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
We are happy to support an NSF PRFB application that makes use of AI to advance microbial cultivation for biotechnological purposes. Deadline=Sept 29th.
More here: uncultured.carinilab.com/p/were-looki...
More here: uncultured.carinilab.com/p/were-looki...
We're Looking to Sponsor Postdoc Fellows in AI-Driven Microbial Cultivation
NSF Postdoctoral Research Fellowships in Biology
uncultured.carinilab.com
September 8, 2026 at 3:47 PM
We are happy to support an NSF PRFB application that makes use of AI to advance microbial cultivation for biotechnological purposes. Deadline=Sept 29th.
More here: uncultured.carinilab.com/p/were-looki...
More here: uncultured.carinilab.com/p/were-looki...
Reposted by Arkadiy Garber
Ever wondered why diverse organism shrink their genome in specific cells? We try to make sense of these curious cases of programmed DNA elimination in a review that came out today @naturerevgenet.bsky.social trebuchet.public.springernature.app/get_content/... @sandraduharcourt.bsky.social
September 8, 2026 at 3:10 PM
Ever wondered why diverse organism shrink their genome in specific cells? We try to make sense of these curious cases of programmed DNA elimination in a review that came out today @naturerevgenet.bsky.social trebuchet.public.springernature.app/get_content/... @sandraduharcourt.bsky.social
Reposted by Arkadiy Garber
The 100 Diatom Genomes Project journals.plos.org/plosbiology/... #jcampubs
The 100 Diatom Genomes Project
This Community Page presents the 100 Diatom Genomes Project, which aims to sequence the genomes and transcriptomes of 100 diatom species across major lineages, life forms and ecological strategies. Th...
journals.plos.org
September 2, 2026 at 4:14 PM
The 100 Diatom Genomes Project journals.plos.org/plosbiology/... #jcampubs
Reposted by Arkadiy Garber
Foldseek-Interface enables fast search/clustering of the protein interface universe! We clustered 3.1M PDB dimers into 77,167 groups and found new interfaces keep appearing even as fold discovery plateaus. 🧵
📄 www.biorxiv.org/content/10.6...
🔎 search.foldseek.com/interface
🌐 interface.foldseek.com
📄 www.biorxiv.org/content/10.6...
🔎 search.foldseek.com/interface
🌐 interface.foldseek.com
August 26, 2026 at 5:26 PM
Foldseek-Interface enables fast search/clustering of the protein interface universe! We clustered 3.1M PDB dimers into 77,167 groups and found new interfaces keep appearing even as fold discovery plateaus. 🧵
📄 www.biorxiv.org/content/10.6...
🔎 search.foldseek.com/interface
🌐 interface.foldseek.com
📄 www.biorxiv.org/content/10.6...
🔎 search.foldseek.com/interface
🌐 interface.foldseek.com
Reposted by Arkadiy Garber
Complete Genome Sequences of Mycobacteriophages TribleTrouble, TClif, Llorens and CallaLilly #micropublication #biology #data #caltechlibrary #Bacteriophage #GenomeAnnouncements #NewFinding https://micropublication.org/journals/biology/micropub-biology-002251
August 11, 2026 at 7:12 PM
Complete Genome Sequences of Mycobacteriophages TribleTrouble, TClif, Llorens and CallaLilly #micropublication #biology #data #caltechlibrary #Bacteriophage #GenomeAnnouncements #NewFinding https://micropublication.org/journals/biology/micropub-biology-002251
Reposted by Arkadiy Garber
Genome Sequence and Antimicrobial Production of Pseudomonas crudilactis #micropublication #biology #data #caltechlibrary #Pseudomonas #GenomeAnnouncements #NewFinding https://micropublication.org/journals/biology/micropub-biology-002227
August 12, 2026 at 12:47 AM
Genome Sequence and Antimicrobial Production of Pseudomonas crudilactis #micropublication #biology #data #caltechlibrary #Pseudomonas #GenomeAnnouncements #NewFinding https://micropublication.org/journals/biology/micropub-biology-002227
What lurks in the dark? An innovative framework for studying diverse wild insect microbiota
link.springer.com/article/10.1...
link.springer.com/article/10.1...
What lurks in the dark? An innovative framework for studying diverse wild insect microbiota - Microbiome
Microbiome - Symbiotic microorganisms can profoundly impact insect biology, including their life history traits, population dynamics, and evolutionary trajectories. However, microbiota remain...
link.springer.com
August 12, 2026 at 3:45 PM
What lurks in the dark? An innovative framework for studying diverse wild insect microbiota
link.springer.com/article/10.1...
link.springer.com/article/10.1...
