iiinova — where your digital self keeps evolving

Reposted by Alexey Markin

Louise H. Moncla @lhmoncla.bsky.social · 23/09/2026

Our lab just put out a new preprint! Led by Maria Maltepes, we've been working with @tavisanderson.bsky.social and @alexey-markin.bsky.social to understand how host species impacts the fundamentals of how influenza viruses evolve. TLDR, reassortment and selection rates vary widely across species.

scholar.google.com

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Reposted by Alexey Markin

Society for Molecular Biology and Evolution @official-smbe.bsky.social · 12/03/2026

🧬EvolCompGen presents: Christian Landry on the Evolution of gene duplication, from redundancy to dependency @christianlandry.bsky.social 🗓️ Join us on Monday, March 23 at 11:00 AM EDT 📌 Register here: us02web.zoom.us/webinar/regi...

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Reposted by Alexey Markin

Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 28/02/2026

So I pleased to announce the conceptual spawn of FigTree: PearTree (acronym still to be finalised). If you want to dive right in it is hosted as a web app here: artic-network.github.io/peartree (click the “Example...” button for immediate candy and then click every button you can find).

artic-network.github.io

PearTree — Phylogenetic Tree Viewer

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Alexey Markin @alexey-markin.bsky.social · 22/01/2026

An exciting result showing the statistical consistency of ASTRAL-pro under the dup+loss+coalescence model of gene evolution. A lot of empirical validation challenging various assumptions too (with a nice method TREE-QMC). Was great to be a part of this project led by Rachel Parsons and Erin Molloy

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Reposted by Alexey Markin

ISCB News @iscb.bsky.social · 28/11/2025

🗓️ One week to go until our next ISCBacademy webinar, presented by the EvolCompGen COSI. 🔬 Michael Barnett will discuss new experimental evidence on the evolution of evolvability in bacterial populations.

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Alexey Markin @alexey-markin.bsky.social · 24/09/2025

Excited to share a new preprint! “Ordered Leaf Attachment (OLA) Vectors can Identify Reticulation Events even in Multifurcated Trees” We link reticulations (eg introgression or virus recombination) to an ordering of taxa, which opens some new directions! arxiv.org/pdf/2509.16405 1/3

arxiv.org

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Alexey Markin @alexey-markin.bsky.social · 11/08/2025

TreeSort is out at MBE! Fresh off the press so DOI below is not yet working, but you can find the article here: academic.oup.com/mbe/article/... 💡If you want to apply it to your data - please see the tutorial here github.com/flu-crew/Tre...

academic.oup.com

Revealing Reassortment in Influenza A Viruses with TreeSort

Abstract. Reassortment among influenza A viruses (IAV) facilitates evolution and has been associated with interspecies transmission and pandemics. We intro

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Alexey Markin @alexey-markin.bsky.social · 10/07/2025

Good overview of what’s been happening with HPAI H5N1 recently

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Alexey Markin @alexey-markin.bsky.social · 21/06/2025

A new paper out: fast (n logn) computation of cophenetic distances between phylogenetic trees. What’s great is that our algorithm applies to a very broad class of cophenetic distances including the popular Kendall-Colijn distance - check it out! journals.plos.org/ploscompbiol...

journals.plos.org

Computing generalized cophenetic distances under all Lp norms: A near-linear time algorithmic framework

Author summary Biological research often relies on large-scale comparisons of evolutionary trees to extract valuable insights across different subfields of biology. To effectively compare trees on a l...

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Alexey Markin @alexey-markin.bsky.social · 23/04/2025

Phylogenetics don’t let you go even on vacation. Also, never seen sea dragons before, they look insane

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Alexey Markin @alexey-markin.bsky.social · 21/04/2025

Late repost but thanks to the TWiV team for revisiting our human -> 🐷 reverse-zoonoses of influenza A viruses paper. Discussion is from ~9:00 to ~40:00 for anyone interested in IAV interface between humans and pigs. The dementia paper discussion was also fascinating

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Alexey Markin @alexey-markin.bsky.social · 10/02/2025

Anyone knows what’s happening with the Rocky bioinformatics conference and if they plan to continue it? I never had a chance to go so far, but really wish they would continue

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Reposted by Alexey Markin

Louise H. Moncla @lhmoncla.bsky.social · 20/12/2024

Just in time for the holidays, our lab has just submitted our first lab led paper www.biorxiv.org/content/10.1...! We use phylodynamics to reconstruct how H5N1 got to North America and spread so rapidly. Full thread coming post holidays, but for now, super proud of @lambod50.bsky.social

biorxiv.org

Intensive transmission in wild, migratory birds drove rapid geographic dissemination and repeated spillovers of H5N1 into agriculture in North America

Since late 2021, a panzootic of highly pathogenic H5N1 avian influenza virus has driven significant morbidity and mortality in wild birds, domestic poultry, and mammals. In North America, infections i...

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Alexey Markin @alexey-markin.bsky.social · 02/12/2024

EvolCompGen presents an online seminar: Megan Smith on Using machine learning to accommodate complexity in phylogenetics and population genetics. Join us on Friday, December 6, at 11 am EST through iscb.junolive.co For non-ISCB members, registration here: iscb.swoogo.com/ISCBnucleus-...

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