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Jesse Shapiro

@bjesseshapiro.bsky.social
1.9K followers 861 following 668 posts

Macrobe qui aime les microbes www.shapirolab.ca

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Reposted by Jesse Shapiro
Craig MacLean @craigmaclean.bsky.social · 1h
Postdoc position available in my group to work on ERC funded project on evolutionary biology of antibiotic resistance. Looking for someone with expertise in bacterial genetics, AMR, and evolutionary biology. www.jobs.ac.uk/job/DSZ416/p...
jobs.ac.uk
Postdoctoral Research Associate at University of Oxford
Explore an exciting academic career as a Postdoctoral Research Associate. Don't miss out on other academic jobs. Click to apply and explore more opportunities.
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Prasad Jallepalli, MD, PhD @prasad.bsky.social · 29/09/2026
5 potatoes cubed is still 5 potatoes because potatoes are root vegetables
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Pleuni Pennings @pleunipennings.bsky.social · 19h
I am hiring a postdoc! Are you interested to work on population genetics/ drug resistance/ data? Want to work in Montpellier, France? Fastq files don't scare you? PhD required, start date hopefully Nov 1! (end date Sep 30 2028) Please share! abetterscientist.wordpress.com/2026/09/29/p...
abetterscientist.wordpress.com
Postdoc position on drug resistance evolution in Montpellier, France
I have some exciting news (again!). I got money from the region (Occitanie) to hire a postdoc (and later an engineer / technician) to work on drug resistance evolution in malaria (P. faciparum) and…
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Dave Jorgenson @davejorgenson.bsky.social · 26/09/2026
🎃 Pumpkin Spice GLP-1 season 🍂
Smoothie King’s new pumpkin spice GLP-1 smoothie??
And
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Christian Landry @christianlandry.bsky.social · 17h
Single-cell biologists: I am trying to find examples in which people have encapsulated individual cells into droplets, let them grow and performed PCR at two loci with droplet-specific barcoded primers to link the genotypes at these loci using sequencing.
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Kate Baker @ksbakes.bsky.social · 25/09/2026
We have an open Assistant/Associate Professor position in Pathogen Biology at the Department of Genetics - come and join us! 🦠 🧫 🧬https://www.cam.ac.uk/jobs/assistantassociate-professor-in-pathogen-genetics-pc51175
cam.ac.uk
Assistant/Associate Professor in Pathogen Genetics
Applications are invited for an Assistant or Associate Professorship in Pathogen Genetics to be held in the Department of Genetics. We are searching for a talented individual with a track record of fu...
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Jesse Shapiro @bjesseshapiro.bsky.social · 23h
Our latest, spearheaded by the truly indefatigable @emderrick.bsky.social in which we search for selective sweeps in nature and genetic targets of selection within a species in the context of a diverse background community @isme-microbes.bsky.social doi.org/10.1093/isme... 🧵 1/n
doi.org
Validate User
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Asaf Levy @asaflevylab.bsky.social · 29/09/2026
Our new preprint is out. www.biorxiv.org/content/10.6... We applied an XGBoost algorithm with genomic and biochemical features to detect all T6SS effectors in bacterial genomes. Next, we validated 3 novel effectors that serve as antibacterial or anti-euk toxins. One of the effectors, from
biorxiv.org
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Carl T. Bergstrom @carlbergstrom.com · 29/09/2026
"I believe that science derives its authority from something more than mastering the pipeline from data generation to publication. Rather, it comes from interactions within a community of people trained to interrogate evidence and answer for the conclusions they draw from it."
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Will Ratcliff @wcratcliff.bsky.social · 28/09/2026
New paper out with @kaylastoy.bsky.social: academic.oup.com/evlett/advan...
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Jesse Shapiro @bjesseshapiro.bsky.social · 27/09/2026
Bittersweet watching these familiar streets from an ocean away! #UCI
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Lianet Noda @lianetn.bsky.social · 24/09/2026
Akos beat me to announce the paper! Glad it got your attention! Thank you!
