Arkadiy Garber
@ironark.bsky.social
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
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
Reposted by Arkadiy Garber
... 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 👍
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
... 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 👍
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 👍
Reposted by Arkadiy Garber
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
arkadiy describes a way, read his paper and learn the surprising role of TmRNA (10Sa RNA still when john @mcsymbiont.bsky.social ...
#SymbioSky #MicroSky
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...
www.biorxiv.org/content/10.6...
February 9, 2026 at 1:55 AM
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
arkadiy describes a way, read his paper and learn the surprising role of TmRNA (10Sa RNA still when john @mcsymbiont.bsky.social ...
#SymbioSky #MicroSky
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...
www.biorxiv.org/content/10.6...
February 8, 2026 at 2:08 AM
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...
www.biorxiv.org/content/10.6...
Reposted by Arkadiy Garber
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
Efficient and scalable Python implementation of ANCOM-BC for omics differential abundance testing https://www.biorxiv.org/content/10.64898/2026.01.26.701398v1
Reposted by Arkadiy Garber
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
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
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
Reposted by Arkadiy Garber
Reposted by Arkadiy Garber
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”
#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
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”
#microsky
Reposted by Arkadiy Garber
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)
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
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)
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)
Reposted by Arkadiy Garber
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
Kinetic modeling of multiple-strain artificial consortium to improve fengycin production of Bacillus subtilis.
Reposted by Arkadiy Garber
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/...
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/...
January 27, 2026 at 8:23 PM
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/...
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/...
Reposted by Arkadiy Garber
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/...
(=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
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/...
(=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/...
Reposted by Arkadiy Garber
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...
- 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
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...
- 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...
Reposted by Arkadiy Garber
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...
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
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...
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...
Reposted by Arkadiy Garber
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
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
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
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
Reposted by Arkadiy Garber
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/...
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
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/...
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/...
Reposted by Arkadiy Garber
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
Prototaxites reconstruction by Matt Humpage
January 21, 2026 at 7:25 PM
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
Prototaxites reconstruction by Matt Humpage
Reposted by Arkadiy Garber
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
Viral theft of light: A cyanophage protein dismantles cyanobacterial photosynthesis to accelerate infection www.cell.com/cell-host-mi...
Reposted by Arkadiy Garber
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
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
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
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
Reposted by Arkadiy Garber
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...
January 17, 2026 at 10:12 PM
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...
Reposted by Arkadiy Garber
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...
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
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...
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...
Reposted by Arkadiy Garber
🚨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
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...
January 9, 2026 at 4:49 PM
🚨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
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...
Reposted by Arkadiy Garber
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/...
"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/...
January 9, 2026 at 4:56 PM
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/...
"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/...
Reposted by Arkadiy Garber
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
Interaction and co-evolution among parasites, host insects, and gut microbiota.
Reposted by Arkadiy Garber
Genomic signatures of evolution and domestication in the button mushroom Agaricus bisporus
-in @currentbiology.bsky.social
www.cell.com/current-biol...
-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
Genomic signatures of evolution and domestication in the button mushroom Agaricus bisporus
-in @currentbiology.bsky.social
www.cell.com/current-biol...
-in @currentbiology.bsky.social
www.cell.com/current-biol...
Reposted by Arkadiy Garber
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
Targeting biofilm resistance in meat production: Postbiotics as a clean-label alternative, a bibliometric analysis review.