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Jesse Shapiro

Jesse Shapiro

@bjesseshapiro.bsky.social

1.8K followers 750 following 450 posts

Macrobe qui aime les microbes

http://www.shapirolab.ca/

Jesse M. Shapiro is an American economist who has served as the George Gund Professor of Economics and Business Administration at Harvard University since 2022. He was previously the George S. and Nancy B. Parker Professor of Economics at Brown University from 2015 to 2019, and the Eastman Professor of Political Economy at Brown from 2019 to 2021. He received a MacArthur Fellowship in 2021. .. more

Economics 40%

Political science 16%

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Jesse Shapiro @bjesseshapiro.bsky.social · Jul 1

One of my favourite serendipitous results from the lab came about because we were long-read sequencing bacterial:

Vibrio cholerae, which is "supposed to" have TWO circular chromosomes (3 + 1 million base pairs) often has just ONE fused chromosome (4 Mbp).

www.nature.com/articles/s41...

(1/n)

Prevalent chromosome fusion in Vibrio cholerae O1 - Nature Communications

The pathogenic bacterium Vibrio cholerae typically has two circular chromosomes. Here, Cuénod et al. analyse 467 clinical isolates and identify several independent chromosome fusion events that are li...

Jesse Shapiro @bjesseshapiro.bsky.social · 2d

A beautiful opportunity to enrage a copy-editor by (a) alternating between the two, or even better, (b) using the cursed "deletion-born(e) fusions."

Jesse Shapiro @bjesseshapiro.bsky.social · 2d

Very cool paper, and I look forward to the fight with the copy editor about whether it should be "deletion-born fusions" or "deletion-borne fusions"!
(I think both could work?!)

Michael Baym @baym.lol · 5d

New preprint from my lab (with Arya Kaul, @fernpizza.bsky.social, and @brinda.eu), in which we explore new genes hitchhiking on the beneficial deletion that fused them together, and find them in the LTEE, M. Tb/bovis, and across the bacterial tree of life

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 6d

Novel genes arise from genomic deletions across the bacterial tree of life https://www.biorxiv.org/content/10.64898/2026.01.05.697752v1

Jesse Shapiro @bjesseshapiro.bsky.social · 2d

I really enjoyed the paper! It left me wondering how many pseudogenes are actually due to beneficial deletions. We (meaning @gmdouglas.bsky.social & I) tend to assume that pseudogenes (decaying genes) are roughly neutral, but of course some could be adaptive!

www.nature.com/articles/s41...

Client Challenge

Jesse Shapiro @bjesseshapiro.bsky.social · 2d

Full points for eye protection, but the pipetting technique needs work.

Reposted by Jesse M. Shapiro

/r/Habs @habsonreddit.bsky.social · 2d

There’s no place in the NHL like the Bell Centre in Montreal.

Just listen to the Habs crowd on Alexandre Texier’s hat trick goal 🔥

Reposted by Jesse M. Shapiro

Vaughn Cooper @vscooper.micropopbio.org · 2d

🚨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

Reposted by Jesse M. Shapiro

T. Green, MLS 👩🏽‍💻📚🇵🇭🇺🇲 @flipinthestacks.bsky.social · 3d

Enjoy this again from one of the "untenured faculty members and staff holding the institution together."

(Sobs at markout of the office of diversity, equity, and inclusion) #AcademicChatter
#AcademicHumor

An Accurate Organizational Chart of Your University

Our 20th most-read article of 2025. - - -In accordance with our informal tradition of updating documents every thirty years, whether they need it ...

www.mcsweeneys.net

Reposted by Jesse M. Shapiro

Heather Hendrickson @drhhnz.bsky.social · 3d

We’re looking for a postdoc to join the Hendrickson lab!
The project will involve dissecting the molecular mechanisms of a fascinating mobile element in our honeybee biocontrol phages. Sound like something you would be interested in? Get in touch! Details:
jobs.canterbury.ac.nz/jobdetails/a...

Research Associate / Postdoctoral Fellow - Honeybee Bacteriophages and Advanced Biotechnology - University of Canterbury | Te Whare Wānanga o Waitaha

jobs.canterbury.ac.nz

Reposted by Jesse M. Shapiro

McGill Global Health Programs @mcgillghp.bsky.social · 3d

Applications are now open for the 2026 Global Health Scholars program. McGill undergraduates from all faculties and programs can gain hands-on global health research experience with a faculty supervisor during summer 2026 and receive up to $6,000 in funding. www.mcgill.ca/globalhealth...

