Pinned
Matthew Hahn
@3rdreviewer.bsky.social
· Mar 7
It's official--we're escaping for a year!
Happy to say that we'll be on leave at the Wissenschaftskolleg in Berlin from August 2025-July 2026.
Looking forward to beer, travel, and scholarly learning ;)
Happy to say that we'll be on leave at the Wissenschaftskolleg in Berlin from August 2025-July 2026.
Looking forward to beer, travel, and scholarly learning ;)
Reposted by Matthew Hahn
noooooooooooooooooo!
(nice figure btw, with time of duplication vs probability)
(nice figure btw, with time of duplication vs probability)
New paper with @smishra677.bsky.social!
How many different trees can be generated by just one duplication event? It turns out A WHOLE LOT, if you consider the coalescent process.
1/
www.biorxiv.org/content/10.6...
How many different trees can be generated by just one duplication event? It turns out A WHOLE LOT, if you consider the coalescent process.
1/
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 23, 2026 at 5:00 PM
noooooooooooooooooo!
(nice figure btw, with time of duplication vs probability)
(nice figure btw, with time of duplication vs probability)
Reposted by Matthew Hahn
New paper with @smishra677.bsky.social!
How many different trees can be generated by just one duplication event? It turns out A WHOLE LOT, if you consider the coalescent process.
1/
www.biorxiv.org/content/10.6...
How many different trees can be generated by just one duplication event? It turns out A WHOLE LOT, if you consider the coalescent process.
1/
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 23, 2026 at 11:10 AM
New paper with @smishra677.bsky.social!
How many different trees can be generated by just one duplication event? It turns out A WHOLE LOT, if you consider the coalescent process.
1/
www.biorxiv.org/content/10.6...
How many different trees can be generated by just one duplication event? It turns out A WHOLE LOT, if you consider the coalescent process.
1/
www.biorxiv.org/content/10.6...
New paper with @smishra677.bsky.social!
How many different trees can be generated by just one duplication event? It turns out A WHOLE LOT, if you consider the coalescent process.
1/
www.biorxiv.org/content/10.6...
How many different trees can be generated by just one duplication event? It turns out A WHOLE LOT, if you consider the coalescent process.
1/
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 23, 2026 at 11:10 AM
New paper with @smishra677.bsky.social!
How many different trees can be generated by just one duplication event? It turns out A WHOLE LOT, if you consider the coalescent process.
1/
www.biorxiv.org/content/10.6...
How many different trees can be generated by just one duplication event? It turns out A WHOLE LOT, if you consider the coalescent process.
1/
www.biorxiv.org/content/10.6...
Reposted by Matthew Hahn
Reposted by Matthew Hahn
An interesting bit of history:
In 1916, Denmark sold the Danish West Indies to the US. You may know of them as the US Virgin Islands. As part of this sale, the US recognized Danish authority over Greenland.
The text of the complete, ratified agreement is here: www.govinfo.gov/content/pkg/...
In 1916, Denmark sold the Danish West Indies to the US. You may know of them as the US Virgin Islands. As part of this sale, the US recognized Danish authority over Greenland.
The text of the complete, ratified agreement is here: www.govinfo.gov/content/pkg/...
January 19, 2026 at 7:06 AM
An interesting bit of history:
In 1916, Denmark sold the Danish West Indies to the US. You may know of them as the US Virgin Islands. As part of this sale, the US recognized Danish authority over Greenland.
The text of the complete, ratified agreement is here: www.govinfo.gov/content/pkg/...
In 1916, Denmark sold the Danish West Indies to the US. You may know of them as the US Virgin Islands. As part of this sale, the US recognized Danish authority over Greenland.
The text of the complete, ratified agreement is here: www.govinfo.gov/content/pkg/...
My first PopGroup—it was great! Thanks to all the organizers, especially.
January 10, 2026 at 2:57 PM
My first PopGroup—it was great! Thanks to all the organizers, especially.
Reposted by Matthew Hahn
Earlier this week, David Marques, my beloved PhD brother, died after a battle with cancer. He was an amazing person, friend, father, husband, scientist, collaborator, birder, among other things. I am immensely grateful for many years of friendship and close collaboration with him. We miss you!
January 10, 2026 at 9:14 AM
Earlier this week, David Marques, my beloved PhD brother, died after a battle with cancer. He was an amazing person, friend, father, husband, scientist, collaborator, birder, among other things. I am immensely grateful for many years of friendship and close collaboration with him. We miss you!
Final version of paper with @smishra677.bsky.social now published in a wonderful issue of GENETICS!
academic.oup.com/genetics/art...
academic.oup.com/genetics/art...
