Xiaowei Jiang
@johnjxw.bsky.social
Computational and evolutionary biologist, studying virus, microbial and cancer evolution. Views my own.
Targeting a "hairy" spike is hard! www.nature.com/articles/s41... www.nature.com/articles/s41... www.nature.com/articles/s41...
Vaccination generates broadly cross-neutralizing antibodies to the HIV Env apex - Nature
A vaccination strategy using heterologous HIV Env trimers covalently coupled to liposomes for multivalent display generates cross-neutralizing HIV serum antibody responses in non-human primates, mimic...
nature.com
This may be justified as their hosts are bacteria, but then what's next? Safe viral vectors for gene therapies? www.science.org/doi/10.1126/...
Generative design of bacteriophages with genome language models
Many important biological functions arise not from single genes but from complex interactions encoded by entire genomes. We report the first generative design of complete bacteriophage genomes using g...
science.org
Have a look at this one, it is getting better, and can use your local env, three different popular agent harness systems: github.com/aipoch/open-...
GitHub - aipoch/open-science: Open Science is an open-source, local-first, model-agnostic AI research workbench for scientific discovery.
Open Science is an open-source, local-first, model-agnostic AI research workbench for scientific discovery. - aipoch/open-science
github.com
Fitness flux: more interactive data, too, and Trevor also shows that the adaptation of SARS-COV-2 well follows the expectation of Fisher's fundamental theorem! blab.github.io/fitness-flux/ , also check Meijers et al, but what genetic mechanisms make this prediction challenging now, recombination?
Fitness flux in SARS-CoV-2 and influenza H3N2
blab.github.io
Xiaowei Jiang@johnjxw.bsky.social · 6mo agoFinally, got the whole idea, it just took 10+ years to get there. It seems to connect everything since Fisher and Wright, etc. www.pnas.org/doi/10.1073/...
A true foundational "virtual-cell" should learn from an "evolutionary tape" that can play the whole spectrum of organismal evolution. www.nature.com/articles/s41...
Whole-genome duplication shaped cell-type evolution in the vertebrate brain - Nature
Analyses of brain single-cell transcriptomes from human, mouse, lizard, lamprey and amphioxus reveal that duplicated genes (ohnologues) played a pivotal part in early vertebrate cell-type diversificat...
nature.com
Not sure about the ecological changes of reservoir animals for emerging/re-emerging viral pathogens this year: yaleclimateconnections.org/2026/06/may-...
May 2026 was the world's second-warmest May on record » Yale Climate Connections
Global sea surface temperatures were the second-highest on record for May.
yaleclimateconnections.org
If I let Fable 5 work on my codebase...cancer, virus, and bacteria...and the key word pathogen...will it get crazy...hmm...
Evolutionary genetics of ageing www.nature.com/articles/s41...
Evolutionary genetics of ageing - Nature Reviews Genetics
Modern humans increasingly live long enough to experience late-life consequences of genetic and molecular systems shaped by natural selection. In this Review, the authors integrate evolutionary geneti...
nature.com
Complete genome of the Hondius outbreak hantavirus (and tree): virological.org/t/complete-s...
Complete sequence of Orthohantavirus andesense virus: Swiss resident 2026
Posted on behalf of the Swiss National Reference Center for Emerging Viral Infections, Geneva University Hospitals and the Institute of Medical Virology, University of Zurich (Partner Laboratory Natio...
virological.org
BEAST!
Trevor Graham@trevorgraham.bsky.social · 4mo agoIn colon, stem cells divide & so do the crypts they reside in: a multi-level evolutionary process. D Mallo, P Bousquets @heathergrant.bsky.social @calumgabbutt.bsky.social have made "PhyPhum" to lineage trace somatic evolution in human glandular tissues www.biorxiv.org/content/10.6... @icr.ac.uk
🚨New paper!🚨 Our study showing that H5N1 influenza viruses can remain infectious in unpasteurised milk for, basically, as long as you are likely to encounter that milk has now been published: www.microbiologyresearch.org/content/jour...
How somatic evolution affects health? www.nature.com/articles/s41...
