Our new pre-print, investigating a few important questions when we train S2F models on different types of MPRA datasets. Congrats to Yilun and @xinmingtu.bsky.social www.biorxiv.org/content/10.1...
Investigating Data Size, Sequence Diversity, and Model Complexity in MPRA-based Sequence-to-Function Prediction
We created the MPRA Dataset Collection (MDC), a curated resource of MPRA data from 12 studies comprising over 150 million labeled DNA subsequences. These datasets include both random and natural genom...
www.biorxiv.org
March 15, 2025 at 3:02 AM
Our new pre-print, investigating a few important questions when we train S2F models on different types of MPRA datasets. Congrats to Yilun and @xinmingtu.bsky.social www.biorxiv.org/content/10.1...
Our collaboration with Tony Mustoe's lab us out today. MPRA libraries and possible cryptic splicing in MPRA reporters, or reporters in general. The additional novelty here is that such events are controlled or influenced by AU-rich sequences.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
U-rich elements drive pervasive cryptic splicing in 3’ UTR massively parallel reporter assays - Nature Communications
Massively parallel reporter assays (MPRAs) are powerful technologies for measuring the impact of non-coding sequences on gene expression. Here, the authors demonstrate that MPRA reporters often underg...
www.nature.com
July 25, 2025 at 10:17 AM
Our collaboration with Tony Mustoe's lab us out today. MPRA libraries and possible cryptic splicing in MPRA reporters, or reporters in general. The additional novelty here is that such events are controlled or influenced by AU-rich sequences.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Check out this fascinating MPRA in human hematopoietic cells from Satish Nandakumar, @tewhey.bsky.social, and team!! www.biorxiv.org/content/10.6...
February 21, 2026 at 4:43 PM
Check out this fascinating MPRA in human hematopoietic cells from Satish Nandakumar, @tewhey.bsky.social, and team!! www.biorxiv.org/content/10.6...
My non-MPRA phd work! 😄
New, from @navya-shukla.bsky.social and me:
You have a new genome and want to test it for acceleration against other genomes:
Tired: add it to an existing WGA with much toil and tears
Wired: use our new approach to only add conserved regions!
🧬🧪🖥️
You have a new genome and want to test it for acceleration against other genomes:
Tired: add it to an existing WGA with much toil and tears
Wired: use our new approach to only add conserved regions!
🧬🧪🖥️
Lift&Add - rapid and robust addition of new species to alignments of conserved non-coding sequences https://www.biorxiv.org/content/10.1101/2025.10.14.682260v1
October 15, 2025 at 10:49 PM
My non-MPRA phd work! 😄
Happy to share work spearheaded by former grad student Colin Shew testing shared duplicated cis regulatory elements (CREs) using an MPRA. While we find some high effect CREs, collectively paralog differences represent modest effects accounting for observed gene expression divergence.
Influence of cis-regulatory elements on regulatory divergence in human segmental duplications https://www.biorxiv.org/content/10.1101/2025.10.03.680410v1
October 7, 2025 at 2:31 AM
Happy to share work spearheaded by former grad student Colin Shew testing shared duplicated cis regulatory elements (CREs) using an MPRA. While we find some high effect CREs, collectively paralog differences represent modest effects accounting for observed gene expression divergence.
My preprint on keju, a statistical tool for Massively Parallel Reporter Assay (MPRA) data, is out! keju improves sensitivity, calibration, and reliability over previous methods by closely modeling important uncertainty sources in MPRAs. Check it out: www.biorxiv.org/content/10.6... (1/n)
www.biorxiv.org
March 2, 2026 at 6:59 PM
My preprint on keju, a statistical tool for Massively Parallel Reporter Assay (MPRA) data, is out! keju improves sensitivity, calibration, and reliability over previous methods by closely modeling important uncertainty sources in MPRAs. Check it out: www.biorxiv.org/content/10.6... (1/n)
alfugme faz mpra mim plss
August 1, 2025 at 1:30 AM
alfugme faz mpra mim plss
@juruehle.bsky.social's PhD work is now out in Genome Biology 📚🧬 : Lentiviral single-cell MPRA of synthetic enhancers reveals motif affinity-based encoding of cell state specificity
link.springer.com/article/10.1186/s13059-026-04186-9
Julia achieved three cool things with this work...🧵
link.springer.com/article/10.1186/s13059-026-04186-9
Julia achieved three cool things with this work...🧵
Lentiviral single-cell MPRA of synthetic enhancers reveals motif affinity-based encoding of cell state specificity - Genome Biology
Background Cell state-specific gene expression programs emerge from the interplay between cis-regulatory elements (CREs), such as enhancers, and transcription factors (TFs). Massively parallel reporte...
