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Pia Rautenstrauch

@prauten.bsky.social

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Pia Rautenstrauch @prauten.bsky.social · Jan 24

1/4 🧵 Preprint alert: In "Metrics Matter: Why We Need to Stop Using Silhouette in #SingleCell #Benchmarking," we reveal critical flaws in common #Evaluation metrics for #Integration and propose robust alternatives. @uweohler.bsky.social
www.biorxiv.org/content/10.1...

Metrics Matter: Why We Need to Stop Using Silhouette in Single-Cell Benchmarking

Current-day single-cell studies comprise complex data sets affected by nested batch effects caused by technical and biological factors, relying on advanced integration methods. Silhouette is an establ...

www.biorxiv.org

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Reposted by Pia Rautenstrauch

Yun S. Song @yun-s-song.bsky.social · 17d

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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Reposted by Pia Rautenstrauch

Constantin Pape @cppape.bsky.social · 22d

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

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Pia Rautenstrauch @prauten.bsky.social · 25d

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.

Dubravka Vucicevic @dr-dusa.bsky.social · 29d

I am so happy to share that our paperis officially published in Cell Genomics! In this paper, we describe TESLA-seq, which combines pooled CRISPR activation with targeted single-cell RNA-seq to map enhancer-gene connections at high sensitivity.

Link to the full story: www.cell.com/cell-genomic...

Reposted by Pia Rautenstrauch

Michael Love @mikelove.bsky.social · Sep 8

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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Reposted by Pia Rautenstrauch

France Culture @franceculture.fr · 29d

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.
➡️ https://l.franceculture.fr/1LI

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Reposted by Pia Rautenstrauch

Tuomo Hartonen @tuomohartonen.bsky.social · Aug 27

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...

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...

www.nature.com

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Reposted by Pia Rautenstrauch

Alex Diaz-Papkovich @alexandr.bsky.social · Aug 27

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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Reposted by Pia Rautenstrauch

Dmitry Kobak @hippopedoid.bsky.social · Aug 27

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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Reposted by Pia Rautenstrauch

Emma Dann @emmamarydann.bsky.social · Aug 25

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

scverse @scverse.bsky.social · Aug 25

💰 Travel Grants Available for scverse conference 2025! 💰
Did you know we are offering grants to help anyone in financial need attend our annual conference? 🌍
🧵

#scverse #scverse2025 #SingleCell #Conference #StanfordUniversity #TravelGrant

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Reposted by Pia Rautenstrauch

Yun S. Song @yun-s-song.bsky.social · Aug 15

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

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

t.co

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Pia Rautenstrauch @prauten.bsky.social · Aug 12

Thanks, @paubadiam.bsky.social! That makes sense. Excited for the results 🔎.

Pia Rautenstrauch @prauten.bsky.social · Aug 12

Very well set up benchmark and informative comparisons! I might have missed it, but did you also compare the performance of the same methods using either truly paired vs synthetically paired multimodal data as input in terms of your performance evaluation metrics, in addition to network consistency?

Pia Rautenstrauch @prauten.bsky.social · Aug 12

By now, I’ve heard from many people who’ve noticed inconsistencies when using silhouette-based metrics for horizontal data integration evaluation. I hope we’ve helped shed light on why these metrics fall short and that our recommendations prove useful to you!

Reposted by Pia Rautenstrauch

Simon Haas @simonhaas.bsky.social · Aug 7

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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Reposted by Pia Rautenstrauch

Liana Lareau @lianafaye.bsky.social · Aug 7

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...

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...

www.biorxiv.org

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Pia Rautenstrauch @prauten.bsky.social · Aug 6

Lucky to have inspiring and supportive mentors by my side! @mikelove.bsky.social

Reposted by Pia Rautenstrauch

Michael Love @mikelove.bsky.social · Aug 5

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

Nature Biotechnology @natbiotech.nature.com · Jul 30

Shortcomings of silhouette in single-cell integration benchmarking - @uweohler.bsky.social @prauten.bsky.social @mdc-bimsb.bsky.social @mdc-berlin.bsky.social @humboldtuni.bsky.social go.nature.com/4fcQzZr

Shortcomings of silhouette in single-cell integration benchmarking - Nature Biotechnology

Silhouette score is unsuitable as a metric for single-cell data integration.

go.nature.com

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Reposted by Pia Rautenstrauch

Nature Biotechnology @natbiotech.nature.com · Jul 30

Shortcomings of silhouette in single-cell integration benchmarking - Nature Biotechnology

Silhouette score is unsuitable as a metric for single-cell data integration.

go.nature.com

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Pia Rautenstrauch @prauten.bsky.social · Aug 1

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!

Andrea Ganna @andganna.bsky.social · Jul 30

Leena Peltonen School of Human Genetics in full-swing!

@gosiatrynka.bsky.social
@dgmacarthur.bsky.social
@bpasaniuc.bsky.social
@tuuliel.bsky.social
@hilarycmartin.bsky.social
@sashagusevposts.bsky.social
@zkutalik.bsky.social
@mashaals.bsky.social
@alemedinarivera.bsky.social

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Reposted by Pia Rautenstrauch

Peter Koo @pkoo562.bsky.social · Jul 16

*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

Peter Koo @pkoo562.bsky.social · Jul 16

Our work on "Evaluating the representational power of pre-trained DNA language models for regulatory genomics" led by @AmberZqt with help from @NiraliSomia & @stevenyuyy is finally published in Genome Biology! Check it out!

genomebiology.biomedcentral.com/articles/10....

Evaluating the representational power of pre-trained DNA language models for regulatory genomics - Genome Biology

Background The emergence of genomic language models (gLMs) offers an unsupervised approach to learning a wide diversity of cis-regulatory patterns in the non-coding genome without requiring labels of ...

genomebiology.biomedcentral.com

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Reposted by Pia Rautenstrauch

Valentine Svensson @nxn.se · Jun 2

The duplication crisis: the other replication crisis - www.worksinprogress.news/p/the-duplic...

The duplication crisis: the other replication crisis

How bad publishing incentives hinder long-term thinking in computational biology research

www.worksinprogress.news

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Reposted by Pia Rautenstrauch

Stein Aerts @steinaerts.bsky.social · Jun 4

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

VIB.AI @vibai.bsky.social · Jun 4

We want to connect:
To link model builders with data generators.
To bring together scientists asking why cells behave the way they do, and others figuring out how to model that behavior.

If you're working on AI in biology, consider joining!
https://tinyurl.com/y35m6khy

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Reposted by Pia Rautenstrauch

Gherman Novakovsky @gnovakovsky.bsky.social · May 29

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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Reposted by Pia Rautenstrauch

recombseq.bsky.social @recombseq.bsky.social · Apr 25

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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Reposted by Pia Rautenstrauch

Emma Chory, Ph.D. @chorye.bsky.social · Apr 14

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

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