Ali Hakimzadeh
@bioinfo94.bsky.social
PhD fellow in Bioinformatics
#Bioinformatics #eDNA #metabarcoding #metagenomics
#RNA-Seq #GWAS #multi-omics
#Bioinformatics #eDNA #metabarcoding #metagenomics
#RNA-Seq #GWAS #multi-omics
Reposted by Ali Hakimzadeh
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
mycokeys.pensoft.net/article/1616...
#fungi #taxonomy #PacBio #classification #eDNA
October 20, 2025 at 5:27 PM
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
mycokeys.pensoft.net/article/1616...
#fungi #taxonomy #PacBio #classification #eDNA
Reposted by Ali Hakimzadeh
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...
- "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...
Redirecting
doi.org
September 10, 2025 at 3:57 PM
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...
- "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...
Reposted by Ali Hakimzadeh
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-...
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...
ut.ee
June 18, 2025 at 11:20 AM
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-...
Reposted by Ali Hakimzadeh
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
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...
doi.org
May 6, 2025 at 8:04 AM
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
Reposted by Ali Hakimzadeh
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...
If so, you might this little project: github.com/rrwick/conda...
GitHub - rrwick/condaenvlist: a simple tool for listing conda environments with descriptions
a simple tool for listing conda environments with descriptions - rrwick/condaenvlist
github.com
March 27, 2025 at 4:34 AM
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...
If so, you might this little project: github.com/rrwick/conda...
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
🔗 Read more: doi.org/10.1111/fwb....
#eDNA #FreshwaterBiology #conservation
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...
doi.org
February 3, 2025 at 10:09 AM
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
🔗 Read more: doi.org/10.1111/fwb....
#eDNA #FreshwaterBiology #conservation
Reposted by Ali Hakimzadeh
EUKARYOME v1.9.3 now available in eukaryome.org
A special release of long reads of marine microeukaryotes
A special release of long reads of marine microeukaryotes
January 23, 2025 at 6:48 AM
EUKARYOME v1.9.3 now available in eukaryome.org
A special release of long reads of marine microeukaryotes
A special release of long reads of marine microeukaryotes
Reposted by Ali Hakimzadeh
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
November 17, 2024 at 7:23 AM
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
Reposted by Ali Hakimzadeh
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
December 24, 2024 at 8:21 AM
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
Reposted by Ali Hakimzadeh
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...
www.biorxiv.org/content/10.1...
December 10, 2024 at 4:14 PM
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...
www.biorxiv.org/content/10.1...