Jason Shapiro
@jshap.bsky.social
Senior Bioinformatician at the University of Chicago. Also interested in phages, bacteria, and coevolution.
Reposted by Jason Shapiro
🦠🧍♀️From bacterial to human immunity.
We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social
www.science.org/doi/10.1126/...
We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social
www.science.org/doi/10.1126/...
www.science.org
July 24, 2025 at 6:23 PM
🦠🧍♀️From bacterial to human immunity.
We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social
www.science.org/doi/10.1126/...
We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social
www.science.org/doi/10.1126/...
Reposted by Jason Shapiro
We are on the lookout for postdocs for two different projects at the intersection of ecology, evolution, and the human microbiome.
See thread for more information and reach out!
See thread for more information and reach out!
July 22, 2025 at 7:34 PM
We are on the lookout for postdocs for two different projects at the intersection of ecology, evolution, and the human microbiome.
See thread for more information and reach out!
See thread for more information and reach out!
Reposted by Jason Shapiro
New #Rstats blog post: Plot Data Along a Genome with karyoploteR. Demos: genome density, per-base coverage, structural variation, GWAS Manhattan plots, combine multiple data types, gene expression results from DESeq2, epigenetic regulation from ENCODE doi.org/10.59350/dqs...
July 7, 2025 at 11:00 AM
New #Rstats blog post: Plot Data Along a Genome with karyoploteR. Demos: genome density, per-base coverage, structural variation, GWAS Manhattan plots, combine multiple data types, gene expression results from DESeq2, epigenetic regulation from ENCODE doi.org/10.59350/dqs...
Reposted by Jason Shapiro
Are you a recent PhD (or soon to be PhD) from outside Canada looking to do a postdoc in Quebec?
Get in touch if you are excited about microbes, evolution, ecology, genomics (or all of the above!) and I'd be happy to help develop a project together!
www.mcgill.ca/gps/funding/...
Get in touch if you are excited about microbes, evolution, ecology, genomics (or all of the above!) and I'd be happy to help develop a project together!
www.mcgill.ca/gps/funding/...
PBEEE/Quebec Merit Scholarship for Foreign Postdocs and Visiting Research Student and Visiting Researchers
**Note that the FRQ is in the process of revamping their webpages. We will update links soon as we can with the current 2025 year's information. Be sure to check back to see if any eligibility or docu...
www.mcgill.ca
June 11, 2025 at 7:00 PM
Are you a recent PhD (or soon to be PhD) from outside Canada looking to do a postdoc in Quebec?
Get in touch if you are excited about microbes, evolution, ecology, genomics (or all of the above!) and I'd be happy to help develop a project together!
www.mcgill.ca/gps/funding/...
Get in touch if you are excited about microbes, evolution, ecology, genomics (or all of the above!) and I'd be happy to help develop a project together!
www.mcgill.ca/gps/funding/...
Reposted by Jason Shapiro
We have a new 3-year postdoc position in our group at the @hifmb.de to study plasmids and plasmids systems of the marine environment to survey their utility in microbial responses to environmental change.
Please see the official job ad here, and spread the word:
jobs.awi.de/Vacancies/20...
Please see the official job ad here, and spread the word:
jobs.awi.de/Vacancies/20...
PostDoc in ecology and evolution of plasmids in polar waters at HIFMB (f/d/m)
Layout AWI HIPP extern, englisch
jobs.awi.de
June 5, 2025 at 8:09 AM
We have a new 3-year postdoc position in our group at the @hifmb.de to study plasmids and plasmids systems of the marine environment to survey their utility in microbial responses to environmental change.
Please see the official job ad here, and spread the word:
jobs.awi.de/Vacancies/20...
Please see the official job ad here, and spread the word:
jobs.awi.de/Vacancies/20...
Reposted by Jason Shapiro
The Wadsworth Center is expanding it's research focus on #virology /vector-borne diseases!
www.asmcareerconnections.org/job/research-scientist-5-g-31/78488664/
This is a unicorn assistant prof equivalent position with 12-month hard money salary and no teaching commitments (!)
Reposts appreciated 🙏
www.asmcareerconnections.org/job/research-scientist-5-g-31/78488664/
This is a unicorn assistant prof equivalent position with 12-month hard money salary and no teaching commitments (!)
