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Reposted by Judith Kribelbauer

Jacob Schreiber @jmschreiber91.bsky.social · 1d

Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians!

The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.

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Judith Kribelbauer @jk-swietek.bsky.social · Aug 14

While over here discussions are about slashing Science funding, the Swiss are proposing to put it center stage on their currency. And I thought I was returning to the "Mecca of Science", not leaving it... 😅 Also, is this even real money? www.neuebanknotenserie.ch/detailview.h...

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Judith Kribelbauer @jk-swietek.bsky.social · Aug 7

Beautifully controlled system to delineate primary from context-specific TF binding, revealing how chromatin state shapes TF binding specificity during differentiation and vice versa!

Schubeler Lab @schubelerlab.bsky.social · Aug 7

Excited to see this published with additional data following our preprint a while back. Cool combination (in our biased view) of controlled TF expression and machine learning to decode chromatin sensitivity. www.sciencedirect.com/science/arti....

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Judith Kribelbauer @jk-swietek.bsky.social · Aug 5

Excited to see that our study on context-specific transcription factors was named as one of 8 remarkable outputs of 2024 by the Swiss Institute of Bioinformatics.

SIB Swiss Institute of Bioinformatics @sib.swiss · Jul 31

“This study offers a significant advancement in understanding enhancer-mediated gene regulation by identifying context-specific transcription factor interactions."
🥁That’s what the committee said about this #SIBRemarkableOutputs 2024
👉Discover the output: tinyurl.com/53arz2rz

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Reposted by Judith Kribelbauer

Chromatin Haiku @chromatinhaiku.bsky.social · Jul 2

The Range Extender
For enhancers to function
At long distances

#ChromatinHaiku

Evgeny Kvon @evgenykvon.bsky.social · Jul 2

Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/

Range extender mediates long-distance enhancer activity - Nature

The REX element is associated with long-range enhancer–promoter interactions.

www.nature.com

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Judith Kribelbauer @jk-swietek.bsky.social · Jun 27

Congrats!

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Judith Kribelbauer @jk-swietek.bsky.social · Jun 23

same here. Have an 18-month-old and the only time I get anything done is at night when he sleeps 🫠 You are not alone, hang in there!

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Judith Kribelbauer @jk-swietek.bsky.social · May 28

Agree, there are definitely cases where syntax is important, the question is more how to model it well when it isn't. I would think the latter is important for accuracy, which is where models tend to start underperforming (e.g. predicting activity for personalised genomes). I like your suggestion!

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Judith Kribelbauer @jk-swietek.bsky.social · May 27

might be time to reconsider how we train machine learning models. Almost every model I come across uses convolutional filters that attempt to learn syntax, when perhaps none is present...

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Judith Kribelbauer @jk-swietek.bsky.social · May 27

Really cool work using a gene synteny-based strategy to identify enhancer conservation across species w/o seq similarity. Last figure is my favorite: while TFBS content is conserved, TFBS syntax is not! Aligns with our findings on TF cooperativity, where a specific syntax was not required.

Daniel Ibrahim @danielibrahim.bsky.social · May 27

How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...

Conservation of regulatory elements with highly diverged sequences across large evolutionary distances

Nature Genetics - Combining functional genomic data from mouse and chicken with a synteny-based strategy identifies positionally conserved cis-regulatory elements in the absence of direct sequence...

rdcu.be

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Judith Kribelbauer @jk-swietek.bsky.social · May 16

As a scientist and mom of a little boy this story really touched me. The rewards of science funding go way beyond $ return on investment (& NIH's ROI is unparalleled). Hats off to the parents making this incredibly tough decision, paving the way for future treatments. www.nytimes.com/2025/05/15/h...

