iiinova — where your digital self keeps evolving

Reposted by Melanie Weilert

Zeitlinger Lab @zeitlingerlab.bsky.social · 05/02/2026

The new updates for Charles McAnany’s preprint “Positional Interpretation of Cis-Regulatory Code and Nucleosome Organization with Deep Learning Models” (www.biorxiv.org/content/10.1...) are up! We introduce PISA, a tool to visualize the cis-regulatory code. See a recap below:

biorxiv.org

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Reposted by Melanie Weilert

Zeitlinger Lab @zeitlingerlab.bsky.social · 09/01/2026

The @zeitlingerlab.bsky.social is pleased to announce @sergio-gma91.bsky.social’s preprint “High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo” (www.biorxiv.org/content/10.6...). TLDR; TFIID behaves differently depending on promoter type. More below:

biorxiv.org

High-resolution binding data of TFIID and cofactors show promoter-specific differences in vivo

TFIID is instrumental in recognizing promoter sequences and initiating transcription, yet a cohesive understanding of how this complex interacts with and functions at different promoter types in vivo ...

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Reposted by Melanie Weilert

Julia Zeitlinger @juliazeitlinger.bsky.social · 19/11/2025

Very proud of our new paper! Great job @mweilert.bsky.social, our experimentalists and modeling collaborator Rosa Martinez-Corral. It was fun to see the story grow and get feedback from various experts. Thank you all!

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Melanie Weilert @mlweilert.bsky.social · 19/11/2025

It’s been fun figuring out why some degenerate motifs matter while others don’t. Turns out there’s a whole syntax behind it, relying on cooperativity!

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Reposted by Melanie Weilert

Julia Zeitlinger @juliazeitlinger.bsky.social · 07/05/2025

Like regulatory genomics? Don’t miss this very fun meeting! May 7 is the deadline for early registration and abstract submission www.asbmb.org/meetings-eve...

asbmb.org

Evolution and core processes in gene expression

June 26–29, 2025 | Kansas City, Mo.

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Reposted by Melanie Weilert

GenomeTDCC @genometdcc.org · 23/04/2025

🚨PRE-PRINT 🧪🧬🖥️👩‍🔬 Long-range massively parallel reporter assay reveals rules of distal enhancer-promoter interactions From Barak Cohen's lab at @washu.bsky.social Read the pre-print 👇 doi.org/10.1101/2025... Learn more about the research from the Cohen lab: bclab.wustl.edu

From the BioRxiv pre-print article "Long-range massively parallel reporter assay reveals rules of distal enhancer-promoter interactions" by Yawei Wu et al.
Fig. 1. Design of long-range MPRA. a, Design of the enhancer landing pad and the promoter landing
pad. The enhancer landing pad contains a dual promoter driving expression of an mTagBFP fluorescent
protein and a thymidine kinase (TK) gene for counterselection, flanked by FRT and F3 sites for RMCE.
available under aCC-BY-NC 4.0 International license.
was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made
bioRxiv preprint doi: https://doi.org/10.1101/2025.04.21.649048; this version posted April 22, 2025. The copyright holder for this preprint (which
The promoter landing pad expresses the mEmerald fluorescent protein and iCaspase9 for
counterselection and is flanked by loxFAS and loxP sites for orthogonal RMCE. b-c, Workflow of
long-range MPRA. eBC: enhancer barcode; rBC: random barcode; dBC: distance barcode. A barcoded
enhancer library is integrated into pooled long-range landing pad cells through Flpase-facilitated
recombination. After counterselection with Ganciclovir, cells with successful integration are enriched.
Cells are sorted into different bins based on mScarlet fluorescence level. Genomic DNA is extracted from
each bin; barcodes are amplified and sequenced. Reporter gene expression of each enhancer at each
distance is calculated as the weighted average of fluorescence levels across bins.

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Reposted by Melanie Weilert

Julia Zeitlinger @juliazeitlinger.bsky.social · 08/04/2025

Our new preprint is out! Want to better visualize what your sequence-to-function profile learned? Here is PISA. It also comes in a new BPNet package, which can be used to train many genomics data sets, including MNase-seq data.

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Reposted by Melanie Weilert

Stein Aerts @steinaerts.bsky.social · 04/04/2025

Very proud of two new preprints from the lab: 1) CREsted: to train sequence-to-function deep learning models on scATAC-seq atlases, and use them to decipher enhancer logic and design synthetic enhancers. This has been a wonderful lab-wide collaborative effort. www.biorxiv.org/content/10.1...

biorxiv.org

CREsted: modeling genomic and synthetic cell type-specific enhancers across tissues and species

Sequence-based deep learning models have become the state of the art for the analysis of the genomic regulatory code. Particularly for transcriptional enhancers, deep learning models excel at decipher...

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Reposted by Melanie Weilert

Stowers Institute @stowersinstitute.bsky.social · 03/03/2025

We're thrilled that Investigator @juliazeitlinger.bsky.social is co-chairing the 2025 @asbmb.bsky.social meeting in #KansasCity, which will delve into the core processes of #geneexpression from #developmental and evolutionary perspectives. Read more: bit.ly/41Czvqy

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Reposted by Melanie Weilert

Julia Zeitlinger @juliazeitlinger.bsky.social · 04/03/2025

This a great interdisciplinary gene expression meeting, where everyone is welcome. Please consider attending and submitting your abstract: www.asbmb.org/meetings-eve...

asbmb.org

Evolution and core processes in gene expression

June 26–29, 2025 | Kansas City, Mo.

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Melanie Weilert @mlweilert.bsky.social · 29/01/2025

5 minutes on this platform and it's already clear leaving Twitter was a great call, glad to see everyone <3

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