George Bouras
@gbouras13.bsky.social
📤 1194
📥 345
📝 67
Bioinformatics @ Adelaide University - phages, microbes and more
pinned post!
Phold's manuscript is now available
@narjournal.bsky.social
thanks to
@susiegriggo.bsky.social
@npbhavya.bsky.social
@vijinim.bsky.social
@linsalrob.bsky.social
@martinsteinegger.bsky.social
@milot.bsky.social
@eunbelivable.bsky.social
& others not on bsky
#phagesky
academic.oup.com/nar/article/...
add a skeleton here at some point
4 months ago
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reposted by
George Bouras
naturepoker
about 6 hours ago
I've been wondering about role of reference assembly contiguity when training/tuning an ONT basecaller model. Stumbled into implementing a crude forward pass in
#Julia
with tuned weights, contig level genome ref vs complete genome ref. Model behaves very differently on same POD5 signal input! 💻🧬
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reposted by
George Bouras
Ryan Cook
11 days ago
During my PhD,
@milja001.bsky.social
and I started counting phage genomes, and tried to make them available in useful formats with useful metadata. We also described the extent of sequenced phage genomes at the time. Five years on, we've had a look at what's changed
www.biorxiv.org/content/10.6...
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https://www.biorxiv.org/content/10.64898/2026.05.06.722914v1
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reposted by
George Bouras
Vijini Mallawaarachchi
12 days ago
🎉 Excited to share that our paper, “agtools: A Software Framework to Manipulate Assembly Graphs”, has been accepted in Bioinformatics Advances. (1/n) 🔗 GitHub:
github.com/Vini2/agtools
📄 Paper:
academic.oup.com/bioinformati...
#bioinformatics
#genomics
#openscience
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agtools: A Software Framework to Manipulate Assembly Graphs
AbstractMotivation. Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap info
https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbag126/8670094
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reposted by
George Bouras
Sam Horsfield
14 days ago
Our new preprint is out! We train a transformer on gene order and gene content of bacterial pathogens, applying it to a range of epidemiological and evolutionary analyses (1/8)
www.biorxiv.org/content/10.6...
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reposted by
George Bouras
Rob Edwards
14 days ago
Want to find
#prophage
in your
#bacteria
genomes? We built PhiSpy a long time ago, and now we've created a new web page for it:
linsalrob.github.io/PhiSpyWeb/
Best of all, the data never leaves your computer!
#phage
#phagesky
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PhiSpyWeb – Browser-based Prophage Prediction
Browser-based prophage prediction using PhiSpy, Pyodide, and WebAssembly
https://linsalrob.github.io/PhiSpyWeb/
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reposted by
George Bouras
Marie-Eve VAL
15 days ago
This one means a lot. Our paper, “Large extrachromosomal replicons are widespread across bacterial lineages and show coordinated replication termination and spatial coupling with the chromosome,” is out!
doi.org/10.1038/s414...
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Large extrachromosomal replicons are widespread across bacterial lineages and show coordinated replication termination and spatial coupling with the chromosome - Nature Communications
Bacterial genomes often include extrachromosomal replicons, ranging from small plasmids to chromosome-scale replicons. Here, Czarnecki et al. analyse more than 40,000 complete bacterial genomes and sh...
https://doi.org/10.1038/s41467-026-72671-7
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reposted by
George Bouras
Rafal Mostowy
20 days ago
🎉 New in
@plosbiology.org
: Temperate phages of Klebsiella pneumoniae show capsule-driven host tropism — but how? The working assumption was depolymerases: enzymes that chew through the bacterial sugar capsule. Turns out that's not the whole story. 🧵
journals.plos.org/plosbiology/...
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reposted by
George Bouras
Bohdana Hurieva🇺🇦
26 days ago
🎉Excited to share our new preprint! TIR domains from diverse animals, including human TLR4, are catalytically active and produce cyclic ADP-ribose (cADPR). This enzymatic activity is widespread in animals and conserved across the tree of life.
www.biorxiv.org/content/10.6...
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https://www.biorxiv.org/content/10.64898/2026.04.20.719644v1
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reposted by
George Bouras
Kotaro Chihara
29 days ago
Happy to share our new work on how phages escape bacterial immunity. We show that a phage homing endonuclease drives segmental amplification of anti-defense genes, pointing to a versatile and rapid mode of adaptation.
www.nature.com/articles/s41...
