cartalop.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

Xenium product updates : RNA and protein multiomics workflow @10xgenomics.bsky.social #AGBT2025 #AGBT25

submitted 9 days ago • 0 comments

FOMO on all the cool science & tech at #AGBT25. on Feb 28th, we’re spilling all the beans on our fave developments in #ngs #spatial #multiomics #singlecell. Register: www.genengnews.com/multimedia/g... @jlemieux.bsky.social @biomath.bsky.social @catharineaquino.bsky.social @jessie-no.bsky.social

submitted 11 days ago • 0 comments

📝 FeatureForest: the power of foundation models, the usability of random forests. Nomen est omen! We use features of the biggest models and train a handy random forest based pixel classifier with them. 👍 Hit bioRxiv recently… check it out! www.biorxiv.org/content/10.1...

submitted 22 days ago • 3 comments

Best practices for single-cell analysis across modalities go.nature.com/4gJkk3c #ExpertRecommendation by @lukasheumos.bsky.social et al. (from the @fabiantheis.bsky.social lab) - now nearing 250k accesses! Free to read here: rdcu.be/eabUB

submitted 16 days ago • 1 comment

📢 Calling all female African scientists. Applications open for the EMBL-UNESCO 3-month residencies in infection biology: 🪴 Grow your network 🧪Develop your skills 🧠Exchange knowledge with international colleagues Deadline: 31 March 2025 www.embl.org/about/info/s... #WomenInSTEM #WomenInScience

submitted 22 days ago • 2 comments

Today my postdoc presented on his NSF-funded project modeling the evolution of intersectional identity signaling, and my grad students sardonically dubbed it “The Last Hurrah of Quantitative Woke Studies.”

submitted 28 days ago • 1 comment

"Anything threatening to be a subculture is commodified before it can walk" - www.dezeen.com/2014/12/18/w...

submitted 29 days ago • 0 comments

If you think you are missing some spice in your life, move to Germany and use Deutsche Bahn. It’s the rollercoaster of your life 👻🚝😅

submitted 30 days ago • 1 comment

Researchers have shown that patches of muscle grown from stem cells can help to repair a failing heart https://go.nature.com/4hEsuL3

submitted 31 days ago • 2 comments

Yet another reminder that a statistical test is only as good as its null hypothesis, which is as good as the noise model. And, I suppose, that the number of replicates is always the bottleneck.

submitted 31 days ago • 0 comments

TL;DR: "Evaluating the accuracy-error trade-off in the search for differentially expressed genes leads us to advocate rank-based methods and Bayesian statistics to mitigate the limitations of binary classifications and communicate uncertainty." www.biorxiv.org/content/10.1...

submitted 32 days ago • 1 comment

Now out in @science.org w/ @jshendure.bsky.social we present 'Genome-shuffle-seq': a method to shuffle mammalian genomes and characterize the impact of structural variants (SVs) with single-cell resolution in one experiment. www.science.org/doi/10.1126/...

submitted 33 days ago • 3 comments

www.nytimes.com/2025/01/31/w...

submitted 32 days ago • 0 comments

SFI President David Krakauer's quarterly column "Beyond Borders" is now available on Substack! Read his latest on knowledge of the 1st & 2nd kinds and how thinkers from the last century have explored these concepts through games. substack.com/home/post/p-15...

submitted 32 days ago • 1 comment

Reminder that @europepmc.org is a mirror of Pubmed with better search and that it indexes all bioRxiv preprints (as well as ResearchSquare), not just the ones funded by NIH like chauvinist Pubmed

submitted 32 days ago • 9 comments

Hello BlueSky! Follow us to stay up to date on the inspiring science published in our journals and more. To get started, check out our #starterpack to meet all the Cell Press journals currently on the platform, with more to come🧪🔬🤖🧬🌳🪲 go.bsky.app/TdKYuS7

submitted 33 days ago • 0 comments

We're delighted to share our work on scrambling the human genome using prime editing, repetitive elements, and recombinases in @science.org , led by @jonaskoeppel.bsky.social , @f-raphael.bsky.social , with @proftomellis.bsky.social and George Church. www.science.org/doi/10.1126/...

submitted 33 days ago • 2 comments

🤯🤯🤯 www.nature.com/articles/s41...

submitted 33 days ago • 0 comments

JOB OPPORTUNITY: Join us as a scientific programmer to advance tools for multi-omics data at Heidelberg University. Details can be found at shorturl.at/OcnOa and please spread the word!

submitted 33 days ago • 0 comments

Somewhere outside Milovice, Czechia. 📷 Kiev-4a & Jupiter-8M 50mm f/2.0 🎞️ Kodak Tri-X 400

submitted 33 days ago • 0 comments

I’m super excited to share what I’ve been working on for the last (many) years: a spatial + genomic + transcriptomic characterization of how the breast cancer microenvironment evolves through immunotherapy! (1/x) 🧪🧬 🖥️ #AcademicSky #MLSky #ImmunoSky www.biorxiv.org/content/10.1...

