Finally a good take

Sophie Huiberts@sophie.huiberts.me · 7d ago

Guest blog by me

I’m excited to share our new preprint introducing HipHap, a tool for assigning long reads to haplotype-resolved diploid reference assemblies! With Max Marin, Matthew Meyerson, and @lh3lh3.bsky.social Preprint: www.biorxiv.org/content/10.6... 🧵 1/6

HipHap: Haplotype Assignment and Confidence Scoring for Diploid Reference Genomes

Diploid genome assemblies are now routinely available, but most read aligners were designed for haploid references, which have long been the gold standard. When reads are aligned to a diploid assembly...

biorxiv.org

You should be fascinated hitting the power button on your computer.

 Every boot on an x86 machine iterates through the entire sequence of computing evolution in a few milliseconds:

This.

Katie Spoon@kspoon.bsky.social · 5d ago

We found that the most gendered experience wasn’t work-life balance, the focus of most retention efforts. It was feeling devalued, in formal evaluations, but particularly in everyday interactions. Unlike every other topic, the gender gap in devaluation was larger among more senior faculty.

(very) nice results plus love the notion of student-generated paper

Pavel Veselý@pavelvesely.bsky.social · 5d ago

Excited to share a *student-generated* paper: arxiv.org/abs/2610.18347 (to appear at SODA). It's about data sketches (streaming algos.) for approximating data distributions with high accuracy for the tails. The credit goes to my PhD student Tomáš Domes who worked hard on the problem for a few years

2) The scientists whose papers Swartz downloaded were already paid. We’re paid to do research; we aren’t paid when papers come out. The people you pay to access papers are publishers, which often have a bigger profit margin than Big Pharma. So the two are not equivalent. Scientists were not victims.

Aaron Swartz, coding prodigy and hacktivist who helped develop RSS and was a co-founder of Reddit, died by suicide after facing $1 million in fines and 35 years in prison for felony charges, just for downloading pdfs of research papers with the intention of making them accessible to the public.

Julie S. Lalonde@julieslalonde.bsky.social · 5d ago

Being GenX/Millennial is such a trip. In our lifetimes, we saw people our age getting wild criminal penalties for pirating music and now have to sit and watch as companies gobble up our work with impunity.

In a bid to tackle the deluge of manuscripts it now receives, preprint server arXiv has announced a cap of two papers per month for each submitting researcher go.nature.com/4dBP2MT

ArXiv versus AI slop: will capping preprint submissions work?

Major preprint platform tightens its rules to curb a surge of submissions, including those generated by artificial-intelligence tools.

go.nature.com

Katie Zacharia sat on the advisory board of an organization that calls for women who have abortions to be executed “in the public square,” and for pro-choice Americans to lose their right to hold public office.

Trump’s New Press Secretary Supports the Death Penalty for Abortion Patients

10.13.26

jessica.substack.com

Sebastiano Vigna: PHastR: Faster Minimal Perfect Hashing with Rotated Layouts https://arxiv.org/abs/2610.17833 https://arxiv.org/pdf/2610.17833 https://arxiv.org/html/2610.17833

Coding learning need to change! -> advice to -Write modular code -Comments -Think about code organization -Respect standards ...

It'S Gonna Be A Big Adjustment Daniel Larusso

ALT: It'S Gonna Be A Big Adjustment Daniel Larusso

static.klipy.com

Nature@nature.com · 7d ago

Programming is still an essential skill, but how you do it needs to change, says Jacques Cornwell go.nature.com/3Uj26QK

I tried to cook mac&cheese several times. Consistently failed. Thought it was French DNA preventing a catastrophe. Turns out, it was not. The key ingredient, my friends, is Maroilles!

Many people are (correctly) saying this: www.seangoedecke.com/llms-reward-...

Skani (github.com/bluenote-157...) is now v0.4.0! Big performance update: **~2.5x faster** and ~30-40% less RAM for average nucleotide identity (ANI) comparison of genomes. The database format has changed (breaks forward compatibility; watch out!).

GitHub - bluenote-1577/skani: Fast average nucleotide identity (ANI) calculator for bacterial genomes, MAGs, and contigs. Supports genome comparisons and large-scale database searches.

Fast average nucleotide identity (ANI) calculator for bacterial genomes, MAGs, and contigs. Supports genome comparisons and large-scale database searches. - bluenote-1577/skani

github.com

How much do PhD students earn? The first comprehensive overview of PhD income shows vast imbalances across much of Europe Read the full story: www.nature.com/articles/d41...

