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Pedro Ribeiro

@pedrogribeiro.bsky.social
277 followers 307 following 23 posts

Postdoc at Petr Nguyen's lab. Lepidoptera genomics | Chromosomal evolution | Phylogenetics Science (and some personal life too) 🇧🇷🇨🇿🦋🍻

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Pedro Ribeiro @pedrogribeiro.bsky.social · 26/09/2026
It was an extremely rewarding experience to fully supervise a student, who defended her BSc with excellent grade! We worked on the identification of Wolbachia from genomic data to explore infection in a butterfly family. Thanks a lot to @pavelmatosm.bsky.social for the guidance and help throughout!
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Graham Coop @gcbias.bsky.social · 10/09/2026
I’m looking to hire an NIH funded postdoc to join our lab here at Davis (please RT). Ongoing areas of interest include: 1) polygenic signals of selection from time series, ARGs, GWAS, etc 2) The interpretation of GWAS, polygenic scores, & sources of confounding
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Pedro Ribeiro @pedrogribeiro.bsky.social · 08/09/2026
Another great event by the @10klepgenomes.bsky.social !
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Charlotte Wright @charlottewright.bsky.social · 26/08/2026
Delighted this huge team effort is out! By surveying >20,000 people from >100 countries, we used to butterflies to show that aesthetic biases distort scientific research & environmental policy. Understanding this bias is a key step towards more balanced decision-making 🦋 www.doi.org/10.1016/j.cu...
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Henry North @henrylnorth.bsky.social · 24/08/2026
Congrats to @cd-williams.bsky.social on his first first-author paper! We developed a sequential SDM approach to quantitatively incorporate information about local adaptation into range forecasts for invasive species. Feedback welcome! www.biorxiv.org/content/10.6...
biorxiv.org
Genetically informed distribution models refine predictions for the overwintering range of Helicoverpa armigera in North America
The ecological and economic threat posed by invasive pests demands proactive mitigation. Species distribution models (SDMs) are widely used in efforts to predict where invasive species might spread af...
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Casey Dunn @caseywdunn.bsky.social · 25/08/2026
My new book, Phylogenetic Biology, is now published. Available online for free at dunnlab.org/phylogenetic... . Physical copies can be purchased at shop.lightningsource.com/b/085?params... or your favorite bookstore.
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Noah Whiteman @nkwhiteman.bsky.social · 06/08/2026
I’m thrilled to share that our search for a tenure-track colleague in my *truly wonderful and collegial* Genetics, Genomics, Evolution and Development Division in the MCB Department at Berkeley @berkeleymcb.bsky.social is live! Please share this broad search widely: aprecruit.berkeley.edu/JPF05481
aprecruit.berkeley.edu
Assistant Professor -Genetics, Genomics, Evolution, and Development - Molecular and Cell Biology
University of California, Berkeley is hiring. Apply now!
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KamilSJaron.bsky.social @kamilsjaron.bsky.social · 23/07/2026
New preprint: 338 coleopteran genomes reveal exceptional rearrangement variation compared to other insect orders. Big congrats to @arf-mln.bsky.social, for getting this giant piece together. Big collaboration of @joanameier.bsky.social's and my groups. 🧵👇 doi.org/10.64898/202...
Phylogeny of 338 species with tips painted by the chromosomal ancestry of their contemporary genomes (well separated colours indicate only few changes, while blending indicates rearrangements). Colouring of the branches is by the number of rearrangements. The ring between paints and phylogeny indicates wether the chromosomal rearrangement was fusion dominated (brown) or fission dominated (teal) process.  
Photo credits: Udo Schmidt, Lech Borowiec, JL Tachet, David Navrátil, Fred Chevaillot, Siga, Cosmin Manci, John Hallmén, Igor Souza-Gonçalves, Alex Hyde, H. Coiffait, David Ignace, Yves Bousquet.
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Pável Matos @pavelmatosm.bsky.social · 14/07/2026
A glimpse of our work on the population genomics of the critically endangered Alcon blue (Phengaris alcon) in Czechia. Many thanks to Jihoceska televize for featuring our research! 🦋
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Project Psyche @projectpsyche.bsky.social · 03/07/2026
(2/3) Great talk by @charlottewright.bsky.social from @sangerinstitute.bsky.social, one of our coordinators, on widening participation in genome generation! @10klepgenomes.bsky.social is scaling Lepidoptera genome curation across Europe: 30 trained curators, 14 countries, 120+ genomes curated 🦋👀
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Joana Meier @joanameier.bsky.social · 02/07/2026
Enjoying an excellent Entomology Congress #ECE2026 in Tours, France. Jean-Michel Drezen and I hosted a genomics symposium. Lots of @projectpsyche.bsky.social members here. @pedrogribeiro.bsky.social gave an excellent talk on the @10klepgenomes.bsky.social COST Action.
