|
Alex Crits-Christoph@acritschristoph.bsky.social |
846 followers 723 following 503 posts
Computational microbiologist
|
Marco Galardini
@mgalactus.bsky.social
[ View ] |
Do you want to run a microbial GWAS but are put off by installing a dozen different bioinformatic tools, are unsure about best practices, and how to transform the list of threshold passing variants into a neat annotated table?
Then we have just the thing for you!
www.biorxiv.org/content/10.1...
1 replies 5 reposts 4 likes
|
Jack A Gilbert
@gilbertjacka.bsky.social
[ View ] |
It's that time of year again. The Applied Microbiology International's Horizon Award applications are due. You can nominate yourself or someone else here appliedmicrobiology.org/membership-c...
0 replies 2 reposts 2 likes
|
|
Alex Crits-Christoph
@acritschristoph.bsky.social
[ View ] |
Repeated plague infections across six generations of Neolithic Farmers
www.nature.com/articles/s41...
Yersinia genomes from a plague 5000 years ago:
0 replies 8 reposts 9 likes
|
Jim Shaw
@jimshaw.bsky.social
[ View ] |
Our paper, Floria, is now out in the ISMB 2024 Bioinformatics proceedings!
Floria can obtain strain-level haplotypes of metagenomes for *noisy long reads* or *short reads* in minutes
With Jean-Sebastien Gounot, Hanrong Chen, Niranjan Nagarajan, Yun William Yu
academic.oup.com/bioinformati...
1 replies 5 reposts 11 likes
|
|
Alex Crits-Christoph
@acritschristoph.bsky.social
[ View ] |
2025 EMBL events:
www.embl.org/about/info/c...
0 replies 2 reposts 3 likes
|
|
Alex Crits-Christoph
@acritschristoph.bsky.social
[ View ] |
Simultaneous multi-site editing of individual genomes using retron arrays
for making multiple genomic edits concurrently
www.biorxiv.org/content/10.1...
0 replies 1 reposts 2 likes
|
|
Alex Crits-Christoph
@acritschristoph.bsky.social
[ View ] |
*newly available Loki culture, not new culture
www.microbiologyresearch.org/content/jour...
1 replies 1 reposts 2 likes
|
|
Alex Crits-Christoph
@acritschristoph.bsky.social
[ View ] |
A story behind the new Loki culture: "one culture collection declined our request to deposit the strain- For the other three, two unfortunately could not preserve the strain and only one culture collection succeeded – Japan Collection of Microorganisms"
microbiologysociety.org/blog/appreci...
1 replies 1 reposts 4 likes
|
bioRxiv Microbiology
@biorxiv-microbiol.bsky.social
[ View ] |
Genome-resolved year-round dynamics reveal a broad range of giant virus microdiversity www.biorxiv.org/content/10.1101/2024.07.08.602415v1
0 replies 3 reposts 4 likes
|
Anne Kupczok
@annecmg.bsky.social
[ View ] |
New paper with Nikos Vakirlis: we found thousands of species-specific genes in the human gut microbiome (some with evidence of selection) and they mostly seem to be "grown locally" in bacteria, rather than transferred from phages. genome.cshlp.org/content/earl...
1 replies 4 reposts 2 likes
|
|
Andrew Rambaut
@arambaut.bsky.social
[ View ] |
We are delighted to announce BEAST X v10.5.0 (beta 1) - the X is to differentiate it from the project 'BEAST2' & to denote these are orthogonal with a common origin.
Website: beast.community
Github: github.com/beast-dev/be...
Many new models, performance enhancements and features (and a new logo)
2 replies 26 reposts 26 likes
|
Mike Blazanin
@mikeblazanin.bsky.social
[ View ] |
Glad to see this out! gcplyr is an R package that makes it easy to wrangle and analyze microbial growth curve data. In the paper, I highlight what it adds compared to other software
(a new version is up too! update to get the latest features)
#microbiomesky #MicroSky 🧬🖥️🦠🔬
doi.org/10.1186/s128...
