joe-wade.bsky.social
@joe-wade.bsky.social
Reposted by joe-wade.bsky.social
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 9:42 PM
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by joe-wade.bsky.social
Brand new preprint from my lab, showing that TnpB, the ancestor of Cas12, acts as a gene drive in plasmids! And it turns out in conjugative plasmids that it acts as a primitive anti-self defense system, providing a potential link between its transposon effect and becoming CRISPR!
What is the best strategy to win any contest?
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
November 20, 2025 at 10:17 PM
Brand new preprint from my lab, showing that TnpB, the ancestor of Cas12, acts as a gene drive in plasmids! And it turns out in conjugative plasmids that it acts as a primitive anti-self defense system, providing a potential link between its transposon effect and becoming CRISPR!
Reposted by joe-wade.bsky.social
Apply through APHL to be a summer intern at the Wadsworth Center. Both basic science research and public health opportunities available.
November 19, 2025 at 3:49 PM
Apply through APHL to be a summer intern at the Wadsworth Center. Both basic science research and public health opportunities available.
Reposted by joe-wade.bsky.social
The University at Albany Biomedical Sciences Department is hiring at the Assistant Professor level. We are looking for researchers at the intersection of infectious disease and artificial intelligence:
albany.interviewexchange.com/jobofferdeta...
#infectiousdisease #artificialintelligence
albany.interviewexchange.com/jobofferdeta...
#infectiousdisease #artificialintelligence
albany.interviewexchange.com
November 18, 2025 at 10:45 PM
The University at Albany Biomedical Sciences Department is hiring at the Assistant Professor level. We are looking for researchers at the intersection of infectious disease and artificial intelligence:
albany.interviewexchange.com/jobofferdeta...
#infectiousdisease #artificialintelligence
albany.interviewexchange.com/jobofferdeta...
#infectiousdisease #artificialintelligence
Reposted by joe-wade.bsky.social
Canonical transcription termination mechanisms explain a minority of operons in cyanobacteria https://www.biorxiv.org/content/10.1101/2025.11.10.687660v1
November 11, 2025 at 3:17 AM
Canonical transcription termination mechanisms explain a minority of operons in cyanobacteria https://www.biorxiv.org/content/10.1101/2025.11.10.687660v1
Reposted by joe-wade.bsky.social
First 🟦 post - my main postdoc work is out in the world! We designed a Cas12a-based genetic screen to identify host factors that contribute to infection by the tickborne pathogen Rickettsia parkeri, and stumbled across a really exciting direct interaction between host and bacterium🦠. Check it out!
Host cyclophilin-mediated maturation of an obligate intracellular bacterial surface virulence factor https://www.biorxiv.org/content/10.1101/2025.10.28.684717v1
November 3, 2025 at 7:03 PM
First 🟦 post - my main postdoc work is out in the world! We designed a Cas12a-based genetic screen to identify host factors that contribute to infection by the tickborne pathogen Rickettsia parkeri, and stumbled across a really exciting direct interaction between host and bacterium🦠. Check it out!
Reposted by joe-wade.bsky.social
The Wilkinson Lab is open for science! @mskcancercenter.bsky.social
🧬We'll be finding funky new RNA biology, mainly by looking at reverse transcriptases (i.e. the Best Enzymes In The World)🧬
annnd: I'm hiring - come join! Especially postdocs and PhD students - please get in touch (NYC is great)
🧬We'll be finding funky new RNA biology, mainly by looking at reverse transcriptases (i.e. the Best Enzymes In The World)🧬
annnd: I'm hiring - come join! Especially postdocs and PhD students - please get in touch (NYC is great)
Wilkinson Lab
We discover and study reverse transcriptases
wilkinsonlab.bio
October 31, 2025 at 7:00 PM
The Wilkinson Lab is open for science! @mskcancercenter.bsky.social
🧬We'll be finding funky new RNA biology, mainly by looking at reverse transcriptases (i.e. the Best Enzymes In The World)🧬
annnd: I'm hiring - come join! Especially postdocs and PhD students - please get in touch (NYC is great)
🧬We'll be finding funky new RNA biology, mainly by looking at reverse transcriptases (i.e. the Best Enzymes In The World)🧬
annnd: I'm hiring - come join! Especially postdocs and PhD students - please get in touch (NYC is great)
Reposted by joe-wade.bsky.social
De-DUFing the DUFs 🧩 @franznarberhaus.bsky.social lab uncovers how small DUF1127 proteins regulate #phosphate uptake by binding the sensor kinase PhoR. Their conserved role from Agrobacterium to E. coli highlights how even small DUFs can shape bacterial physiology 🦠
buff.ly/jJd9Eho
buff.ly/jJd9Eho
October 21, 2025 at 7:02 AM
De-DUFing the DUFs 🧩 @franznarberhaus.bsky.social lab uncovers how small DUF1127 proteins regulate #phosphate uptake by binding the sensor kinase PhoR. Their conserved role from Agrobacterium to E. coli highlights how even small DUFs can shape bacterial physiology 🦠
buff.ly/jJd9Eho
buff.ly/jJd9Eho
Reposted by joe-wade.bsky.social
Thrilled to share our multidisiplinary work on how genome-wide DNA bridging by H-NS reshapes the stationary phase bacterial nucleoid and affects the transcriptional landscape. With Xindan Wang and @meyerroc.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 21, 2025 at 10:01 AM
Thrilled to share our multidisiplinary work on how genome-wide DNA bridging by H-NS reshapes the stationary phase bacterial nucleoid and affects the transcriptional landscape. With Xindan Wang and @meyerroc.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by joe-wade.bsky.social
My lab is hiring a postdoc! Official job ad and application instructions here:
healthresearch.wd1.myworkdayjobs.com/en-US/HRI_Ca...
