Tom Mathers
@tom-mathers.bsky.social
Evolutionary biologist. Genomics, aphids and gardening.
Senior Computer Biologist at Wellcome Sanger Institute.
Senior Computer Biologist at Wellcome Sanger Institute.
Pinned
Tom Mathers
@tom-mathers.bsky.social
· May 16
Struggling to find the tiny microchromosomes in draft bird genome assemblies?
Our new #preprint introducing MicroFinder can help: www.biorxiv.org/content/10.1...
🧵 below
(1/n)
@sangerinstitute.bsky.social
Our new #preprint introducing MicroFinder can help: www.biorxiv.org/content/10.1...
🧵 below
(1/n)
@sangerinstitute.bsky.social
Reposted by Tom Mathers
Does anyone have a photo of Charles W. Metz by any chance? He originally isolated the Holo2 line of Bradysia coprophila we still use after more than 100 years after their original capture.
November 18, 2025 at 12:21 PM
Does anyone have a photo of Charles W. Metz by any chance? He originally isolated the Holo2 line of Bradysia coprophila we still use after more than 100 years after their original capture.
Reposted by Tom Mathers
Join us! 🧬🪰🎉🔬
We are currently advertising two #PhD projects to study the #evolution, #development and #genomics of sexual traits in stalk-eyed flies.
Deadline for applying is Wednesday, January 7, 2026. Get in touch for more info!
We are currently advertising two #PhD projects to study the #evolution, #development and #genomics of sexual traits in stalk-eyed flies.
Deadline for applying is Wednesday, January 7, 2026. Get in touch for more info!
November 17, 2025 at 3:58 PM
Join us! 🧬🪰🎉🔬
We are currently advertising two #PhD projects to study the #evolution, #development and #genomics of sexual traits in stalk-eyed flies.
Deadline for applying is Wednesday, January 7, 2026. Get in touch for more info!
We are currently advertising two #PhD projects to study the #evolution, #development and #genomics of sexual traits in stalk-eyed flies.
Deadline for applying is Wednesday, January 7, 2026. Get in touch for more info!
Reposted by Tom Mathers
Preprint Alert! 🦥
We produced complete genomes for 2 Xenarthra and placed them in a mammalian comparative framework. We found that Xenarthra harbour the largest number of retrocopies in mammals! www.biorxiv.org/content/10.1...
We produced complete genomes for 2 Xenarthra and placed them in a mammalian comparative framework. We found that Xenarthra harbour the largest number of retrocopies in mammals! www.biorxiv.org/content/10.1...
Retrocopy formation and domestication shape genome evolution in sloths and other xenarthrans
Xenarthrans, comprising sloths, anteaters, and armadillos, represent one of the most morphologically and physiologically specialised mammalian clades, yet the genomic basis of their adaptations remain...
www.biorxiv.org
October 2, 2025 at 9:16 PM
Preprint Alert! 🦥
We produced complete genomes for 2 Xenarthra and placed them in a mammalian comparative framework. We found that Xenarthra harbour the largest number of retrocopies in mammals! www.biorxiv.org/content/10.1...
We produced complete genomes for 2 Xenarthra and placed them in a mammalian comparative framework. We found that Xenarthra harbour the largest number of retrocopies in mammals! www.biorxiv.org/content/10.1...
Second cut of the year for the rosemary hedge. The most fragrant job in the garden!
October 4, 2025 at 10:01 AM
Second cut of the year for the rosemary hedge. The most fragrant job in the garden!
Reposted by Tom Mathers
Now out! Paper led by @philmor1964.bsky.social and the The Cetacean Genomes Project. An effort by many, we present 13 new, high-quality reference genomes for cetaceans 🐬🐋 following @vertebrategenomes.bsky.social and @ebpgenome.bsky.social standards for a group that is very hard to sample from.
July 18, 2025 at 9:16 AM
Now out! Paper led by @philmor1964.bsky.social and the The Cetacean Genomes Project. An effort by many, we present 13 new, high-quality reference genomes for cetaceans 🐬🐋 following @vertebrategenomes.bsky.social and @ebpgenome.bsky.social standards for a group that is very hard to sample from.
