Sign in

Ali Hakimzadeh

@bioinfo94.bsky.social
154 followers 365 following 8 posts

Postdoctoral researcher in Max Planck Institute for marine microbiology #Bioinformatics Developing pipelines and custom modules for multiomics data analysis of microbiome, cancer and environmental data

PostsRepliesMedia
Reposted by Ali Hakimzadeh
Physalia-courses@ONLINE @physaliacourses.bsky.social · 23/09/2026
Closing our Machine Learning for Multi-Omics Integration course today! 🧬 Huge thanks to @oskolkov.bsky.social and to everyone who joined us from all over the globe this week🌍 It was a pleasure learning and connecting with you all! Next edition in February: www.physalia-courses.org/courses-work...
031
Reposted by Ali Hakimzadeh
Mycology and Microbiology Center @myco-microbio.bsky.social · 09/09/2026
#Eukaryome 2.1 has arrived—download it from the dedicated version page here: eukaryome.org #bioinformatics #taxonomy
eukaryome.org
HOME | EUKARYOME
023
Reposted by Ali Hakimzadeh
israelm03.bsky.social @israelm03.bsky.social · 20/08/2026
Our @myco-microbio.bsky.social from University of Tartu had a fantastic time at #ISME20 in Auckland! 🇳🇿 Insightful sessions & so many inspiring new connections. Honored to present my PhD poster & chat with everyone who stopped by! #FungalEcology #PhDLife
174
Reposted by Ali Hakimzadeh
Sten Anslan @sanslan.bsky.social · 08/08/2026
Benchmarking Illumina 2×500, PacBio and Oxford Nanopore for full-length ITS metabarcoding. PacBio performed best overall. More broadly, representative sampling is essential for reliably detecting land-use effects on soil biodiversity! onlinelibrary.wiley.com/doi/10.1111/...
174
Reposted by Ali Hakimzadeh
Leho Tedersoo @tedersoo.bsky.social · 26/06/2026
Major fungal genome-based global biogeography study published in New Phytologist by Yi-Hong Ke et al.: the success story of Suillus luteus. doi.org/10.1111/nph....
doi.org
Global population structures and demographic history of Suillus luteus, a pine co‐introduced ectomycorrhizal fungus associated with exotic forestry and invasion
Global phylogenomic tree and phylogenetic network of Suillus luteus and its closely related species.
0125
Reposted by Ali Hakimzadeh
Umeå Plant Science Centre @umeaplantsciencecentre.se · 24/03/2026
🧪🌾VACANCY - Postdoc in fungal ecology & modelling🧬 This 2-year postdoc focuses on mycorrhizal fungal biogeography using large-scale metabarcoding data and species distribution models.🌍 Join the group of @frewecologist.bsky.social and work with us @umeaplantsciencecentre.se! 📅 Apply by 30 April
01113
Reposted by Ali Hakimzadeh
Leho Tedersoo @tedersoo.bsky.social · 08/04/2026
African fungi mapped within a PhD project led by John Kupagme, an African PhD student. www.bioacad.com/article/doi....
083
Reposted by Ali Hakimzadeh
Inovine Conferences @inovineconferences.bsky.social · 08/04/2026
🌿 Session Highlight: Microbial Ecology & Plant Microbiomes 2nd International Conference on Plant Science and Molecular Biology (IPMB 2026) 📅 November 23–24, 2026 📍 Paris, France 📢 Submit your abstract: plantscience.inovineconferences.com/submit-abstr... #ipmb2026 #microbialecology #plantmicrobiome
122
Reposted by Ali Hakimzadeh
Ming Tommy Tang @tommytang.bsky.social · 07/04/2026
I built a personal AI assistant on a Mac Mini. Within 48 hours, cheap models had poisoned its memory with fabricated colleagues, fictional file shares, and an imaginary costume party. Here is what I learned.
141
Reposted by Ali Hakimzadeh
Ming Tommy Tang @tommytang.bsky.social · 03/04/2026
1/ Last year I was running a 6-hour alignment job on a remote server. Then I realized: I forgot to start screen or tmux. My laptop was about to die. Panic mode. Here's exactly how I saved that process without killing it:
151
Reposted by Ali Hakimzadeh
Mycology and Microbiology Center @myco-microbio.bsky.social · 13/03/2026
Nice progress — one of our members has just published her first paper on her PhD journey. The study shows how different soil sampling designs can dramatically change biodiversity estimates across animals, bacteria, and fungi. 🐀🦠🍄🧬
032
Reposted by Ali Hakimzadeh
Vladimir Mikryukov @vmikk.bsky.social · 11/03/2026
How much does sampling design matter in soil biodiversity surveys? A lot. Our new manuscript shows how diversity changes with sampling design, depth, subsample number, and pooling. I'm especially happy this is the first manuscript from Meirong Chen's PhD work, and very proud of her progress.
Heatmap comparing richness ranks across soil sampling designs for three organism groups: animals, bacteria, and fungi. Three side-by-side panels, with various sampling designs by rows, and habitats (marked by tree icons) by columns.
272
Reposted by Ali Hakimzadeh
Mycology and Microbiology Center @myco-microbio.bsky.social · 24/03/2026
New publications are springing up rapidly among our PhD students — like fungi after rain! Nice work — and ironically, this time it's all about the desert mycobiome! Who would’ve thought our publication “rainfall” comes from a desert? 😄
041
Reposted by Ali Hakimzadeh
Ming Tommy Tang @tommytang.bsky.social · 23/03/2026
I've been building Claude Code skills for a month. Turns out I was missing half the picture. Thariq from Anthropic just published lessons from hundreds of skills they use internally. 9 categories, dozens of patterns.
2122
Reposted by Ali Hakimzadeh
israelm03.bsky.social @israelm03.bsky.social · 19/03/2026