0 replies 17 reposts 23 likes
|
|
Alex Crits-Christoph
@acritschristoph.bsky.social
[ View ] |
meh, no answer but to post more
0 replies 0 reposts 3 likes
|
Michael Kuhn
@biocs.bsky.social
[ View ] |
"Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries" from @fasnicar.bsky.social @cibiocm.bsky.social
www.sciencedirect.com/science/arti...
1 replies 1 reposts 1 likes
|
Roland Hatzenpichler
@environmicrobio.bsky.social
[ View ] |
New preprint, 1st authored by GeorgeSchaible, coauthored by collaborators EMSL and MSU grad student Jen Crandall, addresses a gap in single cell isotope labeling: how well do results from SIP-Raman and SIP-NanoSIMS compare tinyurl.com/33375zfa
9 replies 4 reposts 5 likes
|
|
Roland Hatzenpichler
@environmicrobio.bsky.social
[ View ] |
It was a privilege to work with @markabelan.bsky.social on an infographic that summarizes the role of microbes in methane cycling, both cells that make or break methane. We have English, German and Spanish versions! Use widely and freely :)
3 replies 6 reposts 8 likes
|
Bkoskella
@bkoskella.bsky.social
[ View ] |
Job alert!! Join Integrative Biology at UC Berkeley. We are hiring an Assistant Professor in the area of global change biology with emphasis on the Ecology and Evolution of Host-Microbe Interactions (pathogens, mutualists, microbiomes).
aprecruit.berkeley.edu/JPF04476
0 replies 71 reposts 38 likes
|
Gregg Gonsalves
@gregggonsalves.bsky.social
[ View ] |
So proud of my old friend @peterstaley.bsky.social for standing up for EcoHealth Alliance when no one else will. www.statnews.com/2024/07/08/e...
0 replies 12 reposts 31 likes
|
|
Alex Crits-Christoph
@acritschristoph.bsky.social
[ View ] |
Evolution and host-specific adaptation of Pseudomonas aeruginosa
www.science.org/doi/10.1126/...
0 replies 2 reposts 3 likes
|
Dave Baltrus 🦦
@surtlab.bsky.social
[ View ] |
Does anyone have an npt2 promoter sequence that can be synthesized into a plasmid (and works for expression?) Or, other strong promoter that works across Gram negative bacteria? TIA
0 replies 8 reposts 3 likes
|
Brett Baker
@archaeal.bsky.social
[ View ] |
See also the accompanying paper showing the archaeal ancestors are likely more compkex than previously thoght!
www.biorxiv.org/content/10.1...
0 replies 3 reposts 6 likes
|
Anupama Khare
@anukharelab.bsky.social
[ View ] |
New preprint from our lab! We found that Staph aureus evolves tolerance to pyocyanin produced by Pseudomonas aeruginosa via CodY mutations. Project was started by @saraalexander.bsky.social and then led by @tmartini.bsky.social who tested so many possibilities to pin down the mechanism!
0 replies 4 reposts 6 likes
|
bioRxiv Genetics
@biorxiv-genetic.bsky.social
[ View ] |
Sedentary chromosomal integrons as biobanks of bacterial anti-phage defence systems www.biorxiv.org/content/10.1101/2024.07.02.601686v1
0 replies 1 reposts 1 likes
|
|
bioRxiv Microbiology
@biorxiv-microbiol.bsky.social
[ View ] |
The archaeal class Nitrososphaeria is a key player of the reproductive microbiome in sponges during gametogenesis www.biorxiv.org/content/10.1101/2024.07.03.601946v1
0 replies 2 reposts 3 likes
|
Thiago Carvalho
@cyrilpedia.bsky.social
[ View ] |
'Birkholz et al. have discovered that a mobile intron containing a homing endonuclease found within a viral RNA polymerase gene in one bacteriophage blocks productive infection by a related and competing coinfecting bacteriophage.'
www.science.org/doi/10.1126/...
0 replies 11 reposts 9 likes
|
|
Brett Baker
@archaeal.bsky.social
[ View ] |
After many years of work we present a preprint that doubles the numbers of Asgard genomes, revealing lots of new insights into their metabolism. Notably, lineages closely related to eukaryotes are capable of aerobic respiration!
www.biorxiv.org/content/10.1...
