Mark Borris Aldonza (보리스)
@precursorcell.bsky.social
@elife.bsky.social ambassador '25. Researcher/PhD @KAISTPR × @SeoulNatlUni. Passionately working on cancer👾 and evolution🪸🦈. Fanconi anemia survivor🟥.
https://sites.google.com/view/borrisaldonza/
https://sites.google.com/view/borrisaldonza/
Pinned
My first💙post (skeet?) and a PhD status update:
Excited to start a new research chapter as a visiting research fellow in Dr. Hanseul Yang's lab at my alma mater #KAIST for my final PhD year. Hanseul is a brilliant young scientist and mentor who trained with Dr. Elaine Fuchs at
#Rockefeller.
Excited to start a new research chapter as a visiting research fellow in Dr. Hanseul Yang's lab at my alma mater #KAIST for my final PhD year. Hanseul is a brilliant young scientist and mentor who trained with Dr. Elaine Fuchs at
#Rockefeller.
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
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.
Multimodal learning enables chat-based exploration of single-cell data - @bocklab.bsky.social @cemm.oeaw.ac.at @meduniwien.ac.at go.nature.com/3WPGJnW
Multimodal learning enables chat-based exploration of single-cell data - Nature Biotechnology
CellWhisperer uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data.
go.nature.com
November 11, 2025 at 11:39 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.
Free up a time of your weekend for this and also watch www.pictureascientist.com
November 8, 2025 at 12:57 PM
Free up a time of your weekend for this and also watch www.pictureascientist.com
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...
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
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...
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...
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...
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
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...
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
November 5, 2025 at 7:03 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
Reposted by Mark Borris Aldonza (보리스)
Required reading for cell biologists to get a sense of basic statistical principles!
www.nature.com/articles/s41...
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
Required reading for cell biologists to get a sense of basic statistical principles!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
😆
Nature suggests you use their "Manuscript Adviser" bot to get advice before submitting
I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:
I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:
November 4, 2025 at 5:27 PM
😆
Reposted by Mark Borris Aldonza (보리스)
This is interesting for a number of reasons. www.nature.com/articles/s41...
Mesenchymal thymic niche cells enable regeneration of the adult thymus and T cell immunity - Nature Biotechnology
T cell immunity declines with thymic atrophy, but thymic cell grafts rescue T cell function.
www.nature.com
November 3, 2025 at 4:05 PM
This is interesting for a number of reasons. www.nature.com/articles/s41...
Reposted by Mark Borris Aldonza (보리스)
The new Wiley journal review system is an absolute nightmare. Editorial assistants have been replaced by a clunky, AI-enabled website that makes it harder to find and invite reviewers. Associate editor workloads have increased. I'm not convinced the invitations to reviewers are even going through.
October 6, 2025 at 3:22 PM
The new Wiley journal review system is an absolute nightmare. Editorial assistants have been replaced by a clunky, AI-enabled website that makes it harder to find and invite reviewers. Associate editor workloads have increased. I'm not convinced the invitations to reviewers are even going through.
Reposted by Mark Borris Aldonza (보리스)
Here's a first collection of great life science institutes worldwide you can follow to help you get back in the loop. 🌍🔬
Did we miss any? Let us know, and we'll add them!
go.bsky.app/A5Jrf8N
Did we miss any? Let us know, and we'll add them!
go.bsky.app/A5Jrf8N
February 4, 2025 at 8:25 AM
Here's a first collection of great life science institutes worldwide you can follow to help you get back in the loop. 🌍🔬
Did we miss any? Let us know, and we'll add them!
go.bsky.app/A5Jrf8N
Did we miss any? Let us know, and we'll add them!
go.bsky.app/A5Jrf8N
Reposted by Mark Borris Aldonza (보리스)
🧵1/17
📣Thrilled to share our latest study just out in Cancer Discovery!
➡️
aacrjournals.org/cancerdiscov...
📣Thrilled to share our latest study just out in Cancer Discovery!
➡️
aacrjournals.org/cancerdiscov...
