Mark Borris Aldonza (보리스)
banner
precursorcell.bsky.social
Mark Borris Aldonza (보리스)
@precursorcell.bsky.social
@elife.bsky.social ambassador '25. PhD cand @KAISTPR × @SeoulNatlUni. Passionately working on drug off-targets💊, cancer👾, genomics & evolution of extremophiles🪸🦈. Fanconi anemia survivor🟥.
Reposted by Mark Borris Aldonza (보리스)
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...
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.
matsen.group
December 11, 2025 at 5:36 PM
Reposted by Mark Borris Aldonza (보리스)
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
December 31, 2025 at 3:24 PM
Reposted by Mark Borris Aldonza (보리스)
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... !
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...
github.com
January 15, 2026 at 11:01 PM
Reposted by Mark Borris Aldonza (보리스)
Revealing a coherent cell-state landscape across single-cell datasets with CONCORD - @zevgartner.bsky.social @ucsanfrancisco.bsky.social go.nature.com/4jsNxSL
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.
go.nature.com
January 5, 2026 at 4:44 PM
Reposted by Mark Borris Aldonza (보리스)
I was invited by @focalplane.bsky.social to write a short description about it:

focalplane.biologists.com/2025/12/12/a...
December 15, 2025 at 8:40 AM
Reposted by Mark Borris Aldonza (보리스)
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...
December 11, 2025 at 7:51 PM
Reposted by Mark Borris Aldonza (보리스)
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🧵:
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.
www.nature.com
December 11, 2025 at 5:54 PM
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.
November 30, 2025 at 10:48 AM
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...
November 29, 2025 at 4:54 PM
Reposted by Mark Borris Aldonza (보리스)
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.

👇
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.
bit.ly
November 27, 2025 at 4:11 PM
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
November 25, 2025 at 2:11 AM
Reposted by Mark Borris Aldonza (보리스)
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! ⬇️
November 23, 2025 at 12:27 AM
A huge step for systematically mapping IDRs across the protein universe in different contexts
www.cell.com/cell/fulltex...
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...
www.cell.com
November 22, 2025 at 10:48 PM
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...
www.medrxiv.org
November 22, 2025 at 3:06 AM
Reposted by Mark Borris Aldonza (보리스)
Also, here’s an accessible video intro:
November 15, 2025 at 5:33 PM
Reposted by Mark Borris Aldonza (보리스)
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
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...
biorxiv.org
November 12, 2025 at 9:26 PM
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.
November 11, 2025 at 11:39 PM
Free up a time of your weekend for this and also watch www.pictureascientist.com
November 8, 2025 at 12:57 PM
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...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 8, 2025 at 12:52 PM
Reposted by Mark Borris Aldonza (보리스)
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...
November 5, 2025 at 6:53 PM
>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
November 5, 2025 at 7:03 PM
Reposted by Mark Borris Aldonza (보리스)
Required reading for cell biologists to get a sense of basic statistical principles!

www.nature.com/articles/s41...
Ten essential tips for robust statistics in cell biology - Nature Cell Biology
Statistical thinking is a core part of solid, trustworthy biology. However, many studies still include insufficient sample sizes, have poor experimental design or select an incorrect statistical metho...
www.nature.com
November 4, 2025 at 7:23 PM