#PhageSky
#MicroSky
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Phage homing endonuclease amplifies anti-defense genes to evade bacterial immunity - Nature Communications
Phages employ diverse counter-defense strategies to overcome bacterial immune systems. Here, the authors reveal that the phage homing nuclease SegB facilitates immune evasion by promoting the segmenta...
https://www.nature.com/articles/s41467-026-71036-4
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reposted by
George Bouras
Sebastian Deorowicz
about 1 month ago
10 years after the first FAMSA paper, its successor is now published in Nat Biotech! We believe that FAMSA2 can enable analyses of large protein collections that were previously unattainable. Thank you, Andrzej and Cedric, for great collaboration
www.nature.com/articles/s41...
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Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2 - Nature Biotechnology
FAMSA2 accurately aligns millions of protein sequences at high speed.
https://www.nature.com/articles/s41587-026-03095-3
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George Bouras
Rob Edwards
about 1 month ago
Have you developed a new
#bioinformatics
tool to understand
#phage
or
#virus
? Make sure you add it to
#awesome-virome
github.com/shandley/awe...
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Whenever I presented Phold, I was frequently asked "can you do the same beyond phages?" We (
@oschwengers.bsky.social
@linsalrob.bsky.social
@binomicalabs.org
et al) finally did it with Baktfold
github.com/gbouras13/ba...
www.biorxiv.org/content/10.6...
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GitHub - gbouras13/baktfold: Rapid & standardized genome annotation using protein structural information
Rapid & standardized genome annotation using protein structural information - gbouras13/baktfold
https://github.com/gbouras13/baktfold
about 1 month ago
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reposted by
George Bouras
Rob Edwards
about 1 month ago
Want to annotate a bacterial genome with structures?
@oschwengers.bsky.social
bakta and
@gbouras13.bsky.social
phold got together, and the result is Baktfold: protein annotation across the microbial tree of life using structures
www.biorxiv.org/content/10.6...
#phagesky
#microsky
#microbiomesky
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https://www.biorxiv.org/content/10.64898/2026.03.31.715528v1
0
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reposted by
George Bouras
Vivek Mutalik
about 2 months ago
📣Huge preprint 🔔 Today we share something our group has been working toward for a long time, led by
@lucasmoriniere.bsky.social
We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.
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reposted by
George Bouras
Aude Bernheim
about 2 months ago
How diverse is bacterial immunity ? We report in
@science.org
how language models allowed us to predict 2.4M antiphage proteins spanning >23K novel potential systems. 👏
@emordret.bsky.social
,
@alexhv.bsky.social
& al
doi.org/10.1126/scie...
Explore them here
defensefinder.mdmlab.fr/wiki/refseq_...
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https://www.science.org/doi/10.1126/science.adv8275
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reposted by
George Bouras
about 2 months ago
45 novel protein folds in the updated AFESM (AFDB + ESMatlas) manuscript: • 12 high-confidence folds in AFESM • 33 by ColabFold-repredicting 2.3M low-quality domains We show AFDB captures most domains already and ESMfold struggles with novelty 🌏
afesm.foldseek.com
📄
biorxiv.org/content/10.1...
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AFESM Clusters
Foldseek clustered 820M AlphaFold DB + ESMatlas structures
https://afesm.foldseek.com
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reposted by
George Bouras
Ryan Hesse
about 2 months ago
New review paper hot off the presses in
@natureportfolio.nature.com
, check it out if you wanna reframe your understanding of viral ecology!
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reposted by
George Bouras
naturepoker
about 2 months ago
Happy to have made a small contribution for
@gbouras13.bsky.social
's study. Hope this is just one of many examples in independent researcher collaboration with academic scientists!
#archaeasky
folks, this pipeline rules for global baseline annotation for archaea
doi.org/10.64898/202...
💻🧬🧫🦠
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reposted by
George Bouras
Zamin Iqbal
about 2 months ago
New paper from Hugh Cottingham,
@katholt.bsky.social
,
@yekwah.bsky.social
@nenadmacesic.bsky.social
and co. Great to see the speed/accuracy tradeoff info here, I don't think I've seen it laid out like this before.
www.microbiologyresearch.org/content/jour...
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reposted by
George Bouras
Pedro Beltrao
about 2 months ago
We have updated the yeast AlphaFold3 co-folding map. The 15GB docker also has an updated streamlit app that is more responsive and easier to search through if you want to just browse the results. There will be many false positives ! We added known interactions for those wanting to filter.
add a skeleton here at some point
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reposted by
George Bouras
Sam Horsfield
about 2 months ago
ggCaller v1.5.0 is out! We've removed the integrated clustering to enable users to benefit from new Panaroo features. Now, ggCaller generates GFFs that can be used with any clustering method. But for fans of an integrated ggCaller pangenome workflow read on...
github.com/bacpop/ggCal...
