iiinova — where your digital self keeps evolving

Reposted by Benjamin Schuster-Böckler

Yun S. Song @yun-s-song.bsky.social · 23/09/2026

Please help spread the word! We are recruiting multiple Postdoctoral Fellows as part of the recently launched Bakar Computational Biomedicine Initiative (BCBI) at UC Berkeley and UCSF. BCBI website: bcbi.berkeley.edu Apply by Nov 1, 2026: berkeley.infoready4.com#freeformComp... (1/n)

bcbi.berkeley.edu

Bakar Computational Biomedicine Initiative | Bakar Computational Biomedicine Initiative

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Benjamin Schuster-Böckler @dagams.bsky.social · 16/09/2026

I think the logical thing to do would be to accept the will of the people: erect a tall and solid border around Piddington, withdraw everyone's UK passports, and treat every Piddingtonian who enters the UK as an illegal immigrant unless they apply for a work visa. It's literally what they voted for!

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Ian Sudbery @iansudbery.bsky.social · 12/09/2026

Holy moly, @ensembl.org killed biomart! Hope many R scripts are there out there that depend on biomaRt? How many people have informatics practicals, or undergraduate project instructions that depend on a web interface for bulk selection of data?

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Roger Highfield @rogerhighfield.bsky.social · 22/08/2026

More than 50 studies on cell ageing have apparently used the wrong antibody to identify a key protein in experiments, according to a science sleuth. www.nature.com/articles/d41...

nature.com

Sleuth identifies dozens of studies that used the wrong antibody

The case is the latest example of a scientific workhorse being misused in experiments.

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Reposted by Benjamin Schuster-Böckler

John Cocker @joecocker.bsky.social · 22/08/2026

For Lia 🪨

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Oxford Mathematics @oxfordmathematics.bsky.social · 16/08/2026

'Riffing with Roger', an Oxford Mathematics Unoriginal starring Roger Penrose. And another Roger (sort of).

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Reposted by Benjamin Schuster-Böckler

Lucy Siegle @lucysiegle.bsky.social · 16/08/2026

Hot hooves strikes again!

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Count Binface @countbinface.bsky.social · 16/08/2026

A brief note for Nadhim Zahawi.

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John Cocker @joecocker.bsky.social · 16/08/2026

On this day in 1942, a 5 year old Dutch Jewish girl arrived at Auschwitz with her mother and sister (12) where they were murdered in the gas chamber after selection. The father perished on the 30 Sep 1942. Her name was Betty Stodel Please support @auschwitzmemorial.bsky.social

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Reposted by Benjamin Schuster-Böckler

John Cocker @joecocker.bsky.social · 16/08/2026

On this day in 1942, a 7 month old Dutch Jewish girl arrived at Auschwitz with her mother where they were murdered in the gas chamber after selection. The father perished on the 30 Sep 1942. Her name was Edith Poppelsdorf Please support @auschwitzmemorial.bsky.social

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Count Binface @countbinface.bsky.social · 12/08/2026

For thousands of years, a solar eclipse has been a prophetic harbinger of a spectacular, epoch-making event. Just saying. #VoteBinface #Clacton

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Benjamin Schuster-Böckler @dagams.bsky.social · 12/08/2026

"It's difficult to organise science after publication. Science should be published in a machine-readable form from the outset." It's 2026 and we're coming up with the semantic web. Maybe an XML-based format?! 🤦‍♂️ Wasn't the promise of AI that we DON'T have to invent new "machine-readable" formats?

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Reposted by Benjamin Schuster-Böckler

Count Binface @countbinface.bsky.social · 07/08/2026

In Clacton right now. (Real, not AI!) #VoteBinface

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Benjamin Schuster-Böckler @dagams.bsky.social · 17/07/2026

This is the work of @killercup.de - a lot of careful engineering went into this. Seems to pass most (if not all?) htslib tests. The other benefit is that it removes dynamic link dependencies introduced by rust-htslib

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Benjamin Schuster-Böckler @dagams.bsky.social · 17/07/2026

BTW: while we were trying to optimise IO from bam/cram in our rust-based methylation/variant calling tool "rastair", we ended up re-implementing htslib with a focus on better pileup performance: docs.rs/seqair/lates... It seems to make a big speed difference for us, would love to get feedback

docs.rs

seqair - Rust

Pure-Rust BAM/SAM/CRAM/FASTA reader, pileup engine, and VCF/BCF writer.

