29 Aug 2024
Are you looking for a #bioinformatics #pipeline to analyse #spike_in #ChIP_seq data? Check out our latest work now online in NAR Genomics and Bioinformatics!! Kudos to @BrexDavide and thanks to our collaborators!! doi.org/10.1093/nargab/lqae1…
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25 Feb 2023
Anyone aware of the computational pipeline that can be impemented in @RStudio for analyzing cut and run data set? #Bioinformatics #computational_biology #cut_and_run #Chip_seq #Genomics
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24 Jun 2020
「Fig1:」 Advice from the book "Computational epigenetics and diseases" chapter2 @generegulation @ChIP_seq
「Fig2:」Also learned a pkg from @Bioconductor normR
The impression: easy to use and well-written vignette bioconductor.org/packages/re…
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21 Apr 2020
Hi guys, what #genomics resources (websites, blog, pdfs, githubs,manuals,books etc.,) do you use to learn #DataAnalytics of your #ngs data?Please share your experiences or suggestions with me
#DataScience #epigenetics #ChIP_seq #RNA_seq #R #python #phdchat #phdpandemic #phdadvice
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26 Oct 2019
Absolute quantification of cohesin and CTCF in human cells. There are ~250K cohesin complexes of which ~ a half bound to ~120K CTCF sites including ~ 60K single motifs and ~30K dual motifs (unresolved by ChIP_Seq) which sum up to ~120K single ones indeed ! doi.org/10.7554/eLife.46269
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20 Aug 2019
An excellent example of @ChiP_seq & @RNA_seq integration! Our customers @UF have uncovered potential therapeutic targets for treating a cancer-causing virus. doi.org/10.1128/JVI.01978-18
#Bioinformatics
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3 Jun 2019
Articulo con resultados espectaculares y protocolo de #ChIP_seq en single cells #cancerdemama Marcas asociadas a resistencia de #quimioterapia High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer
nature.com/articles/s41588-0… #FelizLunes
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26 Mar 2019
A very useful tool for the @ChIP_seq community
A #new antibody search engine with publication data. #Free online platform for academic scientists!
landing.benchsci.com/academi… #openaccess #openscience #phdchat
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18 Mar 2019
Thank you guys !! I want to see binding sites in the genome, nothing to do with repeats, so good to proceed with only unique mapping reads.
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18 Mar 2019
Depends of the scientific question. If we are interested in repeats then obviously multi-mapping reads are the key reads and they can be e.g. mapped to a dedicated "genome assembly" composed of the repeat of interest to compare normalised read coverage between two cell conditions
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18 Mar 2019
In @ChIP_seq data, what do u do with multi mapping reads ? Do you exclude them completely or take one best alignment reported by bowtie. Any suggestions cc @pundhir_sachin @tangming2005 @AltunaAkalin @generegulation
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4 Feb 2019
Proximity assisted dimerization of two CTCF proteins bound inside ChIP_Seq peaks with the dual rather than single CBS motifs is conserved from Drosophila to humans: e.g., the Fab‐8 insulator depends on essential dual dCTCF binding sequence shown herein embor.embopress.org/content/…
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15 Oct 2018
This is my PhD thesis on regulation of secondary metabolites summed up in a paper. @eLife @ChIP_seq @LeibnizHKI
15 Oct 2018
Excited to see our new paper out in @eLife using @ChIP_seq towards understanding fungal secondary metabolites production doi.org/10.7554/eLife.40969 Special thanks to @JulianeFischer5 and @tina_netzker and also @JSMC_Info and ILRS @LeibnizHKI for funding.
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15 Oct 2018
Excited to see our new paper out in @eLife using @ChIP_seq towards understanding fungal secondary metabolites production doi.org/10.7554/eLife.40969 Special thanks to @JulianeFischer5 and @tina_netzker and also @JSMC_Info and ILRS @LeibnizHKI for funding.
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4 Sep 2018
snakePipes: a collection of #snakemake based workflows for the analysis of NGS data #ChIP_seq #RNA_seq #HiC #scRNA_seq #ATAC_seq @mpi_ie snakepipes.readthedocs.io #bioRxiv biorxiv.org/content/early/20…
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31 Jan 2018
@CTCF_Papers Did you hear about "binary CTCF code" conserved within 2xCTCF-bound @ChIP_seq-peaks analyzed for cancer associated mutations in the bulk of recent @CTCF_Papers referenced in the #CanEpi17 @StanInScience review ? @CEEHRC #CanEpi17
31 Jan 2018
@StanInScience Dear Stanley: Did you hear about "binary CTCF code" conserved within CTCF @ChIP_seq peaks analyzed for cancer-associated mutations in @CTCF_Papers referenced in your review ?
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31 Jan 2018
@boris_ctcf Did you hear about "binary CTCF code" conserved within 2xCTCF-bound @ChIP_seq-peaks analyzed for cancer associated mutations in the bulk of recent @CTCF_Papers referenced in the #CanEpi17 @StanInScience review ? x.com/StanInScience/status/9…
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31 Jan 2018
@StanInScience Dear Stanley: Did you hear about "binary CTCF code" conserved within CTCF @ChIP_seq peaks analyzed for cancer-associated mutations in @CTCF_Papers referenced in your review ?
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3 Dec 2017
Wig-> bigWig ->ChIPWig! @mkim158 Great to see NarrowPeaks R package being applied on @ChIP_seq data in WIG format @Bioconductor #BioInformatics #rstats {doi.org/doi:10.18129/B9.bioc…} x.com/mkim158/status/9237267…
31 Oct 2017
Discovering BINARY CTCF CODE with a little help from 'CTCF Like' BORIS is available from PubMed ncbi.nlm.nih.gov/pubmed/2907…
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