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Reposted by Jesse Shapiro
Colin Carlson @colincarlson.bsky.social · 24/09/2026
Oh, you can listen to the Morning Edition story on our new Nature article! www.npr.org/2026/09/24/n...
npr.org
New research suggests human actions could be driving increase in disease outbreaks
Infectious disease outbreaks are on the rise worldwide. A new analysis finds human actions, from deforestation to climate change, are partly responsible.
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Eduardo Rocha @epcrocha.bsky.social · 22/09/2026
Fun collaboration with the Van Melderen lab, led by Ludovic Belot on the acquisition and erosion of toxin-antitoxin systems in bacterial chromosomes. academic.oup.com/mbe/article/...
academic.oup.com
Acquisition and erosion of toxin-antitoxin systems in bacterial chromosomes
Abstract. Toxin-antitoxin systems (TAs) are widespread in bacterial genomes. Yet, their integration, persistence, and impact in chromosome dynamics remain
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lukelukeluke @lukelukeluke.bsky.social · 17/09/2026
Here is a nice mushroom
A big beautiful bear’s head tooth mushroom growing on a perimortuous maple tree. The green undergrowth climbs around it on all sides, and yellow summer sun infuses the woodscape. All photos by me
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Asher Cutter @asherdcutter.bsky.social · 17/09/2026
Come to @romtoronto.bsky.social and EEB in Toronto! ROM is seeking entomologist/arachnologist curator who would also be faculty in EEB at UofT royalontariomuseum.applytojob.com/apply/mdMTpA...
royalontariomuseum.applytojob.com
Curator of Insects & Arachnids - Royal Ontario Museum - Career Page
Apply to Curator of Insects & Arachnids at Royal Ontario Museum in Toronto, ON, Canada.
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Dmitri Petrov @petrovadmitri.bsky.social · 17/09/2026
We are searching for an Assistant Professor in Evolutionary Biology! Looking for colleagues asking fundamental questions relating to evolutionary processes and drivers of evolutionary patterns. If you think it is you, please do apply! And please repost. facultypositions.stanford.edu/jobs/assista...
facultypositions.stanford.edu
Assistant Professor in Evolutionary Biology - Stanford University, California, United States
The Department of Biology at Stanford University seeks applicants for a tenure-track Assistant Professor in Evolutionary Biology. A successful candidate will conduct research that asks fundamental que...
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Jesse Shapiro @bjesseshapiro.bsky.social · 17/09/2026
French TGV 🚆 folks are heroes. After delays caused by the Deutchbahn, the heroic and classy French have rebooked me in 1st class so I can (hopefully) make it home tonight. Merci ! 🇫🇷 🫡
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Kevin A. Scott, PhD @sculpturatus.bsky.social · 17/09/2026
found at ucsf
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Will Ratcliff @wcratcliff.bsky.social · 15/09/2026
1/17 Submissions are now open for the 2027 Microbial Population Biology GRC! We expect this meeting to be extraordinarily oversubscribed. If you want to come, time is of the essence--apply ASAP! June 27–July 2 • Andover, NH www.grc.org/microbial-po...
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Fiona J Whelan @whelanfj.bsky.social · 14/09/2026
Lovely news from @microbiologysociety.org that our recent Perspective was one of the most viewed article in MGen last month. The idea was all @halllab.bsky.social 's. We gravitate towards using the newest, shiniest methods to answer a Q but sometimes the tried and true is still the best option.
microbiologyresearch.org
An ode to the 16S rRNA gene: its history, importance, caveats and future in microbiome research
The 16S rRNA gene has - and continues to - play an important role in microbiology. It’s universality across prokaryotes and variation across species has allowed the sequencing of its hypervariable reg...
