Judith Kribelbauer
@jk-swietek.bsky.social
Gabilan Assistant Professor of Biological Sciences @ USC - Molecular and Computational Biology Section
Reposted by Judith Kribelbauer
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.
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.
October 7, 2025 at 3:24 PM
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.
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.
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...
August 14, 2025 at 6:10 AM
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...
Beautifully controlled system to delineate primary from context-specific TF binding, revealing how chromatin state shapes TF binding specificity during differentiation and vice versa!
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....
August 7, 2025 at 8:12 PM
Beautifully controlled system to delineate primary from context-specific TF binding, revealing how chromatin state shapes TF binding specificity during differentiation and vice versa!
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.
“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
🥁That’s what the committee said about this #SIBRemarkableOutputs 2024
👉Discover the output: tinyurl.com/53arz2rz
August 5, 2025 at 8:51 PM
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.
Reposted by Judith Kribelbauer
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
July 2, 2025 at 11:02 PM
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.
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...
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
May 27, 2025 at 7:31 PM
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.
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
May 16, 2025 at 5:03 AM
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...
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
April 29, 2025 at 6:39 PM
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
Reposted by Judith Kribelbauer
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...
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
April 22, 2025 at 8:51 PM
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...
genome.cshlp.org/content/earl...
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
April 21, 2025 at 9:43 PM
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...
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
February 12, 2025 at 11:46 PM
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
Finally out! We present EXTRA-seq, a new EXTended Reporter Assay to quantify endogenous enhancer-promoter communication at kb scale!
www.biorxiv.org/content/10.1...
A 🧵about what it can do:
#SynBio #DeepLearning #GeneRegulation
www.biorxiv.org/content/10.1...
A 🧵about what it can do:
#SynBio #DeepLearning #GeneRegulation
EXTRA-seq: a genome-integrated extended massively parallel reporter assay to quantify enhancer-promoter communication
Precise control of gene expression is essential for cellular function, but the mechanisms by which enhancers communicate with promoters to coordinate this process are not fully understood. While seque...
biorxiv.org
December 16, 2024 at 2:39 PM
Finally out! We present EXTRA-seq, a new EXTended Reporter Assay to quantify endogenous enhancer-promoter communication at kb scale!
www.biorxiv.org/content/10.1...
A 🧵about what it can do:
#SynBio #DeepLearning #GeneRegulation
www.biorxiv.org/content/10.1...
A 🧵about what it can do:
#SynBio #DeepLearning #GeneRegulation
Neat study introducing a new system to study enhancer cooperativity across large distances in endogenous (!) contexts - showing that there is still much to learn about E-E and E-P communication. Enhancer order, distance, and strength, & CTCF sites all matter, and in a context-specific manner!
By definition, enhancers can activate from a distance. But with increased distance between enhancer and promoter, the activation drops. To study this systematically, we build a synthetic locus: www.cell.com/molecular-ce... 1/12
Redirecting
doi.org
December 4, 2024 at 9:04 PM
Neat study introducing a new system to study enhancer cooperativity across large distances in endogenous (!) contexts - showing that there is still much to learn about E-E and E-P communication. Enhancer order, distance, and strength, & CTCF sites all matter, and in a context-specific manner!
and here the flagship manuscript #Codebook
(1/7) Thrilled to reveal the results of the Codebook Project, an international effort to identify accurate DNA-binding motifs and genomic binding loci for the >300 uncharacterized human transcription factors (TFs) doi.org/10.1101/2024...
Perspectives on Codebook: sequence specificity of uncharacterized human transcription factors
We describe an effort (“Codebook”) to determine the sequence specificity of 332 putative and largely uncharacterized human transcription factors (TFs), as well as 61 control TFs. Nearly 5,000 independ...
doi.org
November 15, 2024 at 8:51 PM
and here the flagship manuscript #Codebook
Curious to learn more about the Codebook Project? years-long, multi-center effort to identify binding specificities for poorly characterized human TFs. Read below if you want to learn more about 'dark' TFs (1/5 preprints in total).
(1/8) 🚀 Excited to share our findings on a large-scale ChIP-seq assay for 166 previously uncharacterized human transcription factors (TFs) and their roles in both regulatory regions, and more strikingly, the “dark matter” genome. 🌌 doi.org/10.1101/2024....
Extensive binding of uncharacterized human transcription factors to genomic dark matter
Most of the human genome is thought to be non-functional, and includes large segments often referred to as “dark matter” DNA. The genome also encodes hundreds of putative and poorly characterized tran...
doi.org
November 15, 2024 at 8:49 PM
Curious to learn more about the Codebook Project? years-long, multi-center effort to identify binding specificities for poorly characterized human TFs. Read below if you want to learn more about 'dark' TFs (1/5 preprints in total).
Reposted by Judith Kribelbauer
(1/12) Excited to present the results of the large-scale benchmarking of DNA motif discovery tools using the Codebook data compendium on poorly studied human transcription factors and the Codebook Motif Explorer: dx.doi.org/10.1101/2024..., mex.autosome.org ⬇️.
November 14, 2024 at 1:04 PM
(1/12) Excited to present the results of the large-scale benchmarking of DNA motif discovery tools using the Codebook data compendium on poorly studied human transcription factors and the Codebook Motif Explorer: dx.doi.org/10.1101/2024..., mex.autosome.org ⬇️.
Reposted by Judith Kribelbauer
(12/12) Kudos to the Codebook and GRECO-BIT consortium members including @bartdeplancke.bsky.social, see the whole team at ibis.autosome.org/docs/about_us
IBIS Challenge
ibis.autosome.org
November 14, 2024 at 1:04 PM
(12/12) Kudos to the Codebook and GRECO-BIT consortium members including @bartdeplancke.bsky.social, see the whole team at ibis.autosome.org/docs/about_us
Reposted by Judith Kribelbauer
(1/8)📢Excited to announce the bioRxiv submission of my work from the past three years! Introducing meSMiLE-seq, a microfluidic assay aimed to understand how DNA modifications impact transcription factor (TF) binding, as part of the large Codebook/GRECO-BIT collab dx.doi.org/10.1101/2024... ✨🧵 ⬇️
https://dx.doi.org/10.1101/2024.11.11.619598✨
November 14, 2024 at 1:49 PM
(1/8)📢Excited to announce the bioRxiv submission of my work from the past three years! Introducing meSMiLE-seq, a microfluidic assay aimed to understand how DNA modifications impact transcription factor (TF) binding, as part of the large Codebook/GRECO-BIT collab dx.doi.org/10.1101/2024... ✨🧵 ⬇️
looks like a great lineup!
New conference that will explore gene regulation mechanisms at molecular resolution. We bring bring together a fine crowd that uses microscopy, genomics and theory to chart the future of the booming fields of #singlemoleculegenomics and #singlemoleculemicroscopy. Join us July 15-18th 2025 at EMBL
November 14, 2024 at 9:40 AM
looks like a great lineup!