Xiaowei Jiang
@johnjxw.bsky.social
Computational and evolutionary biologist, studying virus, microbial and cancer evolution. Views my own.
Somatic and germline mutational processes across the tree of life
www.researchsquare.com/article/rs-8...
www.researchsquare.com/article/rs-8...
Somatic and germline mutational processes across the tree of life
The characterisation of mutational processes active in somatic and germline cells in vivo has predominantly focused on human cancers, normal tissues and model organisms. Beyond mammals, little is know...
www.researchsquare.com
January 26, 2026 at 3:55 AM
Somatic and germline mutational processes across the tree of life
www.researchsquare.com/article/rs-8...
www.researchsquare.com/article/rs-8...
"...progression to colorectal cancer requires traversing a rugged fitness landscape, whereas subsequent CNA evolution is constrained by negative selection."
aacrjournals.org/cancerdiscov...
aacrjournals.org/cancerdiscov...
Negative Selection Maintains Grossly Altered but Broadly Stable Karyotypes in Metastatic Colorectal Cancer
AbstractAneuploidy is near-ubiquitous in cancer and contributes to tumor biology. However, the temporal evolutionary dynamics that select for aneuploidy remain uncharacterized. We performed longitudin...
aacrjournals.org
January 25, 2026 at 3:53 AM
"...progression to colorectal cancer requires traversing a rugged fitness landscape, whereas subsequent CNA evolution is constrained by negative selection."
aacrjournals.org/cancerdiscov...
aacrjournals.org/cancerdiscov...
Reposted by Xiaowei Jiang
This first probable case of highly pathogenic avian influenza in a dairy cow in Europe raises two points. First, it suggests that virus incursion is possible in the Dutch housing system, which differs from that in the southern U.S., where cows were first infectted. www.science.org/content/arti...
Bird flu antibodies found in cow in the Netherlands, a first outside of U.S.
Dead cat led to discovery, but officials stress no further spread of H5N1 has been detected
www.science.org
January 24, 2026 at 8:02 AM
This first probable case of highly pathogenic avian influenza in a dairy cow in Europe raises two points. First, it suggests that virus incursion is possible in the Dutch housing system, which differs from that in the southern U.S., where cows were first infectted. www.science.org/content/arti...
Will there be convergent evolution in the GP RBD for NPC1 for ongoing and future outbreaks assuming they are from different zoonotic reservoirs? www.biorxiv.org/content/10.1...
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Molecular characterization of Ebola virus glycoprotein V75A substitution in the 2018–2020 epidemic
An Ebola virus glycoprotein mutant, which emerged early during the 2018–2020 epidemic,
enhances viral infectivity through multiple mechanisms and may have contributed to
its dominance in the outbreak.
www.cell.com
January 23, 2026 at 4:54 AM
Will there be convergent evolution in the GP RBD for NPC1 for ongoing and future outbreaks assuming they are from different zoonotic reservoirs? www.biorxiv.org/content/10.1...
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Interesting blog about a Dutch software entrepreneur and his approach to fight his own cancer. centuryofbio.com/p/sid
Going Founder Mode On Cancer
Sid Sijbrandij's extraordinary care journey
centuryofbio.com
January 23, 2026 at 12:54 AM
Interesting blog about a Dutch software entrepreneur and his approach to fight his own cancer. centuryofbio.com/p/sid
I guess it wont work well is because many genes and their carriers/genomes evolve in a way determined by non-fixed population genetic parameters, and current data do not cover their changing evolutionary landscapes spanning vast biological complexity. www.biorxiv.org/content/10.6...
www.biorxiv.org
January 21, 2026 at 3:17 AM
I guess it wont work well is because many genes and their carriers/genomes evolve in a way determined by non-fixed population genetic parameters, and current data do not cover their changing evolutionary landscapes spanning vast biological complexity. www.biorxiv.org/content/10.6...
