Tue Sparholt Jørgensen
@tuesparholt.bsky.social
📤 317
📥 100
📝 44
pinned post!
Bacterial telomeres are common, just not so much in RefSeq 'complete' genomes. But they can be added by the new tool David Faurdal wrote. I am thrilled to see this out as a preprint here:
www.biorxiv.org/content/10.1...
@tilmweber.bsky.social
@thombooth.bsky.social
4 months ago
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Sam Williams
2 days ago
Check out our paper in
@asm.org
Applied and Environmental Microbiology 🍾 OSMAC guided bioprospecting of Atlantic sponges reveals novel bacterial species and the antimicrobial thiazole alkaloid agrochelin II | Applied and Environmental Microbiology
journals.asm.org/doi/10.1128/...
#secmet
#microsky
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OSMAC guided bioprospecting of Atlantic sponges reveals novel bacterial species and evidence for the antimicrobial thiazole alkaloid agrochelin II | Applied and Environmental Microbiology
Bioactive microbial natural products remain the preeminent source of new lead compounds for drug development. Due to the increasingly high levels of strain and compound rediscovery from terrestrial en...
https://journals.asm.org/doi/10.1128/aem.01877-25
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Tue Sparholt Jørgensen
Matt Hutchings
4 days ago
Research into filamentous actinomycetes, the antibiotic producers, is in steep decline. Loads of natural products chemistry research worldwide but not much aimed at understanding their biology and ecology. The latter is key to unlocking their specialised metabolism
link.springer.com/article/10.1...
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Revitalizing actinobacteria research: an urgent response to the antimicrobial resistance crisis - Natural Products and Bioprospecting
Abstract The crisis of antimicrobial resistance (AMR) is escalating while the antibiotic pipeline remains stagnant. Our bibliometric analysis of eight decades of literature reveals a critical imbalanc...
https://link.springer.com/article/10.1007/s13659-025-00587-8
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Albert Vilella, PhD.
7 days ago
Another example of a custom-made 3D-printed 96-well magnet bead purification device, triggered by a "pipette eject" event on the OpenTrons. Essentially, if the OpenTrons is thought as a flexible pipetter, then
@plasmidsaurus.bsky.social
turn pipette events into other MolBio tasks.
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Tue Sparholt Jørgensen
Albert Vilella, PhD.
7 days ago
Another interesting use of 3D printed plastic adapters, in this case to turn the OpenTrons bays into racks of Oxford
@nanoporetech.com
PromethION flowcells.
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Tue Sparholt Jørgensen
Adam Phillippy
18 days ago
Time for a thread on our Christmas preprint “Origin and evolution of acrocentric chromosomes in human and great apes”. I had so much fun with this project and paper. It will be hard to summarize in a thread, but I’ll try
www.biorxiv.org/content/10.6...
[1/21]
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Oliver Schwengers
18 days 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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Jonathan Jacobs
23 days ago
First fully phased reference genome for the Yarrowia liploytica type-strain is out!
academic.oup.com/jimb/advance...
Super fun project in collaboration with James Crill at Syracuse University as well. Important platform organism for industrial microbiology and biomanufacturing as well.
#genomics
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Complete Diploid Genome of the Type Strain Yarrowia lipolytica YB-423 (ATCC 18942™)
Abstract. Here, we present the first complete, fully phased diploid genome of type strain Yarrowia lipolytica YB-423 (=ATCC 18942™), constructed using a co
https://academic.oup.com/jimb/advance-article/doi/10.1093/jimb/kuag002/8417173?login=false
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Adam Phillippy
22 days ago
New tool from
@alexsweeten.bsky.social
to find and classify all your satellites: "AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates" 📄
www.biorxiv.org/content/10.6...
📦
github.com/marbl/anianns
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Daniel Figeys
23 days ago
Exploring
#microbiome
data? MetaTree makes statistically based hierarchical tree comparisons easy and accessible.
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My understanding of MDPI as the biggest polluter of science gets some quantitative basis in this cool study. How about we as researchers stop publishing there and stop reading it leaving the special issues with another issue: absence of honest science.
add a skeleton here at some point
25 days ago
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Keith Robison
25 days ago
ONT Axes P2 Solo, Roiling Community 🧬🖥️
omicsomics.blogspot.com/2026/01/ont-...