Reposts appreciated 🙏
June 3, 2025 at 9:35 PM
The Wadsworth Center is expanding it's research focus on #virology /vector-borne diseases!
www.asmcareerconnections.org/job/research-scientist-5-g-31/78488664/
This is a unicorn assistant prof equivalent position with 12-month hard money salary and no teaching commitments (!)
Reposts appreciated 🙏
www.asmcareerconnections.org/job/research-scientist-5-g-31/78488664/
This is a unicorn assistant prof equivalent position with 12-month hard money salary and no teaching commitments (!)
Reposts appreciated 🙏
Reposted by Jason Shapiro
Metabolites are not genes — avoiding the misuse of pathway analysis in metabolomics
www.nature.com/articles/s42...
www.nature.com/articles/s42...
Metabolites are not genes — avoiding the misuse of pathway analysis in metabolomics - Nature Metabolism
Pathway analysis, originally developed for gene expression data, has been adapted for metabolomics. However, owing to the unique characteristics and constraints of metabolites compared with genes, pat...
www.nature.com
April 18, 2025 at 4:18 PM
Metabolites are not genes — avoiding the misuse of pathway analysis in metabolomics
www.nature.com/articles/s42...
www.nature.com/articles/s42...
Reposted by Jason Shapiro
Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social:
rdcu.be/eg4OA
1/
rdcu.be/eg4OA
1/
Efficient and robust search of microbial genomes via phylogenetic compression
Nature Methods - Phylogenetic compression achieves performant and lossless compression of massive collections of microbial genomes, facilitating fast BLAST-like search and versatile alignment tasks.
rdcu.be
April 9, 2025 at 9:07 PM
Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social:
rdcu.be/eg4OA
1/
rdcu.be/eg4OA
1/
Reposted by Jason Shapiro
I'm delighted to share a useful FREE web-based app portal of powerful bioinformatics tools for microbial genomes and shotgun microbiome sequences!
It's called Micromics and is built by Middle Author Bioinformatics, led by co-founder @ironark.bsky.social
omix.midauthorbio.com
It's called Micromics and is built by Middle Author Bioinformatics, led by co-founder @ironark.bsky.social
omix.midauthorbio.com
Microbial Omics
A suite of bioinformatics tools for microbial genome and metagenome analysis.
omix.midauthorbio.com
April 8, 2025 at 12:11 PM
I'm delighted to share a useful FREE web-based app portal of powerful bioinformatics tools for microbial genomes and shotgun microbiome sequences!
It's called Micromics and is built by Middle Author Bioinformatics, led by co-founder @ironark.bsky.social
omix.midauthorbio.com
It's called Micromics and is built by Middle Author Bioinformatics, led by co-founder @ironark.bsky.social
omix.midauthorbio.com
Reposted by Jason Shapiro
Our extension to ska, 'ska lo' (for 'left-out') which can additionally, and still very quickly, find indels and SNPs closers than the k-mer distance is now out: academic.oup.com/mbe/advance-...
This addresses a long standing challenge for reference-free variant callers
This addresses a long standing challenge for reference-free variant callers
Reference-free variant calling with local graph construction with ska lo (SKA)
Abstract. The study of genomic variants is increasingly important for public health surveillance of pathogens. Traditional variant calling methods from who
academic.oup.com
April 4, 2025 at 9:56 AM
Our extension to ska, 'ska lo' (for 'left-out') which can additionally, and still very quickly, find indels and SNPs closers than the k-mer distance is now out: academic.oup.com/mbe/advance-...
This addresses a long standing challenge for reference-free variant callers
This addresses a long standing challenge for reference-free variant callers
Reposted by Jason Shapiro
Today we report a new compendium of human gut microbiomes with >168,000 samples
By analyzing this massive dataset, we discovered distinct microbiome patterns across the globe, and show we can predict where a person lives just from their gut bacteria
Now out in Cell:
www.cell.com/cell/fulltex...
By analyzing this massive dataset, we discovered distinct microbiome patterns across the globe, and show we can predict where a person lives just from their gut bacteria
Now out in Cell:
www.cell.com/cell/fulltex...
Integration of 168,000 samples reveals global patterns of the human gut microbiome
The Human Microbiome Compendium is a unified database of publicly available human
gut microbiome 16S samples, built with the integrated data from hundreds of independent
projects. The compendium is us...
www.cell.com
January 22, 2025 at 5:12 PM
Today we report a new compendium of human gut microbiomes with >168,000 samples
By analyzing this massive dataset, we discovered distinct microbiome patterns across the globe, and show we can predict where a person lives just from their gut bacteria
Now out in Cell:
www.cell.com/cell/fulltex...