This is fun: "By the year 2000, the United Kingdom will be simply a small group of impoverished islands, inhabited by some 70 million hungry people. —Ehrlich (1968)"
"Prediction in ecology and evolution"
academic.oup.com/bioscience/a...
"Prediction in ecology and evolution"
academic.oup.com/bioscience/a...
Prediction in ecology and evolution
Abstract. Prediction is frequently asserted to be the sine qua non of science, but prediction means different things to different people in different conte
academic.oup.com
January 15, 2026 at 10:17 AM
This is fun: "By the year 2000, the United Kingdom will be simply a small group of impoverished islands, inhabited by some 70 million hungry people. —Ehrlich (1968)"
"Prediction in ecology and evolution"
academic.oup.com/bioscience/a...
"Prediction in ecology and evolution"
academic.oup.com/bioscience/a...
Happy New Year with a nice pint of IPA.
December 31, 2025 at 4:00 PM
Happy New Year with a nice pint of IPA.
One comment I like is that many of the "working" methods are like "cooking recipes", and you also need diversity for future success in this field.
www.youtube.com/watch?v=7u-D...
www.youtube.com/watch?v=7u-D...
EP20: Yann LeCun
YouTube video by The Information Bottleneck
www.youtube.com
December 22, 2025 at 2:54 AM
One comment I like is that many of the "working" methods are like "cooking recipes", and you also need diversity for future success in this field.
www.youtube.com/watch?v=7u-D...
www.youtube.com/watch?v=7u-D...
Generally bacteria can have large effective population size, and there are less genetic redundancy due to effective selection, so gene copy number can be very useful in certain context for predictive modelling.
www.nature.com/articles/s44...
www.nature.com/articles/s44...
Gene copy-number features generalize better than SNPs for antimicrobial resistance prediction in Staphylococcus aureus - npj Antimicrobials and Resistance
npj Antimicrobials and Resistance - Gene copy-number features generalize better than SNPs for antimicrobial resistance prediction in Staphylococcus aureus
www.nature.com
December 22, 2025 at 12:59 AM
Generally bacteria can have large effective population size, and there are less genetic redundancy due to effective selection, so gene copy number can be very useful in certain context for predictive modelling.
www.nature.com/articles/s44...
www.nature.com/articles/s44...
Using LLMs responsibly should be taught from primary schools now.
Closing out my year with a journal editor shocker 🧵
Checking new manuscripts today I reviewed a paper attributing 2 papers to me I did not write. A daft thing for an author to do of course. But intrigued I web searched up one of the titles and that's when it got real weird...
Checking new manuscripts today I reviewed a paper attributing 2 papers to me I did not write. A daft thing for an author to do of course. But intrigued I web searched up one of the titles and that's when it got real weird...
December 20, 2025 at 11:24 AM
Using LLMs responsibly should be taught from primary schools now.
Reposted by Xiaowei Jiang
Absolutely stoked to have this published in @plosbiology.org
We looked at the metabolism of #Klebsiella pneumoniae 🦠🧫. We not only demonstrated lineage-specific #metabolism, but that lineages can cross-feed and support each other.
journals.plos.org/plosbiology/...
#MicroSky #microbiology 🧬 🧪 💊
We looked at the metabolism of #Klebsiella pneumoniae 🦠🧫. We not only demonstrated lineage-specific #metabolism, but that lineages can cross-feed and support each other.
journals.plos.org/plosbiology/...
#MicroSky #microbiology 🧬 🧪 💊
A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and capacity for intra-species co-operation
Why are there so many co-circulating Klebsiella pneumoniae clones? Using genomics and large-scale metabolic modelling of >7000 isolates, this study identifies structured, clone-specific metabolic spec...
journals.plos.org
December 13, 2025 at 9:46 AM
Absolutely stoked to have this published in @plosbiology.org
We looked at the metabolism of #Klebsiella pneumoniae 🦠🧫. We not only demonstrated lineage-specific #metabolism, but that lineages can cross-feed and support each other.
journals.plos.org/plosbiology/...
