Arkadiy Garber
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ironark.bsky.social
Arkadiy Garber
@ironark.bsky.social
170 followers 400 following 91 posts
PhD, Microbiology
MS, Geological Sciences
BS, Neuroscience

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
Posts Replies Media Videos
Reposted by Arkadiy Garber
stcmicrobeblog.bsky.social
... worked on it in the mid-90s.)

john and I chatted about TmRNA/10Sa RNA in STC... but none of us could have anticipated how useful it might be for endosymbionts. great work 👍
Of Terms in Bi­ol­ogy: Trans-Trans­la­tion
by John McCutcheon, Janie and Christoph — This could become a very short explainer of the term "trans-trans­lation", as gi­ven by Vioque and de la Cruz in their mini­review: "Trans-trans­lation is…
smallthingsconsidered.blog
February 9, 2026 at 1:55 AM
Reposted by Arkadiy Garber
stcmicrobeblog.bsky.social
have you ever wondered how endosymbionts cope with the many pseudogenes in their genomes (before they generously reduce them by a factor of ~10)?
arkadiy describes a way, read his paper and learn the surprising role of TmRNA (10Sa RNA still when john @mcsymbiont.bsky.social ...

#SymbioSky #MicroSky
ironark.bsky.social Arkadiy Garber @ironark.bsky.social · 2d
Happy to share a preprint—the last chapter of my dissertation with @mcsymbiont.bsky.social and Co—on what happens when bacterial endosymbionts accumulate huge numbers of pseudogenes during early genome reduction.

www.biorxiv.org/content/10.6...
Diagram illustrating early genome erosion during the transition from a free-living Sodalis bacterium to two host-associated endosymbionts inside the long-tailed mealybug. Circular genomes show intact genes in blue and pseudogenes in red, highlighting increased pseudogene accumulation in symbiotic forms. Caption asks: “What are the downstream molecular consequences of early genome erosion?”
February 9, 2026 at 1:55 AM
ironark.bsky.social
Happy to share a preprint—the last chapter of my dissertation with @mcsymbiont.bsky.social and Co—on what happens when bacterial endosymbionts accumulate huge numbers of pseudogenes during early genome reduction.

www.biorxiv.org/content/10.6...
Diagram illustrating early genome erosion during the transition from a free-living Sodalis bacterium to two host-associated endosymbionts inside the long-tailed mealybug. Circular genomes show intact genes in blue and pseudogenes in red, highlighting increased pseudogene accumulation in symbiotic forms. Caption asks: “What are the downstream molecular consequences of early genome erosion?”
February 8, 2026 at 2:08 AM
Reposted by Arkadiy Garber
biorxiv-bioinfo.bsky.social
Efficient and scalable Python implementation of ANCOM-BC for omics differential abundance testing https://www.biorxiv.org/content/10.64898/2026.01.26.701398v1
January 28, 2026 at 9:46 PM
Reposted by Arkadiy Garber
zhuqiyun.bsky.social
We introduce a Python implementation of ANCOM-BC that is 100x faster than the original R code, while preserving statistical validity. Scales to much larger omics datasets and enables ML workflows with repeated inference (feature selection, sensitivity, stability, etc.) #Bioinformatics #Microbiome
biorxiv-bioinfo.bsky.social bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 12d
Efficient and scalable Python implementation of ANCOM-BC for omics differential abundance testing https://www.biorxiv.org/content/10.64898/2026.01.26.701398v1
January 31, 2026 at 9:24 PM
Reposted by Arkadiy Garber
gittacoaker.bsky.social
www.science.org/doi/10.1126/...
Multiple protein structure alignment at scale with FoldMason
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
www.science.org
January 30, 2026 at 7:12 PM
Reposted by Arkadiy Garber
fabricejpierre.bsky.social
Cool stuff!

“A quorum-sensing molecule from Pseudomonas aeruginosa induces defensive multicellularity in a coinfecting pathogen”

#microsky
A quorum-sensing molecule from Pseudomonas aeruginosa induces defensive multicellularity in a coinfecting pathogen | PNAS
Microorganisms commonly exist in polymicrobial communities, where they can respond to interspecies secreted molecules by altering behaviors and phy...
www.pnas.org
January 29, 2026 at 11:06 AM
Reposted by Arkadiy Garber
lauriebelch.bsky.social
Calling all OrthoFinder users!

We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.

GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...

(1/10)
www.biorxiv.org
January 29, 2026 at 12:07 PM
Reposted by Arkadiy Garber
thedailypub.bsky.social
Kinetic modeling of multiple-strain artificial consortium to improve fengycin production of Bacillus subtilis.
Kinetic modeling of multiple-strain artificial consortium to improve fengycin production of Bacillus subtilis.
Published in Biotechnology for biofuels and bioproducts
doi.org
January 29, 2026 at 2:00 AM
Reposted by Arkadiy Garber
jerorb.bsky.social
New paper out in @pnas.org, and it made the cover! 👁️

We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve.