Reposted by Tom Mathers
Albuquerque characterized the satellitome of the pea aphid, with results suggesting that satDNAs contribute to genome evolution, biotype divergence, and the “fast-X” effect.
🔗 doi.org/10.1093/gbe/evaf104
#genome #satellitome
🔗 doi.org/10.1093/gbe/evaf104
#genome #satellitome
Exploring the Satellitome of the Pest Aphid Acyrthosiphon pisum (Hemiptera, Aphididae): Insights Into Genome Organization and Intraspecies Evolution
Abstract. Satellite DNAs (satDNAs), ubiquitous sequences in eukaryotic genomes, play a crucial role in genome organization, function, and evolution. The pe
doi.org
July 10, 2025 at 4:18 PM
Albuquerque characterized the satellitome of the pea aphid, with results suggesting that satDNAs contribute to genome evolution, biotype divergence, and the “fast-X” effect.
🔗 doi.org/10.1093/gbe/evaf104
#genome #satellitome
🔗 doi.org/10.1093/gbe/evaf104
#genome #satellitome
😱 Simultaneously curating all 8 haplotypes of octaploid Carpinus betulus (European hornbeam).
One set of chromosomes down, many more to go...
@sangerinstitute.bsky.social Darwin Tree of Life.
One set of chromosomes down, many more to go...
@sangerinstitute.bsky.social Darwin Tree of Life.
July 1, 2025 at 7:52 PM
😱 Simultaneously curating all 8 haplotypes of octaploid Carpinus betulus (European hornbeam).
One set of chromosomes down, many more to go...
@sangerinstitute.bsky.social Darwin Tree of Life.
One set of chromosomes down, many more to go...
@sangerinstitute.bsky.social Darwin Tree of Life.
Reposted by Tom Mathers
Heaven @saskiahogenhout.bsky.social et al. generated chromosome-level genomes for three psyllid species that are plant disease vectors, revealing detoxification gene expansions and genetic substructure across Europe.
🔗 doi.org/10.1093/gbe/evaf116
#genome #entomology
🔗 doi.org/10.1093/gbe/evaf116
#genome #entomology
June 30, 2025 at 7:42 AM
Heaven @saskiahogenhout.bsky.social et al. generated chromosome-level genomes for three psyllid species that are plant disease vectors, revealing detoxification gene expansions and genetic substructure across Europe.
🔗 doi.org/10.1093/gbe/evaf116
#genome #entomology
🔗 doi.org/10.1093/gbe/evaf116
#genome #entomology
Helenium Moerheim Beauty doing well in the dry conditions.
June 28, 2025 at 7:06 AM
Helenium Moerheim Beauty doing well in the dry conditions.
Reposted by Tom Mathers
Join us on the Wellcome Genome Campus of the Sanger Institute and EBI for a symposium on biodiversity genomics from 27th-29th October! Abstract deadline on 14 July. There is also an option to join via Zoom, but in-person is much nicer if you can make it.
Present your insights from studies into #eukaryotic genomes at our #Biodiversity25 conference! 📈
🗓️ 27-29 October 2025
Submit by 14 July 📩
We encourage submissions showcasing best practices for applying new methods and resources to analyse #biodiversity genomes at scale 🌳🧬
📎 bit.ly/4j3vAZ9
🗓️ 27-29 October 2025
Submit by 14 July 📩
We encourage submissions showcasing best practices for applying new methods and resources to analyse #biodiversity genomes at scale 🌳🧬
📎 bit.ly/4j3vAZ9
June 27, 2025 at 1:57 PM
Join us on the Wellcome Genome Campus of the Sanger Institute and EBI for a symposium on biodiversity genomics from 27th-29th October! Abstract deadline on 14 July. There is also an option to join via Zoom, but in-person is much nicer if you can make it.
First group three clematis flowers. Early this year due to the hot spring.
June 15, 2025 at 10:32 AM
First group three clematis flowers. Early this year due to the hot spring.