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ONT Axes P2 Solo, Roiling Community
Oxford Nanopore has a serious case of user community unrest, triggered by the announcement that the P2 Solo (aka P2s) will be phased out sta...
https://omicsomics.blogspot.com/2026/01/ont-axes-p2-solo-roiling-community.html?m=1
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Tue Sparholt Jørgensen
Ryan Wick
about 1 month 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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Stephen Turner
about 1 month ago
Ultra-high-throughput mapping of genetic design space
www.nature.com/articles/s41...
(read free:
rdcu.be/eY6E2
) 🧬🖥️🧪
github.com/cbashorlab/C...
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Unpacking my stuff in my new
@ssi-dk.bsky.social
office, I came across this post which resonated enough that I printed it out and hung it up on my wall. It's going back up now. I think from
@danpsimpson.bsky.social
?
about 1 month ago
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Rasmus Kirkegaard
about 1 month ago
Been doing a lot of
@nanoporetech.com
sequencing for soil and sediment lately and it appears that no matter how much DNA or how little we still get decent yields. So pretty robust performance. Yield clearly depends on pore count.
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Manuel Ares-Arroyo
about 1 month ago
Bacteria chromosomes contain Genomic Islands that provide virulence, antibiotic resistance, MGE-defence,... They transfer between cells, but the mechanism of most remains elusive. Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
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https://www.biorxiv.org/content/10.64898/2026.01.13.699239v1
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Heng Li
about 1 month ago
I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see
hlilab.github.io/vacancies
. RTs appreciated!
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HLi Lab - Vacancies
Openings
https://hlilab.github.io/vacancies
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How delightful to start the year with a neat overview of the sequencing field from the most capable watcher of the space.
add a skeleton here at some point
about 1 month ago
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Keith Robison
about 2 months ago
Sequencing Instrumrnt Outlook 2026 My observations & predictions on sequencing instrument companies 🧬🖥️
omicsomics.blogspot.com/2026/01/sequ...
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Sequencing Instrument Outlook 2026
A computational biologist's personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery
https://omicsomics.blogspot.com/2026/01/sequencing-instrument-outlook-2026.html?m=1
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Stephen Turner
about 2 months ago
Staying Current in Data Science and Computational Biology: 2026 Edition. Part 3 in a series of posts going back 14 years.
doi.org/10.59350/2na...
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Staying Current in Data Science and Computational Biology: 2026 Edition
Part 3 in a series of posts going back 14 years
https://doi.org/10.59350/2naqr-4m048
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Matt Hutchings
about 2 months ago
New preprint. Work led by
@ainsley-beaton.bsky.social
& Rebecca Devine. They show the highly conserved Streptomyces MtrAB two component system activates ectoine production and triggers sporulation in response to osmotic stress in Streptomyces venezuelae
www.biorxiv.org/content/10.6...
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MtrAB activates ectoine production and triggers sporulation in response to osmotic stress in Streptomyces venezuelae
The MtrAB two-component system is a master regulator of antibiotic biosynthesis in Streptomyces species. MtrA is also required for sporulation under certain growth conditions, which means that on some...
https://www.biorxiv.org/content/10.64898/2025.12.19.695424v1
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Microbiology Society
2 months ago
Born
#OnThisDay
in 1922, Esther Lederberg was the first to isolate the lambda phage in 1951. She characterised the lysogenic phase, whereby the phage are able to integrate into the bacterial genome, staying dormant. This discovery made them a model tool of study, leading to many more breakthroughs.
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Torsten Seemann
2 months ago
💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because
@oschwengers.bsky.social
already has an excellent replacement called Bakta you can migrate to.
#bioinformatics
#microbiology
#genomics
github.com/tseemann/pro...
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Release Heading into the sunset · tseemann/prokka
The future This is probably the last release of Prokka. I won't be making any code changes except bug fixes. I will update the databases occasionally. I strongly recommend you use Bakta by @oschwen...
https://github.com/tseemann/prokka/releases/tag/v1.15.6
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Holly Bik
2 months ago
DNA is the best kind of time machine - really feels like we’re in a golden age of big data studies like this. Can’t wait to read!
add a skeleton here at some point
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Simon Roux
2 months ago
🧬🦠🚨 Another new paper alert, this time led by
@maureenbug.bsky.social
! In collaboration with the Emerson lab and
@titus.idyll.org
lab (
@taylorreiter.bsky.social
), both at UC Davis. Asking the question: what are we missing in short-read metagenome assembly, and why ?
doi.org/10.1093/narg...
