John Mariani
@johnmariani.bsky.social
Asst Prof at University of Rochester
Glial-biased Neuroscientist
Bioinformaticist (All the 'omics)
Pianist
Meme enthusiast
Glial-biased Neuroscientist
Bioinformaticist (All the 'omics)
Pianist
Meme enthusiast
Reposted by John Mariani
CellWhisperer
From Transcriptome to Text
A great LLM-Chatbot explorer for CELLxGENE & GEO & your own data!
Contrastive language image pretraining
Geneformer
BioBERT
>1 million bulk/pseudo-bulk transcriptomes
cellwhisperer.bocklab.org
#NatBiotech 2025
www.nature.com/articles/s41...
From Transcriptome to Text
A great LLM-Chatbot explorer for CELLxGENE & GEO & your own data!
Contrastive language image pretraining
Geneformer
BioBERT
>1 million bulk/pseudo-bulk transcriptomes
cellwhisperer.bocklab.org
#NatBiotech 2025
www.nature.com/articles/s41...
November 22, 2025 at 12:14 PM
CellWhisperer
From Transcriptome to Text
A great LLM-Chatbot explorer for CELLxGENE & GEO & your own data!
Contrastive language image pretraining
Geneformer
BioBERT
>1 million bulk/pseudo-bulk transcriptomes
cellwhisperer.bocklab.org
#NatBiotech 2025
www.nature.com/articles/s41...
From Transcriptome to Text
A great LLM-Chatbot explorer for CELLxGENE & GEO & your own data!
Contrastive language image pretraining
Geneformer
BioBERT
>1 million bulk/pseudo-bulk transcriptomes
cellwhisperer.bocklab.org
#NatBiotech 2025
www.nature.com/articles/s41...
Reposted by John Mariani
VRK2 targeting potentiates anti-PD-1 immunotherapy in hepatocellular carcinoma through MYC destabilization www.nature.com/articles/s4...
October 12, 2025 at 2:15 PM
VRK2 targeting potentiates anti-PD-1 immunotherapy in hepatocellular carcinoma through MYC destabilization www.nature.com/articles/s4...
Reposted by John Mariani
The pitfalls of class prediction in omics 🧵
1/ You think you’ve built the perfect omics predictor.
The accuracy is high. The p-value is low.
But is it real—or just a story your data whispered back?
1/ You think you’ve built the perfect omics predictor.
The accuracy is high. The p-value is low.
But is it real—or just a story your data whispered back?
September 27, 2025 at 1:15 PM
The pitfalls of class prediction in omics 🧵
1/ You think you’ve built the perfect omics predictor.
The accuracy is high. The p-value is low.
But is it real—or just a story your data whispered back?
1/ You think you’ve built the perfect omics predictor.
The accuracy is high. The p-value is low.
But is it real—or just a story your data whispered back?
Reposted by John Mariani
Oligodendrocyte progenitor cell responses to inflammatory demyelination with aging https://www.biorxiv.org/content/10.1101/2025.09.22.677854v1
September 22, 2025 at 11:15 PM
Oligodendrocyte progenitor cell responses to inflammatory demyelination with aging https://www.biorxiv.org/content/10.1101/2025.09.22.677854v1
Reposted by John Mariani
www.cell.com/cell/abstrac...
A host organelle (in sea slugs) integrates stolen chloroplasts for animal photosynthesis
A host organelle (in sea slugs) integrates stolen chloroplasts for animal photosynthesis
A host organelle integrates stolen chloroplasts for animal photosynthesis
Sea slugs steal foreign chloroplasts and store them in specialized organelles that
facilitate photosynthesis and eventual digestion to mediate starvation resistance.
www.cell.com
September 17, 2025 at 5:04 PM
www.cell.com/cell/abstrac...
A host organelle (in sea slugs) integrates stolen chloroplasts for animal photosynthesis
A host organelle (in sea slugs) integrates stolen chloroplasts for animal photosynthesis
Reposted by John Mariani
tgv 0.1.0 release: github.com/zeqianli/tgv
- Rich CIGAR and base visualization
- Allele frequency visualization
- VCF and BED file support
- Mouse dragging and hovering
- Filter alignment
Now 90% of what I need from IGV can be done in the terminal.
Some interesting behind-the-scenes:
- Rich CIGAR and base visualization
- Allele frequency visualization
- VCF and BED file support
- Mouse dragging and hovering
- Filter alignment
Now 90% of what I need from IGV can be done in the terminal.
