iiinova — where your digital self keeps evolving

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Andrea Ganna @andganna.bsky.social · 15/12/2025

🌟 Applications for the 2026 Leena Peltonen School of Human Genetics are open! Back after a great 2025 edition: ~20 global leaders and ~20 PhD students shaping the future of genomics. 📅 July 26–30, 2026 📍 Wellcome Genome Campus, UK 📝 Apply by March 6 → www.lpshg.com

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Camilla Ciolli Mattioli @cciollimattioli.bsky.social · 06/02/2026

Thrilled to announce that I’ve just opened my research lab at @helmholtz-hiri.bsky.social ! A huge thank you to my mentor Roi Avraham (and lab members!) for the incredible training and support that made this possible.

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Wolfgang Huber @wkhuber.bsky.social · 28/01/2026

There is the obvious fraud potential, but I think something much more fundamental is going to happen, too. It will change the meaning of what a "research publication" is. The reason why people read papers is to learn something that they couldn't reproduce in seconds by pushing a few buttons.

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nilswagner.bsky.social @nilswagner.bsky.social · 26/01/2026

How many high-impact developmental variants are we missing by relying only on adult splicing annotations? We address this in our preprint “Aberrant splicing prediction during human organ development”: www.biorxiv.org/content/10.1...

biorxiv.org

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Lisa Buchauer @libuchauer.bsky.social · 07/01/2026

I'm excited to announce we're recruiting a PhD student in Machine Learning for Immunology within the Einstein Center for Early Disease Interception, together with Simon Haas!

lnkd.in

This link will take you to a page that’s not on LinkedIn

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Gioele La Manno @gioelelamanno.bsky.social · 16/10/2025

🧠 The Lipid #Brain Atlas is out now! If you think #lipids are boring and membranes are all the same, prepare to be surprised. Led by @lucafusarbassini.bsky.social with Giovanni D'Angelo's lab, we mapped membrane lipids in the mouse brain at high resolution. www.biorxiv.org/cgi/content/...

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Yun S. Song @yun-s-song.bsky.social · 22/09/2025

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics. www.biorxiv.org/content/10.1... (1/n)

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Constantin Pape @cppape.bsky.social · 16/09/2025

I did not know Taylor Swift was moonlighting in soliciting contributions for fake journals!

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Pia Rautenstrauch @prauten.bsky.social · 13/09/2025

Check out my talented colleagues' study, profiling hundreds of CRISPRa-responsive regulatory elements surrounding PHOX2B, a key player in neuroblastoma, using a targeted scRNA-seq screen in a neuroblastoma cell line.

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Michael Love @mikelove.bsky.social · 08/09/2025

Our first Fall #tidyomics meeting will be this Wed 10 September, early in US / noon in Europe / late in Australia. Feel free to join if you're interested in what we are doing to make omics data more amenable to tidy data analysis. Organized with Stefano @stemang.bsky.social

Meeting agenda

Sep 10, 2025
Attendees:
Links:
Agenda (feel free to add your items):
• Blog almost ready for R blogger linkage thanks to @Izabela Mamede, @Mengyuan Shen and @Maria Doyle
• New posts from many including
@Juan Henao and myself
• Ideas for other posts?
• There is tidybulk v2 ready to be submitted. Some feedback would be nice there.
• Stefano's new speedy code in tidySE
• https://github.com/tidyomics/
genomics-todos/issues/19#is suecomment-3239791713
• https://github.com/tidyomics/t
idySummarizedExperiment/i ssues/106
• Report back from tidyomics workshop at useR! (Justin and Mike)
• Other projects in the works?
• Ideas for engaging new users?
New developers?

