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Reposted by Antoine Limasset

Ethan Mollick @emollick.bsky.social · 8h

I think people are still unprepared for a world where you cannot trust any video content, despite years of warning.

Even when Google & OpenAI include watermarks, those can be easily removed, and open weights AI video models without guardrails are coming. www.404media.co/sora-2-water...

Sora 2 Watermark Removers Flood the Web

Bypassing Sora 2's rudimentary safety features is easy and experts worry it'll lead to a new era of scams and disinformation.

www.404media.co

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Reposted by Antoine Limasset

Ben Langmead @benlangmead.bsky.social · 1d

I've added 7 videos to my Burrows-Wheeler indexing playlist (www.youtube.com/playlist?lis...), rounding out the r-index series and adding a 5-part series on the move structure. Now 27 videos in that playlist. I aim to add videos on prefix-free parsing, PBWT, Wheeler languages/automata in the future.

Burrows-Wheeler Indexing - YouTube

Videos on : (a) the Burrows-Wheeler Transform (BWT), (b) the FM Index, which uses the BWT to construct a full-text index, (c) Wheeler graphs, (d) r-index, an...

www.youtube.com

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Reposted by Antoine Limasset

Titus Brown @titus.idyll.org · 1d

A new paper from the lab! Work led by
@drtamermansour.bsky.social and others not here on bsky. "We propose the Great Genotyper, a population-scale genotyping workflow to address the N+1 problem."

The Great Genotyper: a graph-based method for population genotyping of small and structural variants

Long-read sequencing (LRS) enables high-quality structural variant (SV) discovery. SV genotypers utilize these precise call sets to improve the recall and precision of genotyping in short-read sequenc...

pmc.ncbi.nlm.nih.gov

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Reposted by Antoine Limasset

Bede Constantinides @bedec.bsky.social · 2d

"OpenZL is our answer to the tension between the performance of format-specific compressors and the maintenance simplicity of a single executable binary."
engineering.fb.com/2025/10/06/d...

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Reposted by Antoine Limasset

Javier Santoyo @jsantoyo.bsky.social · 5d

A closed-loop method for precise genome size estimation using HiFi reads. #GenomeSize #HiFi #LongReads #Genomics #Bioinformatics #BMCgenomics 🧬 🖥️
bmcgenomics.biomedcentral.com/articles/10....

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Reposted by Antoine Limasset

Roland Faure @rfaure.bsky.social · 5d

Our preprint on our new metagenomic HiFi assembler Alice is out 🥳 Based on a *new sketching method* (🧵1/6)
👉 Preprint www.biorxiv.org/content/10.1...
👉 Github github.com/rolandfaure/...

Alice: fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching

We introduce Mapping-friendly Sequence Reduction (MSR) sketches, a sketching method for high-fidelity (HiFi) long reads, and Alice, an assembler that operates directly on these sketches. MSR produces ...

www.biorxiv.org

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Reposted by Antoine Limasset

Signal @signal.org · 5d

We are alarmed by reports that Germany is on the verge of a catastrophic about-face, reversing its longstanding and principled opposition to the EU’s Chat Control proposal which, if passed, could spell the end of the right to privacy in Europe. signal.org/blog/pdfs/ge...

signal.org

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Reposted by Antoine Limasset

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 8d

Alice: fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching https://www.biorxiv.org/content/10.1101/2025.09.29.679204v1

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Reposted by Antoine Limasset

RECOMB Conference Series @recombconf.bsky.social · 6d

#RECOMB2026 is now accepting submissions and we'd love to see your best work!

📌 Abstract registration: Nov 7, 2025
📌 Full paper submission: Nov 14, 2025

📜 More info: recomb.org/recomb2026/call_for_papers.html

RECOMB 2026 | CALL FOR PAPERS

Call For Papers

recomb.org

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Reposted by Antoine Limasset

Mike Wiser @drmikewiser.bsky.social · 7d

I got my first "I object to you saying in class that there is no biological basis for a sex binary because the current political situation and also my religious views" email for the term.

Fun times.

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Reposted by Antoine Limasset

Heng Li @lh3lh3.bsky.social · 9d

Do you know ~60% of human SVs fall in ~1% of GRCh38? See our new preprint: arxiv.org/abs/2509.23057 and the companion blog post on how we started this project and longdust: lh3.github.io/2025/09/29/o.... Work with Alvin Qin

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Antoine Limasset @npmalfoy.bsky.social · 9d

What the heck is that ???????