Finally realised what tech companies insisting 'you need to suffer some hurt right now to enjoy a glorious future' reminded me of

I thought it was already commonly accepted (and beyond US politics...)

Elmo Shrugs for NinersUnited

ALT: Elmo Shrugs for NinersUnited

static.klipy.com

Thomas Steinke@stein.ke · last wk.

50 years from now it will be widely accepted that a significant fraction of US politics in the 2020s was driven by hostile foreign actors. People studying history will think everything makes sense through this lens.

Oh sweet, new autocycler version dropped. General performance improvement and unaligned BAM support for processing basecalled output directly (though I feel like regular users would still want a filtered fastq for their assemblies). github.com/rrwick/Autoc...

Release Autocycler v0.8.0 · rrwick/Autocycler

This release: Adds support for unaligned BAM (uBAM) input reads in addition to FASTQ format. uBAM is the default format for basecalled ONT reads. Has miscellaneous code refactoring and optimisatio...

github.com

La honte d'écrire cet article est sans mesure

franceinfo@franceinfo.fr · 2w ago

Le mouvement lycéen se poursuit et la tension reste forte dans les manifestations. Certains CRS sont parfois confrontés à des jeunes du même âge que leurs propres enfants. Franceinfo a recueilli le témoignage de deux d'entre eux.

At this point, it's safe to say that multiple "results" in the OpenAI problems have been "inspired" by the work (sometimes fully spelled out) of researchers interacting with their chatbot How do we, researchers, defend both feeding the monster *and* exposing ourselves to this kind of abuse?

"""And of course there’s a lot for us to learn from the aliens"""

They hounded Aaron Swartz to death for downloading papers from jstor but society is now supposed to just accept mass theft because this thing can write that TPS report *for* you. en.wikipedia.org/wiki/Aaron_S...

Aaron Swartz - Wikipedia

en.wikipedia.org

John Scalzi@scalzi.com · 2w ago

This is your occasional reminder that generative "AI" in particular could have been developed on public domain materials and/or licensed and compensated works but the major players intentionally, methodically and systemically chose to steal labor from working creative folks instead

A species of lungfish found in South America has claimed the title of the animal with the biggest genome sequenced so far. Learn more on #WorldAnimalDay: https://scim.ag/46OMl6v

US social media companies are interfering in the Brazilian elections in favour of the Far Right’s Flávio Bolsonaro. Meta is the latest. It’s just blocked the campaign account of President Lula in the final stretch of the election.

Meta restringe la cuenta de Lula y su partido alerta por posible injerencia extranjera

De cara a las elecciones en Brasil, Lula enfrenta a Meta por restringir su cuenta mientras su partido alerta por posible injerencia extranjera.

elespectador.com

ISMB is ranked A in CORE largely thanks to @yannponty.bsky.social ‘s tireless efforts. I believe ECCB could/should also be ranked A considering the scientific committee’s qualifications, acceptance rate etc. But it takes a lot of work to do the advocacy….

Sina Majidian@sinamajidian.bsky.social · 3w ago

I'm surprised to see ECCB is ranked C in the CORE ranking! Good for ISMB, which is ranked A. No ranking for ACM-BCB! portal.core.edu.au/conf-ranks/?...

Don't tell me - the industry based on the largest wholesale theft in history... stole stuff you gave to it?

Carl Zimmer@carlzimmer.com · 3w ago

Four days ago, a scientist was surprised by the news that Anthropic discovered new virus genes for making DNA. He says he’s been studying them for years—and feeding his data to Anthropic’s AI as part of his own research. Coincidence? Here’s my story. nyti.ms/3VSWayc

Ok comp. bio / bioinformatics / genomics friends. Let's talk about @recombconf.bsky.social and, specifically, the way in which the "proceedings" have evolved. This seems like something that we, as a community, should address. RECOMB now has no "published" proceedings in the classic sense.

Cuttlefish 3.0.3 is out! github.com/COMBINE-lab/... Fun little jaunt with Opus 5.5 to substantially reduce the memory requirement (especially at moderate thread counts). Now it's both non-trivially faster *and* more memory-frugal than the initial C++ implementation!

Trying to achieve something in C++ after having been immersed in the Rust ecosystem for the past few years is *wild*. Incredibly broken build systems, obscure linker errors from three CMakes deep, documentation snippets that don't compile, no info on which class is declared in which header...

SeqKit is now faster and uses 40% less memory when reading large FASTA records, such as human genomes, though it still uses more RAM than tools written in C/C++/Rust. Worth upgrading! github.com/shenwei356/s...

GitHub - shenwei356/seqkit: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation - shenwei356/seqkit

github.com