Reposted by Tom Mathers
super-happy, three TE invasions in Dmel during the last 30 years; the crazy thing - Transib1 spread in just 2-3years in global populations academic.oup.com/mbe/advance-... great work everyone @rpianezza.bsky.social @almoroscarpa.bsky.social @signor-molevol.bsky.social Anna Haider
Spatio-temporal tracking of three novel transposable element invasions in Drosophila melanogaster over the last 30 years
Abstract. Transposable elements (TEs) are repetitive sequences capable of mobilizing within genomes, exerting a sigfinificant influence on evolution throug
academic.oup.com
June 11, 2025 at 11:37 AM
super-happy, three TE invasions in Dmel during the last 30 years; the crazy thing - Transib1 spread in just 2-3years in global populations academic.oup.com/mbe/advance-... great work everyone @rpianezza.bsky.social @almoroscarpa.bsky.social @signor-molevol.bsky.social Anna Haider
Shropshire lad, grown from a cutting.
June 7, 2025 at 6:12 PM
Shropshire lad, grown from a cutting.
Reposted by Tom Mathers
Thanks for posting @reviewcommons.org
If you're interested you can also find the reviewed version here:
doi.org/10.7554/eLif...
Really keen to get people's perspectives on the population genetics of reservoirs, and what they tell us about variation associated with emergent crop pathogens.
If you're interested you can also find the reviewed version here:
doi.org/10.7554/eLif...
Really keen to get people's perspectives on the population genetics of reservoirs, and what they tell us about variation associated with emergent crop pathogens.
April 30, 2025 at 9:01 AM
Thanks for posting @reviewcommons.org
If you're interested you can also find the reviewed version here:
doi.org/10.7554/eLif...
Really keen to get people's perspectives on the population genetics of reservoirs, and what they tell us about variation associated with emergent crop pathogens.
If you're interested you can also find the reviewed version here:
doi.org/10.7554/eLif...
Really keen to get people's perspectives on the population genetics of reservoirs, and what they tell us about variation associated with emergent crop pathogens.
Reposted by Tom Mathers
Our recent paper is out where we propose kmer-based phylogenetics for fungal Starship TEs (which are unalignable as highly variable). We think it could help with spotting bonafide HGT events (and suggest direction of transfer?)
doi.org/10.1093/g3jo...
@mcmullan0.bsky.social @norwichmicro.bsky.social
doi.org/10.1093/g3jo...
@mcmullan0.bsky.social @norwichmicro.bsky.social
Starship giant transposable elements cluster by host taxonomy using k-mer-based phylogenetics
Abstract. Starships are a recently established superfamily of giant cargo-mobilizing transposable elements in the fungal subphylum Pezizomyotina (phylum As
academic.oup.com
May 14, 2025 at 3:19 PM
Our recent paper is out where we propose kmer-based phylogenetics for fungal Starship TEs (which are unalignable as highly variable). We think it could help with spotting bonafide HGT events (and suggest direction of transfer?)
doi.org/10.1093/g3jo...
@mcmullan0.bsky.social @norwichmicro.bsky.social
doi.org/10.1093/g3jo...
@mcmullan0.bsky.social @norwichmicro.bsky.social
Reposted by Tom Mathers
Our paper on phylogenetics of fungal Starship TEs is now on the cover of the June issue of Genetics @genetics-gsa.bsky.social 🙂
academic.oup.com/genetics/iss...
@mcmullan0.bsky.social @earlhaminst.bsky.social @rothamsted.bsky.social
academic.oup.com/genetics/iss...
@mcmullan0.bsky.social @earlhaminst.bsky.social @rothamsted.bsky.social
June 4, 2025 at 1:09 PM
Our paper on phylogenetics of fungal Starship TEs is now on the cover of the June issue of Genetics @genetics-gsa.bsky.social 🙂
academic.oup.com/genetics/iss...
@mcmullan0.bsky.social @earlhaminst.bsky.social @rothamsted.bsky.social
academic.oup.com/genetics/iss...
@mcmullan0.bsky.social @earlhaminst.bsky.social @rothamsted.bsky.social
Reposted by Tom Mathers
New pub on genome sample collection and processing: "Best-practice guidance for Earth BioGenome Project sample collection and processing: progress and challenges in biodiverse reference genome creation"
academic.oup.com/gigascience/...
academic.oup.com/gigascience/...
