Sophie Seidel
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seidels.bsky.social
Sophie Seidel
@seidels.bsky.social
220 followers 250 following 9 posts
PostDoc with @jshendure.bsky.social
Phylogenetics | Statistical Inference | Single-cell
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seidels.bsky.social
Sophie Seidel @seidels.bsky.social · Aug 5
Interested in #Bayesian #phylogenetics for analysing #single-cell lineage data? 🧬 To estimate timed trees 🕒, uncertainty and cell dynamic params!

I am teaching a BEAST 2 and TiDeTree tutorial during the #BC2 conference.
📍Basel, Sep 8, 2025
📅 Apply by Sep 1

Register here: bc2.ch/registration...
Reposted by Sophie Seidel
jhuisman.bsky.social
Have you ever wondered what increasing environmental stress will do to microbial communities?

In our new preprint, @martinadalbello.bsky.social, Jeff Gore and I studied the impact of salinity on microbial community composition and function. 🧵 (1/5)
www.biorxiv.org/content/10.1...
Microbial communities demonstrate robustness in stressful environments due to predictable composition shifts
Environmental stress reduces species growth rates, but its impact on the function of microbial communities is less clear. Here, we experimentally demonstrate that increasing salinity stress shifts com...
www.biorxiv.org
August 25, 2025 at 2:33 PM
Reposted by Sophie Seidel
dhdegroot.bsky.social
Big news! At least for me. I'll start building my own research group at the amazing IMBA in Vienna. Starting from single-cell omics data, we will develop computational tools and theoretical models to understand how single cells make decisions, in particular during development. I think that IMBA is
January 27, 2026 at 1:44 PM
Reposted by Sophie Seidel
troymcdiarmid.bsky.social
Stoked to share our latest work entitled: “Large-scale discovery of neural enhancers for cis-regulation therapies”

shorturl.at/H3Qww

This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon.

Bluetorial below.
November 5, 2025 at 3:09 PM
Reposted by Sophie Seidel
contaminatedsci.bsky.social
We are looking for a postdoc to study single-cell transcriptional heterogeneity in the human skin microbiome.

We have a new protocol mostly developed, but need someone to see it through. Experience with protocol dev or RNAseq appreciated.

Funded by a new grant from MIT-HEALS.
September 12, 2025 at 4:49 PM
Reposted by Sophie Seidel
erictopol.bsky.social
The are many anecdotes for #ChatGPT helping patients. But here's one with fallacious A.I. guidance that resulted in serious complications
www.acpjournals.org/doi/10.7326/...
August 11, 2025 at 5:33 PM
Reposted by Sophie Seidel
seidels.bsky.social
Interested in #Bayesian #phylogenetics for analysing #single-cell lineage data? 🧬 To estimate timed trees 🕒, uncertainty and cell dynamic params!

I am teaching a BEAST 2 and TiDeTree tutorial during the #BC2 conference.
📍Basel, Sep 8, 2025
📅 Apply by Sep 1

Register here: bc2.ch/registration...
August 5, 2025 at 10:55 PM
seidels.bsky.social
Interested in #Bayesian #phylogenetics for analysing #single-cell lineage data? 🧬 To estimate timed trees 🕒, uncertainty and cell dynamic params!

I am teaching a BEAST 2 and TiDeTree tutorial during the #BC2 conference.
📍Basel, Sep 8, 2025
📅 Apply by Sep 1

Register here: bc2.ch/registration...
August 5, 2025 at 10:55 PM
Reposted by Sophie Seidel
const-ae.bsky.social
Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉

www.nature.com/articles/s41...

We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!

🧵
Beeswarm plot of the prediction error across different methods of double perturbations showing that all methods (scGPT, scFoundation, UCE, scBERT, Geneformer, GEARS, and CPA) perform worse than the additive baseline. Line plot of the true positive rate against the false discovery proportion showing that none of the methods is better at finding non additive interactions than simply predicting no change.
August 4, 2025 at 1:52 PM
Reposted by Sophie Seidel
evogytis.bsky.social
Our lab is helping with the organisation of this year's EMBO YSF. We have a great line up of invited speakers from (mostly) the wider Baltic region & a @nightsciencepod.bsky.social workshop on creativity in science (I did it a couple of years ago, it was awesome). Please share & consider joining us!
embo.org EMBO @embo.org · Jul 28
This year's EMBO Young Scientists’ Forum (EYSF) will take place in Vilnius, #Lithuania from 24–26 Sep 2025. The EYSF brings together scientists across #Europe for #networking and scientific exchange – Apply now: meetings.embo.org/event/25-eysf 🧪

