Mark Borris Aldonza (보리스)

Residual Breast Cancer Cells Co-opt SOX5-Driven Endochondral Ossification to Maintain Dormancy aacrjournals.org/cancerdisco...

Can one map the genome-wide binding (1) and its protein partners (2) simultaneously from the same sample?

Yes, one can. with CUT&ID ✂️🪪

Spearheaded — singlehandedly — by @annanordin.bsky.social

No need of transgenesis, cloning and overexpression.

Check it out, it's fast and its works.

🚨 1/ Preprint Alert!

Sex determination outcome is conserved across vertebrates (i.e. generating 2 compatible sexes) ♀️♂️

But are the cell types and gene programs behind them conserved too? 🧬

Spoiler: not really 👀

Find out in our new preprint ⬇️

www.biorxiv.org/content/10.6...

Not something you see in textbooks very often: tripolar mitosis.

A near-complete map of human cytosolic degrons and their relevance for disease

We measured degron potency of >200,000 30-residue tiles from >5,000 human proteins, and trained a model to predict degrons from sequence

Led by @vvouts.bsky.social in @rhp-lab.bsky.social

doi.org/10.1126/scia...

Replaying evolution to learn about the fitness landscape of affinity maturation A five year collaboration with the Victora lab is bearing fruit for evolutionary biology.

Over the past 5+ years I've had the honor of working with @wsdewitt.github.io @victora.bsky.social and many others on a project to "replay" affinity maturation evolution from a fixed starting point.

matsen.group/general/2025...

A study from @danmucida.bsky.social and @victora.bsky.social showed how immune cells in the gut distinguish between food and harmful pathogens, shedding light on the origins of #foodallergies. #RockefellerScience #YearInReview

🔗: https://bit.ly/4hyS18b

Mapping of ENSG_IDs between different release of the Ensembl database · Issue #744 · Ensembl/ensembl Dear members of the Ensembl team, I wasn’t sure who to contact, so I’m starting here. I am writing to ask you questions about the IDMapper tool presented on your website: https://www.ensembl.org/Ho...

A quick story on how we matched genes across two datasets with different Ensembl versions.
1. There must be a tool out there. Ensembl ID History converter ofc!
2. Doesn't match Ensembl search outcomes due to a bug
3. Lesson: use this client instead github.com/Ensembl/ense... !

Revealing a coherent cell-state landscape across single-cell datasets with CONCORD - Nature Biotechnology CONCORD generates denoised cell encodings that preserve key biological structures in single-cell datasets.

Revealing a coherent cell-state landscape across single-cell datasets with CONCORD - @zevgartner.bsky.social @ucsanfrancisco.bsky.social go.nature.com/4jsNxSL

I was invited by @focalplane.bsky.social to write a short description about it:

focalplane.biologists.com/2025/12/12/a...

Have you heard about the Night Science Podcast, where we talk about the creative process of doing science? We explore this with discussions with brilliant scientists & philosophers and artists, to figure out the tricks of the creative scientific trade.
podcasts.apple.com/us/podcast/n...

Causal modelling of gene effects from regulators to programs to traits - Nature Approaches combining genetic association and Perturb-seq data that link genetic variants to functional programs to traits are described.

GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult.

Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:

Passenger mutations link cellular origin and transcriptional identity in human lung adenocarcinomas - Nature Genetics This study shows how the links between somatic passenger mutations in tumors and normal cell transcriptomes can be used to infer cell-of-origin in lung adenocarcinoma.

www.nature.com/articles/s41...

What's stopping the science community from abandoning the term 'basic science' and replacing it with 'fundamental science' across all forms of comms and publishing? "Basic" implies "simple" to the public, when it should be perceived as the foundational bedrock of all innovation.

Risky moves. Can blocking “jumping genes” treat diseases and aging?

A bit late to the party on this @science.org piece. I've always been intrigued by how TEs, are so specifically regulated. Mammalian cancers, for instance, often co-opt L1 activity as a potential mutational escape route from stressful environments.
www.science.org/content/arti...

Mechanisms and treatment of cancer therapy-induced peripheral and central neurotoxicity - Nature Reviews Cancer Neurotoxicity impacting the central and peripheral nervous systems is a considerable adverse effect of both conventional and novel cancer therapies. In this Review, Karschnia et al. outline what is currently known about the mechanisms that underlie the clinical symptoms of central nervous system injury and peripheral neuropathy and the ongoing development of interventions to treat and prevent this unmet medical need.