#MicroSky #microbiology 🧬 🧪 💊
We looked at the metabolism of #Klebsiella pneumoniae 🦠🧫. We not only demonstrated lineage-specific #metabolism, but that lineages can cross-feed and support each other.
journals.plos.org/plosbiology/...
#MicroSky #microbiology 🧬 🧪 💊
Reposted by Xiaowei Jiang
A Man From the Roman Empire Diagnosed With Metastatic Cancer 1,700 Years After His Death
oncodaily.com/oncolibrary/...
#OncoDaily #Oncology #Cancer #Health #Medicine #MedEd #MedOnc #MedNews
oncodaily.com/oncolibrary/...
#OncoDaily #Oncology #Cancer #Health #Medicine #MedEd #MedOnc #MedNews
A Man From the Roman Empire Diagnosed With Metastatic Cancer 1,700 Years After His Death - OncoDaily
A Man From the Roman Empire Diagnosed With Metastatic Cancer 1,700 Years After His Death / cancer, Headlines, OncoDaily, Oncology, Roman Empire,
oncodaily.com
December 13, 2025 at 1:03 AM
A Man From the Roman Empire Diagnosed With Metastatic Cancer 1,700 Years After His Death
oncodaily.com/oncolibrary/...
#OncoDaily #Oncology #Cancer #Health #Medicine #MedEd #MedOnc #MedNews
oncodaily.com/oncolibrary/...
#OncoDaily #Oncology #Cancer #Health #Medicine #MedEd #MedOnc #MedNews
What should we call it? If in the traditional sense evolutionary cell biology context?
nathanlapierre731428.substack.com/p/the-real-v...
nathanlapierre731428.substack.com/p/the-real-v...
The Real Value of the Virtual Cell Challenge
Reflecting on its limitations should guide the future of virtual cell research
nathanlapierre731428.substack.com
December 12, 2025 at 12:28 AM
What should we call it? If in the traditional sense evolutionary cell biology context?
nathanlapierre731428.substack.com/p/the-real-v...
nathanlapierre731428.substack.com/p/the-real-v...
Reposted by Xiaowei Jiang
Spillover of #influenza A viruses from animals to humans represents a threat to our health. In this Perspective, Silke Stertz @virology.uzh.ch discusses emerging research that suggests some influenza A viruses can enter host cells via MHC-II receptors across species 🧪 #virology
A new path to spillover: MHC-II entry of influenza A viruses
Spillover of influenza A viruses from animals to humans represents a threat to our health. This Perspective discusses emerging research that suggests some influenza A viruses can enter host cells via…
plos.io
December 9, 2025 at 5:33 PM
Spillover of #influenza A viruses from animals to humans represents a threat to our health. In this Perspective, Silke Stertz @virology.uzh.ch discusses emerging research that suggests some influenza A viruses can enter host cells via MHC-II receptors across species 🧪 #virology
It feels so so strange, and people are so quiet about this.
Well done to @qmucu.bsky.social for speaking truth about the implosion of the UK HE sector. Too many people are in denial. There are no jobs for us newbies and now they're coming for those fortunate enough to be established. Read this list of the ongoing cut and closures
qmucu.org/qmul-transfo...
qmucu.org/qmul-transfo...
UK HE shrinking
a live page of all the redundancies and restructures happening across UK Higher Education. Page is updated regularly.
qmucu.org
December 9, 2025 at 9:29 AM
It feels so so strange, and people are so quiet about this.
This is expected, particularly interesting is that AlphaFold or similar methods learn the biases in the PDB database.
www.cell.com/structure/ab...
www.cell.com/structure/ab...
Flexibility or uncertainty? A critical assessment of AlphaFold 2 pLDDT
Vander Meersche et al. present a large-scale analysis of the AlphaFold2/AlphaFold3/ESMFold
confidence index pLDDT and flexibility metrics derived from molecular dynamics (MD)
simulations. While genera...
www.cell.com
December 9, 2025 at 2:30 AM
This is expected, particularly interesting is that AlphaFold or similar methods learn the biases in the PDB database.
www.cell.com/structure/ab...
www.cell.com/structure/ab...
