Amanda Clare
@amandaclare.bsky.social
Senior lecturer. Metagenomics, bioinformatics, data science, databases, error analyses and writing code. Aberystwyth, UK. she/her.
Orcid: 0000-0001-8315-3659
Orcid: 0000-0001-8315-3659
Pinned
New preprint: Genome Assemblies and Annotations Are Not Static and Need Support for Tracking Their Evolution. We have version control for software, but for bioinformatics data we're left with filenames, directories or README files. What could version control do for genomics data? 1/6
Reposted by Amanda Clare
The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. www.nature.com/articles/s41... #Bioinformatics #OpenSource
Scikit-bio: a fundamental Python library for biological omic data analysis - Nature Methods
Nature Methods - Scikit-bio: a fundamental Python library for biological omic data analysis
www.nature.com
December 11, 2025 at 5:57 PM
The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. www.nature.com/articles/s41... #Bioinformatics #OpenSource
Reposted by Amanda Clare
The 12th edition of the 2-days workshop “Data Structures in Bioinformatics” (DSB) will take place in Venice (Italy) on February 18-19th, 2026: dsb-meeting.github.io/DSB2026/
DSB 2026 Venice - February 18-19
Workshop Data Structures in Bioinformatics
dsb-meeting.github.io
December 10, 2025 at 2:29 PM
The 12th edition of the 2-days workshop “Data Structures in Bioinformatics” (DSB) will take place in Venice (Italy) on February 18-19th, 2026: dsb-meeting.github.io/DSB2026/
Reposted by Amanda Clare
First let me say that, in practice, t- and Wilcoxon test often give similar results. But when they disagree, I bet the t-test's result is what you prefer. Just try it out, on real or simulated data. The tests have different null hypotheses, are sensitive to different alternatives,
December 10, 2025 at 12:29 PM
First let me say that, in practice, t- and Wilcoxon test often give similar results. But when they disagree, I bet the t-test's result is what you prefer. Just try it out, on real or simulated data. The tests have different null hypotheses, are sensitive to different alternatives,
Reposted by Amanda Clare
🧬🦠🚨 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...
@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...
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
doi.org
December 9, 2025 at 3:25 AM
🧬🦠🚨 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...
@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...
Reposted by Amanda Clare
Lovely to feature alongside the brilliant Birgit Sattler & Tom Battin in this story about life in Earth's dying ice.
www.the-scientist.com/the-ice-is-a...
www.the-scientist.com/the-ice-is-a...
The Ice is Alive: Uncovering the Vanishing World of Glacial Microbes
Glaciers are flush with microbial life. But, as climate change speeds glacial melting, scientists rush to establish microbial biobanks to preserve them.
www.the-scientist.com
December 8, 2025 at 11:28 AM
Lovely to feature alongside the brilliant Birgit Sattler & Tom Battin in this story about life in Earth's dying ice.
www.the-scientist.com/the-ice-is-a...
www.the-scientist.com/the-ice-is-a...
Reposted by Amanda Clare
Lectureship in Zoology at Aberystwyth University! jobs.aber.ac.uk/en/vacancy/l...
Come join our fantastic team at @aberdlsagb.bsky.social @aberuni.bsky.social in beautiful Wales. Application deadline: 14 Dec 2025.
Come join our fantastic team at @aberdlsagb.bsky.social @aberuni.bsky.social in beautiful Wales. Application deadline: 14 Dec 2025.
December 6, 2025 at 12:02 PM
Lectureship in Zoology at Aberystwyth University! jobs.aber.ac.uk/en/vacancy/l...
Come join our fantastic team at @aberdlsagb.bsky.social @aberuni.bsky.social in beautiful Wales. Application deadline: 14 Dec 2025.
Come join our fantastic team at @aberdlsagb.bsky.social @aberuni.bsky.social in beautiful Wales. Application deadline: 14 Dec 2025.