‼️Check Paula’s 🧵 and the paper👇

𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿
www.pnas.org/doi/10.1073/...
Cover of PNAS in which we show plasmids as colourful concentric circles, with dots scattered. The image kind of resembles an eye, although it’s visibly a plot.
January 27, 2026 at 8:23 PM
Reposted by Arkadiy Garber
evolvedbiofilm.bsky.social
Transcription Factor Promiscuity Drives Regulatory Rewiring and Evolvability in Gene Networks in Bacteria
(=Pseudomonas fluorescens)
Advanced Science, perspective by @taylorlabgroup.bsky.social & @alanrice.ie
Uni Bath's 60th anniversary special issue
advanced.onlinelibrary.wiley.com/doi/10.1002/...
Transcription Factor Promiscuity Drives Regulatory Rewiring and Evolvability in Gene Networks in Bacteria
This special issue marking the University of Bath's 60th anniversary offers an opportunity to reflect on nearly a decade of research into the evolution of gene regulatory networks (GRNs) from members....
advanced.onlinelibrary.wiley.com
January 24, 2026 at 11:35 AM
Reposted by Arkadiy Garber
bananabenana.bsky.social
Our new paper on Insertion Sequences (IS) in #Klebsiella

- Lineages have vastly different IS loads and profiles
- An inverse relationship between IS load and metabolic capacity, in particular phosphorus use, consistent with early reductive evolution.

www.microbiologyresearch.org/content/jour...
Exploring the IS-capades of Klebsiella pneumoniae: insertion sequences drive metabolic loss in obscure sub-lineages
Introduction. Klebsiella pneumoniae is an opportunistic pathogen that causes a wide spectrum of infections within healthcare settings and the community. Four K. pneumoniae sub-lineages, defined using ...
www.microbiologyresearch.org
January 22, 2026 at 7:52 PM
Reposted by Arkadiy Garber
vscooper.micropopbio.org
What could mirror bacteria do in nature if created? A story of these prospects and a plan to prevent them.

Titles aside, I hope you'll read it (the tech is NOT close). Thanks to Tom Freeman for writing help & @jfischman.bsky.social for ace editing! www.scientificamerican.com/article/life...
Life’s evil twins, called mirror cells, could wipe us out if scientists don’t stop them
Researchers are close to making “reversed” cells that may wipe us off the planet
www.scientificamerican.com
January 20, 2026 at 7:20 PM
Reposted by Arkadiy Garber
cmdi.bsky.social
Insects in hospitals are potential disease vectors! 🪳🪰

A new systematic review shows that cockroaches, flies, and ants often carry drug-resistant bacteria and can transmit pathogens to patients. 🏥

pubmed.ncbi.nlm.nih.gov/41562025/

#InfectionPrevention #PublicHealth #Microbiology
From infestation to infection: a systematic review of arthropod-mediated microbial transmission in hospitals - PubMed
Arthropods in healthcare environments commonly harbor clinically relevant and antimicrobial-resistant microbes, and limited but compelling evidence supports their potential role in patient transmission. Strengthened pest management and environmental hygiene are essential components of infection prev …
pubmed.ncbi.nlm.nih.gov
January 21, 2026 at 8:43 PM
Reposted by Arkadiy Garber
jabbur.bsky.social
so very happy to share this Perspective piece that I wrote with @hollykay1.bsky.social for @febsletters.bsky.social

in this paper we do an extensive (and long overdue) review of rhythms (of all kinds, not just circadian!) in bacteria, and we ask the +

febs.onlinelibrary.wiley.com/doi/10.1002/...
FEBS Press
Circadian clocks have been identified in very few bacterial species, and only the cyanobacterial clock is understood in detail. Bacterial rhythms have primarily been studied in species in isolation o...
febs.onlinelibrary.wiley.com
January 20, 2026 at 9:30 PM
Reposted by Arkadiy Garber
transitionalform.bsky.social
Our paper on the mysterious Devonian organism Prototaxites has now finally been published! See the paper here (www.science.org/doi/10.1126/...) and our explainer thread below!
Prototaxites reconstruction by Matt Humpage
January 21, 2026 at 7:25 PM
Reposted by Arkadiy Garber
bejalab.bsky.social
Viral theft of light: A cyanophage protein dismantles cyanobacterial photosynthesis to accelerate infection www.cell.com/cell-host-mi...
Viral theft of light: A cyanophage protein dismantles cyanobacterial photosynthesis to accelerate infection
Auxiliary metabolic genes, acquired by cyanobacterial viruses (cyanophages) from their hosts, are thought to manipulate host metabolism during infection. A recent study by Nadel et al. performed in vi...
www.cell.com
January 17, 2026 at 7:25 PM
Reposted by Arkadiy Garber
gthibault.bsky.social
We’ve discovered how the superbug E. faecalis prevents chronic wounds from healing.

It’s not a toxin. It’s metabolism.