Abstract submission by 1 Aug
Registration by 15 Aug
EMBO Young Scientists’ Forum 2025
The EMBO Young Scientists’ Forum (EYSF) brings together young scientists (doctoral and postdoctoral) to engage with colleagues from across the continent and share their findings and interests with it…
meetings.embo.org
July 28, 2025 at 3:48 PM
Reposted by Sophie Seidel
brotmanbaty.bsky.social
POSTDOC ALERT: Applications now open for SeaBridge postdoc fellowship; opportunity to work on leading-edge biotech w/researchers at the Seattle Hub for Synthetic Biology.
brotmanbaty.org/news/new-pos...
@marionpepper.bsky.social
@jshendure.bsky.social
@coletrapnell.bsky.social
New Postdoc Fellowship Program Builds on Innovative SeattleHub Research | Brotman Baty Institute
BBI
brotmanbaty.org
June 16, 2025 at 4:36 PM
Reposted by Sophie Seidel
choijunhong.bsky.social
New preprint with the Shendure lab @jshendure.bsky.social ! We apply the DNA Typewriter lineage recorder to mouse 3D gastruloids, a powerful model of early mammalian development. Led by Sam Regalado and CX Qiu @cxqiu.bsky.social : www.biorxiv.org/content/10.1... (1/13)
Lineage recording in monoclonal gastruloids reveals heritable modes of early development
Mammalian stem cells possess a remarkable capacity for self-organization, a property that underlies increasingly sophisticated in vitro models of early development. However, even under carefully contr...
www.biorxiv.org
May 27, 2025 at 2:57 PM
Reposted by Sophie Seidel
seidels.bsky.social
Interested in #Bayesian #phylogenetics? 🧬
Join the Taming the BEAST workshop — theory + hands-on tutorials incl. #singleCell, #devBio & #lineageTracing!
📍Beijing, July 14–18, 2025
📅 Apply by April 25
I'll teach on TiDeTree & cell trees
🔗 taming-the-beast.org/news/Deadlin...
Application deadline extended for Taming the BEAST in Beijing!
taming-the-beast.org
April 17, 2025 at 7:28 PM
seidels.bsky.social
Interested in #Bayesian #phylogenetics? 🧬
Join the Taming the BEAST workshop — theory + hands-on tutorials incl. #singleCell, #devBio & #lineageTracing!
📍Beijing, July 14–18, 2025
📅 Apply by April 25
I'll teach on TiDeTree & cell trees
🔗 taming-the-beast.org/news/Deadlin...
Application deadline extended for Taming the BEAST in Beijing!
taming-the-beast.org
April 17, 2025 at 7:28 PM
Reposted by Sophie Seidel
sib.swiss
💡 Learn to analyze genetic lineage tracing data with TiDeTree in BEAST 2! Gain hands-on experience in setting up and running analyses, from preparing data to interpreting results.

🔹 Organized by @seidels.bsky.social
& Antoine Zwaans (@ethzurich.bsky.social)

👉 Register: bc2.ch/registration...
March 31, 2025 at 1:06 PM
Reposted by Sophie Seidel
tanjastadler.bsky.social
Quantification of developmental processes (here early Danio rerio development) with our novel Bayesian phylogenetic methodology - leveraging single cell lineage tracing data based on CRISPR/Cas9 technology royalsocietypublishing.org/doi/10.1098/... Antoine Zwaans @seidels.bsky.social Marc Manceau
A Bayesian phylodynamic inference framework for single-cell CRISPR/Cas9 lineage tracing barcode data with dependent target sites | Philosophical Transactions of the Royal Society B: Biological Sciences
Analysing single-cell lineage relationships of an organism is crucial towards understanding the fundamental cellular dynamics that drive development. Clustered regularly interspaced short palindromic repeats (CRISPR)-based dynamic lineage tracing relies ...
royalsocietypublishing.org
February 21, 2025 at 8:37 AM
Reposted by Sophie Seidel
alexeidrummond.bsky.social
Check out our new method for summarising BEAST trees. The CCD0-MAP tree gives much more accurate results than MCC tree. It returns the tree that maximises the product of sampled clade probabilities regardless of whether that tree was sampled. Highly recommend :)