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Reposted by Antoine Limasset

Ryan Wick @rrwick.bsky.social · 9d

Happy to share that the paper describing Autocycler is now 100% up:
doi.org/10.1093/bioi...
(1/3)

Autocycler: long-read consensus assembly for bacterial genomes

AbstractMotivation. Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-l

doi.org

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Reposted by Antoine Limasset

RECOMB Conference Series @recombconf.bsky.social · 12d

#RECOMB2026 will be in Thessaloniki, Greece on May 26-29, 2026. Satellites on May 24-25. Save the date!

Το συνέδριο #RECOMB2026 θα πραγματοποιηθεί στη Θεσσαλονίκη, στις 26-29 Μαΐου 2026. Οι δορυφορικές εκδηλώσεις θα διεξαχθούν στις 24-25 Μαΐου 2026. Σημειώστε την ημερομηνία!

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Reposted by Antoine Limasset

David Monniaux @monniauxd.bsky.social · 13d

Vous pouvez soutenir ma proposition à la Cour des Comptes d'examiner les marchés publics de voyagistes, notamment dans l'ESR :
participationcitoyenne.ccomptes.fr/processes/co...

Les marchés publics de voyagistes - Contributions - 2025 - Aidez-nous à enrichir notre programme de travail - Plateforme de participation de la Cour des Comptes

Corps de la contributionLes administrations et opérateurs publics, notamment ceux de l'enseignement supérieur et de la recherche, fond appel à des agences de voyage (FCM, TravelPlanet…) pour l'hôtelle...

participationcitoyenne.ccomptes.fr

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Reposted by Antoine Limasset

Yann Ponty @yannponty.bsky.social · 12d

Prière de soutenir cette demande (un compte est nécessaire, mais réalisable en 2min chrono, promis !) pour reconsidérer l'utilité des marchés voyages de nos institutions préférées.

David Monniaux @monniauxd.bsky.social · 13d

Vous pouvez soutenir ma proposition à la Cour des Comptes d'examiner les marchés publics de voyagistes, notamment dans l'ESR :
participationcitoyenne.ccomptes.fr/processes/co...

Les marchés publics de voyagistes - Contributions - 2025 - Aidez-nous à enrichir notre programme de travail - Plateforme de participation de la Cour des Comptes

Corps de la contributionLes administrations et opérateurs publics, notamment ceux de l'enseignement supérieur et de la recherche, fond appel à des agences de voyage (FCM, TravelPlanet…) pour l'hôtelle...

participationcitoyenne.ccomptes.fr

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Reposted by Antoine Limasset

Paul Medvedev @pashadag.bsky.social · 13d

Thank you folks for your feedback on our survey about Hash functions in genomic sequence analysis. We've updated the paper and you can see the new version here: tinyurl.com/4kk9ccmt.

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Reposted by Antoine Limasset

SKL🇪🇺🇺🇦 @sklafon1.bsky.social · 13d

OYEZ!OYEZ!
Si vous avez des juicy stories d'agences de voyages de marché ESR avec des pratiques commerciales plus que douteuses, dites-moi en MP et je ferai passer à ma copine Orla.

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Antoine Limasset @npmalfoy.bsky.social · 15d

Since errors are evaluated by aligning them to a reference, we can propose a new metric based on this alignment. This metric could evaluate the frequency of repeated errors at a given position and, more importantly, the deviation from the rate expected under a uniform distribution hypothesis.

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Antoine Limasset @npmalfoy.bsky.social · 15d

Would an "imperfect" measure of uniformity be the proportion of errors that could be corrected at a given read depth using the given technology?

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Antoine Limasset @npmalfoy.bsky.social · 15d

Thank you so much for the clarifications! I am indeed interested in the per-read accuracy, but I must admit I don't understand the importance of distinguishing between Ti and Tv.

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Antoine Limasset @npmalfoy.bsky.social · 15d

This figure is extremely interesting, very surprising and exciting results from current state of sequencing technologies!

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Antoine Limasset @npmalfoy.bsky.social · 15d

What a day for genome assembly!
Congrats to everyone!

Adam Phillippy @aphillippy.bsky.social · 16d

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

A complete diploid human genome benchmark for personalized genomics

Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...

www.biorxiv.org

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Reposted by Antoine Limasset

Adam Phillippy @aphillippy.bsky.social · 16d

Clinically routine T2T genomes are finally in sight! 🧪🧬💯 @genomeinabottle.bsky.social [14/14]

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Reposted by Antoine Limasset

Adam Phillippy @aphillippy.bsky.social · 16d

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

A complete diploid human genome benchmark for personalized genomics

Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...

www.biorxiv.org

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