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ironark.bsky.social
Phd Candidate, Microbiology at ASU https://mccutcheonlab.org/ Founder of MAB: midauthorbio.com GitHub: https://github.com/Arkadiy-Garber https://github.com/Middle-Author-Bioinformatics Google Scholar: https://scholar.google.com/citations?user=SGPloYgAAA
66 posts 124 followers 428 following
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In just 10 generations, birdfeeders selected for Anna's hummingbirds with longer beakers and shorter tempers. Wild stuff from @rachelnuwer.bsky.social -- 🧪 #birds www.science.org/content/arti...

submitted 2 days ago • 3 comments

Have you ever wondered about which genes on your favorite bacterial genome are broken or inactivated? Check out Pseudofinder, which is now available as a GUI, and find all the pseudogenes! omix.midauthorbio.com academic.oup.com/mbe/article/...

submitted 2 days ago • 0 comments

Just out work lead by @mycomile.bsky.social @fungage-lab.bsky.social in A. fumigatus that demonstrate how large scale gene cluster movement is driving heterogeneity in this fungus -- Giant transposons promote strain heterogeneity in a major fungal pathogen pubmed.ncbi.nlm.nih.gov/40353686/

submitted 3 days ago • 1 comment

Patchy burn severity explains heterogeneous soil viral and prokaryotic responses to fire in a mixed conifer forest journals.asm.org/doi/full/10.... #jcampubs

submitted 4 days ago • 0 comments

What lies beneath: microbial quality of rural groundwater explored by shotgun metagenomics link.springer.com/article/10.1... #jcampubs

submitted 4 days ago • 0 comments

Here's the scoop: Scientists explored how gut microbes impact colorectal cancer. They found that certain bacteria, like Dialister pneumosintes and Fusobacterium animalis, are linked to specific gene mutations and influence the cancer's evolution. These microbes shift with certain genetic changes...

submitted 4 days ago • 0 comments

#ViroSky #VirEvol

submitted 4 days ago • 0 comments

Excited to announce a web GUI for FeGenie! Are you interested in iron-related genes in your (meta)genomic datasets, but no experience with the command-line? You can now drag-and-drop and, with the click of a button, find all the iron genes: omix.midauthorbio.com www.frontiersin.org/journals/mic...

submitted 4 days ago • 0 comments

Microbial alkaline proteases are super useful enzymes in industries like food and textiles but face issues like low stability and yield. Exciting new tools like AI and advanced genetic engineering are paving the way for better versions. These upgrades promise more efficient and easily produced en...

submitted 7 days ago • 0 comments

Imagine a future where sunlight powers eco-friendly fuel production. This is happening with a blend of smart materials and nature's own systems. Scientists are using special polymers to build solar-driven biohybrids that improve energy transfers and bolster resilience against environmental pressu...

submitted 6 days ago • 0 comments

E. coli teamwork alert! Under antibiotic threat, resistant strains pump out a byproduct called indole. While it hampers resistant growth, it gives a leg-up to sensitive strains, helping them fight off the antibiotics. Sensitive strains return the favor by managing indole levels. This clever swap...

submitted 6 days ago • 0 comments

SynTracker is shaking up the way microbes are studied. Unlike most tools that focus on tiny DNA changes, this one tracks the order of DNA blocks to spot differences in microbial strains. It's great for dealing with tricky data, especially in phages and plasmids. Using SynTracker can reveal how mi...

submitted 5 days ago • 0 comments

When is microbial cross-feeding evolutionarily stable? | bioRxiv https://www.biorxiv.org/content/10.1101/2025.05.16.654511v1?rss=1

submitted 5 days ago • 0 comments

A giant virus in the genome of Chlamydomonas - this week in @science.org #plantscience Cryptic infection of a giant virus in a unicellular green alga | Science www.science.org/doi/10.1126/...

submitted 7 days ago • 1 comment

Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution @natbiotech.nature.com from @microbiome.bsky.social www.nature.com/articles/s41...

submitted 6 days ago • 0 comments

submitted 6 days ago • 0 comments

www.biorxiv.org/content/10.1... Autocycler, the automated successor to Trycycler from @rrwick.bsky.social has a pre-print out - overall, pretty awesome performance (and is very easy to use) github.com/rrwick/Autoc...

submitted 7 days ago • 2 comments

A clever new system for the introduction and heterologous expression of biosynthetic gene clusters into genome-optimised Streptomyces coelicolor: microbialcellfactories.biomedcentral.com/articles/10....

submitted 8 days ago • 0 comments

Do you have an interesting benchmark experiment? We wanna hear about it! Special issue in Genome Biology live now: www.biomedcentral.com/collections/... Submission Deadline: 28 January 2026 #bioinformatic #genetic #genomics please share with your peers!

submitted 8 days ago • 0 comments

ProGenFixer: an ultra-fast and accurate tool for correcting prokaryotic genome sequences using a mapping-free algorithm www.biorxiv.org/content/10.1... #jcampubs

submitted 8 days ago • 0 comments

🚨 Teaching bioinformatics? Or learning it solo? Check out my free & open Fundamentals of Bioinformatics course materials: lectures, slides, and exercises — no coding background required. 🔬🧬👩‍💻 📚 github.com/lskatz/funda... ⭐️ Star it, share it, and level up! #bioinformatics #opensource #STEMeducation

submitted 10 days ago • 2 comments

Check out our new preprint! We systematically map proteomic and metabolomic interactions between >100 pairs of gut bacteria, detecting metabolic interactions and functionally-related clusters of proteins. www.biorxiv.org/content/10.1... @kiranrpatil.bsky.social

submitted 8 days ago • 0 comments

Ultrafast and accurate sequence alignment and clustering of viral genomes | Nature Methods https://www.nature.com/articles/s41592-025-02701-7

submitted 8 days ago • 1 comment

An antisense RNA regulates production of DnaA and affects sporulation in Bacillus subtilis PLoSGenetics from Alan Grossman journals.plos.org/plosgenetics...