Reposted by Amanda Clare
github.com/bede/deacon
For anyone still using Bowtie2 for filtering or depletion of host sequences or specifics, I can recommend Deacon from @bedec.bsky.social . It is so much faster and easier than Bowtie2, and its performance is equal or better (tested with metagenomes and mitogenomes).🧬 & 🖥️
For anyone still using Bowtie2 for filtering or depletion of host sequences or specifics, I can recommend Deacon from @bedec.bsky.social . It is so much faster and easier than Bowtie2, and its performance is equal or better (tested with metagenomes and mitogenomes).🧬 & 🖥️
GitHub - bede/deacon: Fast DNA search and [host] depletion using minimizers
Fast DNA search and [host] depletion using minimizers - bede/deacon
github.com
December 3, 2025 at 7:40 PM
github.com/bede/deacon
For anyone still using Bowtie2 for filtering or depletion of host sequences or specifics, I can recommend Deacon from @bedec.bsky.social . It is so much faster and easier than Bowtie2, and its performance is equal or better (tested with metagenomes and mitogenomes).🧬 & 🖥️
For anyone still using Bowtie2 for filtering or depletion of host sequences or specifics, I can recommend Deacon from @bedec.bsky.social . It is so much faster and easier than Bowtie2, and its performance is equal or better (tested with metagenomes and mitogenomes).🧬 & 🖥️
Reposted by Amanda Clare
This month @genomeresearch.bsky.social publishes a special @recombconf.bsky.social issue highlighting algorithmic innovations in haplotype assembly and phasing, analysis of genomic variation and its association to phenotype, metagenomic analyses, and more. genome.cshlp.org/content/35/1...
December 3, 2025 at 4:38 PM
This month @genomeresearch.bsky.social publishes a special @recombconf.bsky.social issue highlighting algorithmic innovations in haplotype assembly and phasing, analysis of genomic variation and its association to phenotype, metagenomic analyses, and more. genome.cshlp.org/content/35/1...
Another one of those "the world is very small moments": in part of Prof Panangaden's talk he points out the Wasserstein metric was not invented by Wasserstein but by Kantorovich, and should be named accordingly. I thanked him afterwards because I'd read that was the case but everyone uses ... 1/2
Diolch i'r Athro Jane Hillston a'r Athro Prakash Panangaden am ymweld â ni, ac am eu sgyrsiau rhagorol am algebrâu prosesau, bisimwleiddiadau a metrigau.
Thanks to Prof Jane Hillston and Prof Prakash Panangaden for visiting us, and for excellent talks on process algebras, bisimulations and metrics.
Thanks to Prof Jane Hillston and Prof Prakash Panangaden for visiting us, and for excellent talks on process algebras, bisimulations and metrics.
December 2, 2025 at 6:18 PM
Another one of those "the world is very small moments": in part of Prof Panangaden's talk he points out the Wasserstein metric was not invented by Wasserstein but by Kantorovich, and should be named accordingly. I thanked him afterwards because I'd read that was the case but everyone uses ... 1/2
Reposted by Amanda Clare
We’re preparing workshop materials on debugging and troubleshooting in bioinformatics and computational biology, aimed at audience with bio background. Is anyone aware of relevant courses, workshops, or resources?
December 1, 2025 at 4:16 PM
We’re preparing workshop materials on debugging and troubleshooting in bioinformatics and computational biology, aimed at audience with bio background. Is anyone aware of relevant courses, workshops, or resources?
Reposted by Amanda Clare
Join EMBL's Interdisciplinary Postdoc Programme!
3 years funding, self-designed interdisciplinary project co-led between EMBL PI and PI in one of EMBL's actual, prospect or associate member states.
In particular: AI&Theory, use mathem. models, physics principles and AI
www.embl.org/about/info/p...
3 years funding, self-designed interdisciplinary project co-led between EMBL PI and PI in one of EMBL's actual, prospect or associate member states.
In particular: AI&Theory, use mathem. models, physics principles and AI
www.embl.org/about/info/p...
EIPOD-LinC Fellowship Programme – Postdoctoral Programme
www.embl.org
December 1, 2025 at 11:00 AM
Join EMBL's Interdisciplinary Postdoc Programme!
3 years funding, self-designed interdisciplinary project co-led between EMBL PI and PI in one of EMBL's actual, prospect or associate member states.
In particular: AI&Theory, use mathem. models, physics principles and AI
www.embl.org/about/info/p...
3 years funding, self-designed interdisciplinary project co-led between EMBL PI and PI in one of EMBL's actual, prospect or associate member states.
In particular: AI&Theory, use mathem. models, physics principles and AI
www.embl.org/about/info/p...
Our new preprint, spelling out what a genomic-data-aware version control system could do to make #bioinformatics better for everyone.
It was really fun and hopeful, describing the potential for a better future with @nickdimonaco.bsky.social (QUB) and Martin Vickers (JIC). Although bioRxiv doesn't accept review paper preprints, here it is on Figshare figshare.com/articles/pre... 6/6
Genome Assemblies and Annotations Are Not Static and Need Support for Tracking Their Evolution
For the past 25 years, genomic data has been distributed in two key file formats, FASTA and GFF. These files are used across nearly all genomic analyses and encode both the data of genomic sequences ...
figshare.com
December 2, 2025 at 10:30 AM
Our new preprint, spelling out what a genomic-data-aware version control system could do to make #bioinformatics better for everyone.
