards arrows, respectively. (B) Percentage of our identified cis -mCpGs available in the BLUEPRINT study and the comparison between the two studies regarding the direction of effect and significance of association for the top mSNPs are shown on the left . Comparison between the effect sizes found in our study and in BLUEPRINT are shown on the right .

Article Snippet: Cell viability was accessed by acridine orange/propidium iodine staining and CD4 + T cells were isolated using a positive selection strategy implemented with Miltenyi magnetic CD4 MicroBeads (130-045-101).

Techniques: Comparison, Functional Assay

(A) The top 3 colocalized MS- cis -mQTL effects are illustrated (posterior probability >0.95 for colocalization between MS susceptibility and ≥ 1 cis -mQTL effect). The MS GWAS rows ( blue dots) show −log( p -value) of association between SNPs and MS susceptibility in the discovery phase of the 2019 IMSGC GWAS. CpG rows ( plum dots) show −log( p -value) of association between SNPs and the specified cis -CpGs methylation levels. Locations of the local CpGs measured with the Infinium MethylationEPIC kit are shown using light blue vertical lines. Gene exon/intron positions are based on Ensembl 93. Chromatin state annotations for CD4 + T cells are downloaded from the Roadmap Epigenomics Project (sample #E043). Green vertical lines represent the genomic location of the colocalized CpGs: Long vertical lines traversing all rows represent the top specified CpGs, while other vertical lines represent the additional colocalized cis -mCpGs with posterior probability >0.8. All genomic positions are in GRCh37 (hg19) coordinates. (B) Comparison between MS- cis -mQTL colocalization posterior probabilities using mQTL summary statistics from our study and BLUEPRINT for the available common CpGs. Vertical red line represents the threshold for high colocalization posterior probability in our study (i.e. 0.8). (C) The cis -mQTL, cis -eQTL, and CpG-mRNA association for the chromosome 5 top MS- cis -mQTL colocalized effect. Methylation levels are shown in M-values. Gene expression values are in TPM.

Journal: bioRxiv

Article Title: Impact of genetic susceptibility to multiple sclerosis on the T cell epigenome: proximal and distal effects

doi: 10.1101/2020.07.11.198721

Figure Lengend Snippet: (A) The top 3 colocalized MS- cis -mQTL effects are illustrated (posterior probability >0.95 for colocalization between MS susceptibility and ≥ 1 cis -mQTL effect). The MS GWAS rows ( blue dots) show −log( p -value) of association between SNPs and MS susceptibility in the discovery phase of the 2019 IMSGC GWAS. CpG rows ( plum dots) show −log( p -value) of association between SNPs and the specified cis -CpGs methylation levels. Locations of the local CpGs measured with the Infinium MethylationEPIC kit are shown using light blue vertical lines. Gene exon/intron positions are based on Ensembl 93. Chromatin state annotations for CD4 + T cells are downloaded from the Roadmap Epigenomics Project (sample #E043). Green vertical lines represent the genomic location of the colocalized CpGs: Long vertical lines traversing all rows represent the top specified CpGs, while other vertical lines represent the additional colocalized cis -mCpGs with posterior probability >0.8. All genomic positions are in GRCh37 (hg19) coordinates. (B) Comparison between MS- cis -mQTL colocalization posterior probabilities using mQTL summary statistics from our study and BLUEPRINT for the available common CpGs. Vertical red line represents the threshold for high colocalization posterior probability in our study (i.e. 0.8). (C) The cis -mQTL, cis -eQTL, and CpG-mRNA association for the chromosome 5 top MS- cis -mQTL colocalized effect. Methylation levels are shown in M-values. Gene expression values are in TPM.

Article Snippet: Cell viability was accessed by acridine orange/propidium iodine staining and CD4 + T cells were isolated using a positive selection strategy implemented with Miltenyi magnetic CD4 MicroBeads (130-045-101).

Techniques: Methylation, Comparison, Gene Expression