Leo Martins (he/him)
@leomrtns.bsky.social
Computational Biologist. Tenure Track Fellow in Health at the University of Liverpool. 🇧🇷🇯🇵🇪🇸🇬🇧🇨🇭
Phylogenomics and Chemometrics. Prog Rock and Post-Punk. C and Python.
@leomrtns@mstdn.science
Phylogenomics and Chemometrics. Prog Rock and Post-Punk. C and Python.
@leomrtns@mstdn.science
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)
Now we're learning how (not to) handle a bully in a planetary scale.
"He's always been like this, it's the world that changed"
"If we follow his every demand, he promised to retire in a few years and leave us alone"
"He hasn't bullied **me** so far, everything is fine"
"He's always been like this, it's the world that changed"
"If we follow his every demand, he promised to retire in a few years and leave us alone"
"He hasn't bullied **me** so far, everything is fine"
January 21, 2026 at 5:26 PM
Now we're learning how (not to) handle a bully in a planetary scale.
"He's always been like this, it's the world that changed"
"If we follow his every demand, he promised to retire in a few years and leave us alone"
"He hasn't bullied **me** so far, everything is fine"
"He's always been like this, it's the world that changed"
"If we follow his every demand, he promised to retire in a few years and leave us alone"
"He hasn't bullied **me** so far, everything is fine"
Reposted by Leo Martins (he/him)
Even after Trump is gone, the world will remember that he threatened to forcibly seize the territory of a peaceful democratic ally, and our institutions failed to immediately remove him. That makes US dangerously unreliable, not just one senile gangster.
His not being impeached by the end of the business day as a result of this threat is as much a problem as the threat itself. It’s not just Trump that the world has to worry about, it’s a GOP that supports him and Democrats who suck their thumbs and refuse to even discuss pushing to remove him
January 21, 2026 at 2:46 PM
Even after Trump is gone, the world will remember that he threatened to forcibly seize the territory of a peaceful democratic ally, and our institutions failed to immediately remove him. That makes US dangerously unreliable, not just one senile gangster.
Reposted by Leo Martins (he/him)
Sad to hear that Oxford Nanopore wants to discontinue the P2Solo later this year in favor of the P2i (the very pricey P2Solo that comes with a GPU to do the basecalling in it)
It feels like such a big step in the wrong direction. They are a great sequencing company, not a great GPU upseller...
It feels like such a big step in the wrong direction. They are a great sequencing company, not a great GPU upseller...
nanoporetech-customers - Sign In
community.nanoporetech.com
January 20, 2026 at 8:50 PM
Sad to hear that Oxford Nanopore wants to discontinue the P2Solo later this year in favor of the P2i (the very pricey P2Solo that comes with a GPU to do the basecalling in it)
It feels like such a big step in the wrong direction. They are a great sequencing company, not a great GPU upseller...
It feels like such a big step in the wrong direction. They are a great sequencing company, not a great GPU upseller...
Reposted by Leo Martins (he/him)
Americans are realizing that unfettered federal power to detain and arrest is a very dangerous thing. I learned that lesson as a child when they put us into internment camps just for looking like the enemy. Don’t go further down this road.
January 20, 2026 at 10:30 PM
Americans are realizing that unfettered federal power to detain and arrest is a very dangerous thing. I learned that lesson as a child when they put us into internment camps just for looking like the enemy. Don’t go further down this road.
Reposted by Leo Martins (he/him)
For those of us interested in software development, data structure design etc in science, this is a must-read. A taste of what is happening in communities letting AI agents go wild writing code, creating PRs, writing documentation : spoiler - humans get addicted, lose perspective, slop everywhere.
Weekend thoughts on Gas Town, Beads, slop AI browsers, and AI-generated PRs flooding overwhelmed maintainers. I don't think we're ready for our new powers we're wielding. lucumr.pocoo.org/2026/1/18/ag...
Agent Psychosis: Are We Going Insane?
What’s going on with the AI builder community right now?
lucumr.pocoo.org
January 19, 2026 at 7:40 AM
For those of us interested in software development, data structure design etc in science, this is a must-read. A taste of what is happening in communities letting AI agents go wild writing code, creating PRs, writing documentation : spoiler - humans get addicted, lose perspective, slop everywhere.
Reposted by Leo Martins (he/him)
January 19, 2026 at 12:02 PM
Reposted by Leo Martins (he/him)
Black folks and immigrants have long lived in a "perogative state" when it comes to law enforcement, and maybe pundits at the largest national outlets should recognize that their past support for punitive policing and immigration enforcement laid the groundwork for the current moment.