link.springer.com
July 16, 2026 at 1:52 PM
@juruehle.bsky.social's PhD work is now out in Genome Biology 📚🧬 : Lentiviral single-cell MPRA of synthetic enhancers reveals motif affinity-based encoding of cell state specificity
link.springer.com/article/10.1186/s13059-026-04186-9
Julia achieved three cool things with this work...🧵
link.springer.com/article/10.1186/s13059-026-04186-9
Julia achieved three cool things with this work...🧵
5/ We therefore performed MPRA both at baseline and after Wnt stimulation, a key pathway controlling NPC proliferation and cortical development.
September 23, 2026 at 1:54 PM
5/ We therefore performed MPRA both at baseline and after Wnt stimulation, a key pathway controlling NPC proliferation and cortical development.
🧪🖥️🧬 It's here!! Our second MPRA, which is totally different from the first. For starters, there's no human sequences anywhere!
Instead there's marsupials, wolves, pandas and a lot of hard work from lab members past & present, chief amongst them @navya-shukla.bsky.social (looking for a postdoc btw)
Instead there's marsupials, wolves, pandas and a lot of hard work from lab members past & present, chief amongst them @navya-shukla.bsky.social (looking for a postdoc btw)
Dissecting functional regulatory convergence over 160 million years of therian evolution https://www.biorxiv.org/content/10.1101/2025.07.10.662670v1
July 11, 2025 at 9:46 PM
🧪🖥️🧬 It's here!! Our second MPRA, which is totally different from the first. For starters, there's no human sequences anywhere!
Instead there's marsupials, wolves, pandas and a lot of hard work from lab members past & present, chief amongst them @navya-shukla.bsky.social (looking for a postdoc btw)
Instead there's marsupials, wolves, pandas and a lot of hard work from lab members past & present, chief amongst them @navya-shukla.bsky.social (looking for a postdoc btw)
🚀 Very excited to share the first major work from my PhD!!
We combined MPRA and CRISPRa in excitatory neurons to test and validate cis-regulation therapies for hundreds of haploinsufficient neurodevelopmental disorder genes. 🧬🔬
www.biorxiv.org/content/10.1...
We combined MPRA and CRISPRa in excitatory neurons to test and validate cis-regulation therapies for hundreds of haploinsufficient neurodevelopmental disorder genes. 🧬🔬
www.biorxiv.org/content/10.1...
November 6, 2025 at 11:57 PM
🚀 Very excited to share the first major work from my PhD!!
We combined MPRA and CRISPRa in excitatory neurons to test and validate cis-regulation therapies for hundreds of haploinsufficient neurodevelopmental disorder genes. 🧬🔬
www.biorxiv.org/content/10.1...
We combined MPRA and CRISPRa in excitatory neurons to test and validate cis-regulation therapies for hundreds of haploinsufficient neurodevelopmental disorder genes. 🧬🔬
www.biorxiv.org/content/10.1...
What's your favorite MPRA*? Mine is StephenSTARR-seq
* massively Philadelphian restaurant assay
* massively Philadelphian restaurant assay
June 8, 2026 at 7:16 PM
What's your favorite MPRA*? Mine is StephenSTARR-seq
* massively Philadelphian restaurant assay
* massively Philadelphian restaurant assay
They are, but tbh for this mission MQs, MPRA, and maybe AWACS are the way to go for what the target set ostensibly is
I think this is the most likely reason
bsky.app/profile/mike...
I think this is the most likely reason
bsky.app/profile/mike...