Excited to share my first PhD paper! "Desert mycobiome of Saudi Arabia is driven by vegetation patterns" doi.org/10.3897/myco... Really happy to contribute to a better understanding of fungal diversity in extreme environments. #Mycology #DesertEcology @myco-microbio.bsky.social
mycokeys.pensoft.net
Desert mycobiome of Saudi Arabia is driven by vegetation patterns
Deserts are home to diverse microbial communities important in many ecological processes and strategies for responding to a changing climate. We recorded the biodiversity of soil-inhabiting fungi and ...
031
Reposted by Ali Hakimzadeh
Oliver Schwengers @oschwengers.bsky.social · 27/02/2026
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.
033
Reposted by Ali Hakimzadeh
Rob Waterhouse @rmwaterhouse.bsky.social · 03/03/2026
#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
sib.swiss
095
Reposted by Ali Hakimzadeh
Leho Tedersoo @tedersoo.bsky.social · 17/02/2026
Our review about plant endophytes an other leaf-inhabiting fungi out - check it out: authors.elsevier.com/a/1mdbN6Do0q...
authors.elsevier.com
Please wait whilst we redirect you
All content on this site: Copyright © 2026 Elsevier B.V., its licensors, and contributors. All rights are reserved, including those for text and data mining, AI training, and similar technologies. For all open access content, the relevant licensing terms apply.
041
Reposted by Ali Hakimzadeh
Leho Tedersoo @tedersoo.bsky.social · 17/02/2026
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
zenodo.org
GloSED - Global standardised soil eukaryome dataset
Global Standardised Soil Eukaryome Dataset (GloSED) Dataset description The GloSED dataset is a metabarcoding-based dataset encompassing the entire spectrum of soil eukaryotes collected and analysed u...
0122
Reposted by Ali Hakimzadeh
Boas Pucker @bpucker.bsky.social · 17/02/2026
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
Summary of the Plant Bioinformatics course. AI-generated image (ChatGPT) showing some of the central elements. Details: https://github.com/bpucker/PlantBioinformatics
12211
Ali Hakimzadeh @bioinfo94.bsky.social · 16/02/2026
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.
2111
Reposted by Ali Hakimzadeh
Nextflow @nextflow.io · 30/01/2026
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
hubs.la
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.
054
Reposted by Ali Hakimzadeh
Jessica Tierney @leafwax.bsky.social · 23/01/2026
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/...
pnas.org
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...
110445
Reposted by Ali Hakimzadeh
EMBL @embl.org · 22/01/2026
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-...
111044
Ali Hakimzadeh @bioinfo94.bsky.social · 17/01/2026
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.
030
Reposted by Ali Hakimzadeh
Steven Salzberg @stevensalzberg.bsky.social · 16/01/2026
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...
embl.org
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.
1014581
Ali Hakimzadeh @bioinfo94.bsky.social · 05/12/2025
🧬 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
peerj.com
Are we throwing away good data? Evaluation of chimera detection algorithms on long-read amplicons reveals high false-positive rates across algorithms
Long-read amplicon sequencing has enabled us to return to full-length DNA barcodes, which benefit from the higher taxonomic resolution in metabarcoding-based biodiversity studies. However, chimeric se...
062
Reposted by Ali Hakimzadeh
Leho Tedersoo @tedersoo.bsky.social · 20/10/2025
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 fungal phylum-level system, with red font indicating novel taxa and size taxonomic diversity.
02413
Reposted by Ali Hakimzadeh
Dan Portik @dportik.bsky.social · 10/09/2025
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...
doi.org
Redirecting
185
Reposted by Ali Hakimzadeh
Mycology and Microbiology Center @myco-microbio.bsky.social · 18/06/2025
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-...
ut.ee
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...
051
Reposted by Ali Hakimzadeh
Emilia Hannula @ehannula.bsky.social · 06/05/2025
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
doi.org
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...
14021
Reposted by Ali Hakimzadeh
Ryan Wick @rrwick.bsky.social · 27/03/2025
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...
github.com
GitHub - rrwick/condaenvlist: a simple tool for listing conda environments with descriptions
a simple tool for listing conda environments with descriptions - rrwick/condaenvlist
17840
Ali Hakimzadeh @bioinfo94.bsky.social · 03/02/2025
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
doi.org
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...
021
Reposted by Ali Hakimzadeh
Leho Tedersoo @tedersoo.bsky.social · 23/01/2025
EUKARYOME v1.9.3 now available in eukaryome.org A special release of long reads of marine microeukaryotes
0124
Reposted by Ali Hakimzadeh
Dr.Kat Stewart @ecoevoedna.bsky.social · 17/11/2024
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
6111258
Reposted by Ali Hakimzadeh
Stephen Turner @stephenturner.us · 24/12/2024
End-to-end simulation of nanopore sequencing signals with feed-forward transformers academic.oup.com/bioinformatics/adv… 🧬🖥️🧪 github.com/ZKI-PH-ImageAnalysis/seq…
095
Reposted by Ali Hakimzadeh
Daniel Vaulot @daniel-vaulot.bsky.social · 10/12/2024
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...
0149