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Kristian G. Andersen @kgandersen.bsky.social · 11/09/2026
Good read. What truly baffles me seeing this "AI-designed-printed-in-the-lab-bioweapon will kill us all" guff is the fact that we have *the* biggest, out-of-control, Gain-of-Function experiment, in BSL-0, already running rampant in the US. In cattle 🐮. Yet, 🦗. www.theatlantic.com/health/2026/...
theatlantic.com
The AI Pandemic Isn’t On Its Way
Yet plenty of others might be, thanks to evolution.
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Ellinor Alseth @ellinoralseth.bsky.social · 11/09/2026
What a Friday, finally seeing this published in @cp-trendsmicrobiol.bsky.social! We hope this will be of interest to anyone working in the bacterial immune system field (or microbiology in general), and who wants an evolutionary take on it 🦠🧫 Open Access link: authors.elsevier.com/a/1nllx,L%7E...
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Graham Coop @gcbias.bsky.social · 10/09/2026
I’m looking to hire an NIH funded postdoc to join our lab here at Davis (please RT). Ongoing areas of interest include: 1) polygenic signals of selection from time series, ARGs, GWAS, etc 2) The interpretation of GWAS, polygenic scores, & sources of confounding
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Meaghan Castledine @mcastd.bsky.social · 10/09/2026
🦠Fully funded PhD project with myself, Angus Buckling, Jo Lello and Phil Mitchelmore🦠 How should we design phage therapeutics for bacterial co-infections? How do interactions between pathogens affect treatment efficacy? Please get in touch if you have any Qs 💃 shorturl.at/39Xea
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Alvaro Sanchez @asanchezlab.bsky.social · 21/08/2026
New preprint from the lab: The Latent Simplicity of Microbial Ecological Interactions www.biorxiv.org/content/10.6... We're excited about this one. We find that high-order microbial interactions often obey simple linear laws making microbial communities far more predictable than one might expect
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Sam Yeaman @samyeaman.bsky.social · 08/09/2026
I'm looking to hire a postdoc to work on the RepAdapt + MacroMar projects, analysing genomic data from >130 species of plants, animals, and fungi (VCFs are processed, ready to go). Lots of potential for creativity and collaboration! yeamanlab.weebly.com/uploads/5/7/...
Picture shows fireweed in foreground and Mt. Lougheed in background
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Rachel M. Wheatley @rachelmwheatley.bsky.social · 09/09/2026
🔔 New preprint from our lab: how does the chemical composition of infection-like environments shape how costly (or not) antibiotic resistance mutations are? We find that efflux pump regulator mutants can have a selective advantage in synthetic human urine + identify likely component driving this.
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Tami Lieberman @contaminatedsci.bsky.social · 08/09/2026
Two announcements regarding AccuSNV, which calls high precision SNVs across microbial genomes: Version 1.1 is now incredibly easy to install, run, and perform downstream analyses with (see image of typical output!). The manuscript was also published this summer in Genome Research! Links next...
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Montréal Bioinformatics User Group (MonBUG) @mon-bug.bsky.social · 08/09/2026
Tomorrow, Wed., Sept. 9: Georgi Merhi ( @georgimerhi.bsky.social ) will open the MonBUG evening with "A genome in the lice-stack: metagenomic recovery of Bartonella quintana." | #MonBUG #Bioinformatics #Education #MetaGenomics | | CC/ @bjesseshapiro.bsky.social monbug.ca/en/
monbug.ca
MonBUG
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Montréal Bioinformatics User Group (MonBUG) @mon-bug.bsky.social · 08/09/2026
Demain, mercredi 9 septembre: Georgi Merhi ( @georgimerhi.bsky.social ) ouvrira la soirée MonBUG avec « A genome in the lice-stack: metagenomic recovery of Bartonella quintana » | #MonBUG #Bioinformatics #Education #MetaGenomics | CC/ @bjesseshapiro.bsky.social monbug.ca/fr/
monbug.ca
MonBUG
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Jesse Shapiro @bjesseshapiro.bsky.social · 08/09/2026
Who needs a pickup truck?(Montpellier edition)
Photo of a person pedaling a bike with large front and back cargo platforms along a cobbled street
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Reposted by Jesse Shapiro
Ché Pillay @chepillay.bsky.social · 08/09/2026
The cited Microbiology Spectrum paper is here: journals.asm.org/doi/10.1128/... Interesting reading - the way I was taught aseptic technique may have just been a waste of time.