Some interesting behind-the-scenes:
September 7, 2025 at 11:47 PM
tgv 0.1.0 release: github.com/zeqianli/tgv
- Rich CIGAR and base visualization
- Allele frequency visualization
- VCF and BED file support
- Mouse dragging and hovering
- Filter alignment
Now 90% of what I need from IGV can be done in the terminal.
Some interesting behind-the-scenes:
- Rich CIGAR and base visualization
- Allele frequency visualization
- VCF and BED file support
- Mouse dragging and hovering
- Filter alignment
Now 90% of what I need from IGV can be done in the terminal.
Some interesting behind-the-scenes:
Reposted by John Mariani
Nature research paper: Single-cell transcriptomic and genomic changes in the ageing human brain
go.nature.com/4mRVCl0
go.nature.com/4mRVCl0
Single-cell transcriptomic and genomic changes in the ageing human brain - Nature
Sequencing analyses of human prefrontal cortex from donors ranging in age from 0.4 to 104 years show that ageing correlates with an accumulation of somatic mutations in short housekeeping genes and a reduction in the expression of these genes.
go.nature.com
September 7, 2025 at 11:36 AM
Nature research paper: Single-cell transcriptomic and genomic changes in the ageing human brain
go.nature.com/4mRVCl0
go.nature.com/4mRVCl0
Reposted by John Mariani
H3K79 methylation and H3K36 trimethylation synergistically regulate gene expression in pluripotent stem cells
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
H3K79 methylation and H3K36 trimethylation synergistically regulate gene expression in pluripotent stem cells
H3K79me and H3K36me3 synergistically dampen gene expression to facilitate cellular differentiation.
www.science.org
September 1, 2025 at 1:16 AM
H3K79 methylation and H3K36 trimethylation synergistically regulate gene expression in pluripotent stem cells
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by John Mariani
Check it out, Chromatin Kids!
Chromatin remodeller does stuff to Transcription Factors!
Functions where it is seldom seen!
Both decreases and increases chromatin accessibility!
How cool is that?
Chromatin remodeller does stuff to Transcription Factors!
Functions where it is seldom seen!
Both decreases and increases chromatin accessibility!
How cool is that?
The chromatin remodeller CHD4 controls both nucleosome integrity and transcription factor binding to promote activity of active regulatory elements and to prevent activation of silent enhancers https://www.biorxiv.org/content/10.1101/2025.08.29.672645v1
August 30, 2025 at 4:18 PM
Check it out, Chromatin Kids!
Chromatin remodeller does stuff to Transcription Factors!
Functions where it is seldom seen!
Both decreases and increases chromatin accessibility!
How cool is that?
Chromatin remodeller does stuff to Transcription Factors!
Functions where it is seldom seen!
Both decreases and increases chromatin accessibility!
How cool is that?
Reposted by John Mariani
How does Epstein- Barr virus induce multiple sclerosis?
The infection leads to B cells that get into the brain, attracting pro-inflammatory T cells (mouse model)
www.nature.com/articles/s41...
The infection leads to B cells that get into the brain, attracting pro-inflammatory T cells (mouse model)
www.nature.com/articles/s41...
EBV induces CNS homing of B cells attracting inflammatory T cells - Nature
Epstein–Barr virus infection generates a neuroinvasive B cell subset, which recruits activated T cells to the central nervous system, promoting multiple sclerosis.
www.nature.com
August 6, 2025 at 3:24 PM
How does Epstein- Barr virus induce multiple sclerosis?
The infection leads to B cells that get into the brain, attracting pro-inflammatory T cells (mouse model)
www.nature.com/articles/s41...
The infection leads to B cells that get into the brain, attracting pro-inflammatory T cells (mouse model)
www.nature.com/articles/s41...
Coming back to a 2 year old script...
July 31, 2025 at 4:02 PM
Coming back to a 2 year old script...
Reposted by John Mariani
Many proteins bind RNA, yet we still don’t know what RNAs most bind because methods map one RBP at a time. In @cp-cell.bsky.social, with the Jovanovic lab, we describe SPIDR – a method for mapping the RNA binding sites of dozens of RBPs in a single experiment. www.sciencedirect.com/science/arti...
July 26, 2025 at 7:15 PM
Many proteins bind RNA, yet we still don’t know what RNAs most bind because methods map one RBP at a time. In @cp-cell.bsky.social, with the Jovanovic lab, we describe SPIDR – a method for mapping the RNA binding sites of dozens of RBPs in a single experiment. www.sciencedirect.com/science/arti...
