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John Mariani

@johnmariani.bsky.social
1.9K followers 2.9K following 23 posts

Asst Prof at University of Rochester Glial-biased Neuroscientist Bioinformaticist (All the 'omics) Pianist Meme enthusiast

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Reposted by John Mariani
Vaughn Cooper @vscooper.micropopbio.org · 25/09/2026
FYI to everyone submitting this October NIH cycle You need to re-certify your ScienCV AFTER Sept 26 (tomorrow) for your application or it may not be accepted. Great timing!
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John Mariani @johnmariani.bsky.social · 04/09/2026
Does anyone have any good recommendations for companies to make iPSCs from PBMCs?
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Ming Tommy Tang @tommytang.bsky.social · 31/07/2026
An extremely fast R package manager, written in Rust. The R equivalent of uv for Python. · GitHub github.com/nbafrank/uvr
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Ming Tommy Tang @tommytang.bsky.social · 24/07/2026
Best practices for differential accessibility analysis in single-cell epigenomics www.nature.com/articles/s4...
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John Mariani @johnmariani.bsky.social · 08/07/2026
This just out of our lab: We engineered a novel AAV vector that enables highly specific and efficient transduction of human GPCs via glymphatic delivery. www.nature.com/articles/s41...
nature.com
Efficient targeting of human glial progenitor cells in vivo with engineered AAV vectors and glymphatic delivery - Nature Biotechnology
Viral vectors delivered through the brain glymphatics achieve widespread targeting of glial cells.
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John Mariani @johnmariani.bsky.social · 23/06/2026
My daughter made me a top 10 list of why I'm the best dad... #6 was "You do great science" - take note NIH
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Ming Tommy Tang @tommytang.bsky.social · 19/06/2026
Heterogeneity-preserving discriminative feature selection for disease-specific subtype discovery www.nature.com/articles/s4...
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Ming Tommy Tang @tommytang.bsky.social · 15/05/2026
Robust integration of single-cell datasets with imbalanced modality composition www.nature.com/articles/s4...
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GregoryAi @gregoryai.bsky.social · 03/05/2026
IGF-I plays an important role in oligodendrocyte survival and myelination. We used human recombinant IGF-I to #MSchat #MS #Neurology #MultipleSclerosis #NeuroSky #MedSky
gregory-ms.com
Insulin-like growth factor-I receptors in normal appearing white matter and chronic plaques in multiple sclerosis
IGF-I plays an important role in oligodendrocyte survival and myelination. We used human recombinant IGF-I to
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Reposted by John Mariani
Maxim Greenberg @maxvcg.bsky.social · 01/05/2026
This a very important, and extremely well-executed study from Ralph Grand’s group @uniheidelberg.bsky.social. Congrats to all the authors! www.biorxiv.org/content/10.6...
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Charlie Gao @shikokuchuo.net · 23/04/2026
Just released mori 0.1.0 on CRAN — a new R package for shared memory across processes. Parallel R no longer has to mean duplicating your dataset in every worker's RAM. opensource.posit.co/blog/2026-04... 🧵 1/3
opensource.posit.co
mori: Shared memory for R objects
mori is a new R package for sharing R objects across processes via OS-level shared memory. Parallel workers get zero-copy, lazy ALTREP access to the same physical pages — share once, read anywhere.
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lyons-lab.bsky.social @lyons-lab.bsky.social · 02/04/2026
Latest offering. How myelin ensheathes axons! Born from chat with Dwight Bergles on "weird things" we saw oligodendrocytes do, like making "bridges" between sheaths. Driven forward by Cody Call, Kelly Monk, and myelin folks @edinburgh-uni.bsky.social Enjoy! www.nature.com/articles/s41...
nature.com
Flexible ensheathment of axons enables myelination of complex CNS networks - Nature
The rate of axon ensheathment varies within individual myelinating processes, resulting in chains of myelin sheaths connected by bridges consisting of thin cytoplasmic processes that provide&nbsp...
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John Bistline @bistline.bsky.social · 01/04/2026
This is my favorite climate change chart. Japanese monks, aristocrats, and emperors kept meticulous records of cherry blossom festivals for 1,200 years and accidentally built the world's longest climate dataset.
