Massively parallel reporter assay for mapping gene-specific regulatory regions at single-nucleotide resolution
04.03.2026 06:01 — 👍 6 🔁 1 💬 0 📌 0
Massively parallel reporter assay for mapping gene-specific regulatory regions at single-nucleotide resolution
04.03.2026 06:01 — 👍 6 🔁 1 💬 0 📌 0
Join us for our next Kipoi Seminar with Sam Boshar, Instadeep
@instadeep.bsky.social
👉 A foundational model for joint sequence-function multi-species modeling at scale for long-range genomic prediction
🗓️ Wed Mar 4, 5:30pm CET
🧬 kipoi.org/seminar
🦋 @kipoizoo.bsky.social
Congress rejected massive cuts to US science budgets for 2026, but much of the money still isn’t flowing to researchers.
The culprit? The White House Office of Management and Budget (OMB) is quietly slow-walking the release of funds. 🧵👇
Congress has appropriated the funds to NSF but OMB is delaying the release. When funds are released, NSF, which has lost almost 1/5 of its staff, will struggle to evaluate proposals. Since they have to award the funds, big projects with established PIs will benefit. This is how US science dies.
02.03.2026 09:14 — 👍 164 🔁 59 💬 2 📌 3
New paper alert 🚀 Our organism-wide single-cell ATAC-seq atlas of mammalian aging is now out in @science.org, led by our fantastic graduate student Ziyu Lu from @rockefeller.edu!
www.science.org/doi/10.1126/...
🎉Proud to present our latest paper, out now in Nature Communications: www.nature.com/articles/s41...
RNA Binding Proteins (RBPs) are often full of intrinsically disordered regions (IDRs), but what these regions do during RNA recognition is often unclear. 1/10
#RNA #IDR #RBP
Check out our new protocol paper on molecular recording of transcriptional events in genomic DNA!
Super fun pulling this together with @jennynathans.bsky.social @chenomics.bsky.social and @jshendure.bsky.social
New to using Jupyter notebooks for the Allen Brain Cell Atlas?
Join us on Feb. 11 for a beginner-friendly webinar focusing on installation, set-up, and common questions.
Register for the meeting link and recording: https://alleninstitute-org.zoom.us/webinar/register/WN_q0sJzndpRbSZWjrSGblu6A#/
A new Phased Variants container track for hg38 and hg19, and brings phased individual-level genotype data from: Human Diversity Genome Project, Simons Genome Diversity Project, gnomad's HGDP+1000 Genomes callset, and the Mexico Biobank.
Learn more at: https://bit.ly/4rxS60Q
Delighted to present Latent Interaction Variational Inference (LIVI), a framework for trans-eQTL mapping at single-cell resolution that I developed during my PhD together with colleagues from @steglelab.bsky.social 1/n
08.02.2026 16:54 — 👍 25 🔁 12 💬 1 📌 3
Ideal candidates:
• Strong ML/statistics training
• Experience with Deep learning in genomics
• Single-cell genomics a plus
• Analytical, independent, collaborative
• Committed to reproducible, rigorous science
If this sounds like you, reach out and apply now via the program links above.
Position with Christoph Dieterich:
Generative AI for Nanopore Direct RNA Sequencing.
Model raw RNA signals to detect modifications & secondary structure.
Combine experimental & computational approaches to understand how sequence, structure, and chemical modifications shape Nanopore reads.
Position with @eileen-furlong.bsky.social:
Decoding gene regulation with deep learning.
Predict how natural genetic variants shape enhancer activity across Drosophila embryonic development using bulk & single-cell ATAC-seq and RNA-seq.
Testable, interpretable models of gene regulation.
Exciting Postdoc Opportunities – Alliance Interinstitutional Program
**Deadline:** March 31, 2026 (5:00 pm CEST)
🔗 Two shared positions: www.syn-gen.de/alliance-pos...
🔗 Full call & application info:: www.health-life-sciences.de/opportunitie...
A near-complete map of human cytosolic degrons and their relevance for disease
We measured degron potency of >200,000 30-residue tiles from >5,000 human proteins, and trained a model to predict degrons from sequence
Led by @vvouts.bsky.social in @rhp-lab.bsky.social
doi.org/10.1126/scia...
