KamilSJaron.bsky.social
@kamilsjaron.bsky.social
Biodiversity genomics; reproduction; k-mers; Evolution of species with weird genomes; frequently featuring diptera and collembola; group leader at the Tree of Life, Wellcome Sanger Institute; dysorthographic
I very excited we finally made a new version of #smudgeplot: Skylight. Much faster, improved inference and interface and finally, we have a new experimental features that might be fun toying with.
github.com/KamilSJaron/...
github.com/KamilSJaron/...
Release Skylight · KamilSJaron/smudgeplot
What's Changed
Lots of bugfixes in the interface and documentation (@samebdon and @KamilSJaron )
Add JSON report and PNG default plot format to output by @jgrg in #215
Fix bug in estimation of err...
github.com
November 25, 2025 at 9:49 AM
I very excited we finally made a new version of #smudgeplot: Skylight. Much faster, improved inference and interface and finally, we have a new experimental features that might be fun toying with.
github.com/KamilSJaron/...
github.com/KamilSJaron/...
Reposted by KamilSJaron.bsky.social
final week to apply for @sangerinstitute.bsky.social PhD programme (due Nov 27th) -- free to apply, open to anyone anywhere, and a superb training opportunity for students interested in genomic approaches applied to biodiversity, pathogens, vectors, and of course us pesky humans.
November 20, 2025 at 12:07 PM
final week to apply for @sangerinstitute.bsky.social PhD programme (due Nov 27th) -- free to apply, open to anyone anywhere, and a superb training opportunity for students interested in genomic approaches applied to biodiversity, pathogens, vectors, and of course us pesky humans.
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.
This, except I think we can take leadership in our hands, we don’t need funders to do it for us…
All of us can avoid publishing and reviewing for for-profits and it does not have to be too much of a sacrifice (plenty of flashy society/nonprofit journals out there). Be the change.
All of us can avoid publishing and reviewing for for-profits and it does not have to be too much of a sacrifice (plenty of flashy society/nonprofit journals out there). Be the change.
Fundamentally, what we need is leadership. But we break with the chorus of most #OpenScience initiatives here and emphasize very strongly that this leadership must come from funders and institutions.
We researchers can support the battle, but we cannot lead the charge. Funders hold the cards.
6/n
We researchers can support the battle, but we cannot lead the charge. Funders hold the cards.
6/n
November 12, 2025 at 10:58 PM
This, except I think we can take leadership in our hands, we don’t need funders to do it for us…
All of us can avoid publishing and reviewing for for-profits and it does not have to be too much of a sacrifice (plenty of flashy society/nonprofit journals out there). Be the change.
All of us can avoid publishing and reviewing for for-profits and it does not have to be too much of a sacrifice (plenty of flashy society/nonprofit journals out there). Be the change.
This looks so good!
Sign up now for EMBO Workshop "Molecular mechanisms of selfish elements and strategies" in Bern, Switzerland, 8–11 February 2026.
Abstract submission/Registration by: 15 December 2025/15 January 2026
https://meetings.embo.org/event/26-selfish-elements
#EMBOselfishElements #GeneSky #EMBOevents 🧪
Abstract submission/Registration by: 15 December 2025/15 January 2026
https://meetings.embo.org/event/26-selfish-elements
#EMBOselfishElements #GeneSky #EMBOevents 🧪
Molecular mechanisms of selfish elements and strategies
Certain genes, chromosomes, organelles, or entire sets of chromosomes can bias their transmission to the next generation, propagating themselves at the expense of the rest of the genome. Referred to …
meetings.embo.org
October 29, 2025 at 8:21 AM
This looks so good!
Understanding life is starting! Looking forwards to the new following days of talks on biodiversity genomics!
October 27, 2025 at 1:05 PM
Understanding life is starting! Looking forwards to the new following days of talks on biodiversity genomics!
Reposted by KamilSJaron.bsky.social
new publication by @amjadkhalaf.bsky.social who mined arthropod reference genome data for hidden microsporidia reads and then did a whole lot of assembling and sleuthing! great job @amjadkhalaf.bsky.social !
