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 👇

Seppe De Winter@seppedewinter.bsky.social · 2y ago

We wrote a review article on modelling and design of transcriptional enhancers using sequence-to-function models. From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design! @natrevbioeng.bsky.social www.nature.com/articles/s44...

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/

Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation - Nature Genetics

Borzoi adapts the Enformer sequence-to-expression model to directly predict RNA-seq coverage, enabling the in-silico analysis of variant effects across multiple layers of gene regulation.

nature.com

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,

Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation - Nature Genetics

Borzoi adapts the Enformer sequence-to-expression model to directly predict RNA-seq coverage, enabling the in-silico analysis of variant effects across multiple layers of gene regulation.

nature.com

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

Johannes Hingerl@johahi.bsky.social · 2y ago

Introducing Flashzoi⚡! We’ve upgraded the Borzoi model with rotary pos. encodings and FlashAttention, resulting in a significant speedup with similar or better accuracy for faster variant effect prediction, quicker model development and more efficient genomic analysis www.biorxiv.org/content/10.1...

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.

bioRxiv Genomics@biorxiv-genomic.bsky.social · 2y ago

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

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

An integrated transcriptomic cell atlas of human neural organoids - Nature

A human neural organoid cell atlas integrating 36 single-cell transcriptomic datasets shows cell types and states and estimates transcriptomic similarity between primary and organoid counterparts, sho...

nature.com

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

Single-molecule states link transcription factor binding to gene expression - Nature

A study uses single-molecule footprinting to measure protein occupancy at regulatory elements on individual molecules in human cells and describes how different properties of transcription factor bind...

nature.com

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...

Adipose tissue retains an epigenetic memory of obesity after weight loss - Nature

Stable epigenetic changes indicate the existence of an obesogenic memory in mouse adipocytes that primes cells for pathological responses in an obesogenic environment and potentially contributes to th...

nature.com

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...