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GitHub - bacpop/ggCaller: Bifrost graph gene caller.
Bifrost graph gene caller. Contribute to bacpop/ggCaller development by creating an account on GitHub.
https://github.com/bacpop/ggCaller
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reposted by
George Bouras
naturepoker
about 2 months ago
#Archaeasky
folks - I'm curious. How do you feel about the dorado polish bacteria mode for your archaeal ONT long read assembled genomes? I know it holds up well with bacteria, but archaea's always been a bit funny. 💻🧬
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reposted by
George Bouras
Hasindu Gamaarachchi
about 2 months ago
The pre-print for Slorado and openfish is out.
biorxiv.org/content/10.6...
You can do
@nanoporetech.com
basecalling with not just NVIDIA GPU, but also using a range of AMD GPU. Would be useful since popular GPUs are now 💸💸💸💸(& hard to buy), Work by
@bonson-wong.bsky.social
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reposted by
George Bouras
Jim Shaw
about 2 months ago
Myloasm, our long-read metagenome assembler, is now published! w/
@mgmarin.bsky.social
and
@lh3lh3.bsky.social
Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback.
rdcu.be/famFj
add a skeleton here at some point
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reposted by
George Bouras
Martin Steinegger 🇺🇦
2 months ago
AlphaFold database has entered the era of complexes. Together with NVIDIA, DeepMind and EBI, we use ColabFold, OpenFold and MMseqs2-GPU to predict ~31 million complexes (homo & hetro-dimers) resulting in 1.8 million high-quality predictions 📄
research.nvidia.com/labs/dbr/ass...
🌐
alphafold.ebi.ac.uk
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George Bouras
EMBL-EBI
2 months ago
You asked, we listened. Millions of AI-predicted protein complex structures are now available in the
#AlphaFold
Database. This spans homodimers from 20 of the most studied species, including humans, as well as the World Health Organization’s priority pathogens list.
www.ebi.ac.uk/about/news/t...
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reposted by
George Bouras
Dr Andrew Lonsdale
2 months ago
Some background to this, and an example I think of Phil's attitudes towards fostering students and encouraging others. I never got a chance to meet Phil in person, but will share his act of generosity that helped myself and
@hdashnow.bsky.social
and I think had in indelible mark on our careers. 1/8
add a skeleton here at some point
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12
8
reposted by
George Bouras
Anton Bushuiev
3 months ago
ProteinTTT is now easy to run on Hugging Face Spaces and Google Colab. We’ll also be presenting the paper at ICLR 2026 🇧🇷 🤗 Hugging Face Space:
huggingface.co/spaces/pimen...
⚙️ Google Colab:
colab.research.google.com/drive/1l_h7c...
🧵👇
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reposted by
George Bouras
Michael Hall
3 months ago
Until joining
@loolibear.bsky.social
's lab in July, I embarrassingly hadn't had much experience with plasmids. So when I started, Leah said "here you go, have a look at this dataset". What a fun ride this has been. Preprint out today and thread below
www.medrxiv.org/content/10.6...
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Novel transposon Tn8026 acts as a global driver of transmissible linezolid resistance in Enterococcus via a linear plasmid
Linezolid is a critical last-resort antimicrobial for multidrug-resistant Enterococcus faecium , particularly against vancomycin-resistant lineages where therapeutic options are severely limited. Whil...
https://www.medrxiv.org/content/10.64898/2026.03.04.26347163v1
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reposted by
George Bouras
Torsten Seemann
3 months ago
Joining the All-The-Bacteria project provides an annualised return on investment of 8.9% bacterial genomes.
add a skeleton here at some point
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reposted by
George Bouras
Zamin Iqbal
3 months ago
Courtesy of
@martibartfast.bsky.social
, we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025.
allthebacteria.readthedocs.io/en/latest/ov...
