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…

I've moved to new pastures, working on AI models for genomics at the excellent @instadeepai, but will carry on supporting the OrthoFinder team in the background. They're going to be working on some great, new functionality so keep an eye open for that: github.com/OrthoFinder/Or…

And with the new OrthoFinder team we have a new website to bookmark for all the latest updates: github.com/OrthoFinder/Or…

We have a new version of OrthoFinder: biorxiv.org/content/10.110… Faster scaling to larger species sets, phylogenetically resolved orthogroups, reduced RAM usage. Thanks to @dr_belcher, Yi Liu & Jonathan Holmes who have joined the team, and as ever OrthoFinder's PI @Steve__Kelly!

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…

SHOOT.bio is powered by OrthoFinder, DIAMOND, IQ-TREE, MAFFT, EPA-ng & phylotree.js with some other clever technologies under the hood to accelerate your search and gene tree inference. Try it👉 shoot.bio Article👉 bit.ly/3qLGb2N

You give SHOOT.bio a query sequence and it builds a gene tree and identifies the orthologs of your gene in other species Try it👉 shoot.bio Article👉 bit.ly/3qLGb2N

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

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):

The source code for the command line version is on GitHub: github.com/davidemms/SHOOT There's also code on GitHub for a SHOOT webserver. If you're interested in adapting it to enable phylogenetic gene search for a genome resource website, let me know!

The preprint for the SHOOT.bio gene search website with @Steve__Kelly has been updated: bit.ly/3BDiyfD SHOOT lets you search a protein sequence & get back a maximum likelihood gene tree for your sequence. It's a robust & easy way to get accurate orthologs.

@Steve__Kelly Thanks Steve, it's been a blast!

Its the end of an era tomorrow... @David__Emms leaves our group for his next adventure. I think its fair to say his impact on science has been huge. OrthoFinder has been game changing & has enabled so much amazing science around the world. Please join us in wishing him luck!