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Benjamin Schuster-Böckler @dagams.bsky.social · 17/07/2026

I should also add that along the way, we re-implemented htslib in Rust, which has an enormous impact on performance for many parallelised streaming operations on bam and cram files: github.com/Softleif/seq...

github.com

GitHub - Softleif/seqair: BAM/SAM/CRAM/FASTA reader, pileup engine, BCF/BAM writing

BAM/SAM/CRAM/FASTA reader, pileup engine, BCF/BAM writing - Softleif/seqair

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Reposted by Benjamin Schuster-Böckler

Oxford Clarion @oxfordclarion.bsky.social · 08/07/2026

Yes - he CAN! (Sorry, we had to).

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Benjamin Schuster-Böckler @dagams.bsky.social · 04/07/2026

That's shocking! @oxfordshirecc.bsky.social I'm appalled by this lack of care and respect for the neighborhood and the conservation area

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Reposted by Benjamin Schuster-Böckler

Headington News @headingtonnews.bsky.social · 04/07/2026

On 6 July 2026 Oxfordshire County Council will repair the lower part of the old stone wall in the alleyway alongside the Mason's Arms in Quarry, but the upper part of the stone wall will be replaced with a metal fence. See this Facebook post plus informative comment www.facebook.com/FriendsofQua...

facebook.com

Facebook

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Reposted by Benjamin Schuster-Böckler

Daphne Jackson Trust @daphnejacksontr.bsky.social · 02/07/2026

Yesterday we attended the launch of the Women in Research Charter with the Secretary of State for Science, Technology and Innovation, Liz Kendall - along with some of our Fellows. See the Trust being included in the Charter’s “Best Practice pack” - www.gov.uk/government/p...

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Reposted by Benjamin Schuster-Böckler

Netherlands Cancer Institute @nkinl.bsky.social · 01/07/2026

We are looking for a Junior Group Leader in Early Cancer Detection: an innovative scientist ready to build an independent research group and bring new ideas to one of our key research themes. Apply: www.nki.nl/news-events/... #tenure #vacancy #juniorPI #faculty #NKI

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Reposted by Benjamin Schuster-Böckler

Nitika Taneja @TanejaLab @nitikataneja.bsky.social · 01/07/2026

Very excited to share our new Nature study! We discovered that replication stress stabilizes CTCF-dependent chromatin loops enclosing stressed nascent DNA, where G9a-mediated heterochromatin protects it from nucleolytic degradation. rdcu.be/frzLg Huge thanks to all our collaborators and co-authors!

nature.com

Replication-stress-induced chromatin loops protect fork stability - Nature

Replication stress induces the formation of transient chromatin loops that enclose de novo heterochromatin-enriched stalled replication forks.

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Reposted by Benjamin Schuster-Böckler

Genetics Society UK @gensocuk.bsky.social · 26/06/2026

Congratulations to Prof Richard Durbin, winner of the 2026 Genetics Society Medal! His pioneering work in computational genomics has transformed how we analyse and understand genome sequences.

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Reposted by Benjamin Schuster-Böckler

UK 🇬🇧 🤝 🇺🇦 □ @ukbastard.bsky.social · 07/06/2026

Scientists ejected from diabetes conference for distributing journal reprints Those ousted included ADA journal editor-in-chief Steven Kahn and former ADA president Desmond Schatz arstechnica.com/science/2026...

arstechnica.com

Scientists ejected from diabetes conference for distributing journal reprints

Those ousted included ADA journal editor-in-chief Steven Kahn and former ADA president Desmond Schatz...

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Reposted by Benjamin Schuster-Böckler

Madhu Pai, MD, PhD @madhupai.bsky.social · 06/06/2026

We need to make sure this editorial goes viral Misguided Brushes of a Pen Continue to Dismantle and Destroy Biomedical Research in the United States: We Can No Longer Afford Complacency and Fear. We Must All Act Now! diabetesjournals.org/care/article...