Really, really happy that our work on microsporidian genomes is now out in @plosbiology.org! A huge thank you to my coauthors, my supervisors @mblaxter.bsky.social & @marakat.bsky.social, the editors @roliroberts.bsky.social & Joseph Heitman, and the reviewers ❤️ plos.io/48HsAQJ
October 22, 2025 at 1:33 PM
new publication by @amjadkhalaf.bsky.social who mined arthropod reference genome data for hidden microsporidia reads and then did a whole lot of assembling and sleuthing! great job @amjadkhalaf.bsky.social !
Reposted by KamilSJaron.bsky.social
Really, really happy that our work on microsporidian genomes is now out in @plosbiology.org! A huge thank you to my coauthors, my supervisors @mblaxter.bsky.social & @marakat.bsky.social, the editors @roliroberts.bsky.social & Joseph Heitman, and the reviewers ❤️ plos.io/48HsAQJ
October 22, 2025 at 10:47 AM
Really, really happy that our work on microsporidian genomes is now out in @plosbiology.org! A huge thank you to my coauthors, my supervisors @mblaxter.bsky.social & @marakat.bsky.social, the editors @roliroberts.bsky.social & Joseph Heitman, and the reviewers ❤️ plos.io/48HsAQJ
This is a really interesting story. Microsporidia have genome architecture as no other creatures! Congrats @amjadkhalaf.bsky.social
#Microsporidia are #parasites of growing importance. @amjadkhalaf.bsky.social @mblaxter.bsky.social @marakat.bsky.social &co present 40 new genomes from #DarwinTreeofLife sequencing of their arthropod hosts, revealing insights into #tetraploidy & #reproduction @plosbiology.org 🧪 plos.io/48HsAQJ
October 22, 2025 at 4:45 PM
This is a really interesting story. Microsporidia have genome architecture as no other creatures! Congrats @amjadkhalaf.bsky.social
Reposted by KamilSJaron.bsky.social
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...
What an achievement. I am so excited ATLASea is going strong!
The ATLASea program is releasing its 100th genome assembly - cephalopods fans rejoice, it is for a Nautilus species.
Article in French:
www.mnhn.fr/fr/actualite...
Article in French:
www.mnhn.fr/fr/actualite...
Une 100e espèce séquencée dans le programme DIVE-Sea !
Le projet DIVE-Sea, qui a débuté en mars 2023, représente le premier volet du programme ATLASea qui vise à constituer un atlas des génomes d’espèces marines (algues, coraux, poissons, coquillages…) de...
www.mnhn.fr
October 3, 2025 at 9:31 AM
What an achievement. I am so excited ATLASea is going strong!
We have a new small GenomeScope based on @jgrg.mstdn.science.ap.brid.gy's pull request. Thanks James!
Main new feature --json_report will generate a json formatted list of all the inputs and outputs which will make automatic processing of genomescope results easier.
github.com/tbenavi1/gen...
Main new feature --json_report will generate a json formatted list of all the inputs and outputs which will make automatic processing of genomescope results easier.
github.com/tbenavi1/gen...
Release v2.1.0 · tbenavi1/genomescope2.0
This version have small improvements to niceness of the code (removing global variables) and minor improvements to the installation script.
The biggest improvement is the option to generate reports...
github.com
October 2, 2025 at 8:35 PM
We have a new small GenomeScope based on @jgrg.mstdn.science.ap.brid.gy's pull request. Thanks James!
Main new feature --json_report will generate a json formatted list of all the inputs and outputs which will make automatic processing of genomescope results easier.
github.com/tbenavi1/gen...
Main new feature --json_report will generate a json formatted list of all the inputs and outputs which will make automatic processing of genomescope results easier.
github.com/tbenavi1/gen...
This is getting a bit awkward. Anyone else feels like chipping in?
Of course it helps. I confess that I don’t understand the logic that society journals with nonprofit publishers should have less right to recoup our costs than corporate publishers have to do so *and* take a cut in profit (which often takes the form of burdensome APCs)...
