Mahwash Jamy
@mjamy.bsky.social
Evolutionary biologist interested in protist diversity and evolution. Postdoc at Swedish University of Agricultural Sciences.
Pinned
Mahwash Jamy
@mjamy.bsky.social
· Sep 3
Hello there 🦋
Happy to share our piece "Towards a trait-based framework for protist ecology and evolution" in @cp-trendsmicrobiol.bsky.social
Let's build a unified trait 📏 database to unlock transformative insights into protist 🔬 ecology 🌍 and evolution ⏳
▶️ doi.org/10.1016/j.ti...
#protistsonsky
Happy to share our piece "Towards a trait-based framework for protist ecology and evolution" in @cp-trendsmicrobiol.bsky.social
Let's build a unified trait 📏 database to unlock transformative insights into protist 🔬 ecology 🌍 and evolution ⏳
▶️ doi.org/10.1016/j.ti...
#protistsonsky
Check out our new paper on adopting a trait-based framework for protist diversity! We make the case for a unified protist trait database, how to build it, and how it could transform research on protist ecology and evolution.
#protistsonsky
#protistsonsky
Reposted by Mahwash Jamy
Just the Browser helps you remove AI features, telemetry data reporting, sponsored content, product integrations, and other annoyances from desktop web browsers.
justthebrowser.com
justthebrowser.com
justthebrowser.com
January 20, 2026 at 3:46 PM
Just the Browser helps you remove AI features, telemetry data reporting, sponsored content, product integrations, and other annoyances from desktop web browsers.
justthebrowser.com
justthebrowser.com
Reposted by Mahwash Jamy
We just released #anvio v9, "eunice" 🎉
This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176.
Read the release notes:
github.com/merenlab/anv...
Visit our up-to-date web page:
anvio.org
This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176.
Read the release notes:
github.com/merenlab/anv...
Visit our up-to-date web page:
anvio.org
January 20, 2026 at 11:48 AM
We just released #anvio v9, "eunice" 🎉
This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176.
Read the release notes:
github.com/merenlab/anv...
Visit our up-to-date web page:
anvio.org
This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176.
Read the release notes:
github.com/merenlab/anv...
Visit our up-to-date web page:
anvio.org
Reposted by Mahwash Jamy
🗜️⚡ If you use gzip/gunzip a lot in your pipelines, switch to the faster"libdeflate" versions instead! They use modern CPU capabilities to achieve a 2-3x speedup.
libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix
github.com/ebiggers/lib...
libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix
github.com/ebiggers/lib...
GitHub - ebiggers/libdeflate: Heavily optimized library for DEFLATE/zlib/gzip compression and decompression
Heavily optimized library for DEFLATE/zlib/gzip compression and decompression - ebiggers/libdeflate
github.com
January 20, 2026 at 1:37 AM
🗜️⚡ If you use gzip/gunzip a lot in your pipelines, switch to the faster"libdeflate" versions instead! They use modern CPU capabilities to achieve a 2-3x speedup.
libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix
github.com/ebiggers/lib...
libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix
github.com/ebiggers/lib...
Reposted by Mahwash Jamy
If you’re interested in extinction risk, please check out our new paper in @science.org led by my former PhD student Cooper: www.science.org/doi/full/10....
January 16, 2026 at 9:39 AM
If you’re interested in extinction risk, please check out our new paper in @science.org led by my former PhD student Cooper: www.science.org/doi/full/10....
Reposted by Mahwash Jamy
New postdoc funding opportunity in Sweden! If you're interested in applying for this 'Data-Driven Life Sciences' fellowship, please get in touch, we'd be happy to host and help with the application (and talk options beyond the 2-year position). www.scilifelab.se/data-driven/...
DDLS Research School Postdoc call 2026
Call for Academic and Industrial Postdoctoral Fellowships in Data-Driven Life Science 2026 Generic Description of the DDLS Postdoc Program The SciLifeLab and Wallenberg National Program for Data-Drive...
www.scilifelab.se
January 13, 2026 at 1:32 PM
New postdoc funding opportunity in Sweden! If you're interested in applying for this 'Data-Driven Life Sciences' fellowship, please get in touch, we'd be happy to host and help with the application (and talk options beyond the 2-year position). www.scilifelab.se/data-driven/...
Reposted by Mahwash Jamy
If you're interested in biodiversity in freshwater ecosystems, there's just a few days to apply for our PhD project: Ecological Surveillance using High-Throughput Quantitative Imaging at @uniofbath.bsky.social .
Deadline: January 16th!
Apply: is.gd/svXBcr
Image: www.planktoscope.org/how-it-works
Deadline: January 16th!
