"A Multiome experiment is a very expensive way to find out that your hypothesis is wrong."
#devbio #collaborate #GeneRegulation #Enhancers
#devbio #collaborate #GeneRegulation #Enhancers
November 25, 2024 at 5:37 PM
"A Multiome experiment is a very expensive way to find out that your hypothesis is wrong."
#devbio #collaborate #GeneRegulation #Enhancers
#devbio #collaborate #GeneRegulation #Enhancers
Check out this great resource of single cell multiome data, cell annotations, regulatory DNA models of cell type resolved chromatin accessibility & comprehensive annotation of motifs & sequence syntax for multiple tissues in early human development 1/
Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human fetal development! www.biorxiv.org/content/10.1... Read on for more: 🧵 1/16 #GeneReg 🧬🖥️
Dissecting regulatory syntax in human development with scalable multiomics and deep learning
Transcription factors (TFs) establish cell identity during development by binding regulatory DNA in a sequence-specific manner, often promoting local chromatin accessibility, and regulating gene expre...
www.biorxiv.org
May 4, 2025 at 1:43 AM
Check out this great resource of single cell multiome data, cell annotations, regulatory DNA models of cell type resolved chromatin accessibility & comprehensive annotation of motifs & sequence syntax for multiple tissues in early human development 1/
🎇Our new paper in @ScienceMagazine
: Kidney Multiome-Based Genetic Scorecard Reveals Convergent Coding and Regulatory Variants.
@Hongbo919Liu science.org/doi/10.1126/...
: Kidney Multiome-Based Genetic Scorecard Reveals Convergent Coding and Regulatory Variants.
@Hongbo919Liu science.org/doi/10.1126/...
Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants
Kidney dysfunction is a major cause of mortality, but its genetic architecture remains elusive. In this study, we conducted a multiancestry genome-wide association study in 2.2 million individuals and...
science.org
February 7, 2025 at 2:25 PM
🎇Our new paper in @ScienceMagazine
: Kidney Multiome-Based Genetic Scorecard Reveals Convergent Coding and Regulatory Variants.
@Hongbo919Liu science.org/doi/10.1126/...
: Kidney Multiome-Based Genetic Scorecard Reveals Convergent Coding and Regulatory Variants.
@Hongbo919Liu science.org/doi/10.1126/...
📡🧵 Excited to release an updated version of our preprint: Zebrahub-Multiome: Uncovering Gene Regulatory Network Dynamics During Zebrafish Embryogenesis
🧪🧬🖥️🐠
doi.org/10.1101/2024...
A tour-de-force by @yangjoonkim with an unexpected discovery!
🧪🧬🖥️🐠
doi.org/10.1101/2024...
A tour-de-force by @yangjoonkim with an unexpected discovery!
January 23, 2026 at 12:08 AM
📡🧵 Excited to release an updated version of our preprint: Zebrahub-Multiome: Uncovering Gene Regulatory Network Dynamics During Zebrafish Embryogenesis
🧪🧬🖥️🐠
doi.org/10.1101/2024...
A tour-de-force by @yangjoonkim with an unexpected discovery!
🧪🧬🖥️🐠
doi.org/10.1101/2024...
A tour-de-force by @yangjoonkim with an unexpected discovery!
Accuracy of gene regulatory network inference is increased by combining multiome single-cell and atlas-scale bulk data go.nature.com/43YySqO
rdcu.be/ebBio
rdcu.be/ebBio
Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data - Nature Biotechnology
Accuracy of gene regulatory network inference is increased by combining multiome single-cell and atlas-scale bulk data.
go.nature.com
March 13, 2025 at 1:25 PM
Accuracy of gene regulatory network inference is increased by combining multiome single-cell and atlas-scale bulk data go.nature.com/43YySqO
rdcu.be/ebBio
rdcu.be/ebBio
December 19, 2025 at 12:37 AM
This is 1) great news and 2) I think I’m gonna sit on the multiome superenhancer story we were gonna submit now… 😂
EPIGENETIC HULK READY TO SMASH AGAIN! GET IN LOSERS!