How somatic evolution affects health - Nature Ecology & Evolution
As somatic evolution becomes directly measurable, integrating eco-evolutionary principles with high-resolution molecular data creates opportunities to anticipate and prevent disease.
nature.com
Paul Ehrlich has died www.nytimes.com/2026/03/15/b..., some say the coming misery of my generation might have something to do with him.
Population doomster and false prophet of ecological apocalypse Paul Ehrlich has died
Paul Ehrlich, the leading false prophet of inevitable environmental doom and author of the infamous 'The Population Bomb,' has died at age 93.
reason.com
Xiaowei Jiang@johnjxw.bsky.social · 8mo agoThis 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...
Riboviruses are cool! A symbiotic origin of the ribosome? academic.oup.com/pnasnexus/ar...
A symbiotic origin of the ribosome?
Abstract. The origin of life is one of the great mysteries of science. Of the multiple unsolved problems, the origin of the translation system (the means b
academic.oup.com
Xiaowei Jiang@johnjxw.bsky.social · 7mo agoSo understanding origin of life and RNA viruses converges? www.science.org/doi/10.1126/...
Chen Ning “Frank” Yang (1922–2025): Profound proponent of symmetry 'Where there is a bang, there is Yang' www.pnas.org/doi/10.1073/...
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
pnas.org
Courtesy of @martibartfast.bsky.social , we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025. allthebacteria.readthedocs.io/en/latest/ov...
Overview — AllTheBacteria documentation
allthebacteria.readthedocs.io
Finally, got the whole idea, it just took 10+ years to get there. It seems to connect everything since Fisher and Wright, etc. www.pnas.org/doi/10.1073/...
Fitness flux and ubiquity of adaptive evolution | PNAS
Natural selection favors fitter variants in a population, but actual evolutionary processes may decrease fitness by mutations and genetic drift. Ho...
pnas.org
A mathematical model from statistical physics can help reveal properties of populations under changing immune selection (changing fitness landscapes/seascapes). www.biorxiv.org/content/10.1...
biorxiv.org
So understanding origin of life and RNA viruses converges? www.science.org/doi/10.1126/...
A small polymerase ribozyme that can synthesize itself and its complementary strand
The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...
science.org
Interesting paper www.nature.com/articles/s41... it seems to be consistent with recent spillover event(s) discovered in a dairy farm in the northern Netherlands, but would be interesting to see how many of those potentially mammal adaptive mutations in this wave of bird migration?
Ecology and environment predict spatially stratified risk of H5 highly pathogenic avian influenza clade 2.3.4.4b in wild birds across Europe - Scientific Reports
Highly pathogenic avian influenza (HPAI) represents a threat to animal and human health, with the ongoing H5N1 outbreak within the H5 2.3.4.4b clade being one of the largest on record. However, it rem...
nature.com
Thijs Kuiken@thijskuiken.bsky.social · 7mo agoInteressante reconstructie van de tijdlijn van de diagnostische tests van katten, koeien en mensen op vogelgriep H5N1 op het Friese melkveebedrijf, en de informatieverstrekking daarover door de overheid, gezien door de bril van dierenarts ‘hogvet51’ uit de V.S. hogvet51.substack.com/p/h5n1-in-ca...
Sec and Tat mediated secretion safeguards Mycobacterium tuberculosis membrane homeostasis www.biorxiv.org/content/10.1...
biorxiv.org
"HLA micropolymorphisms confine neoantigen conformational adaptability and guide T cell receptor selectivity" www.biorxiv.org/content/10.6...
biorxiv.org
Well, that's almost every postdoc's daily life in Oxford or Cambridge. On the positive side, some of the research directions you pursue can be intellectually satisfactory and beneficial to your career even if they did not make it to one of these journals.
Science News@scinews.bsky.social · 7mo agoHow chasing a high-impact publication nearly broke me When my paper was published in Science, others expected me to be happy. www.science.org/content/arti...
Somatic and germline mutational processes across the tree of life 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...
researchsquare.com
"...progression to colorectal cancer requires traversing a rugged fitness landscape, whereas subsequent CNA evolution is constrained by negative selection." 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
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
science.org
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...
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.
cell.com