submitted 35 days ago • 2 comments

👀🦇

submitted 34 days ago • 0 comments

Researchers have mapped the genome of the Iberian ribbed newt and revealed how the composition and organization of the DNA are linked to its ability to regenerate entire body parts. Published in Cell Genomics by @andrassimon.bsky.social et al. news.ki.se/mapping-of-a...

submitted 35 days ago • 1 comment

New Progress article 👇 Rafiq et al. discuss potential applications of artificial intelligence models that generate new data, and how they can be used to advance ecology research rdcu.be/d7UO6

submitted 35 days ago • 0 comments

👇

submitted 35 days ago • 0 comments

“The leaders of the Human Genome Project always knew they were just starting a conversation” The human genome encodes potentially thousands of tiny proteins that were previously overlooked. The search is on to find out what they do https://go.nature.com/3CupmSS

submitted 35 days ago • 0 comments

If you have been affected by the fires in LA, or are concerned about your ability to keep precious Drosophila strains going during the latest funding crisis, we will host your strains as a backup. Please email me. Please amplify. If you are also able to host fly strains, add your name as well.

submitted 35 days ago • 12 comments

As someone who got started into genomics with protozoan parasites, this is a topic close to my heart. Add STRs and transposons to the mix, and you get genomic innovation galore www.nature.com/articles/s41...

submitted 35 days ago • 1 comment

📷 Kiev-4 & Jupiter-8M 50mm f/2 🎞️ Kodak Tri-X 400

submitted 35 days ago • 0 comments

Useful review below of hepatic #organoids and their applications 🧪 If you freeze and thaw organoids, DM me to improve your yield and save time and money.

submitted 36 days ago • 0 comments

We are featuring Nadia Rosenthal as our first extraordinary biologist of the week. Nadia is the Scientific Director of the @jacksonlab.bsky.social, USA, and she drew the first cover image - Adam Emergent - when @dmmjournal.bsky.social was first launched in 2008. #100biologists

submitted 36 days ago • 0 comments

Spatial-Mux-seq is a multimodal spatial platform for simultaneously profiling the transcriptome, chromatin accessibility, histone modifications, and select proteins. www.nature.com/articles/s41...

submitted 37 days ago • 1 comment

Our new paper is finally out, showing that the same enhancer sequences - and likely the same transcription factors recruited to them - affect the activity of distal enhancers and their looping over to target gene promoters. www.nature.com/articles/s41...

submitted 37 days ago • 7 comments

This is DBiT-seq on steroids. Kudos to the authors, I must find some time to take a look at these data www.nature.com/articles/s41...

submitted 36 days ago • 1 comment

Super cool analysis of 10 AML Px using spatial transcriptomics of bone marrow 👀

submitted 36 days ago • 0 comments

Spatial multi-omics has just gone to the next level! www.nature.com/articles/s41... www.nature.com/articles/s41... —Integration of 5 omic modalities w/ spatial resolution at 20 -50 μm —"a new era for characterizing tissue & cellular heterogeneity that single-modality studies alone could not reveal"

submitted 36 days ago • 2 comments

We’re pleased to announce that our paper, “Evolutionary Optimization of Model Merging Recipes,” has been accepted to Nature Machine Intelligence and published today! The latest version includes new experimental results that further validate our approach. www.nature.com/articles/s42...

submitted 36 days ago • 1 comment

I posted a couple days ago about our new paper on building causal graphs from genetic associations + Perturb-seq. Here I want to expand on the value of using DIRECTIONAL information contained in LoF burden tests.🧵 [work led by @minetoota.bsky.social ] bsky.app/profile/jkpr...

submitted 37 days ago • 1 comment

The next generation of in situ multi-omics: www.nature.com/articles/s41...

submitted 36 days ago • 0 comments

Recruitment for the EMBL International PhD Programme is officially open! 🔊 At EMBL, we train young scientists to become skilled and creative future leaders in academia, industry & other sectors. Start your career in the life sciences with us! www.embl.org/about/info/e... 🧪 #AcademicSky #careers

submitted 37 days ago • 0 comments

A note on the relations between mixture models, maximum-likelihood and entropic optimal transport As they note, this is an interesting summary written for clarity rather than a new result. But, I've long tried to convince people that all of ML is deeply interconnected. arxiv.org/abs/2501.12005

submitted 38 days ago • 1 comment

If you need to sample reads (with or without replacement) from FASTQ files you may find the fastQpick utility by Joseph Rich super useful: github.com/pachterlab/f...

submitted 37 days ago • 1 comment

Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease? I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵

submitted 38 days ago • 6 comments

Caturday nights

submitted 38 days ago • 0 comments

While I agree that UMAPs can be problematic, I also think that statisticians have a lot to answer for with regard to the general debasement of modern science towards p-values instead of critical thinking and model building. That has been far more damaging than a couple of silly plots.

submitted 38 days ago • 7 comments

Good Sunday, all. Last week, some truly landmark papers were published in #cancermetabolism and #mitochondrialbiology. Find them in this curated issue: biomed.news/bims-camemi/... @biomednews.bsky.social "I am a part of all that I have met."-Alfred Tennyson

submitted 38 days ago • 0 comments