Apply: is.gd/svXBcr
Image: www.planktoscope.org/how-it-works
January 13, 2026 at 2:07 PM
If you're interested in biodiversity in freshwater ecosystems, there's just a few days to apply for our PhD project: Ecological Surveillance using High-Throughput Quantitative Imaging at @uniofbath.bsky.social .
Deadline: January 16th!
Apply: is.gd/svXBcr
Image: www.planktoscope.org/how-it-works
Deadline: January 16th!
Apply: is.gd/svXBcr
Image: www.planktoscope.org/how-it-works
Reposted by Mahwash Jamy
⚡️Fully funded #PhD position in my lab at Stockholm University / SciLifeLab! If you’re interested in #lichens, #symbiosis, fungal biology, or meta-omics, please apply. Deadline Feb 1. Read more here: su.varbi.com/en/what:job/...
January 12, 2026 at 2:15 PM
⚡️Fully funded #PhD position in my lab at Stockholm University / SciLifeLab! If you’re interested in #lichens, #symbiosis, fungal biology, or meta-omics, please apply. Deadline Feb 1. Read more here: su.varbi.com/en/what:job/...
Reposted by Mahwash Jamy
Nucleotide diversity is a poor predictor of short-term adaptive potential https://www.biorxiv.org/content/10.64898/2026.01.05.697705v1
January 5, 2026 at 9:32 PM
Nucleotide diversity is a poor predictor of short-term adaptive potential https://www.biorxiv.org/content/10.64898/2026.01.05.697705v1
Reposted by Mahwash Jamy
I have a postdoc position in metagenomic exploration available in my group. Candidates with documented experience in phylo & metagenomics and preferably with petabase-scale data mining and GLM workflows are encouraged to apply. Come join us! 🧬🦠💻
Please repost
Apply here: www.wur.nl/en/vacancy/p...
Please repost
Apply here: www.wur.nl/en/vacancy/p...
January 5, 2026 at 10:45 PM
I have a postdoc position in metagenomic exploration available in my group. Candidates with documented experience in phylo & metagenomics and preferably with petabase-scale data mining and GLM workflows are encouraged to apply. Come join us! 🧬🦠💻
Please repost
Apply here: www.wur.nl/en/vacancy/p...
Please repost
Apply here: www.wur.nl/en/vacancy/p...
Reposted by Mahwash Jamy
It was speculated that there's some degree of DNA exchange between algae & sea slug to create the "support system" for the chloroplasts, but in at least one species, that appears not to be the case.
Changes in the expression of the sea slug genes were sufficient to support the kleptoplasty.
Changes in the expression of the sea slug genes were sufficient to support the kleptoplasty.
Chloroplast acquisition without the gene transfer in kleptoplastic sea slugs, Plakobranchus ocellatus
The newly opened genome of a kleptoplastic mollusk, Plakobranchus ocellatus, indicated that sequestered plastids retain their activity within the animal cell without horizontal algal gene transfer to ...
elifesciences.org
December 27, 2025 at 5:02 PM
It was speculated that there's some degree of DNA exchange between algae & sea slug to create the "support system" for the chloroplasts, but in at least one species, that appears not to be the case.
Changes in the expression of the sea slug genes were sufficient to support the kleptoplasty.
Changes in the expression of the sea slug genes were sufficient to support the kleptoplasty.
Reposted by Mahwash Jamy
Everything is everywhere but Escherichia coli adapts to different niches academic.oup.com/ismej/advanc... #jcampubs
December 18, 2025 at 3:06 PM
Everything is everywhere but Escherichia coli adapts to different niches academic.oup.com/ismej/advanc... #jcampubs
Reposted by Mahwash Jamy
Just on time for the holidays! Happy to share the published version of the discovery of leptophytes, a new deep-branching and widespread group of microalgae based on plastid MAGs (ptMAGs). Now with additional support from a mitochondrial MAG (mtMAG) of leptophytes.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Identification of a deep-branching lineage of algae using environmental plastid genomes - Nature Communications
Here, the authors leverage data from the Tara Oceans expeditions to perform a phylogeny-guided plastid genome-resolved metagenomic survey and provide 660 non-redundant plastid genomes from marine alga...
www.nature.com
December 18, 2025 at 9:48 AM
Just on time for the holidays! Happy to share the published version of the discovery of leptophytes, a new deep-branching and widespread group of microalgae based on plastid MAGs (ptMAGs). Now with additional support from a mitochondrial MAG (mtMAG) of leptophytes.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Mahwash Jamy
Just a few days left to apply to the PhD position in our group. It focuses on selfish genes in #fungi and how they might affect the spread of giant #TEs called Starships.