The only thing I can say is that somatic evolution is less studied/understood.
www.nature.com/articles/d41...
www.nature.com/articles/d41...
www.nature.com
November 26, 2025 at 11:13 AM
The only thing I can say is that somatic evolution is less studied/understood.
www.nature.com/articles/d41...
www.nature.com/articles/d41...
Reposted by Xiaowei Jiang
Simulation-based Inference (SBI) brings the power of generative modeling to parameter inference in science and engineering. We have now written a practical guide on how to effectively use these methods across domains 🔭👁️🗨️🦞
Simulation-based inference (SBI) has transformed parameter inference across a wide range of domains. To help practitioners get started and make the most of these methods, we joined forces with researchers from many institutions and wrote a practical guide to SBI.
📄 Paper: arxiv.org/abs/2508.12939
📄 Paper: arxiv.org/abs/2508.12939
Simulation-Based Inference: A Practical Guide
A central challenge in many areas of science and engineering is to identify model parameters that are consistent with prior knowledge and empirical data. Bayesian inference offers a principled framewo...
arxiv.org
November 21, 2025 at 3:17 PM
Simulation-based Inference (SBI) brings the power of generative modeling to parameter inference in science and engineering. We have now written a practical guide on how to effectively use these methods across domains 🔭👁️🗨️🦞
It works as we last tried sequences from an unreleased glycoprotein-host receptor complex, and it predicted a positive interaction score!
Our PLM-interact is out in Nature Communications! We show that jointly encoding protein pairs using protein language models improves protein–protein interaction prediction performance and enables fine-tuning to predict mutation effects in human PPIs. www.nature.com/articles/s41...
PLM-interact: extending protein language models to predict protein-protein interactions - Nature Communications
Protein structure can be predicted from amino acid sequences with unprecedented accuracy, yet the prediction of protein–protein interactions remains a challenge. Here, authors present a sequence-based...
www.nature.com
November 21, 2025 at 12:38 AM
It works as we last tried sequences from an unreleased glycoprotein-host receptor complex, and it predicted a positive interaction score!
Transmissible vaccines, gene drives... and releasing these to ecosystems, oh man: doi.org/10.1073/pnas...
Gene drives, species complexes, and the risks of collateral damage | PNAS
Gene drives, species complexes, and the risks of collateral damage
doi.org
November 17, 2025 at 6:23 PM
Transmissible vaccines, gene drives... and releasing these to ecosystems, oh man: doi.org/10.1073/pnas...
Ok, I am gonna watch some cat clips to cheer me up...
Can't emphasize how damaging this is. A single non-scientist—Peter Bogner—holds all power & makes all decisions at GISAID & provides no justifications for any of them, except blatantly false ones.
He has that power because he conned rich & powerful people into giving it to him. Enough.
He has that power because he conned rich & powerful people into giving it to him. Enough.
I want to spell this out in case the implications aren't clear:
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
November 16, 2025 at 11:29 AM
Ok, I am gonna watch some cat clips to cheer me up...
Useful concepts, when everything is mixing with everything these days or 4.5 billion years ago...
I've often wondered about what we should call organisms whose similarity might be due to acquired genetic material. It got a little complicated, but I made a stab at it here
Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes academic.oup.com/mbe/article/...
Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes academic.oup.com/mbe/article/...
Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes
Abstract. The classification of living systems presents significant challenges due to the prevalence of gene transfer between genomes. Traditional taxonomi
academic.oup.com
November 15, 2025 at 1:45 PM
Useful concepts, when everything is mixing with everything these days or 4.5 billion years ago...
James Kirk! And lots of interesting research: royalsociety.org/news/2025/11...
November 14, 2025 at 3:21 PM
James Kirk! And lots of interesting research: royalsociety.org/news/2025/11...