These are the corresponding times for your meeting:
Location
Local Time
Durham (USA - North Carolina)
Wednesday, September 10, 2025 at 6:00:00 am
Adelaide (Australia - South Australia)
Wednesday, September 10, 2025 at 7:30:00 pm
Paris (France - Paris) |
Wednesday, September 10, 2025 at 12:00:00 noon
Corresponding UTC (GMT)
Wednesday, September 10, 2025 at 10:00:00

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France Culture @franceculture.fr · 10/09/2025

L’effet Matilda n’est pas une fiction. Il est inscrit dans l’histoire scientifique. Il a éclipsé des femmes comme Marthe Gautier, née il y a cent ans, pionnière oubliée de la trisomie 21. ➡️ l.franceculture.fr/1LI

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Tuomo Hartonen @tuomohartonen.bsky.social · 27/08/2025

Are electronic health records (EHR) more predictive of disease onset than polygenic scores? Can we transfer EHR-based prediction models between countries? Our study on these questions using 3 biobank-based studies with N>845K, is out in @natgenet.nature.com today: www.nature.com/articles/s41...

nature.com

Cross-biobank generalizability and accuracy of electronic health record-based predictors compared to polygenic scores - Nature Genetics

Comparison of electronic health record-based phenotype risk scores (PheRS) and polygenic scores (PGS) across 13 common diseases and three biobank-based studies indicates that PheRS and PGS may provide...

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Alex Diaz-Papkovich @alexandr.bsky.social · 27/08/2025

Last year I met a bunch of great researchers who work with high-dimensional data at a Dagstuhl seminar. This week we put out a preprint about the history and philosophy of low-dimensional embedding methods, their applications, their challenges, and their possible future arxiv.org/abs/2508.15929

The participants of Dagstuhl Seminar 24122 standing on steps outside (from https://www.dagstuhl.de/24122)

Multiple types of embeddings (UMAP, t-SNE, Laplacian Eigenmaps, PHATE, PCA, MDS) of Wikipedia text data labelled by a text summaries generated by an LLM. Methods like UMAP and t-SNE show cluster structure that reflect shared subject matter in text, whiel other methods show more continuous structure.

Multiple embedding methods (PCA, Laplacian Eigenmaps, t-SNE, MDS, PHATE, UMAP) of primate brain organoids at different time periods. Different methods highlight different aspects of development, such as clusters of similar cell types or time courses of cell development.

Multiple embedding methods (PCA, Laplacian Eigenmaps, t-SNE, MDS, PHATE, UMAP) of 1000 Genomes Project genotypes. Different methods reflect different aspects of demographic history of populations.

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Dmitry Kobak @hippopedoid.bsky.social · 27/08/2025

We spent a year writing this review of low-dim embeddings and arguing about things like epistemic roles and best practices :-) 20+ authors are all participants of the Dagstuhl seminar we held last year: www.dagstuhl.de/24122. Led by @alexandr.bsky.social and Cyril de Bodt. arxiv.org/abs/2508.15929

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Emma Dann @emmamarydann.bsky.social · 25/08/2025

We're committed to support as many attendees as possible join us at #scverse2025 - feel free to reach out if you have questions!

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Yun S. Song @yun-s-song.bsky.social · 15/08/2025

Antibodies are highly diverse, but most possible sequences are unstable or polyreactive. In this work, just published in Cell Syst., we propose a new source of data for modeling constraints from these properties. Our models show clear improvements in predicting Ab dysfunction. (1/n) t.co/qCZERPUMPF

t.co

https://authors.elsevier.com/a/1lbX08YyDfuZWX

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Simon Haas @simonhaas.bsky.social · 07/08/2025

Excited to share our latest paper @natmethods.nature.com We present a high-throughput framework to map cellular interactions at ultra-high scale – broadly applicable from whole-organism immune response mapping to personalized therapy response prediction (1/4). www.nature.com/articles/s41...

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Liana Lareau @lianafaye.bsky.social · 07/08/2025

This preprint from Helen Sakharova is one of the coolest things to come out of my lab: “Protein language models reveal evolutionary constraints on synonymous codon choice.” Codon choice is a big puzzle in how information is encoded in genomes, and we have a new angle. www.biorxiv.org/content/10.1...

biorxiv.org

Protein language models reveal evolutionary constraints on synonymous codon choice

Evolution has shaped the genetic code, with subtle pressures leading to preferences for some synonymous codons over others. Codons are translated at different speeds by the ribosome, imposing constrai...