June 13, 2025 at 5:56 AM
This is 1) great news and 2) I think I’m gonna sit on the multiome superenhancer story we were gonna submit now… 😂
We're about to release a pretty massive multiome atlas (includes chromatin) of several adult tissues via ENCODE4 + a significant expansion of the bulk DNase and ATAC datasets (already out). Many more regions than ENCODE3.
November 20, 2024 at 3:41 PM
We're about to release a pretty massive multiome atlas (includes chromatin) of several adult tissues via ENCODE4 + a significant expansion of the bulk DNase and ATAC datasets (already out). Many more regions than ENCODE3.
Excited to share our new FinnGen single-nucleus multiome preprint! 🧬
We profiled ~10M PBMCs (snRNA-seq + snATAC-seq) from 1,108 Finnish donors to map how genetic variants drive complex disease through chromatin and gene regulation 🧵👇
🔗 Link: www.medrxiv.org/content/10.1...
We profiled ~10M PBMCs (snRNA-seq + snATAC-seq) from 1,108 Finnish donors to map how genetic variants drive complex disease through chromatin and gene regulation 🧵👇
🔗 Link: www.medrxiv.org/content/10.1...
December 1, 2025 at 3:36 PM
Excited to share our new FinnGen single-nucleus multiome preprint! 🧬
We profiled ~10M PBMCs (snRNA-seq + snATAC-seq) from 1,108 Finnish donors to map how genetic variants drive complex disease through chromatin and gene regulation 🧵👇
🔗 Link: www.medrxiv.org/content/10.1...
We profiled ~10M PBMCs (snRNA-seq + snATAC-seq) from 1,108 Finnish donors to map how genetic variants drive complex disease through chromatin and gene regulation 🧵👇
🔗 Link: www.medrxiv.org/content/10.1...
Excited to share: enhanced capture in vivo multiome Perturb-seq!
Worried about low gRNA recovery and wasting sequencing on cells that can’t assign a perturbation? We engineered gRNA transcripts to stay in the nucleus, enabling efficient multiomic Perturb-seq!
www.biorxiv.org/content/10.6...
Worried about low gRNA recovery and wasting sequencing on cells that can’t assign a perturbation? We engineered gRNA transcripts to stay in the nucleus, enabling efficient multiomic Perturb-seq!
www.biorxiv.org/content/10.6...
March 17, 2026 at 1:23 PM
Excited to share: enhanced capture in vivo multiome Perturb-seq!
Worried about low gRNA recovery and wasting sequencing on cells that can’t assign a perturbation? We engineered gRNA transcripts to stay in the nucleus, enabling efficient multiomic Perturb-seq!
www.biorxiv.org/content/10.6...
Worried about low gRNA recovery and wasting sequencing on cells that can’t assign a perturbation? We engineered gRNA transcripts to stay in the nucleus, enabling efficient multiomic Perturb-seq!
www.biorxiv.org/content/10.6...
Impressive and important work by @ksusztak.bsky.social and team, published in @science.org!
Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants
#Nephsky #Medsky
www.science.org/doi/10.1126/...
Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants
#Nephsky #Medsky
www.science.org/doi/10.1126/...
Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants
Kidney dysfunction is a major cause of mortality, but its genetic architecture remains elusive. In this study, we conducted a multiancestry genome-wide association study in 2.2 million individuals and...
www.science.org
February 7, 2025 at 3:57 AM
Impressive and important work by @ksusztak.bsky.social and team, published in @science.org!
Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants
#Nephsky #Medsky
www.science.org/doi/10.1126/...
Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants
#Nephsky #Medsky
www.science.org/doi/10.1126/...
I hear multiome a whole lot but that usually means two, maybe three modalities.
November 26, 2024 at 7:28 PM
I hear multiome a whole lot but that usually means two, maybe three modalities.
