Xin Hou

Phages with a broad host range are common across ecosystems - Nature Microbiology Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.

Out Now! Phages with a broad host range are common across ecosystems bit.ly/46tteyG #Phages #Microbiology #Ecosystems

DeepSeek-R1 incentivizes reasoning in LLMs through reinforcement learning - Nature A new artificial intelligence model, DeepSeek-R1, is introduced, demonstrating that the reasoning abilities of large language models can be incentivized through pure reinforcement learning, removing the need for human-annotated demonstrations.

DeepSeek-R1 paper is out now, showing that the inference capabilities of large language models (LLMs) can be improved through pure reinforcement learning, reducing the human input work required to enhance performance.​

👉🏻 www.nature.com/articles/s41...

Recent advances in the inference of deep viral evolutionary history | Journal of Virology Phylogenetic studies examining the origins, emergence, and spread of viruses have arguably been one of the most active and successful areas of evolutionary biology and form the bedrock of the flourishing field of genomic epidemiology. This, in part, reflects the ability of viruses, particularly those with RNA genomes, to evolve at rates much greater than their cellular counterparts (1). The rapid rate at which viruses evolve and accumulate mutations enables evolutionary signals to be identified through comparative genomics at short timescales relevant for outbreak investigation and response. The integration of phylogenetics and epidemiology, known as phylodynamics, has become a vital tool in response to numerous viral outbreaks, epidemics, and pandemics, including Ebola (2), Zika (3), and, more recently, COVID-19 (4) and mpox (5).

There’s been a bunch of new approaches looking at deep viral evolutionary history. We’ve put together a mini review highlighting some recent advancements in structural phylogenetics and time-dependent rate models and what they could do for the field 🦠
🔗 journals.asm.org/doi/full/10....

Advancing RNA phage biology through meta-omics Abstract. Bacteriophages with RNA genomes are among the simplest biological entities on Earth. Since their discovery in the 1960s, they have been used as i

I'm happy to share the first publication from my lab @hoerlab.bsky.social, now out in @narjournal.bsky.social! I take a look at the biology of RNA phages, focusing on how meta-omics methods are discovering new RNA phage families and bacterial defense strategies.

#PhageSky

doi.org/10.1093/nar/...

Recent advances in the inference of deep viral evolutionary history | Journal of Virology Phylogenetic studies examining the origins, emergence, and spread of viruses have arguably been one of the most active and successful areas of evolutionary biology and form the bedrock of the flourish...

The rapid rate of virus evolution poses a challenge for accurately estimating viral evolutionary divergence. Recent advancements in computational biology have opened up new avenues and enabled us to reconstructe the deep evolutionary history of viruses.

👉🏻 journals.asm.org/doi/full/10....

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵

Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.

doi.org/10.1101/2024...

Interested in using phylogenetics to study arboviruses? Our new review in @natrevgenet.nature.com‬ by @viralverity.bsky.social‬, @sdellicour.bsky.social‬, and Marta Giovanetti has you covered!

📖 👉 rdcu.be/epH2U

Short 🧵

AI in Virology: Leveraging AI to Advance Our Understanding of Viruses - Area Science Park Artificial intelligence is opening new perspectives in virus research, providing advanced tools to analyze viral evolution and to understand protein structure and dynamics on a large scale. To explore...

🧬 Excited to share our International Workshop: AI in Virology
📆 Sept 9, 2025 - Trieste, Italy
@AreaSciencePark
We’ll explore how #AI is transforming virology — from protein language models to vaccine design and biosecurity.
🔗 Program & details: www.areasciencepark.it/en/events/ai...

Deutschlandkarte der Verteilung der Exzellenzcluster auf Bundesländer und Universitäten.

Die #Exzellenzcluster stehen fest: Heute hat die Exzellenzkommission 70 Projekte zur Förderung ausgewählt. 45 Cluster werden fortgesetzt, 25 neu eingerichtet. Die Förderung beginnt ab 1. Jan. 2026 für 7 Jahre, die Fördersumme beträgt insg. 539 Mio. €/Jahr. Die Liste: www.dfg.de/resource/blo... 1/3

If you love #viruses, #ribosomes, and genomic #darkmatter, this thread is for you!! 💫
We're excited to share our new publication developing Massively Parallel Ribosome Profiling (MPRP), which uncovered ~4,000 hidden proteins in ~700 viral genomes. www.science.org/doi/10.1126/...