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Reposted by Benjamin Schuster-Böckler

Dan Landau @landau.bsky.social · 04/06/2026

Exciting breakthrough technology from the lab, now live in @cellcellpress.bsky.social ! Instead of cutting the genome where proteins bind (e.g., Cut&Tag), D&D-seq scars the DNA with a deaminase, allowing single cell genome mapping of TFs and chromatin remodellers!

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Benjamin Schuster-Böckler @dagams.bsky.social · 31/05/2026

Is it just me, or did @anthropic.com crank up the sycophancy levels again in Opus 4.8? I'm getting a lot of "great idea" and "very good point" comments since moving from 4.7 🤔

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Benjamin Schuster-Böckler @dagams.bsky.social · 30/05/2026

This is really exciting - and more evidence for Rust taking over bioinformatics.

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Reposted by Benjamin Schuster-Böckler

Rob Klose @robklose.bsky.social · 29/05/2026

Help please! We need to do some large(ish) cell culture inhibiting E-cadherin with a monoclonal antibody. Does anyone have the DECMA-1 hybridoma cell line so we could purify our own antibody? or a similar monoclonal that would do the job. Any help greatly appreciated, just DM me. Please repost!

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Benjamin Schuster-Böckler @dagams.bsky.social · 29/05/2026

Cool new paper from Singapore's Gastric cancer consortium. They show that intestinal metaplasia in the stomach invariably features SBS17, just like Barrett's esophagus. They also confirm our findings from 2018 that SBS17 is strongly DNA-replication asymmetrical, but still no answer to what causes it

aacrjournals.org

Mutational Signatures and Clonal Hematopoiesis in Intestinal Metaplasia across Countries with Varying Stomach Cancer Incidence

International analysis of premalignant intestinal metaplasia identifies Helicobacter pylori variants, somatic drivers, mutational signatures, and clonal hematopoiesis as risk factors associated with p...

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Benjamin Schuster-Böckler @dagams.bsky.social · 22/05/2026

I know Sean from when I worked on PFAM, then met him again many times at HHMI's Janelia Farm campus. Seeing his group being destroyed like this is devastating - he's a titan of bioinformatics, his contributions have been transformational for genomics and proteomics. Utter madness!

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Robin Bisson @robinbisson.bsky.social · 22/05/2026

Patrick Vallance has twice written to MPs saying the budget for curiosity-driven research “will grow as the economy grows” But UKRI has flat cash for curiosity-led research through to 2030 When @isaacbarbosa1.bsky.social asked DSIT where the growth would come from, they had no answer A mystery

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Benjamin Schuster-Böckler @dagams.bsky.social · 22/05/2026

Thank you for sleuthing your way through that rabbit hole - shocking levels of deception (and incompetence at that) on the side of Thermo 😱

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Johan Duchêne @johanduchene.bsky.social · 21/05/2026

@sholtodavid.bsky.social Have you seen this WB from ThermoFisher? Still anti-p53 antibody, but another clone (MA-12648 instead MA5-12557). It also looks like that the band in lane 3 was rotated and reused in lane 4. Moreover, it seems that same band was used for the 2 different clones.

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Ian Sudbery @iansudbery.bsky.social · 13/05/2026

Incredible work. Will be going straight in my final year lectures as an example of how to combine genome-wide data with modelling to answer mechanistic hypotheses.

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Benjamin Schuster-Böckler @dagams.bsky.social · 09/05/2026

Extremely cool stuff coming from the team here: re-implementing htslib from scratch, with a focus on performance, compile-time checks and easier API #bioinformatics #ngs

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Reposted by Benjamin Schuster-Böckler

Seth Stadick @ducktapeprogrammer.bsky.social · 03/05/2026

For the most read-data heavy path in perbase, seqair is ~1.5x faster, which is awesome! I need to explore with some more datasets, but that's a pretty awesome win right off the bat.

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Oxford Clarion @oxfordclarion.bsky.social · 09/05/2026

Oxford City Council is to mark Europe Day today, by flying the European flag. Louise Upton, Lord Mayor of Oxford, fresh from her visit to twin town Leiden's Liberation Day celebration, (and re-election on Thursday), is hosting a European Reception in her Parlour at Oxford Town Hall.

Photo from last year's European reception. Around.a dozen people stand in front of an EU flag in a wood panelled room

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