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Michael Love @mikelove.bsky.social · 05/08/2025

Evaluating something like batch correction requires looking at the data, and picking metrics that capture what you care about. Great work @prauten.bsky.social and @uweohler.bsky.social

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Pia Rautenstrauch @prauten.bsky.social · 01/08/2025

Truly grateful for the exceptional opportunity to participate in #LPSHG2025 last week, featuring a stellar ✨ lineup of leading researchers who doubled as tutors, alongside inspiring fellow PhD students. Excited to apply my learnings and see where this collaborative spirit takes genomics next!

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Peter Koo @pkoo562.bsky.social · 16/07/2025

*Easter egg alert* NOT in the published paper. We also benchmarked Evo 2 and while it did better than other gLMs (consistent that scale can improve gLMs), it still falls short of a basic CNN trained using one-hot sequences and far short of supervised SOTA

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Stein Aerts @steinaerts.bsky.social · 04/06/2025

The deadline for the VIB.AI group leader positions is approaching - send in your CV and short research plan before 14th June to start your BioML research lab in Leuven or Ghent

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Gherman Novakovsky @gnovakovsky.bsky.social · 30/05/2025

Excited to share my first contribution here at Illumina! We developed PromoterAI, a deep neural network that accurately identifies non-coding promoter variants that disrupt gene expression.🧵 (1/)

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recombseq.bsky.social @recombseq.bsky.social · 25/04/2025

We finally concluded the meeting. Thanks to all attendees for their scientific contributions and for traveling (near or far) to the meeting! Thanks to the local organizers for the infrastructure and catering, and thanks to the co-organizers @yaronorenstein.bsky.social @camillemrcht.bsky.social!

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Emma Chory, Ph.D. @chorye.bsky.social · 14/04/2025

When investors learn that the trait for green eyes is also ~20 SNPs

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Janelle Shane @janelleshane.com · 13/04/2025

1. LLM-generated code tries to run code from online software packages. Which is normal but 2. The packages don’t exist. Which would normally cause an error but 3. Nefarious people have made malware under the package names that LLMs make up most often. So 4. Now the LLM code points to malware.

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RECOMB Conference Series @recombconf.bsky.social · 15/03/2025

40 days until #RECOMB2025 in Seoul! 523 attendees confirmed—thank you! 🥳 For those who haven't registered yet, we have great news! 📢 Early bird deadline is extended to Friday, March 21st 📢 Register now at recomb2025.com 🎟️

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Soapbox Science Berlin @berlin-soapbox.bsky.social · 21/02/2025

Last day to apply ⏰😱! If you haven’t already done so, now is the time! Apply to be one of the speakers at the #SoapboxScience summer event and present your research in a fun and relaxed atmosphere ✨ #WomenInSTEM #WomenInScience #Scicomm

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Pia Rautenstrauch @prauten.bsky.social · 04/02/2025

Look for the bare necessities with manifold learning... 🐻🎶 Data science meets Disney in the most unexpected places! Credits to the scikit-learn docs: scikit-learn.org/stable/modul... #DataScience #ManifoldLearning #TechHumor

Excerpt from the scikit-learn docs on Manifold learning quoting Baloo's song from the Jungle Book.

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Leif S. Ludwig @leifludwig.bsky.social · 31/01/2025

Join us to connect with the vibrant #singlecell community. 📢Register for the #ISCO'25 Conference "Innovations in #SingleCell #OMICS" in Berlin! 🗓️ 12-13 May 2025 🎤 Fantastic Keynote and Invited Speakers 🫵🏿 Many slots for talks: submit your abstract 🔗http://isco-conference.eu Please spread the word!

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