A plastic EMP1⁺ to LGR5⁺ cell state conversion as a bypass to KRAS-G12D pharmacological inhibition in metastatic colorectal cancer
Abstract. Inhibitors of the oncogene KRAS hold promise for treating metastatic CRC (mCRC). Here we show that a selective, covalent small molecule inhibitor of the active (ON) conformation of RAS-G12D,...
aacrjournals.org
October 23, 2025 at 6:07 PM
🧵1/17
📣Thrilled to share our latest study just out in Cancer Discovery!
➡️
aacrjournals.org/cancerdiscov...
📣Thrilled to share our latest study just out in Cancer Discovery!
➡️
aacrjournals.org/cancerdiscov...
Reposted by Mark Borris Aldonza (보리스)
The Laoui Lab will be well represented at the Tumor Heterogeneity, Plasticity and Therapy (3rd edition) conference #THPT25! Join us to hear more about therapy resistence in #cancer from Anna Obenauf
@obenaufa.bsky.social
Submit your abstract by the 8th of October on vibbio.tech/THPT25
@obenaufa.bsky.social
Submit your abstract by the 8th of October on vibbio.tech/THPT25
October 7, 2025 at 12:27 PM
The Laoui Lab will be well represented at the Tumor Heterogeneity, Plasticity and Therapy (3rd edition) conference #THPT25! Join us to hear more about therapy resistence in #cancer from Anna Obenauf
@obenaufa.bsky.social
Submit your abstract by the 8th of October on vibbio.tech/THPT25
@obenaufa.bsky.social
Submit your abstract by the 8th of October on vibbio.tech/THPT25
Reposted by Mark Borris Aldonza (보리스)
Acidosis is not just a byproduct of an altere Metabolism - it drives cancer cells‘ stress resilience mechanisms. Big congratulations to our friends from the @johanneszuber.bsky.social lab as well as the team around @wilhelmpalm.bsky.social on this wonderful story now out in Science.
Just out in @science.org: Together with the lab of @wilhelmpalm.bsky.social, we used sequential in-vitro/in-vivo CRISPR screens to decipher metabolic adaptations in tumors. We find that acidosis is a dominant factor that shapes energy metabolism and stress resilience. www.science.org/doi/10.1126/...
October 13, 2025 at 8:09 PM
Acidosis is not just a byproduct of an altere Metabolism - it drives cancer cells‘ stress resilience mechanisms. Big congratulations to our friends from the @johanneszuber.bsky.social lab as well as the team around @wilhelmpalm.bsky.social on this wonderful story now out in Science.
This is going to be one of the biggest, most important features of AlphaFold @alphafold.bsky.social if further improved! Glycobiochemistry needs this bestfriend! #glycotime
academic.oup.com/glycob/artic...
academic.oup.com/glycob/artic...
Modeling glycans with AlphaFold 3: capabilities, caveats, and limitations
Abstract. Glycans are complex carbohydrates that exhibit extraordinary structural complexity and stereochemical diversity while playing essential roles in
academic.oup.com
October 31, 2025 at 8:51 PM
This is going to be one of the biggest, most important features of AlphaFold @alphafold.bsky.social if further improved! Glycobiochemistry needs this bestfriend! #glycotime
academic.oup.com/glycob/artic...
academic.oup.com/glycob/artic...
Really important work that integrates long-read WGS, MEI-targeted enrichment, haplotype-resolved donor-specific assemblies, and internal L1 sequence variation to detect ultra-rare somatic mobile element insertions (sMEIs) with high precision!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Multi-platform framework for mapping somatic retrotransposition in human tissues
Mobile element insertions (MEI) shape the human genome in both germline and somatic tissues. While inherited MEIs are well characterized, mapping somatic MEIs (sMEI) in non-cancer tissues remains chal...
www.biorxiv.org
October 22, 2025 at 1:06 PM
Really important work that integrates long-read WGS, MEI-targeted enrichment, haplotype-resolved donor-specific assemblies, and internal L1 sequence variation to detect ultra-rare somatic mobile element insertions (sMEIs) with high precision!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Mark Borris Aldonza (보리스)
Evidence of off-target probe binding in the 10x Genomics Xenium v1 Human Breast Gene Expression Panel compromises accuracy of spatial transcriptomic profilingelifesciences.org/reviewed-pr...