journals.asm.org
As a component of aseptic technique, Bunsen burners do not universally decrease deposition of microbe-containing particles | Microbiology Spectrum
The ability to manipulate and control microbial presence in built environments is imperative to research and medicine. The lack of documented evidence relating Bunsen burner use and airborne contamina...
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Reposted by Jesse Shapiro
Flora Gaudillière-Jami @fgaudilliere.bsky.social · 07/09/2026
Our paper is now out in the @isme-microbes.bsky.social Journal (and selected as editor's choice)! We use an ecological framework to analyze the distribution of small transposable elements in over 30,000 prokaryotic genomes, characterizing their genomic niche doi.org/10.1093/isme...
doi.org
Characterizing the ecological niche of insertion sequences within prokaryotic genomes
Abstract. Insertion sequences (ISs) are widespread prokaryotic transposable elements, often regarded as genomic parasites that primarily cause deleterious
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Amber Barton @amberbarton.bsky.social · 07/01/2026
Really pleased to see our work on yaws, and how mass drug administration shapes Treponema genomes, published in @lancetmicrobe.bsky.social! sanger.ac.uk/news_item/genomics-uncovers-new-ways-to-target-chronic-childhood-disease/ www.thelancet.com/journals/lan...
sanger.ac.uk
Genomics uncovers new ways to target chronic childhood disease
By sequencing the bacteria that cause the neglected disease yaws, researchers have found that while mass treatment can be successful, it can cause resistant strains to develop. They suggest that publi...
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Paul Rainey @paulbrainey.bsky.social · 07/09/2026
A beautiful piece of detective work by @honour.bsky.social + colleagues revealing the origins of Ralstonia disease of bananas on Martinique. As so often, ICEs (ICERs!) prove to be extraordinary capacitors for evolutionary change. Evolution for evolution's sake 🤔 doi.org/10.1093/gbe/...
doi.org
Interspecies Exchange of Mobile Genetic Elements During a Plant Disease Outbreak
Abstract. Outbreak sequencing provides insight into the origin and evolutionary processes acting on emerging pathogens. Sequencing a historic multihost out
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Jesse Shapiro @bjesseshapiro.bsky.social · 05/09/2026
Fully immersing myself in French culture
Photo of my feet wearing Decathlon branded slides
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Canadian History Ehx @cdnhistoryehx.bsky.social · 05/09/2026
On this day in 2025, Ken Dryden died. Born in 1947 in Hamilton, he won six Stanley Cups, five Vezinas, the Calder and the Conn Smythe in his Hall of Fame career. A best-selling author, he served in Parliament from 2004 to 2011. 📸 Bruce Bennett
Ken Dryden in his jersey standing on the ice with vintage pads, blocker, glove and stick, looking focused.
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Saloni @scientificdiscovery.dev · 05/09/2026
This is interesting. You get assigned to being born at a random place and time in history, to see what a typical person's life might have been like then. Unfortunately I was born in 1403 in the valley of Mexico and died at age 4 from dysentery.
anyhumanever.com
Any Human Ever
One life, drawn at random from all who have ever lived.
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Ben Martin @benjaminmartin.bsky.social · 04/09/2026
Come be my colleague! Montreal is a great place to live and work! Tenure Track position at @mcgill.ca in quantitative cell biology with a research program to address fundamental questions in biology. @futurepislack.bsky.social mcgill.wd3.myworkdayjobs.com/McGill_Caree...
mcgill.wd3.myworkdayjobs.com
Assistant Professor in Quantitative Cell Biology - Department of Biology
Please refer to the How to Apply for a Job (for External Candidates) job aid for instructions on how to apply. If you are an active McGill employee (ie: currently in an active contract or position at ...