January 18, 2026 at 1:10 PM
Black folks and immigrants have long lived in a "perogative state" when it comes to law enforcement, and maybe pundits at the largest national outlets should recognize that their past support for punitive policing and immigration enforcement laid the groundwork for the current moment.
Reposted by Leo Martins (he/him)
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
In remembrance of Peer Bork | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
www.embl.org
January 16, 2026 at 6:33 PM
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
Reposted by Leo Martins (he/him)
So, throw the trainees under the bus and keep the PIs unscathed?!? What if the PI created a toxic environment leading to this behaviour? What if the institute creates a toxic environment glorifying CNS papers??? Will you mention these at the retraction note?
Credit in research goes hand in hand with responsibility. In this week’s editorial we argue that when things go wrong & a retraction is needed, if it is clear who among the authors is responsible they should be named in the retraction note. COPE agrees
🧪 #AcademicSky
www.nature.com/articles/d41...
🧪 #AcademicSky
www.nature.com/articles/d41...
January 15, 2026 at 7:25 AM
So, throw the trainees under the bus and keep the PIs unscathed?!? What if the PI created a toxic environment leading to this behaviour? What if the institute creates a toxic environment glorifying CNS papers??? Will you mention these at the retraction note?
Reposted by Leo Martins (he/him)
In the last six months, the administration has dropped three different, overlapping immigration bans based on national origin, each time more extreme and arbitrary than the last. As you can see these bans impact countries in every region of the world.
cato.org/blog/new-ban...
cato.org/blog/new-ban...
January 14, 2026 at 10:20 PM
In the last six months, the administration has dropped three different, overlapping immigration bans based on national origin, each time more extreme and arbitrary than the last. As you can see these bans impact countries in every region of the world.
cato.org/blog/new-ban...
cato.org/blog/new-ban...
Research institutions tout the value of scholarship that crosses disciplines – but academia pushes interdisciplinary researchers out theconversation.com/research-ins...
mstdn.science/@leomrtns/11...
mstdn.science/@leomrtns/11...
Research institutions tout the value of scholarship that crosses disciplines – but academia pushes interdisciplinary researchers out
Researchers who focus on one specialty are more likely to rise through the academic ranks, even though wicked societal problems require crosscutting work to solve.
theconversation.com
January 15, 2026 at 9:04 AM
Research institutions tout the value of scholarship that crosses disciplines – but academia pushes interdisciplinary researchers out theconversation.com/research-ins...
mstdn.science/@leomrtns/11...
mstdn.science/@leomrtns/11...
Reposted by Leo Martins (he/him)
Timeline cleanse
How adorable is this kid
How adorable is this kid
January 14, 2026 at 7:49 PM
Timeline cleanse
How adorable is this kid
How adorable is this kid
Reposted by Leo Martins (he/him)
🧬🖥️ I’m building an open-source framework for easily compiling #bioinformatics pipeline results into pdf/html/xlsx reports. It will have built-in parsers for popular CLI tools
Now looking for a few bioinformaticians for a brief usability feedback interview 👩💻
DM me or respond here if interested 👋
Now looking for a few bioinformaticians for a brief usability feedback interview 👩💻
DM me or respond here if interested 👋
January 14, 2026 at 1:22 PM
🧬🖥️ I’m building an open-source framework for easily compiling #bioinformatics pipeline results into pdf/html/xlsx reports. It will have built-in parsers for popular CLI tools
Now looking for a few bioinformaticians for a brief usability feedback interview 👩💻
DM me or respond here if interested 👋
Now looking for a few bioinformaticians for a brief usability feedback interview 👩💻
DM me or respond here if interested 👋
Reposted by Leo Martins (he/him)
FYI the NIH is proposing revisions to the NIH Genome Data Sharing Policy: grants.nih.gov/grants/guide...
This needs careful consideration.
Responses are requested by mid-March and it goes without saying that many submissions from the global genomics community are strongly encouraged.
This needs careful consideration.
Responses are requested by mid-March and it goes without saying that many submissions from the global genomics community are strongly encouraged.
NOT-OD-26-023: Request for Information on Draft NIH Controlled-Access Data Policy and Proposed Revisions to NIH Genomic Data Sharing Policy
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Request for Information on Draft NIH Controlled-Access Data Policy and Proposed Revisions to NIH Genomic Data Sharing P...
grants.nih.gov
January 12, 2026 at 1:29 PM
FYI the NIH is proposing revisions to the NIH Genome Data Sharing Policy: grants.nih.gov/grants/guide...