Best-practice guidance for Earth BioGenome Project sample collection and processing: progress and challenges in biodiverse reference genome creation
Abstract. The Earth BioGenome Project has the extremely ambitious goal of generating, at scale, high-quality reference genomes across the entire Tree of Li
academic.oup.com
June 3, 2025 at 3:25 PM
New pub on genome sample collection and processing: "Best-practice guidance for Earth BioGenome Project sample collection and processing: progress and challenges in biodiverse reference genome creation"
academic.oup.com/gigascience/...
academic.oup.com/gigascience/...
Reposted by Tom Mathers
Starship giant transposable elements cluster by host taxonomy using k-mer-based phylogenetics. #TransposableElements #TEs #Kmer #Phylogenetics #Genomics #Bioinformatics #G3 🧬 🖥️
academic.oup.com/g3journal/ad...
academic.oup.com/g3journal/ad...
June 2, 2025 at 5:06 PM
Starship giant transposable elements cluster by host taxonomy using k-mer-based phylogenetics. #TransposableElements #TEs #Kmer #Phylogenetics #Genomics #Bioinformatics #G3 🧬 🖥️
academic.oup.com/g3journal/ad...
academic.oup.com/g3journal/ad...
Reposted by Tom Mathers
An update on open postdoc positions, in my group and the adjacent group of Howard Ochman, here at UT-Austin. #SymbioSky
Mine: insect-bacterial symbiosis with emphasis on intracellular endosymbionts and molecular mechanisms.
web.biosci.utexas.edu/moran/contac...
Mine: insect-bacterial symbiosis with emphasis on intracellular endosymbionts and molecular mechanisms.
web.biosci.utexas.edu/moran/contac...
Nancy Moran Contact
web.biosci.utexas.edu
June 2, 2025 at 8:26 PM
An update on open postdoc positions, in my group and the adjacent group of Howard Ochman, here at UT-Austin. #SymbioSky
Mine: insect-bacterial symbiosis with emphasis on intracellular endosymbionts and molecular mechanisms.
web.biosci.utexas.edu/moran/contac...
Mine: insect-bacterial symbiosis with emphasis on intracellular endosymbionts and molecular mechanisms.
web.biosci.utexas.edu/moran/contac...
Reposted by Tom Mathers
Unicore is now published on GBE 🚀
Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n
📃 doi.org/10.1093/gbe/evaf109
Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n
📃 doi.org/10.1093/gbe/evaf109
June 3, 2025 at 6:55 AM
Unicore is now published on GBE 🚀
Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n
📃 doi.org/10.1093/gbe/evaf109
Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n
📃 doi.org/10.1093/gbe/evaf109
Reposted by Tom Mathers
Oh wow, a new lepidopteran fossil dated to 236 My! Along with a reanalysis of molecular data using the new calibration. Are Lepidoptera really older than 300 My?
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Back to the poop: the oldest hexapod scales discovered within a Triassic coprolite from Argentina
Life on Earth nearly came to an end during the end-Permian mass extinction (EPME; c. 252 Ma). In its aftermath, the Triassic witnessed the adaptation …
www.sciencedirect.com
June 3, 2025 at 6:53 AM
Oh wow, a new lepidopteran fossil dated to 236 My! Along with a reanalysis of molecular data using the new calibration. Are Lepidoptera really older than 300 My?
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Reposted by Tom Mathers
if you have an interest in improving the genomic resources available for mosquitoes, please fill in our google form at tinyurl.com/MosquitoReferenceGenomes. please share this with colleagues who might be interested. thank you! [3/3]
Register your interest in participating in the Global Culicidae Reference Genomes Project
We are seeking mosquito biologists around the world who would be interested in collecting and contributing specimens of any vector species that currently lacks a reference genome.
Aim: We are aiming ...
tinyurl.com
February 24, 2025 at 10:51 AM
if you have an interest in improving the genomic resources available for mosquitoes, please fill in our google form at tinyurl.com/MosquitoReferenceGenomes. please share this with colleagues who might be interested. thank you! [3/3]
Rosa Charles de Mills with Geum Totally Tangerine.
May 24, 2025 at 11:40 AM
Rosa Charles de Mills with Geum Totally Tangerine.