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John Lees @johnlees.bacpop.org · 03/09/2026
I am hiring in this round – please do apply if you are interested in: machine learning (protein/genome/gene language models), methods for pathogen data analysis, pangenomes (or share with any students who might want to work with us)
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Jesse Shapiro @bjesseshapiro.bsky.social · 03/09/2026
How it started, how it’s going
Pile of tomatoes, onions, zucchini, eggplant, peppers and rosemaryRatatouille!!
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Jesse Shapiro @bjesseshapiro.bsky.social · 02/09/2026
Without saying your age, what was your favourite film that came out when you were 20 years old
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Jesse Shapiro @bjesseshapiro.bsky.social · 02/09/2026
Sabbatical, day 2.
Photo of a notebook, pen, and e-reader on an outdoor table with a coffee, basket of croissants, and a ceramic garden gnome
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Joshua Weitz @joshuasweitz.bsky.social · 01/09/2026
Delighted to share news that our preprint “Slower-than-exponential viral decay is prevalent and can reshape virus-microbe dynamics” is now online, led by Akash Arani (UMD-BEES PhD), Paul Fremont (UMD-Biology postdoc) and Emma Wachter (former UMD Honors Bio student) www.biorxiv.org/content/10.6...
Examples of viral decay curves spanning biphasic (red), exponential (blue-dashed) fit to data (black points). ~50% are better represented by biphasic rather than exponential.

https://www.biorxiv.org/content/10.64898/2026.08.27.747580v2.full.pdf
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Lucy van Dorp @lucyvandorp.bsky.social · 01/09/2026
Our latest preprint 👉 www.biorxiv.org/content/10.6... 🦠🧬 We explore the genomic legacy of the Second Plague Pandemic across Northern Europe and the Caucasus, analysing 23 newly reconstructed ancient Yersinia pestis genomes from Sweden, Denmark, the Netherlands, Armenia and Iceland. 1/
biorxiv.org
The Genomic Landscape of Post-Black Death Epidemics in Northern Europe and the Caucasus
One of the most devastating events in human history, the Black Death (c.1347-1353), marked the beginning of the Second Plague Pandemic. After initially receding, plague returned in intermittent outbre...
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Will Shoemaker @shoestrapped.bsky.social · 31/08/2026
Overhaul of our work on the macroecology of rRNA **transcripts** from myself, @martinadalbello.bsky.social, and @jacrickets.bsky.social. Highlights below www.biorxiv.org/content/10.6... I'll be talking about this on Thursday Sept. 3rd 17:30h CEST epcp.univie.ac.at/seminars/det...
biorxiv.org
Leveraging rDNA and rRNA dynamics to investigate the link between ecology and physiology in a freshwater microbial community
The dynamics of microbial communities in temporally varying environments are often mediated by the physiological responses of their members. However, physiological measurements remain difficult to obt...
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Brent Toderian @brenttoderian.bsky.social · 28/08/2026
Does replacing parking with bike-lanes hurt restaurant business? Of course not, as this new peer-reviewed STUDY of 15 years of Montreal data showed. ACTUALLY, downtown experienced significant restaurant growth after bike lanes were installed. @momentummag.bsky.social momentummag.com/do-bike-lane...
Separated bike-lane with people riding in Montreal.
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Stephanie Carvin @stephaniecarvin.bsky.social · 27/08/2026
Wake up, babe. The Prime Minister just dropped “hydronym”.
The name Lake Ontario comes from the Wendat word Ontari’io, which, appropriately, means “the lake is beautiful, the lake is big”.

The name is more than 400 years old, predating both the Confederation of Canada and the Declaration of Independence of the United States of America.

We know that America is changing. Their trading relationships, their foreign policies, their national monuments, their hydronyms. 

Canadians also know that naming reality means calling it Lake Ontario – then, now and always.
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