I've been to two bars tonight and both had feels so good playing
July 25, 2025 at 5:25 AM
I've been to two bars tonight and both had feels so good playing
Reposted by John Mariani
With the help of a technique called Massively Parallel Ribosome Profiling, researchers in Science have identified more than 4000 open reading frames—stretches of genetic material that can encode proteins—across 679 human-associated viral genomes. scim.ag/43RoAdF
Pan-viral ORFs discovery using massively parallel ribosome profiling
Defining viral proteomes is crucial to understanding viral life cycles and immune recognition but the landscape of translated regions remains unknown for most viruses. We have developed massively para...
scim.ag
June 20, 2025 at 6:20 PM
With the help of a technique called Massively Parallel Ribosome Profiling, researchers in Science have identified more than 4000 open reading frames—stretches of genetic material that can encode proteins—across 679 human-associated viral genomes. scim.ag/43RoAdF
Reposted by John Mariani
Myelin–axon interface vulnerability in Alzheimer’s disease revealed by subcellular proteomics and imaging of human and mouse brain
www.nature.com/articles/s41...
www.nature.com/articles/s41...
June 13, 2025 at 1:27 PM
Myelin–axon interface vulnerability in Alzheimer’s disease revealed by subcellular proteomics and imaging of human and mouse brain
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by John Mariani
How exercise protects the brain through neurovascular-associated astrocytes and neuroplasticity:
Results of elegant single cell/nuceli studies in the experimental Alzheimer's model
www.nature.com/articles/s41...
Results of elegant single cell/nuceli studies in the experimental Alzheimer's model
www.nature.com/articles/s41...
Protective exercise responses in the dentate gyrus of Alzheimer’s disease mouse model revealed with single-nucleus RNA-sequencing - Nature Neuroscience
Dissecting the adaptive exercise response of the neurogenic stem-cell niche in the dentate gyrus by single-nucleus RNA sequencing reveals the molecular mediators that underlie exercise’s protective ef...
www.nature.com
June 12, 2025 at 2:12 PM
How exercise protects the brain through neurovascular-associated astrocytes and neuroplasticity:
Results of elegant single cell/nuceli studies in the experimental Alzheimer's model
www.nature.com/articles/s41...
Results of elegant single cell/nuceli studies in the experimental Alzheimer's model
www.nature.com/articles/s41...
Reposted by John Mariani
Reposted by John Mariani
Being able to productionize a ML model is often the goal, however there are many things to keep track of when you do. The orbital package lets you translate your fitted scikit-learn or tidymodels model into SQL that that when run produces predictions.
posit.co/blog/databri... #python #rstats
posit.co/blog/databri... #python #rstats
Posit
Accelerate model deployment with Databricks and Orbital for R and Python Scikit-learn/Tidymodels projects.
posit.co
June 9, 2025 at 10:08 PM
Being able to productionize a ML model is often the goal, however there are many things to keep track of when you do. The orbital package lets you translate your fitted scikit-learn or tidymodels model into SQL that that when run produces predictions.
posit.co/blog/databri... #python #rstats
posit.co/blog/databri... #python #rstats
Reposted by John Mariani
At Posit, we love @typst.app:
⚡ Make PDFs in milliseconds, not minutes
✨ The power of LaTeX with today's technologies
✍️ Modern typography (including emojis!)
🧠 Clear mental model
So I'm thrilled to announce that we're now supporting its development: posit.co/blog/posit-a...
#rstats
⚡ Make PDFs in milliseconds, not minutes
✨ The power of LaTeX with today's technologies
✍️ Modern typography (including emojis!)
🧠 Clear mental model
So I'm thrilled to announce that we're now supporting its development: posit.co/blog/posit-a...
#rstats
Posit
We’re happy to announce that we’re supporting Typst by funding one of their full-time engineers.
posit.co
June 3, 2025 at 1:47 PM
At Posit, we love @typst.app:
⚡ Make PDFs in milliseconds, not minutes
✨ The power of LaTeX with today's technologies
✍️ Modern typography (including emojis!)
🧠 Clear mental model
So I'm thrilled to announce that we're now supporting its development: posit.co/blog/posit-a...
#rstats
⚡ Make PDFs in milliseconds, not minutes
✨ The power of LaTeX with today's technologies
✍️ Modern typography (including emojis!)
🧠 Clear mental model
So I'm thrilled to announce that we're now supporting its development: posit.co/blog/posit-a...