Reposted by Jesse M. Shapiro, Trevor A. Branch

Rebecca R Helm @rebeccarhelm.bsky.social · 3d

The world feels rough right now

So please enjoy this shrimp, filmed off Cozumel, Mexico. It may be a larval reef shrimp, but we don’t know what species or how long it lives or what it eats. The world is still full of wonder and beauty and mystery.

🎥 @pedrovalenciam scuba diver on Insta

Jesse Shapiro @bjesseshapiro.bsky.social · 3d

For example, my current postdocs don’t know how to put semi-colons at the end of each line of code. I’ll never lose that skill.

Reposted by Jesse M. Shapiro

The Onion @theonion.com · 3d

RFK Jr. Recommends Drinking Anything That Comes Out Of Cow

Reposted by Jesse M. Shapiro

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 4d

Within-host adaptive evolution is limited by genetic drift in experimental human influenza A virus infections https://www.biorxiv.org/content/10.64898/2026.01.07.698006v1

Reposted by Jesse M. Shapiro, Håvard Kauserud

Pat Schloss @patschloss.bsky.social · 4d

New paper up on bioRxiv! This is my third and hopefully final paper on rarefaction. It's still better than the other available methods.

www.biorxiv.org/content/10.6...

Rarefaction is better than robust Aitchison PCA and other compositional data analysis methods at controlling for uneven sequencing effort

Amplicon sequencing typically results in a wide distribution in the number of sequences obtained from each sample. How best to account for this variation has been a persistent problem in the microbial...

www.biorxiv.org

Reposted by Jesse M. Shapiro, Zen Faulkes

Michael Hendricks 🇨🇦 @michaelhendricks.bsky.social · 4d

As this ramps up and we are asked to cheerlead for it, I remain genuinely shocked that Canada, once again, under the banner of a **nation-building**, has created a funding program that excludes Canadian students and researchers based on presence in Canada. /1

universityaffairs.ca/news/feds-la...

Feds launch $1.7 billion international talent attraction program - University Affairs

The program will provide funding to bring 100 top-tier international research chairs and their teams to Canada.

universityaffairs.ca

Reposted by Jesse M. Shapiro

Ed Feil @edfeil.bsky.social · 4d

It has been a long road, but our paper on Klebsiella plasmids is finally out in Lancet Microbe. Thanks to all co authors but especially Marjorie Gibbon and Natacha Couto www.sciencedirect.com/science/arti...

Convergence and global molecular epidemiology of Klebsiella pneumoniae plasmids harbouring the iuc3 virulence locus: a population genomic analysis

Klebsiella pneumoniae is an important pathogen of humans and animals. In the past five years, increasing reports of convergent strains that carry both…

www.sciencedirect.com

Reposted by Jesse M. Shapiro

Hensley Lab @scottehensley.bsky.social · 4d

We find that subclade K viruses are antigenically advanced; however, this year's flu vaccine surprisingly elicited antibodies in many individuals that efficiently recognized these viruses. The implications are clear: go get this year’s vaccine if you haven’t already!

www.medrxiv.org/content/10.6...

Antibodies elicited by the 2025-2026 influenza vaccine in humans

A new H3N2 variant (named subclade K) possesses several key hemagglutinin substitutions and is circulating widely during the 2025-2026 influenza season. In this report, we completed experiments to det...

www.medrxiv.org

Reposted by Jesse M. Shapiro

Matthew Hahn @3rdreviewer.bsky.social · 4d

While our updated paper is fast approaching book-length, the results remain the same: our method (reconcILS) is still highly accurate.

So if you want to reconcile gene trees and species trees--and you might have any ILS at all--this is the best method out there!

www.biorxiv.org/content/10.1...

reconcILS: A gene tree-species tree reconciliation algorithm that allows for incomplete lineage sorting

Reconciliation algorithms infer the evolutionary history of individual gene trees given a species tree. Many reconciliation algorithms consider only duplication and loss events (and sometimes horizont...

www.biorxiv.org

Reposted by Jesse M. Shapiro

Isaac Bogoch @isaacbogoch.bsky.social · 5d

It’s been a tough flu season in Ontario. The good news is that it likely peaked and is now starting to ease, though we can expect several more weeks of widespread flu activity.