New pre-print out \o/ All about CRISPR, metagenomes, and what you learn when you collect (a lot of) spacers from natural communities, with @apcamargo.bsky.social @urineri.bsky.social @lhug.bsky.social but also Uri Gophna, Nikhil George (not on Bsky I think) & others at JGI doi.org/10.1101/2025...

Hello everyone! I am pleased to share information on the first ever Computational Structural Virology Symposium, conducted August 4th on zoom and highlighting work in this emerging field. You can register for this event here: forms.gle/CNiqskMwQEuV.... Please re-post!

A general substitution matrix for structural phylogenetics. Abstract. Sequence-based maximum likelihood (ML) phylogenetics is a widely used method for inferring evolutionary relationships, which has illuminated the

New paper from the lab from Sriram Garg in my group. We introduce a general substitution matrix for structural phylogenetics. I think this is a big deal, so read on below if you think deep history is important. academic.oup.com/mbe/advance-...

Slides from my talk (with @kamilsjaron.bsky.social) on an history of k-mers in bioinformatics: rayan.chikhi.name/pdf/2025-kme...

Unicore is now published on GBE 🚀
Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n
📃 doi.org/10.1093/gbe/evaf109

Screenshot of the homepage of Pathoplexus, showing tiles to navigate to the supported pathogens CCHF, Ebola Sudan, Ebola Zaire, HMPV, Mpox, RSV-A, RSV-B, and West Nile virus.

📢Today Pathoplexus announces the inclusion of 2 new viral pathogens: RSV (A & B) and HMPV.

These respiratory viruses cause a serious health burden, particularly in infants & the vulnerable, & Pathoplexus aims to support sequence sharing to improve understanding & response.

1/4

GISAID's opaque leadership is antithetical to public health and epidemiology. All viral sequence sharing should move to open source and transparent platforms like @pathoplexus.org

(Folks unaware of GISAID's creepy leadership should read the article in the 2nd post of Kristian's thread)

You might be wondering why we haven't updated outbreak.info for months.

Well, the reason is that GISAID cut our access in January - as they did others. Without telling us.

After a ♾️ back and forth, that is now permanent.

More on that soon - and why GISAID should not be trusted with critical data.

Oh no! 🤦🏻‍♀️

EVE Meeting Expression of Interest

I'm thinking of organising a meeting on endogenous viral elements (RNA, DNA and retroviral) - if you'd potentially be interested, please fill out the form here - forms.gle/wrCiWMw4yXZe... - so I can gauge interest. Please RT or share with anyone maybe interested! 🧪🧬🖥️🦠 #virology #bioinformatics

Thanks again for the organization and invitation, and also thanks for the food, for the help and everything!! Definitely amazing to be in Lisbon to share our work!!!

Lucaprot leverages AI to discover highly-divergent RNA-dependent RNA polymerase sequences, completely revolutionizing the field of RNA Virus discovery! We are ecstatic to have Xin Hou (@xinhou.bsky.social) as one of our invited speakers at the #RdRpSummit2025!

The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2 Recombination-aware evolutionary analyses of the entire genomes of SARS-CoV-1-like and SARS-CoV-2-like viruses indicate that SARS-CoV-1 and SARS-CoV-2 descend from bat coronaviruses that circulated as...

📄 NEW | Genetic Study shows that Wildlife Trade sparked COVID-19 Virus Emergence in Humans

SARS-CoV-2 arrived in Wuhan too quickly for bat hosts to have carried it there.

cell.com/cell/fulltex...

gla.ac.uk/research/az/...

@davidlrobertson.bsky.social
@spyroslytras.bsky.social
@bljog.bsky.social

Introducing our invited speaker for the session on 'Viral Dark Matter' we have Rachel Seongeun Kim from the Seoul National University!!!!

The registrations for on-site & remote participation are still open! More info: RdRp.io
#RdRpSummit2025

Guess who is invited as the keynote speaker for the session on "Data Mining & Metadata Analysis"???

It is Rayan Chikhi!!!

He will introduce us to Logan. You can read the preprint here: tinyurl.com/vx4cykr7

Registrations are still open for #RdRpSummit2025!

Counting down to Lisbon! On May 12, I’ll be speaking at @rdrpsummit.bsky.social about the viral dark matter we’ve uncovered using #LucaProt. Grateful for the invitation—can’t wait to connect!