With this crew anything is possible but my first guess is SOUTHCOM went maximalist with the CONOP they were asked by OSD to produce for counter-narcotics (because that's what any CCMD does when they're asked for a CONOP) and OSD is either too stupid or too committed to tell them no on anything
September 5, 2025 at 5:11 PM
They are, but tbh for this mission MQs, MPRA, and maybe AWACS are the way to go for what the target set ostensibly is
I think this is the most likely reason
bsky.app/profile/mike...
I think this is the most likely reason
bsky.app/profile/mike...
I'm hiring:
1. Research associate (wet-lab w/ phd) to generate mpra perturbation data
2. ML postdoc to build multimodal generative AI for DNA (eg diffusion and LLMs)
3. Bioinformatician (any level) to process and harmonize functional genomics data to train foundation models
DM me if interested!
1. Research associate (wet-lab w/ phd) to generate mpra perturbation data
2. ML postdoc to build multimodal generative AI for DNA (eg diffusion and LLMs)
3. Bioinformatician (any level) to process and harmonize functional genomics data to train foundation models
DM me if interested!
December 23, 2024 at 8:04 PM
I'm hiring:
1. Research associate (wet-lab w/ phd) to generate mpra perturbation data
2. ML postdoc to build multimodal generative AI for DNA (eg diffusion and LLMs)
3. Bioinformatician (any level) to process and harmonize functional genomics data to train foundation models
DM me if interested!
1. Research associate (wet-lab w/ phd) to generate mpra perturbation data
2. ML postdoc to build multimodal generative AI for DNA (eg diffusion and LLMs)
3. Bioinformatician (any level) to process and harmonize functional genomics data to train foundation models
DM me if interested!
Capture C identifies promoter interacting sequences. MPRA tests sequences for regulatory activity. Here, we combined them both to test sequences with their target promoter. Amazing work by @colinearnould.bsky.social, Pia Keukeleire, Martin Kircher and many others.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Capture-C MPRA: A high-throughput method to simultaneously characterize promoter interactions and regulatory activity
Cis regulatory elements (CREs) interact with their target promoters over long genomic distances and can be identified using chromatin conformation capture (3C) assays. Their regulatory activity can be...
www.biorxiv.org
June 15, 2025 at 6:29 PM
Capture C identifies promoter interacting sequences. MPRA tests sequences for regulatory activity. Here, we combined them both to test sequences with their target promoter. Amazing work by @colinearnould.bsky.social, Pia Keukeleire, Martin Kircher and many others.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
See you all on Wed for Lucía Barbadilla's Kipoi seminar on MPRA-trained models!
Join us for our next Kipoi Seminar with Lucía Barbadilla, De Ridder Group
@luciabarmar.bsky.social
@umcutrecht.bsky.social
👉PARM: The regulatory grammar of human promoters uncovered by MPRA-trained deep learning
📅Wed April 2, 5:30pm CET, not recorded!
🧬kipoi.org/seminar/
🦋 @kipoizoo.bsky.social
@luciabarmar.bsky.social
@umcutrecht.bsky.social
👉PARM: The regulatory grammar of human promoters uncovered by MPRA-trained deep learning
📅Wed April 2, 5:30pm CET, not recorded!
🧬kipoi.org/seminar/
🦋 @kipoizoo.bsky.social
March 31, 2025 at 8:54 AM
See you all on Wed for Lucía Barbadilla's Kipoi seminar on MPRA-trained models!
Powerful new method (Capture-C MPRA) to simultaneously characterize promoter
interactions and regulatory activity. Preprint by @colinearnould.bsky.social @nadavahituv.bsky.social & collaborators
🧪🧬
interactions and regulatory activity. Preprint by @colinearnould.bsky.social @nadavahituv.bsky.social & collaborators
🧪🧬
www.biorxiv.org
June 15, 2025 at 7:27 AM
Powerful new method (Capture-C MPRA) to simultaneously characterize promoter
interactions and regulatory activity. Preprint by @colinearnould.bsky.social @nadavahituv.bsky.social & collaborators
🧪🧬
interactions and regulatory activity. Preprint by @colinearnould.bsky.social @nadavahituv.bsky.social & collaborators
🧪🧬
Nature research paper: Regulatory grammar in human promoters uncovered by MPRA-based deep learning
go.nature.com/3ZQcb6Q
go.nature.com/3ZQcb6Q
Regulatory grammar in human promoters uncovered by MPRA-based deep learning - Nature
PARM is a deep-learning model trained on data from massively parallel reporter assays to help predict promoter activity in different human cell types, design synthetic promoters and identify key features of regulatory promoter grammar.