#rstats
Reposted by John Mariani
Double strand breaks drive toxicity in Huntington's disease mice with or without somatic expansion. https://www.biorxiv.org/content/10.1101/2025.05.27.654663v1
May 29, 2025 at 3:18 AM
Double strand breaks drive toxicity in Huntington's disease mice with or without somatic expansion. https://www.biorxiv.org/content/10.1101/2025.05.27.654663v1
Reposted by John Mariani
This is why science funding matters.
We uncovered a hidden signaling system in the brain—one that responds to maternal environment, even to drugs like LSD during pregnancy.
It took 5 years, a brilliant team, and public funding to get here.
Out today in @NatureNeuro: 🧵👇
We uncovered a hidden signaling system in the brain—one that responds to maternal environment, even to drugs like LSD during pregnancy.
It took 5 years, a brilliant team, and public funding to get here.
Out today in @NatureNeuro: 🧵👇
Led by @scienceyael.bsky.social & out today in @natneuro.nature.com: the brain's fluid-secreting organ — the choroid plexus — can reshape neural development through a powerful, little-known process. & it can be hijacked by serotonergic drugs like LSD. 🧠👇 A thread
rdcu.be/eoaSY
rdcu.be/eoaSY
Choroid plexus apocrine secretion shapes CSF proteome during mouse brain development
Nature Neuroscience - The choroid plexus (ChP) provides molecular cues for brain development. However, the underlying mechanisms are unclear. This study identifies an apocrine secretion mechanism...
rdcu.be
May 28, 2025 at 12:59 PM
This is why science funding matters.
We uncovered a hidden signaling system in the brain—one that responds to maternal environment, even to drugs like LSD during pregnancy.
It took 5 years, a brilliant team, and public funding to get here.
Out today in @NatureNeuro: 🧵👇
We uncovered a hidden signaling system in the brain—one that responds to maternal environment, even to drugs like LSD during pregnancy.
It took 5 years, a brilliant team, and public funding to get here.
Out today in @NatureNeuro: 🧵👇
Reposted by John Mariani
I was having a hard time describing how a plate of cultured cells didn’t look healthy to a new undergrad in the lab. He looked at them and said, “oh yeah, the vibes are off.” Thank god for Gen Z.
May 14, 2025 at 6:11 PM
I was having a hard time describing how a plate of cultured cells didn’t look healthy to a new undergrad in the lab. He looked at them and said, “oh yeah, the vibes are off.” Thank god for Gen Z.
Reposted by John Mariani
For those who want a distraction and/ or are interested, here's the latest from the group, led by Phil Braaker
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Activity-driven myelin sheath growth is mediated by mGluR5 - Nature Neuroscience
Employing pharmacology, genetics and all-optical approaches in zebrafish, Braaker et al. find that neuronal activity influences the growth of myelin sheaths along axons by signaling through metabotrop...
www.nature.com
May 14, 2025 at 11:45 AM
For those who want a distraction and/ or are interested, here's the latest from the group, led by Phil Braaker
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by John Mariani
ATAC-seq quality is highly dependent on Tn5 activity, a function of your enzyme AND your sample. It is strongly recommended to perform Tn5 titration experiments to determine the appropriate amount of enzyme. Too much, and you lose chromatin information. Too little, and you lose complexity 1/
PSA: We just finished processing nearly all public ATAC-seq datasets from SRA (about 22,000 datasets). (Not?) Surprisingly, we had to throw-out nearly ~50% because they were low-quality (low signal-to-noise, duplicate rate, etc.). Check quality before analysis (TSS-enrichment is not sufficient!).
May 14, 2025 at 5:43 AM
ATAC-seq quality is highly dependent on Tn5 activity, a function of your enzyme AND your sample. It is strongly recommended to perform Tn5 titration experiments to determine the appropriate amount of enzyme. Too much, and you lose chromatin information. Too little, and you lose complexity 1/
Reposted by John Mariani
Childhood adversity as a risk factor for autoimmune disease: A systematic review and meta-analysis with implications for psychiatry www.sciencedirect.com/science/arti...
Childhood adversity as a risk factor for autoimmune disease: A systematic review and meta-analysis with implications for psychiatry
Autoimmune diseases are a heterogeneous category of disorders caused by an interaction between genetic and environmental factors which lead to a dysre…
www.sciencedirect.com
May 5, 2025 at 2:01 PM
Childhood adversity as a risk factor for autoimmune disease: A systematic review and meta-analysis with implications for psychiatry www.sciencedirect.com/science/arti...