David Emms @David__Emms

Developer of OrthoFinder and https://t.co/pWdIdp8atF, interested in phylogenomics and all things trees. Former postdoc in the @Steve__Kelly lab. github.com/davidemms/Orth… Joined September 2017

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DrBelcher @dr_belcher

11 months ago

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…

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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…

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David Emms @David__Emms

11 months ago

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…

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David Emms @David__Emms

11 months ago

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

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David Emms @David__Emms

11 months ago

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!

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Natasha Glover @Gloveface

3 years ago

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

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Rob Waterhouse also @rmwaterhouse.bsky.social @rmwaterhouse

3 years ago

#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

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Steve Kelly @Steve__Kelly

3 years ago

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

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Genome Biology @GenomeBiology

4 years ago

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…

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David Emms @David__Emms

4 years ago

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

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David Emms @David__Emms

4 years ago

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

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David Emms @David__Emms

4 years ago

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

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Laura Moody @moodytomato

4 years ago

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 😃 🧬 🌱

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John Lovell @_johntlovell

4 years ago

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

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mary williams @PlantTeaching

6 years ago

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!

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John Lovell @_johntlovell

5 years ago

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):

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David Emms @David__Emms

5 years ago

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!

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David Emms @David__Emms

5 years ago

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.