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Pedro Ribeiro @pedrogribeiro.bsky.social · 02/07/2026
If you are interested in the sequencing and analysis of the genomes of European butterflies and moths, do visit the @10klepgenomes.bsky.social website and get in touch! It is a great opportunity to be part of an exciting community driving timely and interesting research! 10klepgenomes.eu
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10kLepGenomes @10klepgenomes.bsky.social · 29/06/2026
@pedrogribeiro.bsky.social gave a wonderful talk about our initiative with @projectpsyche.bsky.social and #LepEU at @ece2026tours.bsky.social panel dedicated to COST Actions. Our goal is to sequence reference genomes from all European Lepidoptera. #10kLepGenomes #Lepidoptera #ECE2026Tours
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Pedro Ribeiro @pedrogribeiro.bsky.social · 29/06/2026
Here at the @ece2026tours.bsky.social to talk about the amazing @10klepgenomes.bsky.social COST Action and how we are collaborating with @projectpsyche.bsky.social and #LepEU to obtain reference genomes of all European moths and butterflies!
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Jessica Foley @jessicafoley14.bsky.social · 16/06/2026
Very excited to finally have this out in the world! The first paper from my PhD (and my first first-author publication) makes the case for a new entrant to the world of long-lived animal models: Heliconius butterflies. Out now in @natcomms.nature.com www.nature.com/articles/s41... (1/10)
nature.com
Evolution of increased longevity and slowed ageing in a genus of tropical butterfly - Nature Communications
Studying long-lived species across the animal kingdom could provide insights into healthy ageing in humans. This study reveals long lifespans and slowed ageing in Heliconius butterflies, identifying t...
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 15/06/2026
People. @ksamuk.bsky.social and others have made this argument before. There’s good software to do this right. Here’s the argument again: Invariant sites matter! They’re not in your standard vcf and many programs pretend they are anyway. academic.oup.com/gbe/article/...
academic.oup.com
A Recipe for a Good π. How to Properly Estimate Population Genetics Summary Statistics and Why we Should Systematically Report Them
Abstract. Many long-standing questions in population genomics can now be addressed through comparative analyses and by leveraging the vast amount of genomi
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Matthew Hahn @3rdreviewer.bsky.social · 02/06/2026
Very happy to announce a big new paper from the lab, led by grad students @smishra677.bsky.social and Laia Pomar-Pallarès (in collaboration with @roblanfear.bsky.social). We introduce a new way to study introgression, with accompanying software (DAFT) 1/n 🧵 www.biorxiv.org/content/10.6...
biorxiv.org
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Rémi Allio @remiallio.bsky.social · 26/05/2026
We are very glad to introduce a new method for designing phylogenetically informative target-enrichment datasets that leverages recent whole-genome alignment methods to identify thousands of shared and homologous regions across a broad range of reference taxa! Please, check out Benjamin's preprint!
GABBI: an automated, open-source pipeline, integrating genome alignments into phylogenetic markers selection
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Niklas Wahlberg @lepphylo.bsky.social · 03/06/2026
Finally we know where the enigmatic Caribbean genus Calisto goes in the tree of life, thanks to the amazing work by Rayner Nunez! Mixture models seem to be the way to go! doi.org/10.1111/syen...
doi.org
Mixture models unveil the origin of the enigmatic Satyrinae butterfly genera Calisto and Llorenteana (Lepidoptera, Nymphalidae, Satyrinae)
We provide the first reliable hypothesis on the phylogenetic position of Calisto and Llorenteana within the tribe Satyrini, based on genomic data representing all subtribes. We apply for the first t.....
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Noah Whiteman @nkwhiteman.bsky.social · 13/05/2026
Excited that the first genome assembly of a Lonomia spp. moth has been published @genetics-gsa.bsky.social by first authors @diler.bsky.social + @samridhi.bsky.social w/our wonderful colleagues at Universidad de los Andes led by Dr. Camila Gonzalez (thanks @cdanielcadena for introducing us!). 1
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Dr Emma Hodcroft @firefoxx66.bsky.social · 10/05/2026
My ANDV #Hantavirus @nextstrain.org phylogenies now pull directly from @pathoplexus.org to incorporate all seqs I'll continue to improve them, & will keep them updated Change the Tip Labels in the left-hand menu. You can see links to all builds, plus tanglegrams at: nextstrain.org/groups/hodcr...
