David Emms

SHOOT, the phylogenetic sequence search engine, has been published! SHOOT is like BLAST, but instead of a list of similar sequences you get a maximum likelihood phylogenetic tree for your query gene sequence. Try it👉 shoot.bio Article👉 bit.ly/3qLGb2N

OrthoFinder just dropped a major update It’s faster, more accurate, and ready for thousands of genomes Let’s break it down (1/10) github.com/OrthoFinder/Or… biorxiv.org/content/10.110…

It has been a while… but an updated, faster & more accurate version of OrthoFinder is now out! Scales to thousands of species on conventional compute resources with higher accuracy than ever before and the same data rich fully phylogenetic outputs 👉biorxiv.org/content/10.110…

We are looking for a postdoc in comparative genomics/bioinformatics! They will be working in a collaborative environment on an exciting project about synteny, orthology, evolution, gene loss and 🍅. Details: tinyurl.com/4fenkydr Please share! @DessimozLab @SebastianSoyk

#PhD or #Postdoc using #genomics🧬 to study non-model eukaryotes 🐸🐌🌿 in #Europe? Join the #European Reference #Genome Atlas @erga_biodiv to participate in webinars, committee actions, #training: collaborative #biodiversity data production & analysis erga-biodiversity.eu/ergacalendar

Please RT Last few days left to apply! 4 positions to join us at Oxford, driving the next phase of development to OrthoFinder 🧬 We have so many cool ideas and fun things to try. Lets enhance the communities comparative genome capability together! 👉shorturl.at/gtHKT

SHOOT, from @David__Emms & @Steve__Kelly, searches for a sequence in a database of phylogenetic trees, identifies the homology group, and places that sequence in the phylogeny. It finds closest related sequence better than BLAST, with similar speed genomebiology.biomedcentral.com/articles/10.11…

We have TWO fully funded PhD studentships available in our group to study 3D growth in plants. Both studentships are available from October 2022. Please get in touch if you’re interested. Please do retweet and/or spread the word 😃 🧬 🌱

The preprint describing our comparative genomics #Rstats package is on bioRxiv (link below). GENESPACE uses synteny to explore variation among multiple genomes. For example, here are the syntenic regions to the human X and chicken Z sex chromosomes across 17 vertebrates

Plant Science Research Weekly plantae.org/plant-science-… X-species sRNAs, SynBio -> N fixation, gene evolution & organelles, land plant evolution, archaeon at the prok–euk interface, SMXL & phloem, reclassifying filamentous pathogens, drought stress & mycobiomes, and more!

Our GENESPACE comparative genomics R package is on github! GENESPACE conducts synteny-constrained comparisons of gene copy number and presence absence variation among genomes of any ploidy, and makes graphics like this (synteny among grasses, colored by rice chromosomes):

Registrations are now open for the 4th edition of the #ComparativeGenomics course with @sedlazeck and Ingo Ebersberger in March 🔗physalia-courses.org/courses-worksh… #Genomics #Bionformatics @PacBio #longreads @nanopore