Baby Is Healed With World’s First Personalized Gene-Editing Treatment

www.nytimes.com

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Judith Kribelbauer @jk-swietek.bsky.social · Apr 29

How is it end of April already? Excited to share that the Kribelbauer Lab is up and running @USC/MCB. Grateful for my first two PhD students @m-finegan.bsky.social @christinagirgis.bsky.social. We are dev scalable, genome-int. tools to study TF & enhancer regulation. Website now live bit.ly/4jo8Tjg

Home - Kribelbauer Lab

USC Dornsife

dornsife.usc.edu

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Reposted by Judith Kribelbauer

Nadav Ahituv @nadavahituv.bsky.social · Apr 22

MPRAbase (mprabase.ucsf.edu) , a customized database for massively parallel reporter assays (MPRAs) to easily find and download MPRA data. Amazing work by Jingjing Zhao, Fotis Baltoumas, Georgios Pavlopoulos, @vagar.bsky.social, ilias Georgakopoulos-Soares & others.

genome.cshlp.org/content/earl...

MPRAbase a Massively Parallel Reporter Assay database

An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms

genome.cshlp.org

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Judith Kribelbauer @jk-swietek.bsky.social · Apr 21

100% agree w Lowe on this: "But how is AGI going to suddenly reveal what is now hidden? The sum total of all the medical information in the world right now is not enough. And it's going to go on being Not Enough for quite some time..." Let's also focus on Exp. Tools! www.science.org/content/blog...

The End of Disease

www.science.org

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Judith Kribelbauer @jk-swietek.bsky.social · Feb 12

Looking for a Postdoc position in #Genomics at the interface of computational and molecular biology? -> The Rube lab at UC Merced is recruiting. I highly recommend you reach out! aprecruit.ucmerced.edu/JPF01874

Postdoctoral Scholar in Genomics

University of California, Merced is hiring. Apply now!

aprecruit.ucmerced.edu

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Judith Kribelbauer @jk-swietek.bsky.social · Dec 18

Thank you! Very complementary to the synthetic platform your lab built. Still challenging to go beyond 5kb for us, so tackling distal enhancer regulation will take a lot more engineering! Looking forward to future work from your lab!

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Judith Kribelbauer @jk-swietek.bsky.social · Dec 17

Scalability is definitely the next big step in the journey. Also in the works a universal replacement cassette. With the current throughput it can still be useful for benchmarking/providing insights into potential shortcoming of "AI" tools.

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Judith Kribelbauer @jk-swietek.bsky.social · Dec 16

Thank you!

Judith Kribelbauer @jk-swietek.bsky.social · Dec 16

Thank you! Been a long time coming...

Judith Kribelbauer @jk-swietek.bsky.social · Dec 16

Looking forward to feedback from the community. We want to move into new applications (SynBio, genAI, ...), reach out if interested!

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Judith Kribelbauer @jk-swietek.bsky.social · Dec 16

Stay tuned, we have some exciting collaborations in the works (@lucapinello.bsky.social lab), applying EXTRA-seq to test cell type specificity & the dynamic range of synthetically created sequences.

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Judith Kribelbauer @jk-swietek.bsky.social · Dec 16

We evaluated combinatorial E-P modifications, finding a new role for the TATA box, which acts as a 'noise suppressor' to prevent expression from weak (1 TFBS) "enhancers". With increasing E strength it switches to activation thus expanding the dynamic range.

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Judith Kribelbauer @jk-swietek.bsky.social · Dec 16

It also allows testing "out-of context" enhancer activities and what enhancer-native molecular features correlate with expression.

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Judith Kribelbauer @jk-swietek.bsky.social · Dec 16

We sys compare it to plasmid-based MPRAs and deep learning models (Enformer @DeepMind), finding new bio insights & suggesting ways to improve predictions.
We resolve expression differences down to distinct TF configurations on DNA, highlighting shortcomings of MPRAs and DL tools.

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Judith Kribelbauer @jk-swietek.bsky.social · Dec 16

EXTRA-seq can be targeted to endogenous loci, allowing us to measure "near-native" gene expression as a function of dozens of newly introduced E-P genotypes (over 2kb apart).

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