Ali Hakimzadeh

Very much looking forward to our 10th (anniversary!) Microbial Genomics Training Course provided by #BiGi @denbi.bsky.social in Gießen.

3 days full of free hands-on microbial genomics training - from QC, assembly and annotation to genome submissions and comparative genomics.

#biodiversity #bioinformatics Summer School ... 21-26 June in Siegen, Germany co-organised by @sib.swiss & @denbi.bsky.social
www.sib.swiss/training/cou...
🟢 eDNA & ecosystems
🟣 pangenome diversity
🔵 population genetics
🟡 comparative genomics
Register to apply, selections will start from March 16th

Our review about plant endophytes an other leaf-inhabiting fungi out - check it out:
authors.elsevier.com/a/1mdbN6Do0q...

Global Soil Mycobiome Consortium dataset now extended to soil protists and animals (GloSED), including 4000 samples. Pre-publication data available at: zenodo.org/records/1782...
#fungi #soil #ecology #database

Summary of the Plant Bioinformatics course. AI-generated image (ChatGPT) showing some of the central elements. Details: https://github.com/bpucker/PlantBioinformatics

Getting ready for “Plant Bioinformatics” 🌱

Big data, command line, cloud computing & reproducible research — plus replicating published studies.

Materials: github.com/bpucker/Plan...

Study in Bonn: www.biologie.uni-bonn.de/de/studium/b...

#Bioinformatics #OpenEducation @puckerlab.bsky.social

Thank you brother 🙏🏻❤️

Ph.D. defended and the long read journey ends in frozen lands.
Deep thanks to @sanslan.bsky.social and @tedersoo.bsky.social. Special thanks to @owenwangensteen.bsky.social for a demanding and fair defence as the main opponent.
Thanks to all @myco-microbio.bsky.social members for their support.

Phil Ewels: Bioinformatics at Scale: nf-core + Nextflow The Bioinformatics CRO Webinar Series February 18, 2026: Phil Ewels gives a talk about Nextflow and nf-core for scalable, reproducible bioinformatics.

Next month, @ewels.bsky.social (Product Manager for OSS at @seqera.io)will be joining the Bioinformatics CRO webinar series to discuss #Nextflow, @nf-co.re, and exciting new features for reproducible bioinformatics at scale. 👇

hubs.la/Q040__J00

Paleoclimate pattern effects help constrain climate sensitivity and 21st-century warming | PNAS Paleoclimates provide examples of past climate change that inform estimates of modern warming from greenhouse-gas emissions, known as Earth’s clima...

Really excited to see this paper out!! Led by @vtcoop.bsky.social we show that if you use cold and warm paleoclimates together, you can reduce uncertainty in Earth's climate sensitivity by quantifying the pattern effect and more precisely constrain future climate change www.pnas.org/doi/10.1073/...

EMBL is deeply saddened by the passing of our Interim Director General Peer Bork, a pioneering scientist who left an indelible imprint on life science research in Europe and beyond.

We extend our deepest condolences to his family, friends, and colleagues.

www.embl.org/news/people-...

Still processing the news of Peer Bork’s passing. During TREC and TARA projects in Estonia, I witnessed firsthand his scientific depth and human warmth. His legacy will echo through generations of microbiome research. RIP.

Oh no… such shocking news. I’m really touched by this. A big loss for the computational biology community. 😓 RIP

In remembrance of Peer Bork  | EMBL EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.

very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...

🧬 Long-read metabarcoding is powerful, but chimera filters can trash good reads. Our new study benchmarks three algorithms on full-length ITS and shows how false positives distort results.
🔗 peerj.com/articles/204...

#Metabarcoding #LongRead #Bioinformatics #Chimeras

New fungal phylum-level system, with red font indicating novel taxa and size taxonomic diversity.

Fungal phylum-level classification update now available! Used "innovative taxonomy" to describe >100 taxa, from species to phylum, based on long reads, characteristic nucleotides and env-samples.
mycokeys.pensoft.net/article/1616...

#fungi #taxonomy #PacBio #classification #eDNA

New #metagenome assembly comparison of PacBio, ONT, and Illumina in human gut #microbiomes.

- "HiFi generated more cMAGs than ONT at every depth with either assembly method"
- "HiFi cMAGs had significantly higher completeness and lower contamination than ONT"

doi.org/10.1016/j.ce...

ERC grant will support placement of tens of thousands of previously unknown fungi on evolutionary tree Leho Tedersoo, Professor of Mycorrhizal Studies at the University of Tartu, has received the Advanced Grant from the European Research Council to systematise and describe members of the 95% majority o...

Read more from here: ERC grant will support placement of tens of thousands of previously unknown fungi on evolutionary tree ut.ee/en/news/erc-...

EukFunc: A Holistic Eukaryotic Functional Reference for Automated Profiling of Soil Eukaryotes The soil eukaryome constitutes a significant portion of Earth's biodiversity that drives major ecosystem functions, such as controlling carbon fluxes and plant performance. Currently, however, we mis...

Looking for a database to functionally assign your 18S (terrestrial)data to trophic groups? Look no further! Our article is published here: doi.org/10.1111/1755... and you can find the database here as a R package: github.com/lentendu/Euk... #soils #eukaryotes #protists #fungi

GitHub - rrwick/condaenvlist: a simple tool for listing conda environments with descriptions a simple tool for listing conda environments with descriptions - rrwick/condaenvlist

Do you (like me) create a bunch of conda environments, then later forget what they're for, when they were last updated, or which tools are in them?

If so, you might this little project: github.com/rrwick/conda...

The Impact of Oil Palm Plantations and Pastures on Benthic Prokaryotic and Fungal Communities in Tropical Streams The expansion of oil palm plantations and cattle grazing lands has a detrimental impact on freshwater ecosystems, causing ecological degradation and biodiversity loss in the tropics, although litt...

While oil palms and pastures alter tropical stream microorganisms, riparian buffers offer a lifeline. 🚑💧 Saving biodiversity could depend on protecting these green corridors.

🔗 Read more: doi.org/10.1111/fwb....
#eDNA #FreshwaterBiology #conservation

EUKARYOME v1.9.3 now available in eukaryome.org

A special release of long reads of marine microeukaryotes

I started an #eDNA starter pack as one didn’t exist yet. Feel free to message me to get your name added. Open to all! go.bsky.app/U2vgV5Q

End-to-end simulation of nanopore sequencing signals with feed-forward transformers https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae744/7930676 🧬🖥️🧪 https://github.com/ZKI-PH-ImageAnalysis/seq2squiggle

New preprint led by Ruben Gonzalez-Miguens for a new coi database that should be useful to annotate metabarcoding datasets with protists.

www.biorxiv.org/content/10.1...