January 8, 2026 at 1:57 PM
Final version of paper with @smishra677.bsky.social now published in a wonderful issue of GENETICS!
academic.oup.com/genetics/art...
academic.oup.com/genetics/art...
While our updated paper is fast approaching book-length, the results remain the same: our method (reconcILS) is still highly accurate.
So if you want to reconcile gene trees and species trees--and you might have any ILS at all--this is the best method out there!
www.biorxiv.org/content/10.1...
So if you want to reconcile gene trees and species trees--and you might have any ILS at all--this is the best method out there!
www.biorxiv.org/content/10.1...
reconcILS: A gene tree-species tree reconciliation algorithm that allows for incomplete lineage sorting
Reconciliation algorithms infer the evolutionary history of individual gene trees given a species tree. Many reconciliation algorithms consider only duplication and loss events (and sometimes horizont...
www.biorxiv.org
January 7, 2026 at 11:22 AM
While our updated paper is fast approaching book-length, the results remain the same: our method (reconcILS) is still highly accurate.
So if you want to reconcile gene trees and species trees--and you might have any ILS at all--this is the best method out there!
www.biorxiv.org/content/10.1...
So if you want to reconcile gene trees and species trees--and you might have any ILS at all--this is the best method out there!
www.biorxiv.org/content/10.1...
Reposted by Matthew Hahn
Cheating on my German beer gardens to taste some good Dutch stuff:
December 30, 2025 at 11:45 AM
Cheating on my German beer gardens to taste some good Dutch stuff:
My year in Christmas markets...
#1 Schloss Charlottenburg
#1 Schloss Charlottenburg
December 26, 2025 at 2:22 PM
My year in Christmas markets...
#1 Schloss Charlottenburg
#1 Schloss Charlottenburg
Biergarten nummer zehn
December 23, 2025 at 5:13 PM
Biergarten nummer zehn
Achievement unlocked: I cancelled a doctor's appointment (for my kid) over the phone **in German**!
December 18, 2025 at 9:35 AM
Achievement unlocked: I cancelled a doctor's appointment (for my kid) over the phone **in German**!
Have you ever wondered: just how strong *is* the evidence for Muller's ratchet on mtDNA?
Well, wonder no more!
(Project led by Yu Mo, with @smishra677.bsky.social and @yadirapga.bsky.social)
"No molecular evidence for Muller's ratchet in mitochondrial genomes"
www.biorxiv.org/content/10.6...
Well, wonder no more!
(Project led by Yu Mo, with @smishra677.bsky.social and @yadirapga.bsky.social)
"No molecular evidence for Muller's ratchet in mitochondrial genomes"
www.biorxiv.org/content/10.6...
No molecular evidence for Muller's ratchet in mitochondrial genomes
Muller's ratchet predicts that non-recombining genomes can accumulate deleterious mutations, though molecular evidence for it is rare. Previous studies have tried to detect ratchet-like behavior in mi...
www.biorxiv.org
December 17, 2025 at 2:36 PM
Have you ever wondered: just how strong *is* the evidence for Muller's ratchet on mtDNA?
Well, wonder no more!
(Project led by Yu Mo, with @smishra677.bsky.social and @yadirapga.bsky.social)
"No molecular evidence for Muller's ratchet in mitochondrial genomes"
www.biorxiv.org/content/10.6...
Well, wonder no more!
(Project led by Yu Mo, with @smishra677.bsky.social and @yadirapga.bsky.social)
"No molecular evidence for Muller's ratchet in mitochondrial genomes"
www.biorxiv.org/content/10.6...
Reposted by Matthew Hahn
No molecular evidence for Muller's ratchet in mitochondrial genomes https://www.biorxiv.org/content/10.64898/2025.12.16.694700v1
December 17, 2025 at 3:33 AM
No molecular evidence for Muller's ratchet in mitochondrial genomes https://www.biorxiv.org/content/10.64898/2025.12.16.694700v1
Biergarten nummer neun
December 12, 2025 at 8:07 PM
Biergarten nummer neun
Reposted by Matthew Hahn
Today the members of the Evolution, Ecology, and Behavior graduate program at Indiana University celebrated the upcoming retirement of Dr. Ellen Ketterson. Ellen was a bastion of civility and scientific excellence. The program would not be what it is without her presence over these past decades.
December 11, 2025 at 11:21 PM
Today the members of the Evolution, Ecology, and Behavior graduate program at Indiana University celebrated the upcoming retirement of Dr. Ellen Ketterson. Ellen was a bastion of civility and scientific excellence. The program would not be what it is without her presence over these past decades.
Hoo- Hoo- Hoo-
Hoosiers!