go.nature.com
February 4, 2026 at 8:02 PM
Nature research paper: Regulatory grammar in human promoters uncovered by MPRA-based deep learning
go.nature.com/3ZQcb6Q
go.nature.com/3ZQcb6Q
MPRA - Make Presidents Respectable Again
December 7, 2025 at 3:39 PM
MPRA - Make Presidents Respectable Again
Our #ASHG25 platform activities:
Vrathasha Vrathasha: 3D genomics & glaucoma. 206AB, W 10.45-11
Winter Bruner: MPRA & childhood obesity. 205ABC, T 11-11.15
Matt Pahl: Ancillary Session, Predicted Effector Genes. 259A, F 1.45-1.15
Struan Grant chairs Metabolic Matrix session. 253ABC, S 10-11
Vrathasha Vrathasha: 3D genomics & glaucoma. 206AB, W 10.45-11
Winter Bruner: MPRA & childhood obesity. 205ABC, T 11-11.15
Matt Pahl: Ancillary Session, Predicted Effector Genes. 259A, F 1.45-1.15
Struan Grant chairs Metabolic Matrix session. 253ABC, S 10-11
October 14, 2025 at 11:20 AM
Our #ASHG25 platform activities:
Vrathasha Vrathasha: 3D genomics & glaucoma. 206AB, W 10.45-11
Winter Bruner: MPRA & childhood obesity. 205ABC, T 11-11.15
Matt Pahl: Ancillary Session, Predicted Effector Genes. 259A, F 1.45-1.15
Struan Grant chairs Metabolic Matrix session. 253ABC, S 10-11
Vrathasha Vrathasha: 3D genomics & glaucoma. 206AB, W 10.45-11
Winter Bruner: MPRA & childhood obesity. 205ABC, T 11-11.15
Matt Pahl: Ancillary Session, Predicted Effector Genes. 259A, F 1.45-1.15
Struan Grant chairs Metabolic Matrix session. 253ABC, S 10-11
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...
3/ To address this, we used a massively parallel reporter assay (MPRA) to test the regulatory activity of ~9,000 cortical structure-associated variants in human neural progenitor cells (NPCs), cells that give rise to neurons of the developing cortex.
September 23, 2026 at 1:53 PM
3/ To address this, we used a massively parallel reporter assay (MPRA) to test the regulatory activity of ~9,000 cortical structure-associated variants in human neural progenitor cells (NPCs), cells that give rise to neurons of the developing cortex.
Capture-C MPRA: A high-throughput method to simultaneously characterize promoter interactions and regulatory activity https://www.biorxiv.org/content/10.1101/2025.06.11.658967v1
June 15, 2025 at 7:32 AM
Capture-C MPRA: A high-throughput method to simultaneously characterize promoter interactions and regulatory activity https://www.biorxiv.org/content/10.1101/2025.06.11.658967v1
📌 A "dying" USA 🇺🇸 empire! 💣
[A "condensed" history of fallen empires]
– "The US empire is 248 yrs old and is showing signs of decline."
#empire #houseofcards #latestagecapitalism
#oligarchy #power #thecollapse #wealth #usa #TheYarbros
'How America Ends'
By The Yarbros
youtu.be/zH-_YfDUytg?...
[A "condensed" history of fallen empires]
– "The US empire is 248 yrs old and is showing signs of decline."
#empire #houseofcards #latestagecapitalism
#oligarchy #power #thecollapse #wealth #usa #TheYarbros
'How America Ends'
By The Yarbros
youtu.be/zH-_YfDUytg?...
How America is Reaping What It Sowed
YouTube video by The Yarbros
youtu.be
March 18, 2025 at 8:31 PM
March 20, 2025 at 5:06 PM