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Michela Palamin @mpalamin.bsky.social · 24/03/2026
ChromSMF preprint is out!🚀 tinyurl.com/ChromSMF We often piece together chromatin regulation layer by layer from separate assays. But this can be limiting! In @arnaudkr.bsky.social's lab, we developed a method to directly study multiple layers on the same DNA molecule! 🧬 What does this unlock? ⬇️
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Arjun Raj @arjunraj.bsky.social · 21/03/2026
One of my very favorite papers from the lab! Shows that individual cells can learn by forming memories. Amazing work by Jess Li!
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Alejandro Montenegro @aemonten.bsky.social · 19/03/2026
Would I have called it reverse translation? No. Do I think it is? Also no. Is it cool? Heck yes. www.nature.com/articles/s41...
nature.com
Single-molecule peptide sequencing through reverse translation of peptides into DNA - Nature Biotechnology
Peptides are sequenced by converting each amino acid into amplifiable DNA barcodes.
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Alejandro Montenegro @aemonten.bsky.social · 10/03/2026
"GRNs, which should provide mechanistic explanations, are increasingly reduced to statistical correlations — ‘hairballs’ that fail to capture molecular causation" By Maizels and @jamesbriscoe.bsky.social www.nature.com/articles/s41...
nature.com
Gene regulatory networks: from correlative models to causal explanations - Nature Reviews Genetics
In this Perspective, Maizels and Briscoe discuss the limitations of current models of gene regulatory networks and outline solutions to harness data abundance without compromising explanatory power.
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Ming Tommy Tang @tommytang.bsky.social · 08/03/2026
Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus www.nature.com/articles/s4...
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Craig Kaplan @triggerloop.bsky.social · 04/03/2026
Just amazing what evolution can come up with. Naturally occurring nuclease deficient Cas12 family members use gRNAs to bind DNA and recruit sigmaE family members that drive txn initiation proximally. 2 papers! 1- describes 2- structure! www.nature.com/articles/s41... www.nature.com/articles/s41...
nature.com
Exapted CRISPR–Cas12f homologues drive RNA-guided transcription - Nature
Specialized σ factors interact with nuclease-dead, CRISPR–Cas12f proteins to form potent, RNA-guided gene activation systems that function independently of fixed promoter motifs.
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Alejandro Montenegro @aemonten.bsky.social · 01/03/2026
"Here, we present SPAtial Cell Exploration (SPACE), a spatial CRISPR screening platform that integrates whole-transcriptome profiling (~18,000 genes), multiplexed protein detection (~68 markers), and CRISPR perturbation mapping at subcellular resolution" www.biorxiv.org/content/10.1...
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Ming Tommy Tang @tommytang.bsky.social · 11/02/2026
R is slow in plotting tens of thousands of points. How to speed up for a million cell scRNAseq data? check out scattermore github.com/exaexa/scat...
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Science Magazine @science.org · 03/02/2026
A new #ScienceImmunology study highlights the limitations of preclinical models for human antibody-based drugs, and demonstrates how a humanized mouse model may improve study outcomes. scim.ag/4t2ye7T
scim.ag
Cross-species cellular mapping and humanization of Fcγ receptors to advance antibody modeling
Preclinical modeling of human IgG–based drugs is enhanced through humanized Fcγ receptor and FcRn expression in a murine knockin model.
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Cell Stem Cell @cp-cellstemcell.bsky.social · 09/01/2026
Human cortical organoids recapitulate inter-individual variability in infant brain-growth trajectories
dlvr.it
Human cortical organoids recapitulate inter-individual variability in infant brain-growth trajectories
Glass, Matoba, et al. demonstrate that human cortical organoid cell-type proportions, cross-sectional area growth, and cell cycle genes in early neural progenitors are associated with inter-individual variability in infant cortical surface area measurements, supporting the fidelity of organoids as a model system.
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Jonathan Coxhead @4130chromo.bsky.social · 02/01/2026
Review | From bulk RNA sequencing to spatial transcriptomics: a comparative review of differential gene expression analysis methods link.springer.com/article/10.1...
link.springer.com
From bulk RNA sequencing to spatial transcriptomics: a comparative review of differential gene expression analysis methods - Human Genomics
Human Genomics - Transcriptome analysis is essential to dissect the molecular mechanisms underlying phenotypic differences and disease mechanisms. Traditionally, microarrays were used, but RNA...
