@ddylus
Joined April 2009
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  • Following124
  • Followers80
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So happy to see our brittle star genome led by 𝗘𝗹𝗶𝘀𝗲 𝗣𝗮𝗿𝗲𝘆 finally published in @NatureEcoEvo highlighting the evolution of echinoderm chromosomes as well as the origin of the regeneration programm nature.com/articles/s41559-0…

The brittle star genome illuminates the genetic basis of animal appendage regeneration

Nature Ecology & Evolution - A newly sequenced genome of the brittle star Amphiura filiformis and gene expression profiling of adult arm regeneration reveal genes with conserved expression...

nature.com
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Excited to release FastOMA, a rewrite of OMA orthology algorithm that scales linearly, while maintaining OMA’s high accuracy. FastOMA can process all >2000 eukaryotic UniProt ref proteomes within 24 hours. Try it out github.com/DessimozLab/FastO… Preprint: biorxiv.org/content/10.1101/… (1/4)
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Happy to see a summary about Read2Tree from our @NatureBiotech paper from my home country @austria (German only sorry): science.apa.at/power-search/… Link to paper nature.com/articles/s41587-0… @cdessimoz @SinaMajidian @ddylus @BCM_HGSC @RiceCompSci
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Did you catch @Gloveface's talk about bringing science to the public at #SMBE2023? Be sure to also check out her GBE article: Homoeolog Inference Methods Requiring Bidirectional Best Hits or Synteny Miss Many Pairs buff.ly/44K6aJN
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📢📢📢 The new 2023-2024 list is out! Please share widely! If you are looking for a faculty position or postdoc in ecology & evolutionary biology check out this great community run resource: docs.google.com/spreadsheets…

ecoevojobs.net 2023-24

docs.google.com
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Could you envision a future where inferring #orthology for thousands of species becomes possible?! The future is already here and I'll be presenting FastOMA in #ISMBECCB2023 in Lyon! See you in EvolCompGen @EvolComp on Thursday 27th at 15:30! Try it out github.com/DessimozLab/FastO…
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Pls RT: 4 weeks until the registration deadline of our #Bioinformatics #Science #Hackathon @BCM_HGSC. Come join us & work on exciting prototypes across @dnanexus @PacBio @nanopore @GREGoR_research @SMaHTnetwork. Prizes for the best teams! Aug30-Sept1: hgsc.bcm.edu/events/hackatho…
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The length distribution of proteins is remarkably uniform across the tree of life ➡️ universal selection force at play. Paper by postdoc extraordinaire @Why_NeverS, with @OdileLecompte & @Gloveface. 📝Blog post + backstory lab.dessimoz.org/blog/2023/0… 📰Paper doi.org/10.1186/s13059-023-0…
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Reminder that we have 2 postdoc openings: 1) position on synteny and gene loss in 🍅w/ @SebastianSoyk xitter.cf/Gloveface/status/16583… 2) evolutionary structural biology to reconstruct the proteome & interactome of the first animal (urmetazoa) w/ @pedrobeltrao xitter.cf/pedrobeltrao/status/16…
Pedro Beltrao@pedrobeltrao8 Jun 2023
We are hiring for a postdoc position in evolutionary structural biology with the lab of @cdessimoz to study the evolution of animal cells. Based either in Zurich or Lausanne depending on personal circumstances. More details at: career5.successfactors.eu/ca…
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This is part of an exciting @snsf_ch -funded interdisciplinary grant with @dirk_fasshauer, @multicellgenome and @steg0s4urus. This position is to develop cutting edge methods for evolutionary structural biology. Please apply or help us spread the word!
Pedro Beltrao@pedrobeltrao8 Jun 2023
We are hiring for a postdoc position in evolutionary structural biology with the lab of @cdessimoz to study the evolution of animal cells. Based either in Zurich or Lausanne depending on personal circumstances. More details at: career5.successfactors.eu/ca…
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Bioinformatics can address these challenges! At SIB, we have researchers on it (e.g. Daniele Silvestro @unifr & @rmwaterhouse @unil), an environmental working group, and we are now looking for a *Director for Environmental Bioinformatics*. Apply or share! apply.refline.ch/499599/0280…
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Replying to @NatureBiotech @unil @ISBSIB @ETH_en @BCM_HGSC @RiceCompSci @uclcs @CloeFor @sedlazeck @ddylus
Co-lead authors @cdessimoz and @sedlazeck go #behindthepaper on a method to build phylogenetic trees directly from raw reads, bypassing time-consuming steps such as genome assembly. Plus: what Read2Tree has in common with the song "Smoke on the Water" go.nature.com/3KAZcz0