3 replies 18 reposts 25 likes
|
Evolution
@journal-evo.bsky.social
[ View ] |
We are now on Bluesky! Follow us for the latest on recent papers and journal updates.
✅ Research on all areas of evolutionary biology
✅ Society-owned (Society for the Study of Evolution)
✅ Free publication for SSE members
Read the latest papers and submit your research at academic.oup.com/evolut
1 replies 46 reposts 57 likes
|
|
Alex Crits-Christoph
@acritschristoph.bsky.social
[ View ] |
Ultrafast and accurate sequence alignment and clustering of viral genomes
www.biorxiv.org/content/10.1...
GitHub: github.com/refresh-bio/...
0 replies 5 reposts 8 likes
|
Bram van Dijk 🏳️🌈
@bramvandijk.bsky.social
[ View ] |
This is such a cool paper, highlighting that "spatial patterning" cannot be assumed, it emerges.
"Our study reveals the intricate interplay between phage predation, microbial spatial self-organization, and plasmid transfer."
www.nature.com/articles/s41...
0 replies 3 reposts 6 likes
|
Erin Cikanek
@erincikanek.bsky.social
[ View ] |
I see a lot of “but I already vote! And one time I marched!” today and people feeling they already “do it all.” Here are three things you might consider to be involved with politics. 1) sign up to GOTV. For a congressional/state/local candidate. Politics is about mobilization & coordination 1/3
3 replies 18 reposts 37 likes
|
Jonathan Friedman
@jfriedman.bsky.social
[ View ] |
Happy to share our latest manuscript we we study evolutionary rescue in a bacterial mutualism:
Reversion to metabolic autonomy underpins evolutionary rescue of a bacterial obligate mutualism
shorturl.at/tFNTw
1 replies 13 reposts 15 likes
|
Craig MacLean
@craigmaclean.bsky.social
[ View ] |
New paper: Antibiotic resistance mutations alter the ability of pathogenic bacteria to compete against commensal competitors.
academic.oup.com/evlett/advan...
Resistance is costly, but sometimes allows pathogen to overcome competitors
Fun collaboration with Wheatley lab: @rwheatley8.bsky.social
1 replies 14 reposts 21 likes
|
Cameron Thrash
@jcamthrash.bsky.social
[ View ] |
RNA-guided RNA silencing by an Asgard archaeal Argonaute www.nature.com/articles/s41... #jcampubs
1 replies 7 reposts 11 likes
|
|
Alex Crits-Christoph
@acritschristoph.bsky.social
[ View ] |
The atmosphere: a transport medium or an active microbial ecosystem? From @greening.bsky.social et al.
academic.oup.com/ismej/articl...
0 replies 3 reposts 4 likes
|
Geo Santiago-Martínez
@geosantiagom.bsky.social
[ View ] |
Interested in microbes, biofilms & nutrient cycles?
The UConn Microbial Ecophysiology Lab is pleased to share this article about the work of Luis E. Valentín‑Alvarado & colleagues from the The Banfield Lab at UC Berkeley
Amplifying diverse voices together!
doi.org/10.1038/s415...
0 replies 2 reposts 2 likes
|
Microplastics Sommelier
@leastactionhero.bsky.social
[ View ] |
einstein sent this to curie in 1911 when she was being harassed by tabloids. it contains everything you’d want in such a letter: (1) your haters are trash (2) you’re a baller, a true queen (3) i have determined the statistical law of motion of the diatomic molecule in planck’s radiation field 🧪⚛️
37 replies 1465 reposts 3943 likes
|
|
Cameron Thrash
@jcamthrash.bsky.social
[ View ] |
Codon bias, nucleotide selection, and genome size predict in situ bacterial growth rate and transcription in rewetted soil www.biorxiv.org/content/10.1... #jcampubs
0 replies 3 reposts 3 likes
|
Molly Przeworski
@mollyprz.bsky.social
[ View ] |
@natanaels.bsky.social's work modeling how mutations accumulate with age and time, now out in PLoS Biology (joint with @marcdemanuel.bsky.social, William Milligan & Guy Sella): journals.plos.org/plosbiology/...