October 22, 2025 at 2:00 AM
Evidence of off-target probe binding in the 10x Genomics Xenium v1 Human Breast Gene Expression Panel compromises accuracy of spatial transcriptomic profilingelifesciences.org/reviewed-pr...
Reposted by Mark Borris Aldonza (보리스)
Shout out for @johanneszuber.bsky.social and team ! Beautiful work with new biology !
Acidosis orchestrates adaptations of energy metabolism in tumors
Malignant tumors are characterized by diverse metabolic stresses, including nutrient shortages, hypoxia, and buildup of metabolic by-products. To understand how cancer cells adapt to such challenges, ...
www.science.org
October 20, 2025 at 7:07 PM
Shout out for @johanneszuber.bsky.social and team ! Beautiful work with new biology !
Reposted by Mark Borris Aldonza (보리스)
Comment🚨
Large biobank projects like #FinnGen help in uncovering genetic factors that influence cancer risk and outcomes, enhancing risk prediction & biomarker and drug target discovery.
@finngen.bsky.social @dalygene.bsky.social @aoxing2.bsky.social
📖 👇
Large biobank projects like #FinnGen help in uncovering genetic factors that influence cancer risk and outcomes, enhancing risk prediction & biomarker and drug target discovery.
@finngen.bsky.social @dalygene.bsky.social @aoxing2.bsky.social
📖 👇
Unlocking the potential of FinnGen to advance cancer research - Nature Reviews Cancer
Large biobank projects such as FinnGen have enabled systematic searches for inherited factors that causally influence a wide range of human traits, including cancer risk and outcome. These explorations provide genetic insights for various aspects of cancer research, including improved risk prediction, enhanced biomarker and drug target discovery, and personalized medicine.
bit.ly
October 20, 2025 at 3:01 PM
Comment🚨
Large biobank projects like #FinnGen help in uncovering genetic factors that influence cancer risk and outcomes, enhancing risk prediction & biomarker and drug target discovery.
@finngen.bsky.social @dalygene.bsky.social @aoxing2.bsky.social
📖 👇
Large biobank projects like #FinnGen help in uncovering genetic factors that influence cancer risk and outcomes, enhancing risk prediction & biomarker and drug target discovery.
@finngen.bsky.social @dalygene.bsky.social @aoxing2.bsky.social
📖 👇
Dogs as naturally evolved models for human cancers!
Similar human driver architecture, hotspot usage, and mutational processes across histologies, not just within breed-associated cancer types. 🐶👨#Dogs #Cancer #Breed #Genomics
www.biorxiv.org/content/10.1...
Similar human driver architecture, hotspot usage, and mutational processes across histologies, not just within breed-associated cancer types. 🐶👨#Dogs #Cancer #Breed #Genomics
www.biorxiv.org/content/10.1...
The shared selection landscape of dog and human cancers
Cancers in pet dogs are prevalent, progress rapidly, and closely resemble human cancers, positioning them as powerful models for precision oncology. While genetic drivers of human cancer often transce...
www.biorxiv.org
October 20, 2025 at 4:53 PM
Dogs as naturally evolved models for human cancers!
Similar human driver architecture, hotspot usage, and mutational processes across histologies, not just within breed-associated cancer types. 🐶👨#Dogs #Cancer #Breed #Genomics
www.biorxiv.org/content/10.1...
Similar human driver architecture, hotspot usage, and mutational processes across histologies, not just within breed-associated cancer types. 🐶👨#Dogs #Cancer #Breed #Genomics
www.biorxiv.org/content/10.1...
Reposted by Mark Borris Aldonza (보리스)
This week’s round-up spans species from birds to sheep, and now, fittingly, to dogs!
We dive into a new study from Japanese researchers, who have successfully established culture conditions for #canine iPSCs.
🐕 Article: https://bit.ly/4gA5zkC
🐩 Discussion: https://bit.ly/4qfiME4
We dive into a new study from Japanese researchers, who have successfully established culture conditions for #canine iPSCs.
