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skoklab

@skoklab

Interested in all things : #gene_regulation #nuclear_Organization #regulatory_elements #3DGenomeinCANCER #3Cmethods

 New York, NY
skoklab.com
Joined January 2019
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  • Followers355
Save the date for our 2nd #IMBGreen Seminar - 21 Jan 2021, 4pm (CET/UCT+1)!🍃 Nikoline Borgermann, founder of @AvaSustain will give us tips on "How to go green in a wet lab". Are you joining us to learn how to be a part of #sustainablescience? Register➡️form.123formbuilder.com/5752…
Image from IMB Mainz (@imbmainz)
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The Skok lab is looking for higly motivated postdocs with experience in CRISPR and 3C technologies.
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The Skok lab is seeking to hire a wet lab postdoc and a computational analyst. If interested, please contact @jane_skok at [email protected] and lab manager [email protected]. 👍
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Yesterday we celebrate the biggest achievement in the lab so far - 99.2% valid pair HiC libraries!! With cake and dumplings 😜😜😜 Thanks for the magic hand of Haley. We homebrewed the method and @ArimaGenomics works equally well😜😜
Image from Xiaotian Zhang (@zxtzhangqian)
Image from Xiaotian Zhang (@zxtzhangqian)
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Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation biorxiv.org/content/10.1101/…
Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation

Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation

Background Ubiquitously expressed CTCF is involved in numerous cellular functions, some of which involve organizing chromatin into TAD structures and others to its role as a transcription factor. In...

biorxiv.org
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bioRxiv viewer disq.us/t/3kforbz Collaborative work with Elphege Nora and Benoit Bruneau investigating the interplay between CTCF and CTCFL and the functions of their different domains in regulating transcription, chromatin looping and insulation.
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Recent publication in Genome Biology:
Jane Skok (@jane_skok) profile pictureJane Skok@jane_skok10 Dec 2019
Happy to share our new paper in Genome biology. Published: 21 November 2019 EpiMethylTag: simultaneous detection of ATAC-seq or ChIP-seq signals with DNA methylation
Check out our new method in Genome Biology!! :D
CTCF Papers 📚 (@CTCF_Papers) profile pictureCTCF Papers 📚@CTCF_Papers23 Nov 2019
EpiMethylTag: simultaneous detection of ATAC-seq or ChIP-seq signals with DNA methylation. dlvr.it/RJwdcm
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Dynamic 3D chromosomal landscapes in acute leukemia biorxiv.org/content/10.1101/…
Dynamic 3D chromosomal landscapes in acute leukemia

Dynamic 3D chromosomal landscapes in acute leukemia

Three-dimensional (3D) chromatin architectural changes can alter the integrity of topologically associated domains (TADs) and rewire specific enhancer-promoter interactions impacting gene expression....

biorxiv.org
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A B-cell acute lymphoblastic leukemia regulatory network defines novel therapeutic targets in IGH-CRLF2 patients biorxiv.org/content/10.1101/…
A B-cell acute lymphoblastic leukemia regulatory network defines novel therapeutic targets in...

A B-cell acute lymphoblastic leukemia regulatory network defines novel therapeutic targets in...

CRLF2 overexpression in B-ALL patients with an IGH-CRLF2 translocation activates JAK-STAT, PI3K and ERK/MAPK signaling pathways. Although inhibitors of these pathways are available, investigating...

biorxiv.org
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We have several rotation projects open for UCSD graduate and undergraduate students as part of the BISB program. Shoot an email if interested: bioinformatics.ucsd.edu/node…
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Happy to share our latest paper: NSD2 overexpression drives clustered chromatin and transcriptional changes in insulated domains biorxiv.org/content/10.1101/…
NSD2 overexpression drives clustered chromatin and transcriptional changes in insulated domains

NSD2 overexpression drives clustered chromatin and transcriptional changes in insulated domains

CTCF and cohesin play a key role in organizing chromatin into TAD structures. Disruption of a single CTCF binding site is sufficient to change chromosomal interactions leading to spreading of active...

biorxiv.org
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Check out our new method that combines ChIPseq/ATAC-seq with Bisulfite Conversion!!
bioRxiv (@biorxivpreprint) profile picturebioRxiv@biorxivpreprint14 Feb 2019
EpiMethylTag simultaneously detects ATAC-seq or ChIP-seq signals with DNA methylation biorxiv.org/cgi/content/shor… #bioRxiv
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Excited to share our new method to simultaneously analze methylation in ATAC-seq and ChIP-seq peaks : EpiMethylTag simultaneously detects ATAC-seq or ChIP-seq signals with DNA methylation biorxiv.org/content/10.1101/…
EpiMethylTag simultaneously detects ATAC-seq or ChIP-seq signals with DNA methylation

EpiMethylTag simultaneously detects ATAC-seq or ChIP-seq signals with DNA methylation

Activation of regulatory elements is thought to be inversely correlated with DNA methylation levels. However, it is difficult to determine whether DNA methylation is compatible with chromatin...

biorxiv.org
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We are happy to share our new paper about our method called "EpiMethylTag" that combines ATAC-seq or ChIP-seq with bisulfite sequencing
bioRxiv (@biorxivpreprint) profile picturebioRxiv@biorxivpreprint14 Feb 2019
EpiMethylTag simultaneously detects ATAC-seq or ChIP-seq signals with DNA methylation biorxiv.org/cgi/content/shor… #bioRxiv
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The Skoklab is seeking to hire wet lab postdocs and computational technicians to work on chromatin architecture and cancer. Please send CV and cover letter to [email protected]
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Just setting up my Twitter. #myfirstTweet
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