Metagenomics deciphers diagenetic processes of ferruginous mineralization in the deep biosphere
www.nature.com/articles/s43...
www.nature.com/articles/s43...
Metagenomics deciphers diagenetic processes of ferruginous mineralization in the deep biosphere - Communications Earth & Environment
Authigenic minerals reflect specific respiration and fermentation pathways leading to diagenetic redistribution of iron and carbon isotopes during burial, according to an in-depth characterization of ...
www.nature.com
August 9, 2026 at 2:44 AM
Metagenomics deciphers diagenetic processes of ferruginous mineralization in the deep biosphere
www.nature.com/articles/s43...
www.nature.com/articles/s43...
An expanded codebook of human transcription factor DNA-binding specificity
www.nature.com/articles/s41...
www.nature.com/articles/s41...
An expanded codebook of human transcription factor DNA-binding specificity - Nature
Results from a panel of assays that analyse different aspects of DNA sequence specificity reveal more than 100 new motifs to aid the characterization of putative human transcription factors.
www.nature.com
August 8, 2026 at 10:16 PM
An expanded codebook of human transcription factor DNA-binding specificity
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Growth characteristics of natural microbial populations are skewed toward bacteria with low specific growth rates
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
Growth characteristics of natural microbial populations are skewed toward bacteria with low specific growth rates | Microbiology Spectrum
All living organisms are constrained by environmental boundaries that govern where
growth is possible, such as minimum and maximum temperatures or pH. An organism’s
maximum specific growth rate places...
journals.asm.org
August 8, 2026 at 10:15 PM
Growth characteristics of natural microbial populations are skewed toward bacteria with low specific growth rates
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
Taxonomic Resolution of 16S rRNA, FastANI, Mash, and FastAAI across 30,495 Prokaryotic Type-Strain Genomes
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Taxonomic Resolution of 16S rRNA, FastANI, Mash, and FastAAI across 30,495 Prokaryotic Type-Strain Genomes
Prokaryotic taxonomy now relies on both marker-gene and genome-wide sequence comparisons, but these methods differ in taxonomic range, scalability, and sensitivity to genome quality. Here, we benchmar...
www.biorxiv.org
August 8, 2026 at 10:15 PM
Taxonomic Resolution of 16S rRNA, FastANI, Mash, and FastAAI across 30,495 Prokaryotic Type-Strain Genomes
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Experimental verification of the error minimization theory using non-standard genetic codes constructed in vitro
elifesciences.org/articles/111...
elifesciences.org/articles/111...
Experimental verification of the error minimization theory using non-standard genetic codes constructed in vitro
The in vitro experiments that used the artificial genetic codes tested here did not provide support for the error minimization theory.
elifesciences.org
August 8, 2026 at 10:15 PM
Experimental verification of the error minimization theory using non-standard genetic codes constructed in vitro
elifesciences.org/articles/111...
elifesciences.org/articles/111...
Genome-wide dissection of tillering responsiveness to neighbour proximity in sorghum
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Genome-wide dissection of tillering responsiveness to neighbour proximity in sorghum
Tillering plasticity is a key adaptive trait in sorghum influencing resource use efficiency via a plant’s ability to adjust branching to neighbour density. Neighbour detection through red:far-red (R:F...
www.biorxiv.org
August 8, 2026 at 10:13 PM
Genome-wide dissection of tillering responsiveness to neighbour proximity in sorghum
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
I am pleased to share the preprint of our MagicLamp paper, in collaboration with the Penn Geomicrobiology Lab headed by Dr. Pérez-Rodríguez:
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
MagicLamp: a web server and software toolkit for targeted gene annotation of microbial functions
Genome and metagenome annotation tools designed for large databases are ill-suited to the discovery of specialized, ecologically relevant microbial functions. MagicLamp (<https://github.com/Arkadiy-Ga...
www.biorxiv.org
August 7, 2026 at 6:48 AM
I am pleased to share the preprint of our MagicLamp paper, in collaboration with the Penn Geomicrobiology Lab headed by Dr. Pérez-Rodríguez:
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Comparative transcriptomics of closely related Geobacter sulfurreducens strains uncovers strain-level variations in extracellular electron transfer
www.frontiersin.org/journals/mic...
www.frontiersin.org/journals/mic...
Frontiers | Comparative transcriptomics of closely related Geobacter sulfurreducens strains uncovers strain-level variations in extracellular electron transfer
Members of Geobacter sulfurreducens are electroactive bacteria that transfer electrons to extracellular solid electron acceptors using extracellular electron...
www.frontiersin.org
August 7, 2026 at 2:38 AM
Comparative transcriptomics of closely related Geobacter sulfurreducens strains uncovers strain-level variations in extracellular electron transfer
www.frontiersin.org/journals/mic...
www.frontiersin.org/journals/mic...
