Chris Clarkson

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...

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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.

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

I'm anxious, overwhelmed and have a bad headache Have you tried consuming nothing but coffee and terrifying news updates?

#vanitas #memes

Really interesting looking position- highly recommend!
www.jobs.gla.ac.uk/job/research...

If genomics is the answer, what's the question? A commentary on PsychENCODE There was much excitement in the press and in the psychiatric research community recently as a flurry of papers was p...

More thoughts on these issues here: If genomics is the answer, what's the question? www.wiringthebrain.com/2018/12/if-g...

Aging clock based on nucleosome reorganisation derived from cell‐free DNA We show that aging is associated with an increase in the distance between nucleosomes, which can be used to predict a person's age and conduct age classification. We developed the first aging clock b...

Most previous epigenetic age predictors were focused on DNA methylation. Our own model suggested nucleosome positioning as an age predictor a year ago onlinelibrary.wiley.com/doi/full/10....

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.

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. 🧪

Thank you so much to everyone who contributed to this work which resulted in a fascinating insight into #RepeatExpansions

These results indicate that THAP11 expansions are rare in the British population and that sequence structures predisposed to expansions may be more common in non-British ancestries.

We showed a linear relationship between the number of CAA interruptions and overall repeat length. Furthermore, we showed that the prevalence of alleles with three CAA interruptions (characteristic of the disease-causing alleles) is most common in African and South Asian genetic ancestries.

We identified expanded repeats in four individuals with learning difficulties without ataxia and in three individuals in UK Biobank, one with hereditary ataxia (also highlighted by Fearnley et al. (2024)), one with hereditary neuropathy, and one with neurodegenerative disease. See an exemplary case:

We explored the repeat size and structure by interrogating data from from Genomics England, the UCL Queen Square Institute of Neurology in-house database (UCL IoN), and the UK Biobank.

Tan et al. (2023) found a CAG repeat expansion in THAP11 was recently found to be associated with spinocerebellar ataxia in two Chinese families. Expanded repeats ranged from 45 to 100 units, with CAA sequence interruptions in the 5′ region and an uninterrupted CAG tract in the 3′ tail.

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

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

congrats Emma!

RNA editing is a molecular clock in unmodified human cells Despite major advances in spatial RNA sequencing, the ability to extract temporal information in RNA sequencing experiments is still limited. Here, we describe Transcriptome Timestamping (T2), a syste...

www.biorxiv.org/content/10.1...