Current deadline says October 13, but this will be extended to be open for ~2 weeks.
healthresearch.wd1.myworkdayjobs.com/en-US/HRI_Ca...
Current deadline says October 13, but this will be extended to be open for ~2 weeks.
Research Affiliate I (Post Doctoral)
Applications to be submitted by October 13, 2025 Compensation Grade: P99 (Research Affiliate I) Compensation Details: Minimum: $62,353.20 - Maximum: $62,353.20 Annually Positions with a designated wor...
healthresearch.wd1.myworkdayjobs.com
October 10, 2025 at 6:44 PM
My lab is hiring a postdoc! Official job ad and application instructions here:
healthresearch.wd1.myworkdayjobs.com/en-US/HRI_Ca...
Current deadline says October 13, but this will be extended to be open for ~2 weeks.
healthresearch.wd1.myworkdayjobs.com/en-US/HRI_Ca...
Current deadline says October 13, but this will be extended to be open for ~2 weeks.
Reposted by joe-wade.bsky.social
Our lab is offering 3 PhD projects this year across 3 different topics: antibiotic resistance mechanisms, evolution of pathogenic bacteria, and fundamental mechanisms of gene regulation.
www.findaphd.com/phds/?Keywor...
www.findaphd.com/phds/?Keywor...
grainger birmingham PhD Projects, Programmes & Scholarships - 3 PhDs Listed
FindAPhD. Search Funded PhD Projects, Programmes & Scholarships in grainger birmingham. Search for PhD funding, scholarships & studentships in the UK, Europe and around the world.
www.findaphd.com
October 7, 2025 at 3:53 PM
Our lab is offering 3 PhD projects this year across 3 different topics: antibiotic resistance mechanisms, evolution of pathogenic bacteria, and fundamental mechanisms of gene regulation.
www.findaphd.com/phds/?Keywor...
www.findaphd.com/phds/?Keywor...
Reposted by joe-wade.bsky.social
Small side-project from my postdoctoral work with @hitenmadhani.bsky.social. We found that blasticidin S can select for Cryptococcus transformants, and made CRISPR-compatible plasmids for other existing markers. Now 7 dominant genetic selection methods in total!
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
CRISPR/Cas9-compatible plasmids enabling seven dominant genetic selection methods for the human fungal pathogen Cryptococcus neoformans | Microbiology Spectrum
Cryptococcus neoformans is the top-ranked World Health Organization priority fungal pathogen due to its widespread
distribution and inadequate treatment options. Additionally, as a basidiomycete yeast...
journals.asm.org
September 26, 2025 at 9:39 PM
Small side-project from my postdoctoral work with @hitenmadhani.bsky.social. We found that blasticidin S can select for Cryptococcus transformants, and made CRISPR-compatible plasmids for other existing markers. Now 7 dominant genetic selection methods in total!
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
Reposted by joe-wade.bsky.social
Our lab website is live, check it out: pokorzynski-lab.squarespace.com
Pokorzynski Lab @ Oregon State University
pokorzynski-lab.squarespace.com
September 16, 2025 at 9:44 PM
Our lab website is live, check it out: pokorzynski-lab.squarespace.com
Reposted by joe-wade.bsky.social
The Tufts IRACDA Program is now accepting applications. The deadline for positions beginning in late fall/early winter 2025–2026 is October 15, 2025. For details, please visit gsbs.tufts.edu/academics/tu...
