iiinova — where your digital self keeps evolving

Reposted by Chris Clarkson

medRxivpreprint @medrxivpreprint.bsky.social · 30/04/2026

Ancestry-specific and multi-ancestry genome-wide association studies of restless legs syndrome www.medrxiv.org/content/10.64898/20…

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Reposted by Chris Clarkson

Teif lab @teiflab.bsky.social · 05/03/2026

Nucleosome aficionados! Our new review "Nucleosome spacing across cell types, diseases, and ages" is out in NAR: academic.oup.com/nar/article/... A huge effort to pull together what we’ve learned about nucleosome spacing in many systems. Enjoy! @milena-bikova.bsky.social @chrsclrksn.bsky.social

Figure 1.(A) Classical gel electrophoresis experiments showing mono-, di-, tri-, tetra-, and further multinucleosome bands upon chromatin digestion. (B) The nucleosome repeat length (NRL) is defined as the genomic distance between the centres of two neighbouring nucleosomes.

Figure 2.Nucleosome mapping using MNase-seq versus ATAC-seq. (A) In MNase-seq, nucleosomes in both open and tightly packed genomic regions are accessible to digestion. MNase preferentially cleaves DNA between nucleosomes and digests DNA until it encounters a histone octamer, which provides a footprint of nucleosome-protected DNA regions. (B) Bulk MNase-seq results in averaged maps across millions of cells, effectively capturing all possible nucleosome positioning configurations. (C) Single-cell MNase-seq (scMNase-seq) results in a noisier and sparser signal. The resulting footprints still represent nucleosome-protected regions, but not all nucleosomes are represented. (D) In ATAC-seq, open regions can be accessed by the enzyme Tn5 transposase, which can insert primers in regions free from the binding of nucleosomes and transcription factors (TFs). (E) For open chromatin regions, nucleosome maps can be obtained from ATAC-seq similar to MNase-seq. (F) Closed, tightly packed chromatin regions may be less represented in ATAC-seq nucleosome maps.

Figure 5.Molecular mechanisms affecting nucleosome spacing. (A) Linker histones H1 and nonhistone chromatin proteins which compete with H1s and modulate nucleosome spacing through structural and electrostatic mechanisms. (B) Chromatin remodellers actively reposition nucleosomes following context-dependent rules. (C) Cell state-dependent chromatin boundaries formed by CTCF and other structural proteins, as well as associated recruitment of chromatin remodellers which space nucleosomes. (D) Gene activity associated with remodeller action and RNA polymerases transcribing through the nucleosomes, leading to smaller distances between nucleosomes in regulatory regions and gene bodies. (E) DNA sequence repeats of different types.

Figure 6. Examples of NRL changes in biological systems. (A) Cell differentiation leads to NRL changes between different cell types, e.g. mouse dorsal root ganglia neurons (NRL ∼165 bp) versus cortical astrocytes (NRL ∼183 bp) [175]. Schematic cell shapes are adapted from an image created in BioRender (https://BioRender.com/89trj2t). (B) Paired normal versus tumour breast tissues show NRL shortening in cancer (figure adapted from [36] under the CC BY 4.0 licence (https://creativecommons.org/licenses/by/4.0/)). (C) Nucleosome positioning derived from cfDNA of human volunteers shows NRL increase with age (figure reprinted from [79] under the CC BY 4.0 licence (https://creativecommons.org/licenses/by/4.0/)).

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Reposted by Chris Clarkson

Nacho Molina @molinalab.bsky.social · 19/05/2025

Time for a short thread! We developed HiddenFoot, a biophysics-inspired approach to decode single-molecule footprinting data and infer TF, nucleosome, and RNA Pol II binding profiles on individual DNA molecules. One molecule at a time! www.biorxiv.org/content/10.1... 1/6

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Reposted by Chris Clarkson

Teif lab @teiflab.bsky.social · 27/03/2025

We have a postdoctoral opening for a researcher with experience in bioinformatics of DNA sequencing and machine learning to work on the development of new methods for cancer diagnostics related to nucleosomes, chromatin and beyond www.jobs.ac.uk/job/DMK060/s.... Application deadline: 21st April 2025

jobs.ac.uk

Senior Research Officer at University of Essex

Searching for an academic job? Explore this Senior Research Officer opening on jobs.ac.uk! Click to view more details and browse other academic jobs.

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Reposted by Chris Clarkson

Nature Portfolio @natureportfolio.nature.com · 21/12/2024

An essay in Nature discusses how it’s an astonishing achievement that all of statistics and much of science depends on probability considering no one’s sure what it is. 🧪

go.nature.com

Why probability probably doesn’t exist (but it is useful to act like it does)

All of statistics and much of science depends on probability — an astonishing achievement, considering no one’s really sure what it is.

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Chris Clarkson @chrsclrksn.bsky.social · 12/12/2024

The lab of (amazing!) Arianna Tucci and I are delighted to share our published work on the repeat expansion locus in THAP11:

movementdisorders.onlinelibrary.wiley.com

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Reposted by Chris Clarkson

Jeremy Allen @jeremy-data.bsky.social · 26/10/2024

My fav starter packs so far, a thread: stats: go.bsky.app/Ki7PjpS stats: go.bsky.app/7TBN5rX causal inference: go.bsky.app/FdemGAZ package devs: go.bsky.app/N1569Qh data peeps: go.bsky.app/8TdEfdK medical stats: go.bsky.app/ArqEz36 bioinformatics: go.bsky.app/Ha64Gmv r-ladies: go.bsky.app/Vgxwa2F

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