ICYMI 🚨

Neurotoxicity impacting the central & peripheral nervous systems is an adverse effect of cancer therapies. In this #Review, Karschnia et al. outline the mechanisms that underlie the clinical symptoms & the need for interventions to treat it.

👇

Hierarchical interactions between nucleolar and heterochromatin condensates are mediated by a dual-affinity protein - Nature Cell Biology Rajshekar et al. show that a hierarchy of affinities layers pericentromeric heterochromatin around nucleoli, with the RNA helicase Pitchoune (DDX18) acting as a key dual-affinity linker in Drosophila ...

Hierarchical interactions between nucleolar and heterochromatin condensates are mediated by a dual-affinity protein #condensates #chromatin
www.nature.com/articles/s41...

People who fund "disruptors" in biotech and health need to be as discerning and thoughtful as what Max showed here, if not more. #biotech #health #genomics #GWAS #IVF

PhD students and Postdocs: The Night Science Podcast (@nightsciencepod.bsky.social) is producing an episode highlighting young scientists talking about their creative process. DM me if you'd like us to consider you for this, & read below what PhD student Davis Garner will contribute! ⬇️

Molecular grammars of predicted intrinsically disordered regions that span the human proteome Grammars inferred using NARDINI+ (GIN) is a resource that uncovers molecular grammars of intrinsically disordered regions (IDRs) across the human proteome, revealing how distinct grammars underlie pro...

A huge step for systematically mapping IDRs across the protein universe in different contexts
www.cell.com/cell/fulltex...

Structural basis of regulated N-glycosylation at the secretory translocon - Nature The structural mechanism of a natively isolated GRP94 folding intermediate tethered to a CCDC134-bound translocon is described, revealing how the nascent chain remodels the translocon to control N-gly...

Structural basis of regulated N-glycosylation at the secretory translocon #glycotime
www.nature.com/articles/s41...

Mind-blowing discovery in Fanconi anemia. A rare embryonic event of incorporating a second polar body in late oogenesis created blood stem cells with a functional FA pathway. These "corrected" cells naturally expanded, rescuing the bone marrow.
www.medrxiv.org/content/10.1...

Also, here’s an accessible video intro:

Proteome-wide in silico screening for human protein-protein interactions Protein-protein interactions (PPIs) drive virtually all biological processes, yet most PPIs have not been identified and even more remain structurally unresolved. We developed a two-step computational...

Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp

This is awesome! CellWhisperer AI enables chat-based analysis of single-cell RNA-seq data. It lets you directly query your datasets, making complex hypothesis testing on sc-transcriptomes intuitive and code-free.

Free up a time of your weekend for this and also watch www.pictureascientist.com

Specificity, length and luck drive gene rankings in association studies - Nature Genetic association tests prioritize candidate genes based on different criteria.

GWAS and burden tests diverge because one ranks trait-specific variants, the other trait-specific genes, not because one is right and the other wrong.

So if you see a top GWAS hit, you might just be looking at a lucky allele that drifted to high frequency.

www.nature.com/articles/s41...

Cover of this week's Nature showing a brain rendering Cover caption from the journal: Brain development: Our ability to process information into complex emotions, behaviours and decisions relies on the rich diversity of cell types that make up the human brain. Uncovering the molecular and cellular events that take place during brain development could reveal not only the mechanisms that give rise to this diversity but also shed light on how this process might go awry in neurodevelopmental disorders such as autism and schizophrenia. In this week’s issue, the BRAIN Initiative Cell Atlas Network (BICAN) builds on its previous work creating atlases of cell types in the adult mouse, non-human primate (NHP) and human brains to present cell-type atlases of the developing human, mouse and NHP brains. Across a suite of papers, nine of which are published in Nature, the researchers uncover the complex programs through which cell types emerge during brain development in humans and animals, revealing both the shared and unique features of the human brain. The latest work, along with future research directions, is summed up in a Perspective article by Tomasz Nowakowski and colleagues

New issue of Nature - with NINE studies on #brain #development from the BRAIN Initiative Cell Atlas Network (BICAN) 🧠🧪🔬

An amazing set of resources for all scientists working on the brain!

🧠 Immersive feature:
www.nature.com/immersive/d4...

🧠 Perspective:
www.nature.com/articles/s41...

>7000 miles away from NYC but we can feel the positive swarm of hopes and dreams. Here's the Autumn-Winter scene at KAIST in Daejeon🇰🇷 to let you in with the vibe

Required reading for cell biologists to get a sense of basic statistical principles!

www.nature.com/articles/s41...