September 26, 2025 at 7:54 PM
This is getting a bit awkward. Anyone else feels like chipping in?
Reposted by KamilSJaron.bsky.social
Last chance to join us next month for the #Biodiversity25 conference.
A fantastic set of speakers, mix of talks & focused workshops, and the chance to meet others in the field of biodiversity genomics 🧬
In-person registration closes next Monday 29th September!
Registration 🔗: bit.ly/4j3vAZ9
A fantastic set of speakers, mix of talks & focused workshops, and the chance to meet others in the field of biodiversity genomics 🧬
In-person registration closes next Monday 29th September!
Registration 🔗: bit.ly/4j3vAZ9
Understanding Life: Using Largescale Biodiversity Reference Genomes — 20251027
Understanding life: Using largescale biodiversity reference genomes
bit.ly
September 24, 2025 at 3:18 PM
Last chance to join us next month for the #Biodiversity25 conference.
A fantastic set of speakers, mix of talks & focused workshops, and the chance to meet others in the field of biodiversity genomics 🧬
In-person registration closes next Monday 29th September!
Registration 🔗: bit.ly/4j3vAZ9
A fantastic set of speakers, mix of talks & focused workshops, and the chance to meet others in the field of biodiversity genomics 🧬
In-person registration closes next Monday 29th September!
Registration 🔗: bit.ly/4j3vAZ9
Reposted by KamilSJaron.bsky.social
Happy to share the Biodiversity Cell Atlas white paper, out today in @nature.com. We look at the possibilities, challenges, and potential impacts of molecularly mapping cells across the tree of life.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
September 24, 2025 at 3:12 PM
Happy to share the Biodiversity Cell Atlas white paper, out today in @nature.com. We look at the possibilities, challenges, and potential impacts of molecularly mapping cells across the tree of life.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
@asn-amnat.bsky.social Did you consider releasing older papers? Asking money for nearly 60 year old papers is a bit... (lacking a good word here) www.journals.uchicago.edu/doi/epdf/10....
Am I the only one weirded by this?!
Am I the only one weirded by this?!
University of Chicago Press Journals: Cookie absent
www.journals.uchicago.edu
September 24, 2025 at 3:06 PM
@asn-amnat.bsky.social Did you consider releasing older papers? Asking money for nearly 60 year old papers is a bit... (lacking a good word here) www.journals.uchicago.edu/doi/epdf/10....
Am I the only one weirded by this?!
Am I the only one weirded by this?!
Reposted by KamilSJaron.bsky.social
Our paper Genomic diversity of the African malaria vector Anopheles funestus was published in Science today! It features inversions, selection in action, museum specimens and putative new ecotypes. doi.org/10.1126/scie...
September 18, 2025 at 6:45 PM
Our paper Genomic diversity of the African malaria vector Anopheles funestus was published in Science today! It features inversions, selection in action, museum specimens and putative new ecotypes. doi.org/10.1126/scie...
It's that time of the year again... Soon the applications for 12 PhD positions at @sangerinstitute.bsky.social will open. Interested in genomics and thinking about doing a PhD? Join us at Sanger. www.sanger.ac.uk/about/study/...
4-Year PhD Programme
The Wellcome Sanger Institute have a 4-year PhD programme and a Clinical PhD programme in genomics and genetics, registered with the University of Cambridge, which are open to UK and overseas applican...
www.sanger.ac.uk
September 18, 2025 at 3:04 PM
It's that time of the year again... Soon the applications for 12 PhD positions at @sangerinstitute.bsky.social will open. Interested in genomics and thinking about doing a PhD? Join us at Sanger. www.sanger.ac.uk/about/study/...
Reposted by KamilSJaron.bsky.social
How many chromosomes can an animal have?
In our paper out now in @currentbiology.bsky.social we show that the Atlas blue butterfly has 229 chromosome pairs- the highest in diploid Metazoa! These arose by rapid autosome fragmentation while sex chromosomes stayed intact.
www.cell.com/current-biol...
