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Reposted by Sophie Seidel

Tami Lieberman @contaminatedsci.bsky.social · 26d

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.

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Reposted by Sophie Seidel

Eric Topol @erictopol.bsky.social · Aug 11

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/...

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Reposted by Sophie Seidel

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...

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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...

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Reposted by Sophie Seidel

Constantin Ahlmann-Eltze @const-ae.bsky.social · Aug 4

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.

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Reposted by Sophie Seidel

Gytis Dudas @evogytis.bsky.social · Jul 28

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 @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

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Reposted by Sophie Seidel

Brotman Baty Institute @brotmanbaty.bsky.social · Jun 16

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

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Reposted by Sophie Seidel

Junhong Choi @choijunhong.bsky.social · May 27

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

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Reposted by Sophie Seidel

Sophie Seidel @seidels.bsky.social · Apr 17

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

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Sophie Seidel @seidels.bsky.social · Apr 17

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

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Reposted by Sophie Seidel

SIB Swiss Institute of Bioinformatics @sib.swiss · Mar 31

💡 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...

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Reposted by Sophie Seidel

Tanja Stadler @tanjastadler.bsky.social · Feb 21

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

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Reposted by Sophie Seidel

Alexei Drummond @alexeidrummond.bsky.social · Feb 14

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

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Reposted by Sophie Seidel

dominik1klein.bsky.social @dominik1klein.bsky.social · Jan 23

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

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Reposted by Sophie Seidel

EvolDir @evoldir.bsky.social · Jan 1

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

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Reposted by Sophie Seidel

Teresa Rayon @trayon.bsky.social · Dec 20

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

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Reposted by Sophie Seidel

Alfonso Martinez Arias @amartinezarias.bsky.social · Dec 17

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

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Reposted by Sophie Seidel

Rob Noble @robjohnnoble.bsky.social · Dec 16

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

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Reposted by Sophie Seidel

Tim Coorens @timcoorens.bsky.social · Dec 6

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...

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Reposted by Sophie Seidel

Diego Ortega-Del Vecchyo @delvecchyo.bsky.social · Dec 2

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

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Reposted by Sophie Seidel

Tanja Stadler @tanjastadler.bsky.social · Dec 5

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

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Sophie Seidel @seidels.bsky.social · Dec 4

Would love to be added too!

Sophie Seidel @seidels.bsky.social · Dec 3

Thank you for highlighting our review!

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Reposted by Sophie Seidel

Fabian Theis @fabiantheis.bsky.social · Dec 3

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

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Reposted by Sophie Seidel

Bertie Gottgens @bertiegottgens.bsky.social · Nov 17

Very happy to share our latest paper:”Time and single-cell resolved model of murine bone marrow hematopoiesis”:
www.sciencedirect.com/science/arti...
With the groups of Kamil Kranc and Donal O’Carroll, we have generated a new hematopoiesis model fit for the single cell genomics era.

A time- and single-cell-resolved model of murine bone marrow hematopoiesis

The paradigmatic hematopoietic tree model is increasingly recognized to be limited, as it is based on heterogeneous populations largely defined by non…

www.sciencedirect.com

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