Reposted by Amanda Clare
New preprint: Genome Assemblies and Annotations Are Not Static and Need Support for Tracking Their Evolution. We have version control for software, but for bioinformatics data we're left with filenames, directories or README files. What could version control do for genomics data? 1/6
December 1, 2025 at 7:07 PM
New preprint: Genome Assemblies and Annotations Are Not Static and Need Support for Tracking Their Evolution. We have version control for software, but for bioinformatics data we're left with filenames, directories or README files. What could version control do for genomics data? 1/6
Reposted by Amanda Clare
We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.
1/n
1/n
Intro to Bedder – The Quinlan Lab
quinlanlab.org
December 2, 2025 at 2:28 AM
New preprint: Genome Assemblies and Annotations Are Not Static and Need Support for Tracking Their Evolution. We have version control for software, but for bioinformatics data we're left with filenames, directories or README files. What could version control do for genomics data? 1/6
December 1, 2025 at 7:07 PM
New preprint: Genome Assemblies and Annotations Are Not Static and Need Support for Tracking Their Evolution. We have version control for software, but for bioinformatics data we're left with filenames, directories or README files. What could version control do for genomics data? 1/6
A genotype-phenotype puzzle in a Christmas Elf format for day one of the STEM advent calendar.
Agorwch ddiwrnod 1 o'n calendr adfent ar-lein ar gyfer her Nadoligaidd: Her Genomau'r Corachod!
Open day 1 of our online advent calendar for a festive challenge: Elf Genome Challenge!
outreach-hub.aber.ac.uk/Seasonal/Xma...
Open day 1 of our online advent calendar for a festive challenge: Elf Genome Challenge!
outreach-hub.aber.ac.uk/Seasonal/Xma...
December 1, 2025 at 6:28 PM
A genotype-phenotype puzzle in a Christmas Elf format for day one of the STEM advent calendar.
Our Compsci dept staff coffee room in Aberystwyth.
How I imagine it must be like to work in a small university town
November 28, 2025 at 3:32 PM
Our Compsci dept staff coffee room in Aberystwyth.
Reposted by Amanda Clare
One of the things that has been on my to do list for a very long time, is building a gallery of all of the charts I've made across #TidyTuesday, #30DayChartChallenge, #30DayMapChallenge, and other miscellaneous projects 📊
And it's finally here!
Link: nrennie.rbind.io/viz-gallery/
#DataViz #RStats
And it's finally here!
Link: nrennie.rbind.io/viz-gallery/
#DataViz #RStats
Data Visualisation Gallery
Gallery of data visualisations created by Nicola Rennie.
nrennie.rbind.io
November 26, 2025 at 1:33 PM
One of the things that has been on my to do list for a very long time, is building a gallery of all of the charts I've made across #TidyTuesday, #30DayChartChallenge, #30DayMapChallenge, and other miscellaneous projects 📊
And it's finally here!
Link: nrennie.rbind.io/viz-gallery/
#DataViz #RStats
And it's finally here!
Link: nrennie.rbind.io/viz-gallery/
#DataViz #RStats
Reposted by Amanda Clare
How does fever work?
Our new Science paper shows how elevated body temperature can protect against severe influenza and that avian-origin viruses escape this defence.
This is likely one reason why bird flus and some pandemic influenzas can be so severe.🧵
www.science.org/doi/10.1126/...
Our new Science paper shows how elevated body temperature can protect against severe influenza and that avian-origin viruses escape this defence.
This is likely one reason why bird flus and some pandemic influenzas can be so severe.🧵
www.science.org/doi/10.1126/...
Avian-origin influenza A viruses tolerate elevated pyrexic temperatures in mammals
Host body temperature can define a virus’s replicative profile—influenza A viruses (IAVs) adapted to 40° to 42°C in birds are less temperature sensitive in vitro compared with human isolates adapted t...
www.science.org
November 27, 2025 at 7:55 PM
How does fever work?
Our new Science paper shows how elevated body temperature can protect against severe influenza and that avian-origin viruses escape this defence.
This is likely one reason why bird flus and some pandemic influenzas can be so severe.🧵
www.science.org/doi/10.1126/...
Our new Science paper shows how elevated body temperature can protect against severe influenza and that avian-origin viruses escape this defence.
This is likely one reason why bird flus and some pandemic influenzas can be so severe.🧵
www.science.org/doi/10.1126/...
Reposted by Amanda Clare
Wow. What on earth is going on @natureportfolio.nature.com?