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Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations
Abstract. Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but stru
https://doi.org/10.1093/nargab/lqaf163
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Heng Li
3 months ago
579 high-quality human genomes from
@humanpangenome.bsky.social
, Arab Pangenome and individual papers (CHM13, CN1, KSA001, I002C, YAO and KOREF1). Sequences available in the AGC format (3.7GB) and FM-index in the ropebwt3 format (20.3GB). For details, see
github.com/lh3/human-asm
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GitHub - lh3/human-asm: A collection of high-quality human genomes
A collection of high-quality human genomes. Contribute to lh3/human-asm development by creating an account on GitHub.
https://github.com/lh3/human-asm
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Tue Sparholt Jørgensen
sylvain Brisse
3 months ago
Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version
doi.org/10.1101/2024...
I will summarize it for you in this thread 👇
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Life Identification Numbers: A bacterial strain nomenclature approach
Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...
https://doi.org/10.1101/2024.03.11.584534
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C-GEM, the NSF Center for Genetically Encoded Materials
3 months ago
✨ New paper in Science: An archaeal genetic code with all TAG codons as pyrrolysine.
www.science.org/doi/10.1126/...
A collaboration with
@innovativegenomics.bsky.social
Congrats to the Banfield lab,
@roeleah.bsky.social
,
@nxhamlish.bsky.social
, and Alanna!
#NSFfunded
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An archaeal genetic code with all TAG codons as pyrrolysine
Multiple genetic codes developed during the evolution of eukaryotes and bacteria, yet no alternative genetic code is known for archaea. We used proteomics to confirm our prediction that certain archae...
https://www.science.org/doi/10.1126/science.adu2404
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Once again inspiring work from Jillian Banfields group "An archaeal genetic code with all TAG codons as pyrrolysine"
pasteur.hal.science/pasteur-0537...
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An archaeal genetic code with all TAG codons as pyrrolysine
Numerous genetic codes developed during the evolution of Eukaryotes and three are known in Bacteria, yet no alternative genetic code has been established for Archaea. Some bacterial and archaeal proteins include selenocysteine or pyrrolysine, the 21 st and 22 nd amino acids, but no evidence establishes the adoption of a genetic code in which a stop codon universally encodes either amino acid. Here, we used proteomics to confirm the prediction that certain Archaea consistently incorporate pyrrolysine at TAG codons, supporting a new archaeal genetic code which we designate Genetic Code 34. This genetic code has 62 sense codons encoding 21 amino acids, and only two stop codons. In contrast with monophyletic genetic code distributions in bacteria, Code 34 occurs sporadically. This, combined with evidence for lateral gene transfer of the code change machinery and anticipated barriers to code reversal, suggests Code 34 arose independently in multiple lineages. TAG codon distribution patterns in Code 34 genomes imply a wide range in time since code switch. We identified many new enzymes containing Pyl residues, raising questions about potential roles of this amino acid in protein structure and function. We used five new PylRS/tRNA Pyl pairs from Code 34 archaea to introduce new-to-nature pyrrolysine analogs into proteins in E. coli , demonstrating their utility for genetic code expansion.
https://pasteur.hal.science/pasteur-05373021/
3 months ago
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Michael Baym
3 months ago
Hot off the press! Our latest paper led by
@fernpizza.bsky.social
, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
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Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
https://www.science.org/doi/10.1126/science.adx0665
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Reyes-Lamothe lab
3 months ago
Happy to share our most recent work
www.pnas.org/doi/10.1073/...
. Here we describe how efficient DNA replication in E. coli is dependent on an interaction between SSB-ssDNA and the DNA polymerase (Pol III). Thanks to all the co-authors for their hard work!
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Genome integrity relies on rapid recycling of DNA Pol III in bacteria | PNAS
DNA replication requires precise coordination between DNA unwinding and DNA synthesis. In all domains of life, protein–protein interactions at the ...
https://www.pnas.org/doi/10.1073/pnas.2511725122
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Samuel Aroney
3 months ago
“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla.
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social
@rhysnewell.bsky.social
🧵1/6
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Thom Booth
4 months ago
Did you know most 'complete' Streptomyces genomes are missing their telomeres? Thanks to David and Tues hard work, we now have a new tool to recover them! A pleasure to be part of a team. :) 🦠🧪💻
#microsky
add a skeleton here at some point
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Ewan Birney
4 months ago
I am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested!
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
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Staff Scientist
About EMBL-EBI EMBL’s European Bioinformatics Institute is a data powerhouse, utilised on a global scale to advance scientific discovery through bioinformatics and solutions to some of the world’s mos...
https://embl.wd103.myworkdayjobs.com/en-US/EMBL/job/Staff-Scientist_JR2425
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Rick Beeloo
4 months ago
Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it:
www.biorxiv.org/content/10.1...