🐕 Article: https://bit.ly/4gA5zkC
🐩 Discussion: https://bit.ly/4qfiME4
October 20, 2025 at 4:48 PM
This week’s round-up spans species from birds to sheep, and now, fittingly, to dogs!
We dive into a new study from Japanese researchers, who have successfully established culture conditions for #canine iPSCs.
🐕 Article: https://bit.ly/4gA5zkC
🐩 Discussion: https://bit.ly/4qfiME4
We dive into a new study from Japanese researchers, who have successfully established culture conditions for #canine iPSCs.
🐕 Article: https://bit.ly/4gA5zkC
🐩 Discussion: https://bit.ly/4qfiME4
This is so cool and a severely overlooked aspect of the TME and stroma: spatially disordered geometries of the microenvironment promote invasion shifts from collective to single mode. #cancer #TME #stroma #invasion www.biorxiv.org/content/10.1...
Substrate heterogeneity promotes cancer cell dissemination
While tumor malignancy has been extensively studied under the prism of genetic and epigenetic heterogeneity, tumor cell states also critically depend on reciprocal interactions with the microenvironme...
www.biorxiv.org
May 30, 2025 at 2:16 PM
This is so cool and a severely overlooked aspect of the TME and stroma: spatially disordered geometries of the microenvironment promote invasion shifts from collective to single mode. #cancer #TME #stroma #invasion www.biorxiv.org/content/10.1...
The "pivot penalty". Such a great concept for capturing a nuanced idea. Larger pivots = lower citations, publication rates & market value. Yet, novelty rises with bold moves! Tough call for early-career scientists navigating expertise vs. exploration. www.nature.com/articles/s41...
May 28, 2025 at 9:31 PM
The "pivot penalty". Such a great concept for capturing a nuanced idea. Larger pivots = lower citations, publication rates & market value. Yet, novelty rises with bold moves! Tough call for early-career scientists navigating expertise vs. exploration. www.nature.com/articles/s41...
Reposted by Mark Borris Aldonza (보리스)
Excited our paper is out in Cell @cp-cell.bsky.social!
🧬⚡ DNA photo-crosslinking proteomics in living cells
🎯 Pinpoints protein-DNA interactions to single amino acids
🌎 Globally quantifies DNA binding for >1800 proteins at a timescale of minutes
🔗 www.cell.com/cell/fulltex...
🧵
🧬⚡ DNA photo-crosslinking proteomics in living cells
🎯 Pinpoints protein-DNA interactions to single amino acids
🌎 Globally quantifies DNA binding for >1800 proteins at a timescale of minutes
🔗 www.cell.com/cell/fulltex...
🧵
The human proteome with direct physical access to DNA
Zero-distance photo-crosslinking reveals direct protein-DNA interactions in living
cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale
of minutes with single-amino-aci...
www.cell.com
May 23, 2025 at 7:06 AM
Excited our paper is out in Cell @cp-cell.bsky.social!
🧬⚡ DNA photo-crosslinking proteomics in living cells
🎯 Pinpoints protein-DNA interactions to single amino acids
🌎 Globally quantifies DNA binding for >1800 proteins at a timescale of minutes
🔗 www.cell.com/cell/fulltex...
🧵
🧬⚡ DNA photo-crosslinking proteomics in living cells
🎯 Pinpoints protein-DNA interactions to single amino acids
🌎 Globally quantifies DNA binding for >1800 proteins at a timescale of minutes
🔗 www.cell.com/cell/fulltex...
🧵
In love with the anterior-posterior double reporter system! Awesome work as usual from Elly Tanaka's group
@imbavienna.bsky.social
Molecular basis of positional memory in limb regeneration
www.nature.com/articles/s41...
@imbavienna.bsky.social
Molecular basis of positional memory in limb regeneration
www.nature.com/articles/s41...
May 23, 2025 at 4:56 AM
In love with the anterior-posterior double reporter system! Awesome work as usual from Elly Tanaka's group
@imbavienna.bsky.social
Molecular basis of positional memory in limb regeneration
www.nature.com/articles/s41...
@imbavienna.bsky.social
Molecular basis of positional memory in limb regeneration
www.nature.com/articles/s41...