submitted 8 days ago • 0 comments

Excited to introduce our lab's latest work describing how bacterial siderophores can provide an advantage to their producers. They can inhibit competitors' specialized metabolism by causing iron deficiency. 1/6 www.biorxiv.org/content/10.1...

submitted 9 days ago • 2 comments

Our EvoWeaver work is now included on the Computational and Theoretical Biology focus page of Nature Communications! The page highlights recent work that reports methodological advances in computational biology. www.nature.com/collections/...

submitted 9 days ago • 0 comments

Emergence and disruption of cooperativity in a denitrifying microbial community academic.oup.com/ismej/advanc... #jcampubs

submitted 10 days ago • 0 comments

Kailash Venkatraman, Nicolas-Frédéric Lipp & @ibudin.bsky.social examine the similarities between prokaryotic intracytoplasmic membranes & mitochondrial IMs, & discuss whether cristae evolution has driven specialisation of the #mito lipidome. journals.biologists.com/jcs/article/... #JCSMitoSI

submitted 11 days ago • 3 comments

Histone-like protein from a Leptospira sp spirochete #MicroSky

submitted 11 days ago • 0 comments

I am speechless... >> First fault movement ever filmed. M7.9 surface rupture filmed near Thazi, Myanmar m.youtube.com/watch?v=77ub...

submitted 11 days ago • 41 comments

In a study with E. coli, scientists found that when the bacteria face gradually increasing doses of tetracycline, they adapt through subtle genetic tweaks. But when hit with big, sudden doses, they bypass normal regulation, constantly pumping out resistance. This reveals how rapid environmental c...

submitted 11 days ago • 0 comments

Clogged wells hurting heat pumps? Shallow aquifers rich in iron can mess with groundwater systems over time, making them less efficient. Early on, it's calcium carbonate and low iron forms causing blockages. Later, microbes and iron oxide make things worse, eventually stabilizing with biofilms. U...

submitted 11 days ago • 0 comments

"Chimpanzees drum with non-random timing & rhythms differ between subspecies. The team say this sheds light on evolutionary origins of a feature that sits at the heart of human social behaviour from conversation to music-making." New from @nakedprimate.bsky.social @andrearavignani.bsky.social & co🧪

submitted 13 days ago • 1 comment

www.scientificamerican.com/article/the-...

submitted 14 days ago • 0 comments

www.biorxiv.org/content/10.1... Searching for lytic phages in bacterial genome assemblies ..!

submitted 15 days ago • 1 comment

Radiolaria, those star-shaped oceanic plankton, aren't just fossils from eons ago; they're alive and essential today! Recent studies reveal they might hold the key to understanding marine ecosystems. Nearly half of their diversity is still a mystery, possibly due to their skeleton-less form. They...

submitted 15 days ago • 0 comments

How do intracellular #bacteria breach vacuoles to enter the host cytosol? @leaswistak.bsky.social @matthijnvos.bsky.social @enningalab.bsky.social &co show that #Shigella uses its T3SS system to damage endomembranes via mechanoporation to initiate cytosolic access @plosbiology.org 🧪 plos.io/4jXrr9Z

submitted 17 days ago • 2 comments

Microbes have cool cell compartments like eukaryotes! This paper shows how new genomic tools are shedding light on mysterious bacterial and archaeal organelles. Magnetotactic bacteria have magnetosomes that evolved a long time ago, while encapsulins help with sulfur metabolism. And those mysterio...

submitted 15 days ago • 0 comments

The tiny but mighty Prochlorococcus and Synechococcus are key players in Earth's waters. They thrive with the right mix of nutrients and light, but face understudied threats from non-viral predators. While scientists have a grip on viral threats, the complex role of other predators is still a puz...

submitted 15 days ago • 0 comments

WTAE filmed us in working with students at Pittsburgh Perry HS, one of more than 30 schools we partner with. This feature shows the value of NIH & NSF funding at work. Thanks: teacher Vicki Ammer, Prof. Cassie Quigley from Education, and our team, feat. Colton as local star. Segment 1:

submitted 15 days ago • 1 comment

This month's editorial is an invitation to submit papers on clinical and translational aspect of the microbiome. This collection is a joint effort with @naturemedicine.bsky.social @natcomms.nature.com and @commsbio.nature.com #MicroSky #MicrobiomeSky 🦠⚕️🧪⚕️ www.nature.com/articles/s41...

submitted 16 days ago • 3 comments

Microalgae cultivated in different locations show varied productivity, with strains thriving in California and struggling in New Mexico. Interestingly, when grown together in New Mexico, these strain differences vanish, highlighting their adaptability to changing environments. Microbial communiti...

submitted 16 days ago • 0 comments

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submitted 17 days ago • 0 comments

I wrote SprayNPray to bridge the gap between genome binning and taxonomic QC. It profiles contigs using taxonomy, coverage, GC content, and gene density—independent of binning. doi.org/10.1186/s128...

submitted 18 days ago • 1 comment

We developed a predictive framework to identify multiheme cytochromes in bacterial genomes, and used it to profile 50,000+ genomes. The result: a broader-than-expected distribution of extracellular electron transport (EET) capacity across phyla. doi.org/10.3389/fmic...

submitted 19 days ago • 1 comment