Delighted to have our Perturb-multiome paper, led by #JorgeMartinRufino and @hemagene.bsky.social from our lab, published today in @science.org. Please check out this powerful approach to decipher gene regulatory networks enriched for genetic variation: www.science.org/doi/10.1126/...
Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes
Most phenotype-associated genetic variants map to noncoding regulatory regions of the human genome, but their mechanisms remain elusive in most cases. We developed a highly efficient strategy, Perturb...
www.science.org
April 3, 2025 at 11:57 PM
Delighted to have our Perturb-multiome paper, led by #JorgeMartinRufino and @hemagene.bsky.social from our lab, published today in @science.org. Please check out this powerful approach to decipher gene regulatory networks enriched for genetic variation: www.science.org/doi/10.1126/...
Diving into Multiome approaches to understand gene specification networks in the zebrafish retina with Juan Ramon Martínez-Morales @jrmarmor.bsky.social
at #ECCN2025
@borrell-lab.bsky.social @r3rt0.bsky.social @zoltan-molnar.bsky.social
at #ECCN2025
@borrell-lab.bsky.social @r3rt0.bsky.social @zoltan-molnar.bsky.social
May 7, 2025 at 9:20 AM
Diving into Multiome approaches to understand gene specification networks in the zebrafish retina with Juan Ramon Martínez-Morales @jrmarmor.bsky.social
at #ECCN2025
@borrell-lab.bsky.social @r3rt0.bsky.social @zoltan-molnar.bsky.social
at #ECCN2025
@borrell-lab.bsky.social @r3rt0.bsky.social @zoltan-molnar.bsky.social
"Plants don't have specialized immune cells, but individual plant cells can flexibly turn into immune hotspots" - 🌱
@tatsuyanobori.bsky.social presented at #RNGS25 on combining single cell multiome data & spatial transcriptomics to study the genetic regulation of plant-microbe interactions.🧬🦠
@tatsuyanobori.bsky.social presented at #RNGS25 on combining single cell multiome data & spatial transcriptomics to study the genetic regulation of plant-microbe interactions.🧬🦠
March 20, 2025 at 4:11 PM
"Plants don't have specialized immune cells, but individual plant cells can flexibly turn into immune hotspots" - 🌱
@tatsuyanobori.bsky.social presented at #RNGS25 on combining single cell multiome data & spatial transcriptomics to study the genetic regulation of plant-microbe interactions.🧬🦠
@tatsuyanobori.bsky.social presented at #RNGS25 on combining single cell multiome data & spatial transcriptomics to study the genetic regulation of plant-microbe interactions.🧬🦠
Come to poster II12 - @luisadema.bsky.social and I are waiting to show you some beautiful UMAPs of single cell multiome data of the ventral hippocampus across the estrous cucle, sex, and peripartum! 🔥 Cool stuff — come say hi!
November 19, 2025 at 5:11 PM
Come to poster II12 - @luisadema.bsky.social and I are waiting to show you some beautiful UMAPs of single cell multiome data of the ventral hippocampus across the estrous cucle, sex, and peripartum! 🔥 Cool stuff — come say hi!
Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants
@science.org @ksusztak.bsky.social
www.science.org/doi/10.1126/...
@science.org @ksusztak.bsky.social
www.science.org/doi/10.1126/...
Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants
Kidney dysfunction is a major cause of mortality, but its genetic architecture remains elusive. In this study, we conducted a multiancestry genome-wide association study in 2.2 million individuals and...
www.science.org
February 7, 2025 at 2:48 AM
Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants
@science.org @ksusztak.bsky.social
www.science.org/doi/10.1126/...
@science.org @ksusztak.bsky.social
www.science.org/doi/10.1126/...
Updated preprint @cincyresearch.bsky.social @emilymiraldi.bsky.social
Multiome-seq links inflammatory bowel disease polygenic risk to TNF inhibitor response
www.biorxiv.org/content/10.1...