The last chapter of my PhD work is now live on MBE. This has been an incredible project, combining genomics, proteomics, as well as transcriptomics that resolves total mRNA from ribosome-associated mRNA (which we infer to be in the process of translation).
@ironark.bsky.social et al. measured transcript abundance, ribosome-associated RNA, and protein abundance in bacterial endosymbionts, suggesting a mechanism for aberrant pseudogene-derived protein removal.
🔗 doi.org/10.1093/molbev/msag153
#societyjournal #evobio #molbio
🔗 doi.org/10.1093/molbev/msag153
#societyjournal #evobio #molbio
August 4, 2026 at 5:25 PM
The last chapter of my PhD work is now live on MBE. This has been an incredible project, combining genomics, proteomics, as well as transcriptomics that resolves total mRNA from ribosome-associated mRNA (which we infer to be in the process of translation).
Reposted by Arkadiy Garber
Interspecies exchange of mobile genetic elements during a plant disease outbreak.
Interspecies exchange of mobile genetic elements during a plant disease outbreak.
Published in Genome biology and evolution
doi.org
July 31, 2026 at 7:00 PM
Interspecies exchange of mobile genetic elements during a plant disease outbreak.
Reposted by Arkadiy Garber
The artist formerly known as #thatmitoriboguy has now become #thatchlororiboguy
Check out some cool tomo from @florentwaltz.bsky.social @phaips.vd.st
Check out some cool tomo from @florentwaltz.bsky.social @phaips.vd.st
July 27, 2026 at 1:18 PM
The artist formerly known as #thatmitoriboguy has now become #thatchlororiboguy
Check out some cool tomo from @florentwaltz.bsky.social @phaips.vd.st
Check out some cool tomo from @florentwaltz.bsky.social @phaips.vd.st
Reposted by Arkadiy Garber
Microbial growth control: integrating protein abundance and activity www.sciencedirect.com/science/arti... #jcampubs
July 27, 2026 at 2:54 PM
Microbial growth control: integrating protein abundance and activity www.sciencedirect.com/science/arti... #jcampubs
Reposted by Arkadiy Garber
Influence of cell-cell distance on the ecology and evolution of microbial communities academic.oup.com/ismej/advanc... #jcampubs
July 27, 2026 at 2:56 PM
Influence of cell-cell distance on the ecology and evolution of microbial communities academic.oup.com/ismej/advanc... #jcampubs
Reposted by Arkadiy Garber
metaSMASH: Scalable Biosynthetic Gene Cluster Detection for Large Metagenomic Assemblies www.biorxiv.org/content/10.6... #jcampubs
July 27, 2026 at 2:57 PM
metaSMASH: Scalable Biosynthetic Gene Cluster Detection for Large Metagenomic Assemblies www.biorxiv.org/content/10.6... #jcampubs
Methyltransferases in Candidate Phyla Radiation: A Weapon or a Simple Shield?
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Methyltransferases in Candidate Phyla Radiation: A Weapon or a Simple Shield?
The Candidate Phyla Radiation (CPR) consists of microorganisms with highly reduced genomes and limited metabolic capabilities, including the inability to synthesize nucleotides and amino acids. Previo...
www.biorxiv.org
July 23, 2026 at 2:54 PM
Methyltransferases in Candidate Phyla Radiation: A Weapon or a Simple Shield?
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Arkadiy Garber
NCBI Hidden Markov Models (HMM) Release 20.0
18,950 prokaryotic protein HMMs maintained by @ncbi ncbiinsights.ncbi.nlm.nih.gov/2026/07/01/h...
#microbiology #bioinforbioinformatics #genomics
18,950 prokaryotic protein HMMs maintained by @ncbi ncbiinsights.ncbi.nlm.nih.gov/2026/07/01/h...
#microbiology #bioinforbioinformatics #genomics
Now Available! NCBI Hidden Markov Models (HMM) Release 20.0 - NCBI Insights
Download release 20.0 of the NCBI protein profile Hidden Markov models (HMMs) used by the Prokaryotic Genome Annotation Pipeline (PGAP). You can search this collection against your favorite prokaryoti...
ncbiinsights.ncbi.nlm.nih.gov
July 17, 2026 at 10:49 PM
NCBI Hidden Markov Models (HMM) Release 20.0
18,950 prokaryotic protein HMMs maintained by @ncbi ncbiinsights.ncbi.nlm.nih.gov/2026/07/01/h...
#microbiology #bioinforbioinformatics #genomics
18,950 prokaryotic protein HMMs maintained by @ncbi ncbiinsights.ncbi.nlm.nih.gov/2026/07/01/h...
#microbiology #bioinforbioinformatics #genomics