Read2Tree infers phylogenetic trees from raw sequencing reads quick and easy

We just published a method to build phylogenetic trees directly from raw reads, bypassing time-consuming steps such as genome assembly. This post gives the short story and the backstory. In particu...

communities.springernature.com
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Super happy that the Read2Tree paper is now out at @NatureBiotech—the centrepiece of @ddylus’s postdoc and a wonderful collaboration with @sedlazeck. Key contributions by @SinaMajidian and @AdrianAltenhoff too. nature.com/articles/s41587-0…

Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree

Nature Biotechnology - Phylogenetic trees are generated from sequencing reads without genome assembly or annotation.

nature.com
Christophe Dessimoz@cdessimoz20 Apr 2022
My favourite application of Read2Tree is depicted below, where it correctly resolves *on the same tree* very different Coronaviridae samples (from mink and bat), as well as minute differences among variants of SARS-CoV-2. Check out biorxiv.org/content/10.1101/… xitter.cf/sedlazeck/status/15167…
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Check out our new paper on "Antibacterial inhibitors targeting the lipoprotein transport pathway". #antibiotics #microbiology #infectiousdiseases doi.org/10.1016/j.bbamcr.202…
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Looking for a #postdoc? We're looking for candidates to apply to the Beatriu de Pinos Postdoc program to join our lab @metazomics @IBE_Barcelona. 3-year contract and competitive salary. Possibility of funding until publication of selected candidates 1/2
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Genome annotation quality affects so many things we do. Our brilliant Yannis Nevers @Why_NeverS devised a tool to assess proteomes—quick and easy. It reports not only *missing* but also *dubious* content! Blog post: lab.dessimoz.org/blog/2022/1… Preprint: doi.org/10.1101/2022.11.25.5…
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David Dylus retweeted
EvolCompGen@EvolComp13 Jul 2022
Replying to @sedlazeck
@sedlazeck presents Read2Tree: a new assembly-free approach to directly infer phylogenetic trees efficiently from raw reads with 0.2x coverage+. Come hear how it applied to Coronaviridae samples Room: G With @ddylus, Adrian Altenhoff, @SinaMajidian, and @cdessimoz #ISMB2022
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Read2Tree: an assembly-free comp. genomics method for small & large-scale projects. Works on @Pacbio @nanopore @illumina& RNA/DNA & low coverage 0.2x+. Get your phylo tree from raw reads in minutes! e.g #COVID19 biorxiv.org/content/10.1101/… @ddylus @cdessimoz @BCM_HGSC #Bioinformatics
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Happy to announce that our (@schierlab, @hilsawh) paper is now available in its final, beautiful, form @NatureEcoEvo! rdcu.be/cB2V8
Maxwell Shafer@maxwellshafer14 Dec 2020
I am happy to present our new preprint "Gene family evolution underlies cell type diversity in the hypothalamus of teleosts" with @hilsawh and @schierlab! biorxiv.org/content/10.1101/…

Gene family evolution underlies cell type diversification in the hypothalamus of teleosts

Hundreds of cell types form the vertebrate brain, but it is largely unknown how similar these cellular repertoires are between or within species, or how cell type diversity evolves. To examine cell...

biorxiv.org
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Important thread with great examples of unconscious bias in scientific careers. Very much worth reading. #inclusion #diversitymatters #HeForShe
Dr. Melanie Blokesch@MBlokesch30 Sep 2021
A🧵 - Serving on many panels & commissions, I realize the good will to help women & minorities in science. But are extra programs for women or temporary solutions the best we can do? In my opinion, not really. Instead, we need to focus more on 𝘂𝗻𝗰𝗼𝗻𝘀𝗰𝗶𝗼𝘂𝘀 𝗯𝗶𝗮𝘀. 1/X
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