We're looking for a PhD student! If you're interested in #fungal #genomics & #TEs, meiotic drive, or pathogens, please consider applying. The project is about toxin/antidote genes in the human fungal pathogen A. fumigatus. uu.varbi.com/en/what:job/...
December 17, 2025 at 6:55 AM
Reposted by Mahwash Jamy
New preprint out! Using ~75k environmental OTUs + 77 fossil calibrations, we reconstructed a Proterozoic timeline of eukaryote evolution. Our results show crown eukaryotes were already diversifying >1.6 Ga, long before the first undisputed fossils (~1.05 Ga).
🔗 DOI: www.biorxiv.org/content/10.6...
🔗 DOI: www.biorxiv.org/content/10.6...
December 15, 2025 at 8:19 AM
New preprint out! Using ~75k environmental OTUs + 77 fossil calibrations, we reconstructed a Proterozoic timeline of eukaryote evolution. Our results show crown eukaryotes were already diversifying >1.6 Ga, long before the first undisputed fossils (~1.05 Ga).
🔗 DOI: www.biorxiv.org/content/10.6...
🔗 DOI: www.biorxiv.org/content/10.6...
Reposted by Mahwash Jamy
Environmental phylogenetics supports a steady diversification of crown eukaryotes starting from the mid Proterozoic https://www.biorxiv.org/content/10.64898/2025.12.12.693929v1
December 15, 2025 at 12:32 AM
Environmental phylogenetics supports a steady diversification of crown eukaryotes starting from the mid Proterozoic https://www.biorxiv.org/content/10.64898/2025.12.12.693929v1
Reposted by Mahwash Jamy
Would you say that Neurospora crassa is declining as a model organism for fungal biology?
💛 No way, that orange fun-guy is alive and well!
🔴 Yeah, not so many people work with it nowadays ...
🔵 Neuro-who?
📅 Ends: December 31, 2025, 10:03 PM UTC
📊 Show results
💛 No way, that orange fun-guy is alive and well!
🔴 Yeah, not so many people work with it nowadays ...
🔵 Neuro-who?
📅 Ends: December 31, 2025, 10:03 PM UTC
📊 Show results
December 10, 2025 at 9:06 PM
Would you say that Neurospora crassa is declining as a model organism for fungal biology?
💛 No way, that orange fun-guy is alive and well!
🔴 Yeah, not so many people work with it nowadays ...
🔵 Neuro-who?
📅 Ends: December 31, 2025, 10:03 PM UTC
📊 Show results
💛 No way, that orange fun-guy is alive and well!
🔴 Yeah, not so many people work with it nowadays ...
🔵 Neuro-who?
📅 Ends: December 31, 2025, 10:03 PM UTC
📊 Show results
Reposted by Mahwash Jamy
I salute the honesty and courage of these authors, and I am sure we all share a collective shiver from knowing that we all could easily make (and maybe have made) similar analysis mistakes in our own work
#academicchatter
#academicchatter
December 5, 2025 at 3:28 PM
I salute the honesty and courage of these authors, and I am sure we all share a collective shiver from knowing that we all could easily make (and maybe have made) similar analysis mistakes in our own work
#academicchatter
#academicchatter
Reposted by Mahwash Jamy
People working with #protists and #fungi might be interested to hear that we in this study sequenced 13.4 mio. eukaryotic rRNA operons from 450 representative samples. #ProtistsOnSky #Metabarcoding
Microflora Danica: What can you learn from collecting and sequencing 10,000+ samples from a single country? Check out our new paper in @nature.com to find out. Incredible work led by Caitlin Singleton, Thomas B. N. Jensen, and Mads Albertsen from @aau.dk. 🦠🧫🧬
www.nature.com/articles/s41...
www.nature.com/articles/s41...
The Microflora Danica atlas of Danish environmental microbiomes - Nature
Microflora Danica—an atlas of Danish environmental microbiomes—reveals that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity.
www.nature.com
December 5, 2025 at 11:03 AM
People working with #protists and #fungi might be interested to hear that we in this study sequenced 13.4 mio. eukaryotic rRNA operons from 450 representative samples. #ProtistsOnSky #Metabarcoding
Reposted by Mahwash Jamy
One more week to apply to this PhD position on working out an endosymbiosis relationship in a protist. Please share widely to prospective PhD student #protistsonsky
We are looking for a PhD student to work on an exciting plastid endosymbiosis in microbial eukaryotes. This position involves sampling, exciting microscopy such as CARDFISH, ExM and FIBSEM, single-cell transcriptomics and more. #protistsonsky 1/2
December 5, 2025 at 8:48 AM
One more week to apply to this PhD position on working out an endosymbiosis relationship in a protist. Please share widely to prospective PhD student #protistsonsky
Reposted by Mahwash Jamy
As computer scientist, I am very excited about our new biogeography simulator: bigrig - my PostDoc Ben Bettisworth implemented two algoritmically totally distinct simulators from scratch to conduct statistical tests for showing that bigrig is correctly implemented: www.biorxiv.org/content/10.1...