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Overview — AllTheBacteria documentation
https://allthebacteria.readthedocs.io/en/latest/overview.html
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reposted by
George Bouras
Zamin Iqbal
3 months ago
@wytamma.bsky.social
's WASM tools have transformed my experience of teaching Python to first year undergraduate biologists this year. Since last year, I've been teaching ~400 undergrads how to code (functions, lists, dictionaries, loops) over (one hour intro lecture +) two 2-hour practicals. 1/n
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reposted by
George Bouras
Rob Edwards
3 months ago
The
@isvm-society.bsky.social
is organising monthly
#virus
of
#microbes
(including
#phage
). Nominate a speaker and register for the upcoming events at
isvm.org/ivom/
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iVoMs – ISVM
https://isvm.org/ivom/
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Super happy that the AllTheBacteria hypothetical proteins are now in AFDB - hopefully we can start to understand the function of some of them at least 😁
add a skeleton here at some point
3 months ago
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reposted by
George Bouras
Zamin Iqbal
3 months ago
Delighted to see over 17 million new protein structure predictions from novel proteins in AllTheBacteria are now integrated into the AlphaFold Database at
@ebi.embl.org
! Huge work from
@gbouras13.bsky.social
@oschwengers.bsky.social
and friends to generate these.
www.ebi.ac.uk/about/news/u...
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AlphaFold Database welcomes community datasets
Latest AlphaFold Database update adds high-value datasets for microbial and viral proteins, generated by specialist communities
https://www.ebi.ac.uk/about/news/updates-from-data-resources/alphafold-database-community-datasets/
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reposted by
George Bouras
Spyros Lytras
3 months ago
Our paper on inferring context dependent entropy using protein language models is officially out in NAR Genomics & Bioinformatics! 🧬🤖 with Adam Strange, Jumpei Ito, and
@systemsvirology.bsky.social
academic.oup.com/nargab/artic...
details below...
#NARGAB
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Inferring context-specific site variation with evotuned protein language models
Abstract. Multiple sequence alignments (MSAs) have been traditionally used for making inferences about site-specific diversity in proteins. Recent advancem
https://academic.oup.com/nargab/article/8/1/lqag018/8468463
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reposted by
George Bouras
John Lees
3 months ago
How do bacterial pangenomes evolve, what controls their dynamics, why do they exist? Fitting a mechanistic model to 450 species from
allthebacteria.org
suggesting fast vs slow gene exchange (i.e. amount of MGEs) is a major differentiating factor, correlated with phylogeny rather than lifestyle
add a skeleton here at some point
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reposted by
George Bouras
Zamin Iqbal
3 months ago
A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by
@martibartfast.bsky.social
a) correcting errors in 4.5 million genomes & their phylogeny b) improving representation of the Global South in public data
www.nature.com/articles/s41...
(thread 1/n)
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Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods
This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.
https://www.nature.com/articles/s41592-025-02947-1
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reposted by
George Bouras
Patrick Bryant
3 months ago
Introducing The Structural History of Eukarya (SHE): The first proteome-scale phylogeny constructed entirely from 3D structure. We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)
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reposted by
George Bouras
Sam Horsfield
3 months ago
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
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Hugging Face – The AI community building the future.
We’re on a journey to advance and democratize artificial intelligence through open source and open science.
https://huggingface.co
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reposted by
George Bouras
Ryan Wick
3 months ago
New blog post: ONT read QC strategies for assembly
rrwick.github.io/2026/02/05/r...
Mini-study comparing a few QC/subsampling approaches, plus practical notes from my experience.
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ONT read QC strategies for assembly
a blog for miscellaneous bioinformatics stuff
https://rrwick.github.io/2026/02/05/read_qc_testing.html
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reposted by
George Bouras
Oliver Schwengers
4 months ago
🦠🧬🖥️ Bakta v1.12.0 is out with tons of tiny improvements and bug fixes, too many to list all: - partial genes on linear seqs - improved errror handlings & runtimes - support Python 3.12 & 3.13 - ... A huge shout out and thank you to all bug reporters and contributors!
github.com/oschwengers/...
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Release v1.12 - Just do it, but don't crash · oschwengers/bakta
This is the twelfth minor release (v1.12) providing more than 10 minor improvements and many bug fixes improving runtime stability, IO compatibility, and last but not least user experience. Compati...
https://github.com/oschwengers/bakta/releases/tag/v1.12.0
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reposted by
George Bouras
Asaf Levy
4 months ago
A new paper from the lab on virus-like particles called eCISs
www.nature.com/articles/s41...
How bacteria evolved thousands of precision nanoinjectors? Some bacteria don’t secrete toxins — they inject them using phage-derived machines called extracellular contractile injection systems (eCISs).
