Joran Martijn
@JoranMartijnMicrobial evolution, phylogenetics, metagenomics, sequencing and all that jazz
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Attending a conference? Consider compensating your carbon footprint using 'All things small and green': allthingssmallandgreen.org.uk/allthingsmalla…
It’s out! Our paper “Marine Sediments Illuminate Chlamydiae Diversity and Evolution” was published in @CurrentBiology today! Below a thread with major highlights 1/11 cell.com/current-biolog…
We present PhyloMagnet, a workflow to screen meta-omics datasets for taxa and genes of interest. Developped by @maxemilschon in the @Ettema_lab academic.oup.com/bioinformatics…
Assembly methods for nanopore-based metagenomic sequencing: a comparative study biorxiv.org/cgi/content/sh… #biorxiv_bioinfo
I'm beyond excited to share our first #plastic-#microbe article on bacterial candidates for colonization and degradation of #marine plastic debris in Environmental Science & Technology pubs.acs.org/doi/full/10.10… and my excellent student Line Roager's very first article 😊👑🦠
Lateral transfers repeatedly remodeled the oxygen detoxification pathway in Diplomonads, likely helping anaerobes like the parasitic Giardia intestinalis adapt to low-oxygen environments like the host digestive tract: buff.ly/2mutnPP @alejimgon @_feifeixu @janandericm
Ever wonder about the accuracy of gene predictions? We did. Turns out that gene callers are 5% or more inaccurate. They are particularly bad at choosing the correct start codon. Our collaboration with the Gonzalez lab at UCSD, now out in Bioinformatics: academic.oup.com/bioinformatics…
This is amazing
OK y'all, it is now my pleasure to show off some of the truly, genuinely heinous plots students in my Reproducible Data Analysis class made. Content warning: these plots are f***ing awful.
Lateral acquisitions repeatedly remodel the oxygen detoxification pathway in diplomonads and relatives #protists latest from @MolEvoUpp @UppsalaProtists @alejimgon @janandericm @_feifeixu academic.oup.com/gbe/advance-ar…
An ERC funded PhD position is open in our lab to work on the phylogeny and genome evolution of Archaea. Students with a strong bioinformatics background are welcome to apply through bit.ly/314PnjW
PhD position co-supervised by David Moreira, Puri Lopez-Garcia and myself. Exciting and challenging project ahead, don't hesitate to apply!
An ERC funded PhD position is open in our lab to work on the phylogeny and genome evolution of Archaea. Students with a strong bioinformatics background are welcome to apply through bit.ly/314PnjW
CB: Both raw read & consensus accuracy continue to improve. We’re seeing some great results from the Community, eg. Soren Karst’s method for long amplicons with UMIs had an error rate of just 0.03% across the whole rRNA operon of 4.4 kb bit.ly/30V2Iv4 #GenomeScience2019
rnaSPAdes: a new de novo transcriptome assembler from the @spadesassembler team and its application to RNA-Seq data doi.org/10.1093/gigasc… #RNAseq
The first plastid symbiosis likely took place in freshwater or terrestrial environments. Did it also occur in warm habitats?
When I die I want the academic publishing industry to lower me into the grave so it can let me down one last time. #academia
AR(10)E we there yet? New blogpost from @kirk3gaard on @nanopore R10 data albertsenlab.org/ar10e-we-there…
Great news everyone, the genome profiling manuscript is on #bioRxiv! We present in there GenomeScope and #smudgeplot. These tools have fundamentally changed my views on genomics, so I feel I should elaborate a bit 🤔
GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes biorxiv.org/cgi/content/sh… #biorxiv_bioinfo
Proud of our new postdoc @PrecambrianGoat who published one of his PhD chapters in @NatureMicrobiol today “An archaeal origin of the Wood–Ljungdahl H4MPT branch and the emergence of bacterial methylotrophy“ nature.com/articles/s4156…
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Who to follow
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Daniel Tamarit
@DanielTamarit -
Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
@Ettema_lab -
Anja Spang (she/her)
@anjspa1 -
Laura Eme
@eme_laura -
Courtney Stairs
@cstairs -
Andrew J. Roger (@andrewjroger.bsky.social)
@andrewjroger -
Fabien Burki
@fburki -
Jimmy Saw
@jimmysaw -
Kasia Zaremba-N
@kasiazarn -
Mahwash Jamy
@JamyMahwash -
Matt Brown
@socialprotist -
Tom Williams
@tweethinking -
Tami Lieberman
@conTaminatedsci -
Stephan Köstlbacher
@koestlste -
Anna Karnkowska
@ania_karnkowska
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