Hoosiers!
The Dems voted 10–0 against the gerrymander, and the Republicans voted against it 21–19.
A majority of the Republican members of the Indiana State Senate just told Trump to go fuck himself.
A majority of the Republican members of the Indiana State Senate just told Trump to go fuck himself.
The Indiana State Senate is 40 Republicans, 10 Democrats. This result is not even close to nothing.
December 11, 2025 at 10:06 PM
Hoo- Hoo- Hoo-
Hoosiers!
Hoosiers!
New paper on minimal NNs for phylogenetic inference, with former grad student, Ben Rosenzweig:
arxiv.org/abs/2512.02223
arxiv.org/abs/2512.02223
On the Approximation of Phylogenetic Distance Functions by Artificial Neural Networks
Inferring the phylogenetic relationships among a sample of organisms is a fundamental problem in modern biology. While distance-based hierarchical clustering algorithms achieved early success on this ...
arxiv.org
December 3, 2025 at 12:29 PM
New paper on minimal NNs for phylogenetic inference, with former grad student, Ben Rosenzweig:
arxiv.org/abs/2512.02223
arxiv.org/abs/2512.02223
Reposted by Matthew Hahn
How to keep in step when your (protein) partner speeds up…
Here we investigated the adaptive remodeling of a protein-protein interaction surface essential for telomere protection.
Congrats to whole team!
www.science.org/doi/10.1126/...
Here we investigated the adaptive remodeling of a protein-protein interaction surface essential for telomere protection.
Congrats to whole team!
www.science.org/doi/10.1126/...
Rapid compensatory evolution within a multiprotein complex preserves telomere integrity
Intragenomic conflict with selfish genetic elements spurs adaptive changes in subunits of essential multiprotein complexes. Whether and how these adaptive changes disrupt interactions within such comp...
www.science.org
November 28, 2025 at 5:22 PM
How to keep in step when your (protein) partner speeds up…
Here we investigated the adaptive remodeling of a protein-protein interaction surface essential for telomere protection.
Congrats to whole team!
www.science.org/doi/10.1126/...
Here we investigated the adaptive remodeling of a protein-protein interaction surface essential for telomere protection.
Congrats to whole team!
www.science.org/doi/10.1126/...
Reposted by Matthew Hahn
Please pass along - We've extended the CAMBIUM fellowship deadline to December 15! Our NSF NRT supports new grad students to harness biodiversity big data to adapt to & mitigate climate change impacts. Great fit for evolutionary genomics, bioinformatics, ecology & more. cambium.arizona.edu 🧬🌐🌎
November 26, 2025 at 7:19 PM
Please pass along - We've extended the CAMBIUM fellowship deadline to December 15! Our NSF NRT supports new grad students to harness biodiversity big data to adapt to & mitigate climate change impacts. Great fit for evolutionary genomics, bioinformatics, ecology & more. cambium.arizona.edu 🧬🌐🌎
Reposted by Matthew Hahn
absolutely LOVE this preprint on tricking LLMs using poetry:
arxiv.org/abs/2511.15304
Like magic spells, you need to use the correct pentameter or the demon won't listen
arxiv.org/abs/2511.15304
Like magic spells, you need to use the correct pentameter or the demon won't listen
Adversarial Poetry as a Universal Single-Turn Jailbreak Mechanism in Large Language Models
We present evidence that adversarial poetry functions as a universal single-turn jailbreak technique for Large Language Models (LLMs). Across 25 frontier proprietary and open-weight models, curated po...
arxiv.org
November 21, 2025 at 2:07 AM
absolutely LOVE this preprint on tricking LLMs using poetry:
arxiv.org/abs/2511.15304
Like magic spells, you need to use the correct pentameter or the demon won't listen
arxiv.org/abs/2511.15304
Like magic spells, you need to use the correct pentameter or the demon won't listen
Reposted by Matthew Hahn
Read this story in The Chaser Annual 2025, available now: chasershop.com/products/the...
November 13, 2025 at 7:28 AM
Read this story in The Chaser Annual 2025, available now: chasershop.com/products/the...
Look-up your software name before publishing it!
Wow, I never really noticed this 'fastp' software. I'm apparently the only one though.
They simply re-used an existing name already employed by popular and historically significant software. How is this kind of thing possible?
academic.oup.com/bioinformati...
They simply re-used an existing name already employed by popular and historically significant software. How is this kind of thing possible?
academic.oup.com/bioinformati...
fastp: an ultra-fast all-in-one FASTQ preprocessor
AbstractMotivation. Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a differ
academic.oup.com
November 17, 2025 at 7:07 PM
Look-up your software name before publishing it!