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Melike Eren @neurowithmelike.bsky.social · 21/12/2025
This is a very new study and needs to be replicated further, but I found it interesting. As a physiotherapist and neuroscientist, what caught my attention more was whether this alleged epigenetic change on the mitochondria has an effect on infants' brain health, www.cell.com/cell-metabol...
cell.com
Paternal exercise confers endurance capacity to offspring through sperm microRNAs
Yin et al. show that paternal exercise improves offspring endurance capacity and metabolic health via sperm microRNAs that reprogram gene expression in early embryos, revealing how exercise benefits c...
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bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 10/12/2025
Neuronal PARIS-STAT3 axis drives tau pathology and glial activation in Alzheimers disease www.biorxiv.org/content/10.64898/20…
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Ming Tommy Tang @tommytang.bsky.social · 01/12/2025
Motif-based models accurately predict cell type-specific distal regulatory elements www.nature.com/articles/s4... "BOM outperforms more complex deep-learning models while using fewer parameters." simplicity is a beauty.
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Hao Yin @haoyin.bsky.social · 22/11/2025
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...
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Ming Tommy Tang @tommytang.bsky.social · 12/10/2025
VRK2 targeting potentiates anti-PD-1 immunotherapy in hepatocellular carcinoma through MYC destabilization www.nature.com/articles/s4...
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Ming Tommy Tang @tommytang.bsky.social · 27/09/2025
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?
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bioRxiv Neuroscience @biorxiv-neursci.bsky.social · 23/09/2025
Oligodendrocyte progenitor cell responses to inflammatory demyelination with aging www.biorxiv.org/content/10.1101/202…
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Harmit Singh Malik @harmitmalik.bsky.social · 17/09/2025
www.cell.com/cell/abstrac... A host organelle (in sea slugs) integrates stolen chloroplasts for animal photosynthesis
cell.com
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.
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Zeqian Li @zeqianli.bsky.social · 08/09/2025
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:
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Nature @nature.com · 07/09/2025
Nature research paper: Single-cell transcriptomic and genomic changes in the ageing human brain go.nature.com/4mRVCl0
go.nature.com
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.
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Carmelo Ferrai @carmeloferrai.bsky.social · 01/09/2025
H3K79 methylation and H3K36 trimethylation synergistically regulate gene expression in pluripotent stem cells www.science.org/doi/10.1126/...
science.org
H3K79 methylation and H3K36 trimethylation synergistically regulate gene expression in pluripotent stem cells
H3K79me and H3K36me3 synergistically dampen gene expression to facilitate cellular differentiation.
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Surfin' NuRD @surfinnurd.bsky.social · 30/08/2025
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?
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Eric Topol @erictopol.bsky.social · 06/08/2025
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...
nature.com
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.
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John Mariani @johnmariani.bsky.social · 31/07/2025
Coming back to a 2 year old script...
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Mitch Guttman @mitchguttman.bsky.social · 26/07/2025
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...
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John Mariani @johnmariani.bsky.social · 25/07/2025
I've been to two bars tonight and both had feels so good playing
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Science Magazine @science.org · 20/06/2025
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
scim.ag
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...
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John Lukens @lukensjohnr.bsky.social · 13/06/2025
Myelin–axon interface vulnerability in Alzheimer’s disease revealed by subcellular proteomics and imaging of human and mouse brain www.nature.com/articles/s41...
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Eric Topol @erictopol.bsky.social · 12/06/2025
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...
nature.com
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...
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Ian Kremer @wolverinebear.bsky.social · 11/06/2025
cuimc.columbia.edu
Upgrading Brain’s “Dishwasher” May Help Clear Alzheimer's Toxins
Columbia scientists have found that boosting the performance of a self-cleansing system in the brain flushed amyloid and tau toxins from the brains of mice and improved cognition.
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Emil Hvitfeldt @emilhvitfeldt.bsky.social · 09/06/2025
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
Posit
Accelerate model deployment with Databricks and Orbital for R and Python Scikit-learn/Tidymodels projects.
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Hadley Wickham @hadley.nz · 03/06/2025
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
posit.co
Posit
We’re happy to announce that we’re supporting Typst by funding one of their full-time engineers.
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bioRxivpreprint @biorxivpreprint.bsky.social · 29/05/2025
Double strand breaks drive toxicity in Huntington's disease mice with or without somatic expansion. www.biorxiv.org/content/10.1101/202…
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Ya’el Courtney, PhD @scienceyael.bsky.social · 28/05/2025
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: 🧵👇
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Mike Feigin 🥯 @mikefeigin.bsky.social · 14/05/2025
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.
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