This needs careful consideration.
Responses are requested by mid-March and it goes without saying that many submissions from the global genomics community are strongly encouraged.
This needs careful consideration.
Responses are requested by mid-March and it goes without saying that many submissions from the global genomics community are strongly encouraged.
Reposted by Leo Martins (he/him)
🧪 Here's a science mystery to start the year.
Why are species names for fish and plants appearing in the scientific literature in papers about firefighter injuries, hearing loss and heart attack?
Is it AI? Translation tools? Something else?
nobreakthroughs.substack.com/p/is-this-fi...
Why are species names for fish and plants appearing in the scientific literature in papers about firefighter injuries, hearing loss and heart attack?
Is it AI? Translation tools? Something else?
nobreakthroughs.substack.com/p/is-this-fi...
January 11, 2026 at 11:34 PM
🧪 Here's a science mystery to start the year.
Why are species names for fish and plants appearing in the scientific literature in papers about firefighter injuries, hearing loss and heart attack?
Is it AI? Translation tools? Something else?
nobreakthroughs.substack.com/p/is-this-fi...
Why are species names for fish and plants appearing in the scientific literature in papers about firefighter injuries, hearing loss and heart attack?
Is it AI? Translation tools? Something else?
nobreakthroughs.substack.com/p/is-this-fi...
one more to the list for acronym-challenged like myself.
SMC={sequentially Markovian coalescent,Sequential Monte Carlo}. LDA={Latent Dirichlet Allocation, Linear Discriminant Analysis}; ML={Machine Learning, Maximum Likelihood}; GP={General Practitioner, Gaussian Process}
SMC={sequentially Markovian coalescent,Sequential Monte Carlo}. LDA={Latent Dirichlet Allocation, Linear Discriminant Analysis}; ML={Machine Learning, Maximum Likelihood}; GP={General Practitioner, Gaussian Process}
In a new GBE Review, @david-peede.bsky.social et al. overview the SMC model and extensions, discuss examples of discoveries made with the help of SMC-based inference, and comment on the assumptions, benefits, and drawbacks of various methods.
🔗 doi.org/10.1093/gbe/...
#genome #evolution #compbio
🔗 doi.org/10.1093/gbe/...
#genome #evolution #compbio
Not Just Ne Ne-More: New Applications for SMC from Ecology to Phylogenies
Abstract. Genomes contain the mutational footprint of an organism’s evolutionary history, shaped by diverse forces including ecological factors, selective
doi.org
January 8, 2026 at 3:57 PM
one more to the list for acronym-challenged like myself.
SMC={sequentially Markovian coalescent,Sequential Monte Carlo}. LDA={Latent Dirichlet Allocation, Linear Discriminant Analysis}; ML={Machine Learning, Maximum Likelihood}; GP={General Practitioner, Gaussian Process}
SMC={sequentially Markovian coalescent,Sequential Monte Carlo}. LDA={Latent Dirichlet Allocation, Linear Discriminant Analysis}; ML={Machine Learning, Maximum Likelihood}; GP={General Practitioner, Gaussian Process}
Reposted by Leo Martins (he/him)
In his defense, I understand why he and his lackeys want to stand behind ICE. We've already seen what happens if you stand in front of them.
January 8, 2026 at 6:09 AM
In his defense, I understand why he and his lackeys want to stand behind ICE. We've already seen what happens if you stand in front of them.
Reposted by Leo Martins (he/him)
“[P]utting data into GISAID is like dropping it in a mail slot in an unmarked building,” says @colincarlson.bsky.social. “It’s wonderful that there’s so much cool stuff in that building. It would be great if we knew who owned it, or who paid for it, or what they plan to do with it.”
#IDsky 🧪
#IDsky 🧪
Fresh conflicts erupt around giant database for flu and COVID-19 sequences
Critics say “autocratic” behavior by GISAID could hamper response to a future pandemic
www.science.org
January 7, 2026 at 9:51 AM
“[P]utting data into GISAID is like dropping it in a mail slot in an unmarked building,” says @colincarlson.bsky.social. “It’s wonderful that there’s so much cool stuff in that building. It would be great if we knew who owned it, or who paid for it, or what they plan to do with it.”
#IDsky 🧪
#IDsky 🧪
In industry partnerships with academia or as staff of not-exactly-academic institutes, the decision to open the code can sometimes be discussed only at the end of project with IP teams (even if we, individually, are pro-open). JOSS is aiming at AI but hitting hard at these collabs.