Reposted by Jesse M. Shapiro

Reposted by Jesse M. Shapiro

Michael Baym @baym.lol · 5d

New preprint from my lab (with Arya Kaul, @fernpizza.bsky.social, and @brinda.eu), in which we explore new genes hitchhiking on the beneficial deletion that fused them together, and find them in the LTEE, M. Tb/bovis, and across the bacterial tree of life

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 6d

Novel genes arise from genomic deletions across the bacterial tree of life https://www.biorxiv.org/content/10.64898/2026.01.05.697752v1

Reposted by Jesse M. Shapiro

Olaya Rendueles @olayarendueles.bsky.social · 5d

📣 preprint alert!
We sampled #klebsiella isolates from💩 patients when they entered the hospital & 🩸 after development of infection.

🎯 We tracked phenotypic changes & correlate them w genotypic changes.
@klebclub.bsky.social
-in collab with Clermont-Ferrand lab
#microsky
🧵
doi.org/10.64898/202...

Within-host evolution of Klebsiella spp. from intestinal carriage to bacteremia

Gut colonization by the Gram-negative bacillus Klebsiella pneumoniae is a significant risk factor for extra-intestinal infections. However, the mechanisms by which this opportunistic pathogen causes d...

Reposted by Jesse M. Shapiro

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 6d

Novel genes arise from genomic deletions across the bacterial tree of life https://www.biorxiv.org/content/10.64898/2026.01.05.697752v1

Reposted by Jesse M. Shapiro, Simon Roux

Laura Suttenfield @lcatherines.bsky.social · 7d

Happy new year! The second big project of my PhD in Rachel Whitaker's lab is now up! 🎉 We look at how provirus infection affects the evolution of the bacterial chromosome with different types of viral induction – with CRISPRs or antibiotics. Take a peek 🦠 www.biorxiv.org/content/10.6...

Provirus induction diversifies adaptive variation in Pseudomonas aeruginosa lysogen populations

Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that forms chronic infections in people with cystic fibrosis. Often P. aeruginosa strains are lysogens, infected with proviruses, that ...

www.biorxiv.org

Reposted by Jonathan A. Eisen, Jesse M. Shapiro, Elena Litchman , and 2 more Jonathan A. Eisen, Jesse M. Shapiro, Elena Litchman, Chris Marshall, Zen Faulkes

Arcadia Science @arcadiascience.com · 13d

A free, open-access library of high-quality organism illustrations for science communication

A free, open-access library of high-quality organism illustrations for science communication

We create vector graphics of model organisms and emerging biological research organisms to enhance our publications. We’re sharing these editable graphics under a CC0 license for other scientists to...

Reposted by Jesse M. Shapiro

Marianne Denton @mariannedenton.bsky.social · 13d

Last night from the Denton Observatory for this morning, Messier 1, the Crab Nebula.

Nearly 970 years ago a star went supernova which was so bright, it was visible during daylight. Definitely on my bucket list to see a supernova like that 🤞💥

🔭 #Astrophotography

The Crab Nebula through an astrophotography telescope. There’s a lot of stars in the field of view. The nebula looks like a pile of multi colored string. Exposure time ≈47 minutes

Reposted by Jesse M. Shapiro

Dr. Dawn Bowdish @msmacrophage.bsky.social · 14d

Publication Alert: One benefit of vaccination that is particularly difficult to quantify is how it reduces antibiotic use and slows the development of antimicrobial resistance. 'Peri–Covid-19 Antibiotic Use and Antimicrobial Resistance in Older Adults' led by Derek MacFadden and Nick Daneman (1/n)

Peri–Covid-19 Antibiotic Use and Antimicrobial Resistance in Older Adults

Antibiotic use during the coronavirus disease 2019 (Covid-19) pandemic was common in the outpatient setting, but was not supported by guidelines. We sought to evaluate the role of this antibiotic u...

evidence.nejm.org

Jesse Shapiro @bjesseshapiro.bsky.social · 15d

We’ve been using a combination of medaka and clair3, if that helps. (But will try breseq now too, just never thought of it)

Reposted by Jesse M. Shapiro

Cult MTL @cultmtl.com · 15d

Food inflation has reached a two-year high

“Meanwhile, Sobeys, Loblaws and Metro have seen $4.3-billion in profit this year.”

Food inflation in Quebec has reached a two-year high

Food inflation in Quebec has reached a two-year high, with grocery prices up 4.7% over the past year as chains make $4.3-billion in profits.

Reposted by Jesse M. Shapiro, Simon Roux

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 17d

High Precision Binary Trait Association on Phylogenetic Trees https://www.biorxiv.org/content/10.64898/2025.12.24.696407v1