MOABS protocols

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MOABS specifications

Information


Unique identifier OMICS_04480
Name MOABS
Alternative name MOdel based Analysis of Bisulfite Sequencing data
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for MOdel based Analysis of Bisulfite Sequencing data

MOABS in pipelines

 (2)
2018
PMCID: 5888657
PMID: 29394393
DOI: 10.1093/nar/gky063

[…] () with paired mode and two allowable mismatches. in total, we identified 14.6 million cpg sites with coverage ≥10 reads and our downstream bioinformatic analyses were based on these cpg sites. moabs () and bseqc () were used to do the quality control and to calculate the methylation ratio for each cpg site. we defined dmrs as the regions between two samples that have an absolute difference […]

2016
PMCID: 4957136
PMID: 27428748
DOI: 10.1038/ng.3610

[…] the low-quality reads were trimmed using bsmap with default. sequencing depth of cpgs at least 5 reads of each sample were extract to calculate the methylation ratio calling [0,1] by the software moabs. a two-state first-order hidden markov model was used to detect the undermethylated regions and larger undermethylated canyons (≥ 3.5 kb) as described previously., to identify differentially […]


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MOABS in publications

 (276)
PMCID: 5945839
PMID: 29780793
DOI: 10.3389/fped.2018.00121

[…] twice with pbs and stained with different combinations of monoclonal antibodies (moab) against cd45, cd19, cd20, anti-igd, and cd27 and incubated in the dark for 15 min at room temperature. the moabs were conjugated with fluorescein isothiocyanate (fitc), phycoerythrin (pe), phycoerythrin-texas-red-tandem (ecd), phycoerythrin-cyanin-5 (pc5) or phycoerythrin-cyanin-7 (pc7). all reagents […]

PMCID: 5904111
PMID: 29666387
DOI: 10.1038/s41598-018-24306-1

[…] only accounting for 1% and 4%. nras mutations are found in about 3–5% and hras mutations were rare in previous studies,., the kras exon 2 mutation was widely regarded as a predictor for anti-egfr moabs resistance among crcs. nevertheless, the majority of kras exon 2 wild-type (wt) patients fail to benefit from anti-egfr moabs, implying the possibility that activating mutations in other kras […]

PMCID: 5915137
PMID: 29707129
DOI: 10.18632/oncotarget.24785

[…] to an impressive and durable clinical benefit in a significant subgroup of patients with advanced non-small cell lung cancer (nsclc). particularly to date we have three monoclonal antibodies (moabs), nivolumab, pembrolizumab and atezolizumab, targeting the programmed cell death 1 (pd1)/programmed cell death 1 ligand (pd-l1) immune-checkpoint, approved by regulatory authorities […]

PMCID: 5842653
PMID: 29514626
DOI: 10.1186/s12859-018-2086-5

[…] methylation differences at individual cpg sites. one such recent method, known as dss [, ], has been compared to several methods (such as methylkit [], bsmooth [], biseq [], radmeth [], and moabs []), using simulated as well as real data and has been found to be more preferable than these methods. moreover, metilene, a recently proposed dmr finder [], was found to be superior to bsmooth […]

PMCID: 5835032
PMID: 29535719
DOI: 10.3389/fimmu.2018.00331

[…] dried for 1 h at 60°c followed by 30 min at room temperature, and fixated in acetone for 10 min. immunohistochemical staining was performed overnight at room temperature using monoclonal antibodies (moabs) against cd3 (igg2a, ps1-ab699, abcam, cambridge, ma, usa) and cd8 (igg2b, 4b11, leica microsystems, rijswijk, netherlands) as markers for t-cell infiltration in the skin and against hla class […]


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