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A comprehensive catalogue of receptor-binding domains in extracellular contractile injection systems - Nature Communications
Extracellular contractile injection systems (eCISs) are bacteriophage tail-derived toxin delivery complexes that are present in many prokaryotes. Here, the authors present an analysis of eCIS tail fib...
https://www.nature.com/articles/s41467-026-68710-y
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reposted by
George Bouras
Martin Steinegger 🇺🇦
4 months ago
FoldMason is out now in
@science.org
. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and
@milot.bsky.social
. 📄
www.science.org/doi/10.1126/...
🌐
search.foldseek.com/foldmason
💾
github.com/steineggerla...
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Multiple protein structure alignment at scale with FoldMason
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
https://www.science.org/eprint/4QQQFGCSQEGFJVGUESWN/full?activationRedirect=/doi/full/10.1126/science.ads6733
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150
reposted by
George Bouras
Hasindu Gamaarachchi
4 months ago
slow5tools v1.4.0 released
github.com/hasindu2008/...
Many bit profiles for ex-zd lossy compression added by @hiruna72, who reduced 275TB of historical @nanopore rawdata at @GenTechGp to 172TB. guide to lossy archive:
hasindu2008.github.io/slow5tools/a...
paper:
doi.org/10.1101/gr.2...
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Release slow5tools-v1.4.0 · hasindu2008/slow5tools
What's Changed slow5tools skim supports the new auxiliary field open_pore_level introduced in latest ONT pod5 slow5tools degrade has new profiles added (by @sashajenner and @hiruna72) and are docu...
https://github.com/hasindu2008/slow5tools/releases/tag/v1.4.0
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8
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reposted by
George Bouras
Jim Shaw
4 months ago
Announcing a new tool for "denoising" long-read amplicon sequences: savont. Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay. 1/4
github.com/bluenote-157...
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GitHub - bluenote-1577/savont: Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads
Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads - bluenote-1577/savont
https://github.com/bluenote-1577/savont
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reposted by
George Bouras
Dongwook Kim
4 months ago
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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AmpliPhy improves gene trees by adding homologs without affecting alignments
In phylogenomics, gene tree reconstruction depends on multiple sequence alignment (MSA) and tree inference, and ongoing work continues to improve inference quality. Denser taxon sampling has been associated with improved gene tree inference, suggesting that adding homologs could be a practical route to higher accuracy as sequence databases continue to expand. However, adding sequences can influence multiple steps of typical inference pipelines, and little is known on its specific effect on the multiple sequence alignment, tree reconstruction, and rooting steps. We performed a large-scale empirical benchmark to quantify how homolog enrichment affects alignment and phylogenetic inference. Using an enrichment-impoverishment design and a measure of tree accuracy based on taxonomic congruence, we found that enrichment consistently improves tree inference quality, while effects on alignment quality are marginal. We show that this improvement is associated with accurate root placement on enriched trees when sensitive homolog search is accompanied. Notably, much of the benefit can be retained with relatively compact alignments produced by sequence addition. Building on these observations, we provide a tool, AmpliPhy, which efficiently improves phylogenetic reconstruction of protein families through homolog enrichment. The AmpliPhy open-source pipeline software is available at https://github.com/DessimozLab/ampliphy. ### Competing Interest Statement The authors have declared no competing interest. Swiss National Science Foundation, https://ror.org/00yjd3n13, 216623, 10005715
https://doi.org/10.64898/2026.01.26.701724
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reposted by
George Bouras
Rob Edwards
4 months ago
New 2026 iVoM series coming up! Each session includes SCR and 3 ECRs, & plenty of opportunities to interact with the speakers and ask questions. Sign up for links/updates:
docs.google.com/forms/d/1hAB...
First up: Viral Biotechnologies Wed, 28 th January at 17:00 CET / 11:00 EST / 08:00 PST
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Registration form for iVoM4
After submitting this form, you will receive the instructions to join our webinars at the email address you provide.
https://docs.google.com/forms/d/1hABmyJirdMcyrHfWX_1y0vibB_iiQFN6CdeaVqyDlCs/viewform?edit_requested=true#settings
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reposted by
George Bouras
Ryan Wick
4 months ago
New blog post with some thoughts on
@nanoporetech.com
and their recent announcement that the P2 Solo will be discontinued:
rrwick.github.io/2026/01/21/p...
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P2 Solo announcement and the trade-offs of a more stable ONT
a blog for miscellaneous bioinformatics stuff
https://rrwick.github.io/2026/01/21/p2_solo.html
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reposted by
George Bouras
Milot Mirdita
4 months ago
My time in
@martinsteinegger.bsky.social
's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring!
mirdita.org
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Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning
Mirdita Lab builds scalable bioinformatics methods.
https://mirdita.org/
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