In our paper out now in @currentbiology.bsky.social we show that the Atlas blue butterfly has 229 chromosome pairs- the highest in diploid Metazoa! These arose by rapid autosome fragmentation while sex chromosomes stayed intact.
www.cell.com/current-biol...
Constraints on chromosome evolution revealed by the 229 chromosome pairs of the Atlas blue butterfly
The genome of the Atlas blue butterfly contains ten times more chromosomes than most
butterflies, and more than any other known diploid animal. Wright et al. show that
this extraordinary karyotype is ...
tinyurl.com
September 11, 2025 at 3:22 PM
How many chromosomes can an animal have?
In our paper out now in @currentbiology.bsky.social we show that the Atlas blue butterfly has 229 chromosome pairs- the highest in diploid Metazoa! These arose by rapid autosome fragmentation while sex chromosomes stayed intact.
www.cell.com/current-biol...
In our paper out now in @currentbiology.bsky.social we show that the Atlas blue butterfly has 229 chromosome pairs- the highest in diploid Metazoa! These arose by rapid autosome fragmentation while sex chromosomes stayed intact.
www.cell.com/current-biol...
Mind blowing chromosomal fragmentation of … everything but sex chromosomes in blues. Great piece by
@charlottewright.bsky.social at al👏
@charlottewright.bsky.social at al👏
September 11, 2025 at 4:36 PM
Mind blowing chromosomal fragmentation of … everything but sex chromosomes in blues. Great piece by
@charlottewright.bsky.social at al👏
@charlottewright.bsky.social at al👏
Rather interesting thread, I always wondered why we don’t peer review preprints more.
Why hasn't Preprint Peer Review caught on more?
I discovered a small, but simple reason - authors are missing out on the JOY of getting feedback because they aren't notified when feedback occurs.
more in thread below!
I discovered a small, but simple reason - authors are missing out on the JOY of getting feedback because they aren't notified when feedback occurs.
more in thread below!
September 8, 2025 at 6:37 PM
Rather interesting thread, I always wondered why we don’t peer review preprints more.
Reposted by KamilSJaron.bsky.social
You may have missed this #ant poster at #ESEB2025, but be sure not to miss the article just published in #openacess in @nature.com: www.nature.com/articles/s41...
One mother for two species via obligate cross-species cloning in ants - Nature
In a case of obligate cross-species cloning, female ants of Messor ibericus need to clone males of Messor structor to obtain sperm for producing the worker caste, resulting in males from the same moth...
www.nature.com
September 4, 2025 at 10:06 AM
You may have missed this #ant poster at #ESEB2025, but be sure not to miss the article just published in #openacess in @nature.com: www.nature.com/articles/s41...
Very nice thread on a big Logan update. This very much looks like the future of querying genomic data.
🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
September 3, 2025 at 9:25 AM
Very nice thread on a big Logan update. This very much looks like the future of querying genomic data.
We had productive 2 days of defining some hard bits of the database as well as figuring out the next steps forward. We will send around notes in the upcoming days. ToS folks are the best, thank you all for taking part and @aruizherrera.bsky.social and @sphaeromeria.bsky.social for organising!
Family photo of the 2025 Workshop of the @treeofsex.bsky.social ! Thanks everyone for attending and see you soon!
August 24, 2025 at 7:15 PM
We had productive 2 days of defining some hard bits of the database as well as figuring out the next steps forward. We will send around notes in the upcoming days. ToS folks are the best, thank you all for taking part and @aruizherrera.bsky.social and @sphaeromeria.bsky.social for organising!
Reposted by KamilSJaron.bsky.social
The day 2 of the #TreeOfSex annual workshop started with a great talk by @yannguiguen.bsky.social about B chromosomes and their role in sex determination in fish. Next up, Sònia Garcia is giving an update on the works of the Literature team.
August 24, 2025 at 9:28 AM
The day 2 of the #TreeOfSex annual workshop started with a great talk by @yannguiguen.bsky.social about B chromosomes and their role in sex determination in fish. Next up, Sònia Garcia is giving an update on the works of the Literature team.