Rather applaud JOSS's revised approach to deal with AI-based submissions. blog.joss.theoj.org/2026/01/prep... , particularly with 'starting open' and at least 'six months developer history'. More of scholarly pub could benefit from such policies methinks.
Preparing JOSS for a generative AI future: From code to human creativity and design | Journal of Open Source Software Blog
Blog for the Journal of Open Source Software • <a href='https://joss.theoj.org'>https://joss.theoj.org</a>
blog.joss.theoj.org
January 6, 2026 at 10:07 AM
In industry partnerships with academia or as staff of not-exactly-academic institutes, the decision to open the code can sometimes be discussed only at the end of project with IP teams (even if we, individually, are pro-open). JOSS is aiming at AI but hitting hard at these collabs.
Reposted by Leo Martins (he/him)
I have a postdoc position in metagenomic exploration available in my group. Candidates with documented experience in phylo & metagenomics and preferably with petabase-scale data mining and GLM workflows are encouraged to apply. Come join us! 🧬🦠💻
Please repost
Apply here: www.wur.nl/en/vacancy/p...
Please repost
Apply here: www.wur.nl/en/vacancy/p...
January 5, 2026 at 10:45 PM
I have a postdoc position in metagenomic exploration available in my group. Candidates with documented experience in phylo & metagenomics and preferably with petabase-scale data mining and GLM workflows are encouraged to apply. Come join us! 🧬🦠💻
Please repost
Apply here: www.wur.nl/en/vacancy/p...
Please repost
Apply here: www.wur.nl/en/vacancy/p...
Reposted by Leo Martins (he/him)
Registrations are open for ACC2026, a free, 2-day online conference on the latest advances in antimicrobial research.
Organised by GARDP & BSAC, with collab partners ADVANCE-ID & Mahidol University.
📆 4–5 Feb 2026
🔗 https://bit.pulse.ly/qmgpewgvig
@bsacandjac.bsky.social I @advance-id.bsky.social
Organised by GARDP & BSAC, with collab partners ADVANCE-ID & Mahidol University.
📆 4–5 Feb 2026
🔗 https://bit.pulse.ly/qmgpewgvig
@bsacandjac.bsky.social I @advance-id.bsky.social
January 5, 2026 at 6:59 AM
Registrations are open for ACC2026, a free, 2-day online conference on the latest advances in antimicrobial research.
Organised by GARDP & BSAC, with collab partners ADVANCE-ID & Mahidol University.
📆 4–5 Feb 2026
🔗 https://bit.pulse.ly/qmgpewgvig
@bsacandjac.bsky.social I @advance-id.bsky.social
Organised by GARDP & BSAC, with collab partners ADVANCE-ID & Mahidol University.
📆 4–5 Feb 2026
🔗 https://bit.pulse.ly/qmgpewgvig
@bsacandjac.bsky.social I @advance-id.bsky.social
Reposted by Leo Martins (he/him)
Reposted by Leo Martins (he/him)
Did you have snow overnight/today? #UKSnow
I’m researching public attitudes towards clearing Snow and Ice in the UK. Are you over the age of 18 and live in the UK? If so, you can take part in my research by clicking this link (details inside)
app.onlinesurveys.jisc.ac.uk/s/liverpool/...
I’m researching public attitudes towards clearing Snow and Ice in the UK. Are you over the age of 18 and live in the UK? If so, you can take part in my research by clicking this link (details inside)
app.onlinesurveys.jisc.ac.uk/s/liverpool/...
Public Attitudes to Snow and Ice on Pavements and Roads
Online surveys is a powerful, easy to use tool for creating online surveys. Run by Jisc, online surveys is used by over 300 different organisations in the UK...
app.onlinesurveys.jisc.ac.uk
January 2, 2026 at 8:41 AM
Did you have snow overnight/today? #UKSnow
I’m researching public attitudes towards clearing Snow and Ice in the UK. Are you over the age of 18 and live in the UK? If so, you can take part in my research by clicking this link (details inside)
app.onlinesurveys.jisc.ac.uk/s/liverpool/...
I’m researching public attitudes towards clearing Snow and Ice in the UK. Are you over the age of 18 and live in the UK? If so, you can take part in my research by clicking this link (details inside)
app.onlinesurveys.jisc.ac.uk/s/liverpool/...
Reposted by Leo Martins (he/him)
In case you thought they just meant undocumented immigrants…
January 2, 2026 at 2:18 AM
In case you thought they just meant undocumented immigrants…