A phylogenetic tree showing linked sequences from the S and L segment of ANDV virus (Andes Hantavirus)
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Pedro Ribeiro @pedrogribeiro.bsky.social · 30/04/2026
@pavelmatosm.bsky.social has a PhD position for someone to work with comparative genomics of rapid evolution in Andean butterflies! If you are looking for a PhD, do apply!
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José Antonio Borrero @borreroja.bsky.social · 15/04/2026
Excited to share our new paper on pollen foraging in Heliconius himera @behavecol.bsky.social! 🦋🌼 academic.oup.com/beheco/artic... We explored how female and male H. himera differ in pollen foraging & sensory traits. 1/6🧵👇
academic.oup.com
Sexual dimorphism in pollen foraging and sensory traits in Heliconius butterflies
Male and female butterflies often face different ecological and sensory demands, yet how this shapes their foraging behaviour remains unclear. In Heliconiu
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Joana Meier @joanameier.bsky.social · 18/01/2026
Working on entomology research? Join us from 29 June to 3 July in Tours, France, for the European Congress of Entomology. The abstract submission deadline was extended to 31 January. If you are interested in genomics and evolutionary novelties, apply for our symposium on this topic. www.ece2026.org
ece2026.org
ECE 2026 - XIII European Congress of Entomology
It is our great pleasure to welcome you to Tours, France, in the heart of the Loire Valley, from June 29 to July 3, 2026.
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Pedro Ribeiro @pedrogribeiro.bsky.social · 02/12/2025
One of the coolest databases (and most important) in ecology and evolutionary biology
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Alena Sucháčková @alenasuchackova.bsky.social · 30/11/2025
Some butterflies may seem more beautiful than others. And believe it or not, this is influencing their conservation and researchers' interest! - Take this 10-min test to contribute to a research into our perception of butterfly beauty: www.unveiling.eu/en_US/introd...
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Pedro Ribeiro @pedrogribeiro.bsky.social · 01/12/2025
@pavelmatosm.bsky.social has a PhD position to work on rapid evolution and adaptation of flight in high altitude butterflies. Fieldwork in Peru + behavioral experiments! If you are looking for a great PhD opportunity, read the position at the link below and contact Pável! pavelmatos.wordpress.com
pavelmatos.wordpress.com
Matos Lab
Visit the post for more.
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KamilSJaron.bsky.social @kamilsjaron.bsky.social · 25/11/2025
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
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...
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Harmit Singh Malik @harmitmalik.bsky.social · 12/11/2025
Are you an early-stage graduate student (2nd or 3rd year) or early-stage postdoc based in the US or Canada, working primarily in Drosophila? Would you like to help improve the experience of all trainees working in Drosophila research? If so, read on. (Please repost to reach a broad audience.)
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Vincent Debat @vincentdebat.bsky.social · 06/11/2025
Finally out in Elife @elife.bsky.social : well done @joledamoisel.bsky.social ! Convergent iridescence and divergent chemical signals in sympatric sister-species of Amazonian butterflies doi.org/10.7554/eLif...
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Pedro Ribeiro @pedrogribeiro.bsky.social · 06/11/2025
Truly great report by Glenn Zorpette at @spectrum.ieee.org on one of the most exciting scientific EU-level projects going on, the @10klepgenomes.bsky.social COST action alongside with @projectpsyche.bsky.social. Sequence all leps in Europe and make discoveries a landmark in genomics and lep biology!
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Charlotte Wright @charlottewright.bsky.social · 05/11/2025
A fantastic writeup by Glenn Zorpette from @spectrum.ieee.org. Glenn joined us in Italy where we collectively sampled hundreds of new species for @projectpsyche.bsky.social. Shoutout to Luigi Avantaggiato for the spectacular photos and @costprogramme.bsky.social funding for bringing groups together.
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Pedro Ribeiro @pedrogribeiro.bsky.social · 18/09/2025
That's it! On Monday I defended my PhD working with the genomics and evolutionary history of the relationship between butterflies and Wolbachia, with a comment on the use of genomics to conservation! Thanks a lot to @pavelmatosm.bsky.social for supervising and mentoring!
