Analyzing your single-cell data by mapping to a reference atlas? Then how do you know the mapping actually worked, and you’re not analyzing mapping-induced artifacts? We developed mapQC, a mapping evaluation tool www.biorxiv.org/content/10.1... from the ‪@fabiantheis lab. Let’s dive in🧵

Join us for our next Kipoi Seminar with Katherine Pollard, Gladstone Institute of Data Science & Biotechnology,UCSF, Biohub @gladstoneinst.bsky.social @czbiohub.bsky.social 👉Human variant interpretation with sequence-to-activity models 📅Wed June 4,5:30pm CET🧬 kipoi.org/seminar/🦋@kipoizoo.bsky.social

This year, the lab has a great representation at the #eshg2025: 3 talks, 2 posters, 1 spin-off stand ! 1/n

Join us for our next Kipoi Seminar with Laura Martens, Gagneur lab, TUM @lauradmartens.bsky.social @gagneurlab.bsky.social @tum.de 🐕scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution 📅Wed May 7, 5:30pm CET 🧬https://kipoi.org/seminar/ 🦋kipoizoo.bsky

and @pedrotomazdasilva.bsky.social will present tomorrow at #probgen25 poster 128 on dependency analysis of DNA language models. Come and see what functional relationships DNA LMs capture, from regulatory code to RNA structures. Preprint: doi.org/10.1101/2024...

Review alert - "Modelling and design of transcriptional enhancers" by Seppe and Vasilis 👇

Tomorrow Johannes Hingerl @johahi.bsky.social gives a talk on scooby at #probgen25. Enjoy learning in the legendary CSHL auditorium how to model RNA-seq and ATAC-seq profiles in individual cells from half a megabase of genomic sequence. Preprint: doi.org/10.1101/2024...

Hello #probgen25! We have 3 contribs this year @lauradmartens.bsky.social starts today, poster 87, presenting scooby modeling scRNA-seq and sc-ATAC-seq profiles from DNA and applications. Shhh... don't tell it further... rumour says there are awesome cute scooby stickers to win ;-)

Join us for our next Kipoi Seminar with with Alexander Sasse @lxsasse.bsky.social @zmbh.uni-heidelberg.de 👉Advanced training strategies for genomic sequence-to-function models 📅 Wed March 5, 5:30pm CET 🧬 kipoi.org/seminar/ 🦋 @kipoizoo.bsky.social

Join us for our next Kipoi Seminar with with Pedro Tomaz da Silva @pedrotomazdasilva.bsky.social @gagneurlab.bsky.social @TU_Muenchen! 👉Nucleotide dependency analysis of DNA language models reveals genomic functional elements 📅Wed Feb 5, 5:30pm CET 🧬https://kipoi.org/seminar/ 🦋kipoizoo.bsky

Congrats to Johannes Linder, David Kelley et al. on the journal publication of Borzoi - a long context sequence models of RNA-seq coverage profiles with many nice applications for transcriptional & post-transcriptional regulation & variant effect prediction. www.nature.com/articles/s41... 1/

Super excited to announce our latest flagship model Borzoi: major props to Johannes & David Kelley et al for advancing it. It's been a long journey from our prior Enformer model into this one. A few innovations: i) longer DNA context, ii) adaptation to predict RNA-seq abundance and splice isoforms,

Super cool to see this paper out! It's also going to make training scooby models lightning fast! 🤩⚡️

Hey reg genomics folks, here is our little x-mas present: Flashzoi. Borzoi. Just as good. 3x faster. Thumbs up to @johahi.bsky.social for the great initiative, conception & implementation. Big thanks to Johannes Linder, David Kelley and colleagues to have created Borzoi and shared it freely.

Flashzoi: An enhanced Borzoi model for accelerated genomic analysis https://www.biorxiv.org/content/10.1101/2024.12.18.629121v1

Excited to share our lab's first preprint: we used spatial transcriptomics to dissect how aging disrupts the cycling ovary! 🧵 This was an incredible team effort w/ @jennifergarrison.bsky.social #TammyLan @davidsebfischer.bsky.social #AlisonKochersberger #RuthRaichur #SophiaSzady

1/7 Planning to build a single-cell atlas? Or wondering how atlases can be useful to your research? Read our guide on single-cell atlases www.nature.com/articles/s41... published in Nature Methods, by @lisasikkema.bsky.social, @khrovatin.bsky.social, Malte Luecken, @fabiantheis.bsky.social et al.

Join us for our next Kipoi Seminar with with Dmitry Penzar, @pensarata.bsky.social @ autosome.org! 👉LegNet: parameter-efficient modeling of gene regulatory regions using modern convolutional neural network 📅Wed Dec 4, 5:30pm CET 🧬 kipoi.org/seminar/

Women are under-represented at senior levels in #academia globally, & across all #science 🧪 disciplines, as shown by these "scissor-shaped curves" ✂️ So how can we ever achieve #gender #equality? We discuss various strategies in this #Cell Commentary #WomeninSTEM www.cell.com/cell/fulltex... 🧵 1/

Super excited to share our Human Neural Organoid Atlas, now out in Nature! Led by @zhisonghe.bsky.social @josch1.bsky.social, and myself, this resource was created from 36 scRNA-seq datasets—totalling over 1.7 million cells! 🔬✨
 www.nature.com/articles/s41...
 Find out how it can serve you ⏬
 🧵1/8

Single-molecule states link transcription factor binding to gene expression www.nature.com/articles/s41...

The Kipoi seminar is now also on BlueSky! 🎉 Follow @kipoizoo.bsky.social for announcements of upcoming speakers

🧬 New in @Nature: Our team found that fat cells keep a “memory” of their previous obese state even after weight loss, helping explain why maintaining weight loss is so challenging. Excited to share this work!! www.nature.com/articles/s41...

My goal is to understand the regulatory role of every nucleotide in the genome, and how this changes across every cell in the human body. If you are interested in doing a Ph.D. with me at UMass Chan Medical (Genomics and Comp Bio Department), see the links below. Deadline is Dec 1st.

Looking forward to the Inaugural Symposium of the Center for AI & Computational Biology vib.ai with a great line-up of speakers at the interface of AI & biology: D. Kelley, J. Gagneur, Z. Avsec, T. Kortemme, B. Lehner, F. Fraternali, A. Tanay & O. Stegle (20Nov) www.vibconferences.be/events/vibai...