I am also happy to discuss potential fellowship projects in my lab.
I am also happy to discuss potential fellowship projects in my lab.
Tufts IRACDA Program | Graduate School of Biomedical Sciences
gsbs.tufts.edu
September 12, 2025 at 12:42 PM
The Tufts IRACDA Program is now accepting applications. The deadline for positions beginning in late fall/early winter 2025–2026 is October 15, 2025. For details, please visit gsbs.tufts.edu/academics/tu...
I am also happy to discuss potential fellowship projects in my lab.
I am also happy to discuss potential fellowship projects in my lab.
Reposted by joe-wade.bsky.social
NOT TO BE MISSED. My awesome colleague Rob Brewster may have COMPLETELY upended our understanding of how TFs work ... a must-read for anyone who cares in the slightest about gene regulation
E. coli transcription factors regulate promoter activity by a universal, homeostatic mechanism | Science www.science.org/doi/10.1126/...
E. coli transcription factors regulate promoter activity by a universal, homeostatic mechanism
Transcription factors (TFs) may activate or repress gene expression through an interplay of different mechanisms, including RNA polymerase (RNAP) recruitment, exclusion, and initiation. However, depen...
www.science.org
September 11, 2025 at 7:21 PM
NOT TO BE MISSED. My awesome colleague Rob Brewster may have COMPLETELY upended our understanding of how TFs work ... a must-read for anyone who cares in the slightest about gene regulation
Check out our new paper: a review of translational coupling, the phenomenon where translation of one prokaryotic gene can promote translation of the gene downstream. We cover the history, and delve into the mechanism, which is still not fully understood. journals.asm.org/doi/10.1128/...
Translational coupling of neighboring genes in prokaryotes | Journal of Bacteriology
Prokaryotic genes are arranged in operons, with functionally related genes often located
adjacent to one another (1). There are several ways in which the operonic organization of genes facilitates
the...
journals.asm.org
September 11, 2025 at 4:45 PM
Check out our new paper: a review of translational coupling, the phenomenon where translation of one prokaryotic gene can promote translation of the gene downstream. We cover the history, and delve into the mechanism, which is still not fully understood. journals.asm.org/doi/10.1128/...
Reposted by joe-wade.bsky.social
Great scientific discussions and community at the Regulating with RNA in Bacteria and Archaea Meeting in Strasbourg 🇫🇷, presenting NIAID research on B. burgdorferi sRNAs and single-cell RNA-seq #rna
September 10, 2025 at 3:48 PM
Great scientific discussions and community at the Regulating with RNA in Bacteria and Archaea Meeting in Strasbourg 🇫🇷, presenting NIAID research on B. burgdorferi sRNAs and single-cell RNA-seq #rna
Reposted by joe-wade.bsky.social
Looking for a new approach to studying or eliminating phages? Check out our study introducing anti-phage ASOs (antisense oligos) out in @Nature today. nature.com/articles/s4158…
September 10, 2025 at 3:40 PM
Looking for a new approach to studying or eliminating phages? Check out our study introducing anti-phage ASOs (antisense oligos) out in @Nature today. nature.com/articles/s4158…
Reposted by joe-wade.bsky.social
De novo engineered guide RNA-directed transposition with TnpB-family proteins reveals features of naturally evolved systems www.biorxiv.org/content/10.1...
De novo engineered guide RNA-directed transposition with TnpB-family proteins reveals features of naturally evolved systems
Programmable DNA integration using CRISPR-associated transposons (CASTs) offers powerful capabilities for genome engineering. The single effector Cas12k CAST examples evolved from a fixed guide TnpB n...
www.biorxiv.org
August 28, 2025 at 12:23 PM
De novo engineered guide RNA-directed transposition with TnpB-family proteins reveals features of naturally evolved systems www.biorxiv.org/content/10.1...
Reposted by joe-wade.bsky.social
Widespread purine bias in bacterial genes driven by runaway transcription https://www.biorxiv.org/content/10.1101/2025.08.25.672197v1
August 26, 2025 at 3:17 AM
Widespread purine bias in bacterial genes driven by runaway transcription https://www.biorxiv.org/content/10.1101/2025.08.25.672197v1
Reposted by joe-wade.bsky.social
🚨 New Preprint Alert 🚨
Our latest work, A Zur-dependent regulatory RNA involved in maintaining zinc homeostasis in Staphylococcus aureus, is now live on bioRxiv! 🧬🦠📄
Check it out here: www.biorxiv.org/content/10.1...