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Pedro Ribeiro @pedrogribeiro.bsky.social · 18/08/2025
@pavelmatosm.bsky.social has a new PhD position opportunity to work with conservation genomics of European butterflies! The project involves very cool collaborations with @projectpsyche.bsky.social, @10klepgenomes.bsky.social and the LepEUConsortium! Deadline Sep 12 pavelmatos.wordpress.com/join-us/
pavelmatos.wordpress.com
Join us
Opportunities Below are the positions currently open in our lab. PhD position (full-time doctoral funding) We are seeking a highly motivated PhD student to join our team. The goal of the project is…
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Rob Waterhouse @rmwaterhouse.bsky.social · 04/07/2025
This month's ERGA BioGenome Analysis & Applications Seminar will feature a talk by speaker Pío Sierra about a new tool, pantera, which allows faster identification of Transposable Elements in genome assemblies. www.erga-biodiversity.eu/post/faster-...
erga-biodiversity.eu
Faster identification of Transposable Elements in full genome assemblies
This month's ERGA BioGenome Analysis & Applications Seminar will feature a talk by speaker Pío Sierra about a new tool, pantera, which allows faster identification of Transposable Elements in genome a...
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Pedro Ribeiro @pedrogribeiro.bsky.social · 25/06/2025
Anybody out there with BayesAss2 experience? I think we are not understanding each other about how the input file has to look like!
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Christopher Wheat @chriswheat.bsky.social · 22/06/2025
🚨Postdoc opportunity🚨: LepEU postdoc: comparative population genomics of European scale adaptation in butterflies 2 year, full-time PD in my group, Stockholm Univ. Applications assed on rolling basis, deadline: 23 August 2025. Planned start 1 Oct. Details: christopherwheatlab.wordpress.com
The aim of this proposal is to place population genomic insights into a comparative framework to gain fundamental insights into the determinants of evolutionary outcomes. The project will work within LepEU, the European Lepidopteran Population Genomics Consortium (https://lepeu.github.io/). LepEU provides access to field samples from European populations of diverse species. Chromosome-scale reference genomes are provided by Project Psyche (https://www.projectpsyche.org/). Networking during the postdoc will be facilitated by participation in the 10kLepGenomes COST Action (https://10klepgenomes.eu/). Existing datasets await analysis, while additional samples need DNA extraction and submission for sequencing. Functional validation capability (CRISPR/Cas9 gene manipulations) is also available to test emergent hypotheses of allele-to-phenotype impacts. Personal research interests of the postdoc will be important to determine the exact project, as the project has a generous sequencing budget.The successful applicant should have a PhD (obtained within 6 years of the application deadline) in a suitable subject area, such as evolutionary biology or population genomics. A strong interest in population genomics, local adaptation, comparative analyses, and experience working with genomic-scale data is essential. The candidate must have a documented publication record demonstrating relevant skills. Experience working with bioinformatic pipelines (e.g., Snakemake), or working with butterflies is welcome but not essential. The net salary is 28,000 SEK/month (~2,430 Euro, not subject to Swedish income tax) and comes directly from the Carl-Trygger Foundation stipend, which is paid out directly to the postdoc. Only PhD candidates acquired outside of the host department can apply. Currently, the lab of Prof. Wheat consists of 3 postdoctoral researchers, while the Dept. of Zoology provides a vibrant and excellent research environment of active, dynamic researchers. 

Applications should include: i) a succinct description of research interests and experience, detailing your contribution to any relevant publications (max 1 page), ii) why you are the ideal candidate for this position in the lab (max 1 page); iii) a CV including a list of publications, and iv) the name and contact information of two personal references. 

Applications will be reviewed on a rolling basis with a deadline of 23 August 2025. The project is planned to start on 1 October, but flexibility in the starting date can be provided for a suitable candidate. Please contact Prof. Wheat for additional information.
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Alexis Stamatakis @stamatak.bsky.social · 15/05/2025
RAxML-NG v2.0 beta is here github.com/amkozlov/rax... Features 1. Difficulty prediction academic.oup.com/mbe/article/... 2. Adaptive search academic.oup.com/mbe/article/... 3. Early Stop www.biorxiv.org/content/10.1... 4. Model selection 5. Rapid bootstrapping academic.oup.com/mbe/article/...