bigrig: A range simulator for the DEC[+J] model
Quality software tools for science are, as a necessity, rigorously tested and verified. However, there is a major challenge to testing software used for phylogenetics and similar analysis. There is a ...
www.biorxiv.org
December 2, 2025 at 11:28 AM
As computer scientist, I am very excited about our new biogeography simulator: bigrig - my PostDoc Ben Bettisworth implemented two algoritmically totally distinct simulators from scratch to conduct statistical tests for showing that bigrig is correctly implemented: www.biorxiv.org/content/10.1...
Reposted by Mahwash Jamy
We just released IRIS (7+yrs project), a tech we believe will transform cell biology by pairing high-resolution cell images with matched #scRNAseq, letting us interpret cellular form by its molecular ground truth.
Huge tx to @JohannesBues, @JoernPezoldt, @CamilleLambert et al.
shorturl.at/zgY8Z
Huge tx to @JohannesBues, @JoernPezoldt, @CamilleLambert et al.
shorturl.at/zgY8Z
December 2, 2025 at 2:18 PM
We just released IRIS (7+yrs project), a tech we believe will transform cell biology by pairing high-resolution cell images with matched #scRNAseq, letting us interpret cellular form by its molecular ground truth.
Huge tx to @JohannesBues, @JoernPezoldt, @CamilleLambert et al.
shorturl.at/zgY8Z
Huge tx to @JohannesBues, @JoernPezoldt, @CamilleLambert et al.
shorturl.at/zgY8Z
Reposted by Mahwash Jamy
Check out our latest paper on mirusviruses, one of the most remarkable new groups of protist viruses - extremely diverse, carry lots of spliceosomal introns (including new homing introns) and are at the evolutionary crossroads between tailed phages and herpesviruses! www.nature.com/articles/s41...
Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes - Nature Microbiology
Environmental metagenomic explorations show that Mirusviricota lineages lack essential replication and transcription genes and contain spliceosomal introns, suggesting nuclear reproduction.
www.nature.com
November 28, 2025 at 4:43 PM
Check out our latest paper on mirusviruses, one of the most remarkable new groups of protist viruses - extremely diverse, carry lots of spliceosomal introns (including new homing introns) and are at the evolutionary crossroads between tailed phages and herpesviruses! www.nature.com/articles/s41...
Reposted by Mahwash Jamy
An adorable Platyhelminthes! I see that the classification has changed, so this is now subphylum Rhabditophora? Anyhoo, a real cutie!
#marineplankton 🦑
#marineplankton 🦑
November 28, 2025 at 8:25 PM
An adorable Platyhelminthes! I see that the classification has changed, so this is now subphylum Rhabditophora? Anyhoo, a real cutie!
#marineplankton 🦑
#marineplankton 🦑
Reposted by Mahwash Jamy
Need to predict whether a given contig in your assembly was circular in the environment?
Here is a new program in #anvio ecosystem that will look into your BAM file and use paired-end read mapping data to conservatively assess circularity:
anvio.org/help/main/pr...
Here is a new program in #anvio ecosystem that will look into your BAM file and use paired-end read mapping data to conservatively assess circularity:
anvio.org/help/main/pr...
anvi-report-circularity
An anvi'o program. Predict contig circularity from paired-end read alignments in a given BAM file.
anvio.org
November 28, 2025 at 9:11 AM
Need to predict whether a given contig in your assembly was circular in the environment?
Here is a new program in #anvio ecosystem that will look into your BAM file and use paired-end read mapping data to conservatively assess circularity:
anvio.org/help/main/pr...
Here is a new program in #anvio ecosystem that will look into your BAM file and use paired-end read mapping data to conservatively assess circularity:
anvio.org/help/main/pr...
Reposted by Mahwash Jamy
According to the microbial ecologist Puri López-García, pictured here at a salt flat in the Chilean Andes, some 25% to 50% of all bacterial cells may be parasites of other cells.
A Cell So Minimal That It Challenges Definitions of Life | Quanta Magazine
The newly described microbe represents a world of parasitic, intercellular biodiversity only beginning to be revealed by genome sequencing.
www.quantamagazine.org
November 25, 2025 at 9:04 PM
According to the microbial ecologist Puri López-García, pictured here at a salt flat in the Chilean Andes, some 25% to 50% of all bacterial cells may be parasites of other cells.