Leo Martins (he/him)
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
- Reposted by Leo Martins (he/him)Super excited to announce the release of gene and intergenic region annotation from the largest bacterial genome and MAG datasets available, including AllTheBacteria, GTDB, SPIRE, HRGM, mOTUs and MGnify - dereplicated and available from HuggingFace huggingface.co/AllTheBacteria
- I was filling a biodefence survey once, where they asked what is IMO the greatest bio threat to the UK. My reply was "Palantir" I stand by it.
- NEW Nerve investigation reveals extent of Palantir's enmeshment in UK state operations Peter Thiel's surveillance company has deals with government bodies amounting to at least £670m – inc. £15m contract with nuclear weapons agency By @carolecadwalla.bsky.social Charlie Young & Max Colbert 🔗⏬
- Open letter from Ian Chapman to research and innovation community www.ukri.org/news/open-le... TL;DR: UKRI’s overall budget is rising, but not for you. If I understood correctly the rising energy costs (AI?) and "type of facilities and services" are to blame.
- Completely unrelated, obvs, to this article claiming that more formal grievances being submitted by students and staff are evidence that the poor senior professors are being targeted, since the grievances are ultimately dismissed. www.timeshighereducation.com/depth/why-ar...
- Reposted by Leo Martins (he/him)I had intended to post something about this new Google DeepMind paper that appeared yesterday in Nature, but the press coverage has added to what there is to say. So this is a long 🧵 www.nature.com/articles/s41...
- bsky.app/profile/simo... in completely unrelated news
- MRC instructs grant review boards to slash funding rates. Boards asked to recommend just three applications for funding, as BBSRC also suspends calls. www.researchprofessionalnews.com/rr-news-uk-r...
- Reposted by Leo Martins (he/him)MRC instructs grant review boards to slash funding rates. Boards asked to recommend just three applications for funding, as BBSRC also suspends calls. www.researchprofessionalnews.com/rr-news-uk-r...
- Reposted by Leo Martins (he/him)4 year's ago today, the Highway Code changed. Did you even hear about it? The changes aimed to improve safety, but too many people still don’t know the rules. We’re urging the government to invest in an awareness campaign that actually reaches people. cyclinguk.org/hwc-4th-anniversary
- A Vida não tá fácil nem pro Dick Tracy
- Reposted by Leo Martins (he/him)Can ever-increasing sequence databases improve phylogenetic reconstruction of a gene family? Our new preprint introduces AmpliPhy, a pipeline that automates homolog enrichment to improve gene tree inference, built on a robust phylogenomic benchmark scheme. 🧵1/n 📃 doi.org/10.64898/2026.01.26.701724
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- Reposted by Leo Martins (he/him)STOP PRETENDING JESUS WAS CRUCIFIED BECAUSE HE PREACHED GOOD VIBES AND PERSONAL GROWTH
- noooooooooooooooooo! (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...
- 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"
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- 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...
- 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.
- 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...
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- 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.
- 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...
- 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...
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- Research institutions tout the value of scholarship that crosses disciplines – but academia pushes interdisciplinary researchers out theconversation.com/research-ins... mstdn.science/@leomrtns/11...
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- 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 👋
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- 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...
- 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}
- 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
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- 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.
- 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...
- Come join us! Soon I will be advertising a postdoc vacancy in my group as part of my @erc.europa.eu AdG project 'DARK ROOTS'. Focus of the project will be on phylo- and metagenomic mining of novel prokaryotic lineages. I will soon post a link here - stay tuned, and please repost! #asgardarchaea
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- Reposted by Leo Martins (he/him)Jan 1. Jan 3.
- 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/...
- Reposted by Leo Martins (he/him)In case you thought they just meant undocumented immigrants…
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- Reposted by Leo Martins (he/him)The other aspect of this story is, academics and NHS staff could and would have done this better and essentially for free if they were given the same data access as Faculty, but they are not allowed it. Government policy is deliberately to frustrate pro bono / non-profit health data research.
- Reposted by Leo Martins (he/him)Every week, Nature publishes yet another breathless puff piece about some AI startup, based only unpublished claims from the company and interviewing only those who work there. How can the leading scientific journal publish piece after piece that would make Kevin Roose blush? I think it's that...
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- Reposted by Leo Martins (he/him)Season's greetings from all of us at New Phytologist and The New Phytologist Foundation!
- Reposted by Leo Martins (he/him)We’ve today formally written to multiple public bodies about BBC reporting on transgender people. Here’s who we’ve contacted and why. 1/6
- "Exceptional young performers reached their peak quickly but narrowly mastered only one interest (e.g., one sport). By contrast, exceptional adults reached peak performance gradually with broader, multidisciplinary practice. However, elite programs are designed to nurture younger talent."
- "Most top achievers (Nobel laureates and world-class musicians, athletes, chess players) demonstrated lower performance than many peers during their early years. Across the highest adult performance, peak performance is negatively correlated with early performance" www.science.org/doi/10.1126/...
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- It's Open Access! if you want a break from binge-watching series during this festive season...
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- Reposted by Leo Martins (he/him)Hiring: Group Leader in Microbiome Studies! ✨ The successful candidate would establish & lead a new research group in human microbiome science, advancing understanding of microbe-microbe and microbe-host interactions in health & disease. Apply by 22 Dec. www.ndorms.ox.ac.uk/jobs/kennedy...
- Reposted by Leo Martins (he/him)I am still actively looking for postdoc positions — please lmk if you (or your friends and colleagues) need a hardworking postdoc with field, lab, and bioinformatic skills! I am broadly interested in evolution in the ocean, conservation and population genetics, and rapid evolution.
- Reposted by Leo Martins (he/him)New Home Office impact assessment finds that cutting skilled and social care visas will cost the UK up to £10 billion with a central estimate of -£5.4 billion. It would be good if this got even a fraction of the coverage devoted to the endless debate about boats, flags and Turkish barber shops
- Reposted by Leo Martins (he/him)Double success as #LivUni researchers receive highly competitive #ERC Consolidator Grants! These grants support academics pursue ground-breaking ideas and help push new boundaries in science 🔬 👏 Congratulations Prof Brianna Heazelwood and Dr Ceren Kabukcu 👉 news.liverpool.ac.uk/2025/12/09/d...
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- Reposted by Leo Martins (he/him)💾 ABRicate 1.2.0 has been released! This 'oversight' lasted 6 years, but with help from @finlaym.bsky.social we got CI working and updated all the databases. #bioconda #conda #bioinformatics #microbiology #genomics github.com/tseemann/abr...
- Reposted by Leo Martins (he/him)We are deeply saddened to share the passing of Amos Bairoch, pioneer of bioinformatics and co-founder of SIB. His lifelong commitment for high-quality, open data transformed global research. We honour his legacy by continuing to build the future of bioinformatics.
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- Reposted by Leo Martins (he/him)Lots of people sharing this clip because it's funny and cathartic but I also genuinely believe it's important. We have to win the narrative battle between "I live in a corrupt society and that's just how it is" and "I live in a corrupt society and we are going to defeat and humiliate these ghouls."