github.com
Release RAxML-NG v2.0-beta2 · amkozlov/raxml-ng
Main new features Adaptive tree search heuristic (Togkousidis 2023) , (Togkousidis 2024) Multiple fast branch support measures Integrated model testing Full Changelog: 1.2.2...2.0-beta2
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Project Psyche @projectpsyche.bsky.social · 20/03/2025
(1/4) In its first year, #ProjectPsyche has engaged with the research community by creating networks with experts in moths and butterflies 🦋 Members of the project have also trained the research community in #GenomeCuration, a key step in the generation of genomes 🧬
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Marc Somssich @somssich.bsky.social · 12/03/2025
This Editorial by Brandon S. Gaut and Claudia A. M. Russo provides some nice insight into how #SocietyJournals work, and why it pays for Scientists to publish with #SocietyOwned Journals. 👇 A Message From the Editors-in-Chief academic.oup.com/mbe/article/... #PlantScience #SciencePublishing
academic.oup.com
A Message From the Editors-in-Chief
We have been Co-Editor-in-Chiefs of Molecular Biology and Evolution (MBE) for 2 years now. In that time, we have learned a great deal about the science of
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Charlotte Wright @charlottewright.bsky.social · 08/03/2025
It's been brilliant to discuss so many aspects of Project Psyche as a community and find ways to make Psyche even better! Big thank you to @lepphylo.bsky.social @lunduniversity.bsky.social for hosting us and COST for making this meeting possible! www.cost.eu/actions/CA23...
cost.eu
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Joana Meier @joanameier.bsky.social · 24/02/2025
Do you use Darwin Tree of Life (DToL) genomes for your work or grant applications? If so, can you please fill out this form? docs.google.com/forms/d/e/1F... We are gathering info on how DToL genomes are used. It will help us raise money to continue producing publicly available high-quality genomes.
docs.google.com
Darwin Tree of Life Impact Assessment
This form is used to share information within DToL about case studies, ongoing research, and funding awards that demonstrate the impact the Darwin Tree of Life consortium project has had on Global and...
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Pedro Ribeiro @pedrogribeiro.bsky.social · 24/02/2025
Official petition for using em-dash in scientific publication (is it used?). It feels to me a bit too flamboyant to use it in a paper, but honestly I see it as a stylish alternative to "i.e" or sometimes colons.
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Niklas Wahlberg @lepphylo.bsky.social · 06/02/2025
A postdoc opportunity to work on Noctuidae (Lepidoptera) functional genomics with me, @jadrankarota.bsky.social and @chriswheat.bsky.social in Lund, Sweden. We aim to leverage the amazing amount of data being generated by @projectpsyche.bsky.social and DToL projects. lu.varbi.com/en/what:job/...
lu.varbi.com
Postdoctoral fellow in Noctuidae functional genomics
Subject description The project will use a comparative functional genomes approach to study a species-rich group of moths, Noctuidae (Lepidoptera). Noctuidae have both a huge negative and positive imp
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KamilSJaron.bsky.social @kamilsjaron.bsky.social · 31/01/2025
🚨Registration open🚨 1st - 6th of June, me, Katie Jenike, @rayanchikhi.bsky.social and Gene Myers will run a week long workshop on k-mers for biodiversity genomics organised by @connectingscience.bsky.social at @sangerinstitute.bsky.social. Join us & get equipped to wrestle large genomic datasets!
https://coursesandconferences.wellcomeconnectingscience.org/event/k-mer-workshop-for-biodiversity-genomics-20250601/
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Pedro Ribeiro @pedrogribeiro.bsky.social · 10/01/2025
@lepphylo.bsky.social was ahead of me to post about our paper together with Pavel Matos, @joanameier.bsky.social and others! I will come back to this to talk a bit more about it. For me, this is the product of amazing collaborations with inspiring people!
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Niklas Wahlberg @lepphylo.bsky.social · 03/01/2025
Happy to have been part of this new article on planthopper (Fulgoromorpha) systematics! A great collaboration between Jagiellonian and Lund Universities! doi.org/10.1111/syen...
doi.org
Phylogenomic insights into the relationship and the evolutionary history of planthoppers (Insecta: Hemiptera: Fulgoromorpha)
Using genomic data from 285 species across 19 planthopper families, we conducted the first phylogenomic study targeting global planthoppers and inferred their phylogeny with the highest resolution s.....
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Pedro Ribeiro @pedrogribeiro.bsky.social · 19/12/2024
In our lab's website, we have a Blog section for more informal articles: our research, "philosophical" discussions from our meetings and journal clubs. I've contributed to two of these blog posts: - Are cryptic species real? - Congresses attended by our [...] pavelmatos.wordpress.com/category/blog/
pavelmatos.wordpress.com
Blog – Matos Lab
Posts about Blog written by admin
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Pedro Ribeiro @pedrogribeiro.bsky.social · 19/12/2024
Left ex-twitter today (finally). There I tried to maintain a strictly science-based profile. Here I will try to be more flexible, bringing some readings, movies, music, personal life in general. But the aim is mostly to engage with researchers! Cheers!
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