0 replies 16 reposts 22 likes
|
Simon Roux
@simrouxvirus.bsky.social
[ View ] |
Reminder - sessions proposals are open for ASM 2025 ! asm.org/events/asm-m...
Come help shape the program of what should be another exciting meeting, by making sure the topics you care about and you find critical to cover are included ! (And as usual, DMs are open if you have any questions!)
0 replies 8 reposts 7 likes
|
|
Alex Crits-Christoph
@acritschristoph.bsky.social
[ View ] |
Very interesting mystery from Tom Delmont, @mkrupovic.bsky.social, @merenbey.bsky.social et al
0 replies 0 reposts 4 likes
|
|
Alex Crits-Christoph
@acritschristoph.bsky.social
[ View ] |
Egoviruses: distant relatives of poxviruses abundant in the gut microbiome of humans and animals worldwide
Novel dsDNA viruses related to poxviruses in the gut - host unclear, but could be either the mammals themselves or a unicellular eukaryote in the gut
www.biorxiv.org/content/10.1...
1 replies 9 reposts 16 likes
|
|
bioRxiv Microbiology
@biorxiv-microbiol.bsky.social
[ View ] |
Giant transposons promote strain heterogeneity in a major fungal pathogen www.biorxiv.org/content/10.1101/2024.06.28.601215v1
0 replies 3 reposts 2 likes
|
Daniel Bolnick
@danielbolnick.bsky.social
[ View ] |
Excited to share a new preprint:
biorxiv.org/cgi/content/...
In 2019 we founded 9 whole lake populations of stickleback, as part of a massive eco-evo experiment. Here, we report the first half decade of host-parasite & immune trait dynamics...
(thread, 1/N)
1 replies 10 reposts 23 likes
|
Michael Wagner
@michiwagner4.bsky.social
[ View ] |
Thank you very much team Aalborg for having invited us to become part of this journey to map the environmental microbiome of an entire country. Super exciting findings and a whole section on #nitrifier diversity and abundance in Denmark #MicroSky 🧪
www.biorxiv.org/content/10.1...
0 replies 2 reposts 14 likes
|
Carl Zimmer
@carlzimmer.bsky.social
[ View ] |
In new experiments, scientists have given bird flu to cows and watched what happens. The results indicate the virus isn't spreading in droplets infecting airways. For those worried about the evolution of a new pandemic, that's good news--for now. Here's my story. 🧪 Gift link: nyti.ms/3RNOYhX
0 replies 15 reposts 48 likes
|
|
Alex Crits-Christoph
@acritschristoph.bsky.social
[ View ] |
Powerful defense of Dr. Athony Fauci by Richard Horton in The Lancet:
www.thelancet.com/journals/lan...
“why is the international scientific community so quiet? ... The answer is self-censorship"
4 replies 24 reposts 37 likes
|
Jesse D. Jenkins
@jessejenkins.bsky.social
[ View ] |
The Supreme Court just blew up four decades of precedent today, in a decision that will make it harder for executive agencies to protect the environment, public health, worker safety and more.
www.axios.com/2024/06/28/s...
6 replies 45 reposts 78 likes
|
|
Alex Crits-Christoph
@acritschristoph.bsky.social
[ View ] |
Microflora Danica: the atlas of Danish environmental microbiomes
10,686 shotgun metagenomes from a variety of environments across Denmark
www.biorxiv.org/content/10.1...
0 replies 9 reposts 14 likes
|
|
Alex Crits-Christoph
@acritschristoph.bsky.social
[ View ] |
Finally, I kinda worry that the discourse out there misses the mark and presents a picture where metagenomics is a fuzzy unknowable black box and the "cleanest" database or algorithm wins out. But no! We can assemble, we can look at the reads and genomes: there are few mysteries in metagenomes n/n
0 replies 0 reposts 5 likes
|
|
Alex Crits-Christoph
@acritschristoph.bsky.social
[ View ] |
There are also false negatives in this work too (and for kraken, false negatives actually beget false positives at the same time): some cool nano-sized bacteria in the whole blood dataset. Likely all contaminants as identical strains exist across samples 8/n
1 replies 0 reposts 0 likes