The bacteria use extracellular electron transport (EET) to electrochemically generate ROS, effectively "freezing" skin cells in place.

doi.org/10.1126/sciadv.aeb5297
Enterococcus faecalis redox metabolism activates the unfolded protein response to impair wound healing
E. faecalis EET generates ROS, which induces the UPR in keratinocytes, inhibiting in vitro migration.
doi.org
January 17, 2026 at 1:26 AM
Reposted by Arkadiy Garber
asm.org
Inspired by cicada wings, mechano-bactericidal surfaces are patterned with nanostructures that poke, cut and tear bacteria to death. Can they transform how we combat biofilms to protect human health? asm.org/articles/202...
Top: Cicada. Bottom: Bacterial cell being punctured by nanopillars.
January 17, 2026 at 10:12 PM
Reposted by Arkadiy Garber
uncultured.carinilab.com
Our revised manuscript is up on BioRxiv and is coming soon to an ASM journal in your neighborhood.

We show that metabolome & transcriptome profiles are frozen in desiccated Arthrobacter and that water vapor induces resuscitation.

Happy to answer any Qs.

www.biorxiv.org/content/10.1...
Transcriptional and metabolic stasis define desiccation-induced dormancy in the soil bacterium Arthrobacter sp. AZCC_0090 until water vapor initiates resuscitation
Microbes inhabiting soils experience periodic water deprivation. The effects of desiccation on DNA, protein, and membrane integrity are well-described. However, the effects of drying and rehydration o...
www.biorxiv.org
January 14, 2026 at 10:21 PM
Reposted by Arkadiy Garber
vscooper.micropopbio.org
🚨Call for papers🚨
Microbial Evolution: Impacts on Human Health
in the society journal Evolution, Medicine, and Public Health

Guest Editors: Bob Woods, Silvie Huijben & Camilo Barbosa
EIC: me

This will be great, please submit and share!
academic.oup.com/emph/pages/m...
Microbial Evolution: Impacts on Human Health Call for Papers A defining characteristic of infectious diseases is that they evolve. The consequences of this evolution are among the most pressing medical issues facing humanity, including emerging pandemics, antibiotic resistance, and the success or failure of vaccines. Pathogen evolution profoundly influences virulence, transmission, and responses to a broad array of human interventions. While the evolutionary dynamics of pathogens have historically been challenging to study, large-scale genomic sequencing, novel computational tools, and experimental methods are rapidly changing the field. We encourage submissions on the broad topic of the evolution of infectious diseases. This Special Issue aims to feature research that blends evolutionary approaches to understanding pathogen heterogeneity and ongoing genetic change in clinical samples and models of human infection. It also seeks to highlight opportunities to design treatment and prevention strategies that remain effective in the face of ongoing pathogen evolution. Submission – open until January 31, 2027 Guest editors Robert Woods, MD PhD, University of Michigan Camilo Barbosa, PhD, University of Michigan Silvie Huijben, PhD, Arizona State University
January 9, 2026 at 4:49 PM
Reposted by Arkadiy Garber
manuelacasasoli.bsky.social
The dawn and evolution of the dinosaurs: always fascinating.

"We know that an asteroid impact ended the age of the dinosaurs. Now, researchers are uncovering the early evolutionary steps that set the stage for their impressive reign."

🧪 #Science #Biology #Paleontology
www.pnas.org/doi/10.1073/...
Image Source: https://www.pnas.org/doi/10.1073/pnas.2535891123 Reptiles ruled the earth during the Triassic. Some of them may have been early ornithischian bird-hipped dinosaurs, a group that would come to include Stegosaurus (pictured) in the Jurassic when dinosaurs reigned. Image credit: Science Source/RICHARD BIZLEY.
January 9, 2026 at 4:56 PM
Reposted by Arkadiy Garber
thedailypub.bsky.social
Interaction and co-evolution among parasites, host insects, and gut microbiota.
Interaction and co-evolution among parasites, host insects, and gut microbiota.
Published in Insect science
doi.org
January 9, 2026 at 2:00 AM
Reposted by Arkadiy Garber
evolvedbiofilm.bsky.social
Genomic signatures of evolution and domestication in the button mushroom Agaricus bisporus

-in @currentbiology.bsky.social

www.cell.com/current-biol...
Genomic signatures of evolution and domestication in the button mushroom Agaricus bisporus
The evolution and domestication of mushrooms remain unclear. Ling et al. show that divergence and gene flow driven by quaternary glacial cycles shape the current mixed origins of A. bisporus populatio...
www.cell.com
January 9, 2026 at 8:21 AM
Reposted by Arkadiy Garber
thedailypub.bsky.social
Targeting biofilm resistance in meat production: Postbiotics as a clean-label alternative, a bibliometric analysis review.
Targeting biofilm resistance in meat production: Postbiotics as a clean-label alternative, a bibliometric analysis review.
Published in Poultry science
doi.org
January 5, 2026 at 8:00 AM