Want to get started?
github.com/rickbeeloo/b...
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Lee Katz
4 months ago
🚀 New in Fasten: fasten_head Unix head, but FASTQ-aware 🧬 ✅ Get first N reads (not just lines!) ✅ Works with paired-end reads ✅ Can limit by bases OR reads ✅ Blazingly fast (it's Rust 🦀) cat huge.fq | fasten_head -r 1000 Stop doing math with -n. Let the tool understand your data.
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Christopher Whitford
4 months ago
Check out this new amazing preprint by David,
@tuesparholt.bsky.social
,
@thombooth.bsky.social
, and
@tilmweber.bsky.social
!
add a skeleton here at some point
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Jaeseung Hahn
4 months ago
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The telomere reconstruction software Telomore is now live here:
github.com/dalofa/telom...
@dalofa.bsky.social
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GitHub - dalofa/telomore: Gotta find them telomeres
Gotta find them telomeres. Contribute to dalofa/telomore development by creating an account on GitHub.
https://github.com/dalofa/telomore
4 months ago
1
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Stephen Turner
4 months ago
From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes
www.nature.com/articles/s41...
🧬🖥️🧪
github.com/HaploTeam/10...
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Keith Robison
4 months ago
ASHG Posters: The Agony and The Ecstasy
#ASHG25
🧬🖥️
omicsomics.blogspot.com/2025/10/ashg...
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ASHG Posters: The Agony and The Ecstasy
ASHG is a huge meeting, probably the second largest I've ever attended after ASCO. ASBMB is similar in size perhaps, though I think a hair ...
http://omicsomics.blogspot.com/2025/10/ashg-posters-agony-and-ecstasy.html
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STCmicrobeblog
4 months ago
𝘚𝘵𝘳𝘦𝘱𝘵𝘰𝘮𝘺𝘤𝘦𝘴 (and 𝘒𝘪𝘵𝘢𝘴𝘢𝘵𝘰𝘴𝘱𝘰𝘳𝘢🙂) aficionadas y aficionados take note 👇 ...and no, the image doesn't show reconstituted 𝘒𝘪𝘵𝘢𝘴𝘢𝘵𝘰𝘴𝘱𝘰𝘳𝘢 telomeres (telomores) 😉
#MicroSky
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Bacterial telomeres are common, just not so much in RefSeq 'complete' genomes. But they can be added by the new tool David Faurdal wrote. I am thrilled to see this out as a preprint here:
www.biorxiv.org/content/10.1...
@tilmweber.bsky.social
@thombooth.bsky.social
4 months ago
2
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James Briscoe
4 months ago
The
@crick.ac.uk
is recruiting Early Career Group Leaders - Lab set-up, research costs, salaries for up to 5 researchers - Support for up to 12 years - Access to our core facilities - Competitive salary - Fantastic colleagues - All areas of biology Deadline 27 Nov
www.crick.ac.uk/careers-stud...
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Early career group leaders
We appoint researchers from across biology and biomedicine to set up their first groups at the Crick.
https://www.crick.ac.uk/careers-study/faculty/early-career-group-leaders
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Oliver Schwengers
5 months ago
Dear community, Bakta needs your help! To further improve the functional annotation of "hypothetical" CDS, me and
@gbouras13.bsky.social
, we are looking for the worst Bakta-annotated bacterial genomes ;-) (1/2)
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Tue Sparholt Jørgensen
John Innes Centre
5 months ago
VACANCY - Independent research fellowships leading to tenured positions We’re inviting applications from outstanding researchers who either hold, or wish to apply for, Independent Research Fellowships. APPLICATION DEADLINE: 10 November 2025 Click here to apply:
jic.link/Fellows
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Tue Sparholt Jørgensen
Subscribe to Radio Free America (link in bio)
5 months ago
RIP Jane Goodall, by all accounts a wonderful woman who loved this Far Side cartoon
add a skeleton here at some point
27
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Zamin Iqbal
5 months ago
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson
@sangerinstitute.bsky.social
- this version much improved over the preprint. Final version should be open access, apols. Thread 1/n
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This tool looks incredible, I've been missing something exactly like this to analyze assembly graphs, which is necessary to understand more complex genome structures.
add a skeleton here at some point
5 months ago
0
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Tue Sparholt Jørgensen
Heng Li
5 months ago
New blog post – A quick look at Roche's SBX
lh3.github.io/2025/09/11/a...
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