Our latest work, A Zur-dependent regulatory RNA involved in maintaining zinc homeostasis in Staphylococcus aureus, is now live on bioRxiv! 🧬🦠📄
Check it out here: www.biorxiv.org/content/10.1...
August 24, 2025 at 6:38 AM
🚨 New Preprint Alert 🚨
Our latest work, A Zur-dependent regulatory RNA involved in maintaining zinc homeostasis in Staphylococcus aureus, is now live on bioRxiv! 🧬🦠📄
Check it out here: www.biorxiv.org/content/10.1...
Our latest work, A Zur-dependent regulatory RNA involved in maintaining zinc homeostasis in Staphylococcus aureus, is now live on bioRxiv! 🧬🦠📄
Check it out here: www.biorxiv.org/content/10.1...
Reposted by joe-wade.bsky.social
Analysis of stress-induced small proteins in Escherichia coli reveals that YoaI mediates cross-talk between distinct signaling systems 🦠 from Yadavalli lab. Ribo-seq study of Mg2+ starvation induced 17 small proteins 💫 #RNAsky #microsky #ribosome #smallproteins doi.org/10.1101/2024...
Analysis of stress-induced small proteins in Escherichia coli reveals that YoaI mediates cross-talk between distinct signaling systems
Bacterial small proteins (≤ 50 amino acids) are an emerging class of regulators that modulate the activity of signaling networks that enable bacterial adaptation to stress. The Escherichia coli genome...
doi.org
August 18, 2025 at 8:48 AM
Analysis of stress-induced small proteins in Escherichia coli reveals that YoaI mediates cross-talk between distinct signaling systems 🦠 from Yadavalli lab. Ribo-seq study of Mg2+ starvation induced 17 small proteins 💫 #RNAsky #microsky #ribosome #smallproteins doi.org/10.1101/2024...
Reposted by joe-wade.bsky.social
Out yesterday. Using a translation reporter on a mini-tn5 transposon, and high freq. mutagenesis, we looked at translation on whole genome scale independently of genome annotation. academic.oup.com/nar/article/...
PIRT-Seq: a high-resolution whole-genome assay to identify protein-coding genes
Abstract. The advent of high-density mutagenesis and data-mining studies suggest the existence of further coding potential within bacterial genomes. Small
academic.oup.com
August 14, 2025 at 7:00 PM
Out yesterday. Using a translation reporter on a mini-tn5 transposon, and high freq. mutagenesis, we looked at translation on whole genome scale independently of genome annotation. academic.oup.com/nar/article/...
Reposted by joe-wade.bsky.social
New cool work from French friends and colleagues: identification of Rho termination sites in B. subtilis! academic.oup.com/nar/article/...
#SubtiWiki @narjournal.bsky.social @inrae-france.bsky.social
#SubtiWiki @narjournal.bsky.social @inrae-france.bsky.social
Comprehensive mapping of transcription terminator Rho utilization (Rut) sites across the Bacillus subtilis genome
Abstract. Recent evidence indicates that the bacterial Rho helicase regulates Bacillus subtilis gene expression in a growth-dependent manner. This regulati
academic.oup.com
August 14, 2025 at 12:01 PM
New cool work from French friends and colleagues: identification of Rho termination sites in B. subtilis! academic.oup.com/nar/article/...
#SubtiWiki @narjournal.bsky.social @inrae-france.bsky.social
#SubtiWiki @narjournal.bsky.social @inrae-france.bsky.social
Reposted by joe-wade.bsky.social
Talk slots full but we can take late breaking poster abstracts until August 7th. Hope to see you in York to hear about your chromosome story 🧬🦠🧫
www.eventsforce.net/biochemsoc/f...
@vslioy.bsky.social @damelab.bsky.social @graingerlab.bsky.social @biochemsoc.bsky.social @biophychrom.bsky.social
www.eventsforce.net/biochemsoc/f...
@vslioy.bsky.social @damelab.bsky.social @graingerlab.bsky.social @biochemsoc.bsky.social @biophychrom.bsky.social
July 25, 2025 at 12:14 PM
Talk slots full but we can take late breaking poster abstracts until August 7th. Hope to see you in York to hear about your chromosome story 🧬🦠🧫
www.eventsforce.net/biochemsoc/f...
@vslioy.bsky.social @damelab.bsky.social @graingerlab.bsky.social @biochemsoc.bsky.social @biophychrom.bsky.social
www.eventsforce.net/biochemsoc/f...
@vslioy.bsky.social @damelab.bsky.social @graingerlab.bsky.social @biochemsoc.bsky.social @biophychrom.bsky.social