Imagine being an author who had a paper rejected by this journal, only to see this AI slop published…
Unless of course nothing is ever rejected by Sci Reports, which it seems must be the case 🤦🏻♀️
Imagine being an author who had a paper rejected by this journal, only to see this AI slop published…
Unless of course nothing is ever rejected by Sci Reports, which it seems must be the case 🤦🏻♀️
"Runctitiononal features"? "Medical fymblal"? "1 Tol Line storee"? This gets worse the longer you look at it. But it's got to be good, because it was published in Nature Scientific Reports last week: www.nature.com/articles/s41... h/t @asa.tsbalans.se
November 27, 2025 at 10:15 PM
Wow. What on earth is going on @natureportfolio.nature.com?
Imagine being an author who had a paper rejected by this journal, only to see this AI slop published…
Unless of course nothing is ever rejected by Sci Reports, which it seems must be the case 🤦🏻♀️
Imagine being an author who had a paper rejected by this journal, only to see this AI slop published…
Unless of course nothing is ever rejected by Sci Reports, which it seems must be the case 🤦🏻♀️
Reposted by Amanda Clare
We’re working on software that tracks changes to genomic DNA sequences, both intentional and the actual results from real-life sequencing. We wrote up a blog post describing how that could work for a bacterial genome: www.genhub.bio/blog/2025/10... (2/5)
GenHub
www.genhub.bio
November 5, 2025 at 11:16 PM
We’re working on software that tracks changes to genomic DNA sequences, both intentional and the actual results from real-life sequencing. We wrote up a blog post describing how that could work for a bacterial genome: www.genhub.bio/blog/2025/10... (2/5)
Reposted by Amanda Clare
Universities are in crisis, and I don’t think it’s helpful to phrase that as “exiting the market”. They’re not mid-range shoe shops, these are educational pillars in society
Chief exec of OfS 'said the OfS believes there are 24 institutions at risk of exiting the market in the next 12 months, seven of which are large providers with more than 3,000 students. There are another 25 or so institutions of various sizes at risk over a two- to three-year period, she added.'
Seven ‘large providers’ at risk of going under in the next year
Skills minister says no higher education institutions are at imminent risk of collapse this year but OfS confirms more than 20 providers are being closely monitored
www.timeshighereducation.com
November 26, 2025 at 10:13 AM
Universities are in crisis, and I don’t think it’s helpful to phrase that as “exiting the market”. They’re not mid-range shoe shops, these are educational pillars in society
Reposted by Amanda Clare
Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
Antimicrobial resistance (AMR) is a growing health threat, making infections harder to treat and complicating routine medical care.
EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.
#WAAW2025 #ActOnAMR
www.ebi.ac.uk/about/news/t...
🧬💻
EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.
#WAAW2025 #ActOnAMR
www.ebi.ac.uk/about/news/t...
🧬💻
A new gateway to global antimicrobial resistance data
New online portal connects bacterial genomes with experimental resistance data to support antimicrobial resistance research.
www.ebi.ac.uk
November 19, 2025 at 12:27 PM
Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
Reposted by Amanda Clare
Taming the reference genome jungle: the refget sequence collection standard. #ReferenceGenomes #Transcriptomes #SequenceCollectionStandards #GA4GH @biorxiv-genomic.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 21, 2025 at 8:31 AM
Taming the reference genome jungle: the refget sequence collection standard. #ReferenceGenomes #Transcriptomes #SequenceCollectionStandards #GA4GH @biorxiv-genomic.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Amanda Clare
🌱 Tomorrow we launch Plant Science Wales at the National Botanic Garden of Wales!
Explore seed banks, herbarium tours & panels on agri-tech, biophilia & more.
Organised by IBERS & NBGW, supported by the Learned Society of Wales. Follow for behind-the-scenes & speaker highlights!
Explore seed banks, herbarium tours & panels on agri-tech, biophilia & more.
Organised by IBERS & NBGW, supported by the Learned Society of Wales. Follow for behind-the-scenes & speaker highlights!
October 20, 2025 at 10:15 AM
🌱 Tomorrow we launch Plant Science Wales at the National Botanic Garden of Wales!
Explore seed banks, herbarium tours & panels on agri-tech, biophilia & more.
Organised by IBERS & NBGW, supported by the Learned Society of Wales. Follow for behind-the-scenes & speaker highlights!
Explore seed banks, herbarium tours & panels on agri-tech, biophilia & more.
Organised by IBERS & NBGW, supported by the Learned Society of Wales. Follow for behind-the-scenes & speaker highlights!