Want to interpret DNA sequence-to-function models to understand the underlying molecular mechanisms? Then this is a must read!
06.02.2026 16:25 — 👍 10 🔁 5 💬 0 📌 0Hot off the press! Jun Cheng presents AlphaGenome at the Kipoi seminar this Wednesday. Don’t miss it.
02.02.2026 21:14 — 👍 4 🔁 2 💬 0 📌 0
The successes of protein structure prediction are widely known. However, its limitations and failures are less known, especially among non-experts.
Most telling are the failures to predict structure types absent from the training data.
⬜️ This is a distinct machine-learning failure, in ...
1/n
Does the noncoding genome actually carry more genetic information than coding seqs? Motivated by this question we mutated every bp in the 10kb MYC locus. Results are even more exciting: Decoding the MYC locus reveals a druggable ultraconserved RNA element www.biorxiv.org/content/10.6...
31.01.2026 01:13 — 👍 128 🔁 47 💬 4 📌 6We are thrilled that our study on the evolution of gene regulation in mammalian cerebellum development – led by @ioansarr.bsky.social, @marisepp.bsky.social and @tyamadat.bsky.social, in collaboration with @steinaerts.bsky.social – is now out in @ScienceMagazine! www.science.org/doi/10.1126/...
29.01.2026 19:23 — 👍 92 🔁 35 💬 3 📌 6Now with a bioinformatics/genomics label 🖥️🧬
29.01.2026 18:07 — 👍 4 🔁 3 💬 0 📌 0
Paper alert! 💻 How many cells do you need to train reliable deep learning models in regulatory genomics? We asked how data quality, sequencing depth, and dataset size affect training of sequence-to-function models from scATAC-seq. Out now www.nature.com/articles/s41...
(details below)
A bird's-eye view of a former Auschwitz II-Birkenau camp showing a wide dirt pathway flanked by parallel rows of barbed-wire fences. Groups of visitors walk along the path, surrounded by the remnants of brick structures and barracks, now reduced to foundations. Green grass contrasts with the somber history of the site, as the path leads toward a guard tower in the distance.
Auschwitz was at the end of a process. We must remember that it did not start from gas chambers.
This hatred gradually developed: from ideas, words, stereotypes & prejudice through legal exclusion, dehumanization & escalating violence... to systematic and industrial murder.
Auschwitz took time.
NanoSimFormer: An end-to-end Transformer-based simulator for nanopore sequencing signal data
Figure 1
Figure 2
Figure 3
NanoSimFormer: An end-to-end Transformer-based simulator for nanopore sequencing signal data [new]
End-to-end Transformer: High-fidelity nanopore signal generation w/ basecaller guidance optimizes accurate basecalling.
Classical enhancers couple cis-regulatory logic with transcriptional condensates and 3D genome architecture https://www.biorxiv.org/content/10.64898/2026.01.23.701252v1
24.01.2026 06:32 — 👍 4 🔁 2 💬 0 📌 0
Excited to share our latest work in @ajhgnews.bsky.social 🧬📄
We mapped the regulatory landscape of human liver at single-nucleus resolution using snMultiome, connecting genetic variants to the cell-type mechanisms underlying cardiometabolic disease.
www.sciencedirect.com/science/arti...
New preprint on technologies to scale up CRISPR screens.
We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells.
We also introduce an approach for cloning lentiviral libraries with billions of elements.
Messenger RNAs with shorter UTRs tend to live longer on average.
This may reflect that shorter UTRs statistically contain fewer destabilizing regulatory elements.
The relationship depends strongly on cellular context, sequence content, and RNA-binding protein availability.
TF-MINDI is out! A new method to learn cis-regulatory codes through rich embeddings of TF binding sites. TF-MINDI decomposes motif neighbourhoods, and works downstream of any sequence-to-function deep learning model. We deeply study the enhancer code in human neural development, check out the thread
15.01.2026 12:32 — 👍 60 🔁 38 💬 1 📌 0