Multiome-seq links inflammatory bowel disease polygenic risk to TNF inhibitor response
www.biorxiv.org/content/10.1...
August 6, 2026 at 6:57 PM
Updated preprint @cincyresearch.bsky.social @emilymiraldi.bsky.social
Multiome-seq links inflammatory bowel disease polygenic risk to TNF inhibitor response
www.biorxiv.org/content/10.1...
Multiome-seq links inflammatory bowel disease polygenic risk to TNF inhibitor response
www.biorxiv.org/content/10.1...
Single cell multiome analysis of transporter accidents reveals a role for forked beard genes in fate acquisition
Right then, our turn
What's your fake Star Trek academic paper
What's your fake Star Trek academic paper
What’s your fake starwars academic paper
September 23, 2026 at 2:47 PM
Single cell multiome analysis of transporter accidents reveals a role for forked beard genes in fate acquisition
Last summer I spent 4 months working at the @alleninstitute.org as a Visiting Scientist. Recently we released some preprints about the work we collaborated on, where from new multiome atlases of CNS regions we tried to decipher underlying enhancer logic with CREsted (among many other things). (1/n)
February 9, 2026 at 11:59 AM
Last summer I spent 4 months working at the @alleninstitute.org as a Visiting Scientist. Recently we released some preprints about the work we collaborated on, where from new multiome atlases of CNS regions we tried to decipher underlying enhancer logic with CREsted (among many other things). (1/n)
I'd like to thank 🙏🏽 @cynthiasc.bsky.social for her 3 years at @lieberinstitute.bsky.social working in my team analyzing data generated by @kr-maynard.bsky.social et al.
Cynthia led our first foray into the world of multi-omics data (snRNA-seq + snATAC-seq)
#multiome #snRNAseq #scATACseq
Cynthia led our first foray into the world of multi-omics data (snRNA-seq + snATAC-seq)
#multiome #snRNAseq #scATACseq
December 17, 2025 at 11:24 PM
I'd like to thank 🙏🏽 @cynthiasc.bsky.social for her 3 years at @lieberinstitute.bsky.social working in my team analyzing data generated by @kr-maynard.bsky.social et al.
Cynthia led our first foray into the world of multi-omics data (snRNA-seq + snATAC-seq)
#multiome #snRNAseq #scATACseq
Cynthia led our first foray into the world of multi-omics data (snRNA-seq + snATAC-seq)
#multiome #snRNAseq #scATACseq
This is quite cool! I can’t seem to find which of this data is multiome RNA+ATAC as opposed to separate RNA and ATAC. Is all data separate or all data multiome and you can pair data by overlapping cell ids?
January 7, 2025 at 11:07 PM
This is quite cool! I can’t seem to find which of this data is multiome RNA+ATAC as opposed to separate RNA and ATAC. Is all data separate or all data multiome and you can pair data by overlapping cell ids?
Update: scE2G is now online at Nature Genetics!
Since the preprint, we added a new benchmark on a fully held-out CRISPR dataset. scE2G continues to show state-of-the-art performance, reinforcing that it generalizes well
nature.com/articles/s41588-026-02695-8
1/
Since the preprint, we added a new benchmark on a fully held-out CRISPR dataset. scE2G continues to show state-of-the-art performance, reinforcing that it generalizes well
nature.com/articles/s41588-026-02695-8
1/
August 4, 2026 at 12:27 AM
Update: scE2G is now online at Nature Genetics!
Since the preprint, we added a new benchmark on a fully held-out CRISPR dataset. scE2G continues to show state-of-the-art performance, reinforcing that it generalizes well
nature.com/articles/s41588-026-02695-8
1/
Since the preprint, we added a new benchmark on a fully held-out CRISPR dataset. scE2G continues to show state-of-the-art performance, reinforcing that it generalizes well
nature.com/articles/s41588-026-02695-8
1/