journals.plos.org/ploscompbiol...
Accurate Bayesian phylogenetic point estimation using a tree distribution parameterized by clade probabilities
Author summary Our research introduces novel methods to analyse a set of phylogenetic tree topologies, such as those generated by Bayesian Markov Chain Monte Carlo algorithms. We define a new model fo...
journals.plos.org
February 14, 2025 at 5:53 AM
Reposted by Sophie Seidel
dominik1klein.bsky.social
Good to see moscot-tools.org published in @nature.com ! We made existing Optimal Transport (OT) applications in single-cell genomics scalable and multimodal, added a novel spatiotemporal trajectory inference method and found exciting new biology in the pancreas! tinyurl.com/33zuwsep
Mapping cells through time and space with moscot - Nature
Moscot is an optimal transport approach that overcomes current limitations of similar methods to enable multimodal, scalable and consistent single-cell analyses of datasets across spatial and temporal...
tinyurl.com
January 23, 2025 at 8:42 AM
Reposted by Sophie Seidel
evoldir.bsky.social
Join the 2025 Workshop on Molecular Evolution at the Marine Biological Laboratory from May 22 to June 1. Apply by January 29, 2025. More info: https://www.mbl.edu/education/advanced-research-training-courses/course-offerings/workshop-molecular-evolution #workshop
Workshop on Molecular Evolution | Marine Biological Laboratory
The workshop serves graduate students, postdocs, and established faculty from around the world seeking to apply the principles of molecular evolution to questions of anthropology, conservation genetics, development, behavior, physiology, and ecology.
www.mbl.edu
January 1, 2025 at 10:46 AM
Reposted by Sophie Seidel
trayon.bsky.social
Join us in Paris 6-9 May 2025 for the #EvoDevoTempo conference (2nd edition) with a fantastic line up of speakers confirmed!!

Organized by @mdiazcuadros.bsky.social
@vanderhaeghenp2.bsky.social
@bassemh.bsky.social and me.

Please RT to spread the word

meetings.embo.org/event/25-dev...
Developmental timing across species: From mechanisms to evolutionary insights
Like choreography, development consists of a highly ordered suite of steps and transitions. Modifying developmental tempo can affect final size and composition of tissues, as well as their plasticity…
meetings.embo.org
December 20, 2024 at 4:32 PM
Reposted by Sophie Seidel
amartinezarias.bsky.social
We've wondered for a while why #gastruloids are so sensitive to initial cell numbers. Here www.biorxiv.org/content/10.1... led by U, Fiuza, we explore this & observe effects of a number of variables on final structure and think what this tells us @ embryogenesis
#IInNumbersWeTrust #NotInTheGenes
December 17, 2024 at 6:52 PM
Reposted by Sophie Seidel
robjohnnoble.bsky.social
Weini Huang, @xiaofu90.bsky.social, Dmitrii Shek and I are excited to be guest editing a BMC Cancer collection on "Spatial tumor heterogeneity". We welcome studies ranging from spatial transcriptomics to math models. For details and submission guidelines see www.biomedcentral.com/collections/... 🧪
Call for papers - Spatial tumor heterogeneity
www.biomedcentral.com
December 16, 2024 at 7:08 PM
Reposted by Sophie Seidel
timcoorens.bsky.social
Spread the word! Registration for the "Mutations in Time and Space" conference is open. The meeting is all about the origins, patterns, and consequences of mutations across cells, individuals, populations, species. Abstract submission deadline is Jan 17th broadinstitute.swoogo.com/mits2025/597...
December 6, 2024 at 2:29 PM
Reposted by Sophie Seidel
delvecchyo.bsky.social
Don't forget to submit your abstract for "Probabilistic Modeling in Genomics 2025". Deadline: January 10th, 2025. meetings.cshl.edu/meetings.asp...
Probabilistic Modeling in Genomics
Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.
meetings.cshl.edu
December 2, 2024 at 5:27 PM
Reposted by Sophie Seidel
tanjastadler.bsky.social
We are excited to share our new preprint „Bayesian phylodynamic inference of multi-type population trajectories using genomic data“ www.biorxiv.org/content/10.1.... Using BEAST2, you can estimate past population sizes and spillover events between populations based on genetic sequencing data. 1/2
Bayesian phylodynamic inference of multi-type population trajectories using genomic data
Phylodynamic methods provide a coherent framework for the inference of population parameters directly from genetic data. They are an important tool for understanding both the spread of epidemics as we...
www.biorxiv.org
December 5, 2024 at 8:45 AM
Reposted by Sophie Seidel
fabiantheis.bsky.social
Interested in recording cell dynamics? Beautiful review from colleagues around Tanja Stadler and Martin Tran @NatureRevGenet on DNA recording in single cells and lienages. With lots of exciting opportunities for single cell modeling. nature.com/articles/s41576-024-00788-w
December 3, 2024 at 9:30 AM