By analyzing this massive dataset, we discovered distinct microbiome patterns across the globe, and show we can predict where a person lives just from their gut bacteria
Now out in Cell:
www.cell.com/cell/fulltex...
Reposted by Jason Shapiro
Application review for the 2025 Gordon Research Conference on Microbial Population Biology begins on Jan 20. Maximize your chance of acceptance and $ support by submitting your application with a poster abstract before that date! Details: www.grc.org/microbial-po...
January 9, 2025 at 10:49 PM
Application review for the 2025 Gordon Research Conference on Microbial Population Biology begins on Jan 20. Maximize your chance of acceptance and $ support by submitting your application with a poster abstract before that date! Details: www.grc.org/microbial-po...
Reposted by Jason Shapiro
We developed a microscopy-based technique🔬 to measure attachment of viruses #phages to host cells. 🦠
The paper was posted online today:
www.pnas.org/doi/10.1073/...
#phagesky #microsky
The paper was posted online today:
www.pnas.org/doi/10.1073/...
#phagesky #microsky
December 19, 2024 at 10:10 PM
We developed a microscopy-based technique🔬 to measure attachment of viruses #phages to host cells. 🦠
The paper was posted online today:
www.pnas.org/doi/10.1073/...
#phagesky #microsky
The paper was posted online today:
www.pnas.org/doi/10.1073/...
#phagesky #microsky
Reposted by Jason Shapiro
The first review article from my lab, helmed by @celiasouque.bsky.social, "From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance" is now online and open access at Annual Reviews Microbiology:
www.annualreviews.org/content/jour...
www.annualreviews.org/content/jour...
November 21, 2024 at 3:27 PM
The first review article from my lab, helmed by @celiasouque.bsky.social, "From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance" is now online and open access at Annual Reviews Microbiology:
www.annualreviews.org/content/jour...
www.annualreviews.org/content/jour...
Reposted by Jason Shapiro
Our paper on identifying novel origins of transfer by conjugation is out! One can now expand the known oriTs from 1% to 80% in species like Acinetobacter baumannii. This contributes to unravel hitcher plasmid mobility beyond model elements. #microsky www.nature.com/articles/s41...
Expanding the diversity of origin of transfer-containing sequences in mobilizable plasmids - Nature Microbiology
Characterization of known plasmid oriT features facilitates identification of 21 oriT-containing sequence families which, alongside candidate sequence validation, expands our understanding of plasmid ...
www.nature.com
November 11, 2024 at 8:18 AM
Our paper on identifying novel origins of transfer by conjugation is out! One can now expand the known oriTs from 1% to 80% in species like Acinetobacter baumannii. This contributes to unravel hitcher plasmid mobility beyond model elements. #microsky www.nature.com/articles/s41...
Reposted by Jason Shapiro
Seeing a bunch of new followers, so I just tidied up my Evolutionary Biologists starter pack—mostly trying to represent folks' fields right, and get in some topical journals/societies
Hope it's useful, but I'd also love to see packs from other folks, to better cover the field
go.bsky.app/TUNHbNu
Hope it's useful, but I'd also love to see packs from other folks, to better cover the field
go.bsky.app/TUNHbNu
November 7, 2024 at 9:17 PM
Seeing a bunch of new followers, so I just tidied up my Evolutionary Biologists starter pack—mostly trying to represent folks' fields right, and get in some topical journals/societies
Hope it's useful, but I'd also love to see packs from other folks, to better cover the field
go.bsky.app/TUNHbNu
Hope it's useful, but I'd also love to see packs from other folks, to better cover the field
go.bsky.app/TUNHbNu
Reposted by Jason Shapiro
Out in Nature Microbiology, we predicted phage-bacteria interactions in E. coli species using only genomic information.
Adsorption, not defense systems, is the main driver at this scale (relevant for a phage therapy context), leading to tailored cocktails!
www.nature.com/articles/s41...
🧵👇
Adsorption, not defense systems, is the main driver at this scale (relevant for a phage therapy context), leading to tailored cocktails!
www.nature.com/articles/s41...
🧵👇
Prediction of strain level phage–host interactions across the Escherichia genus using only genomic information - Nature Microbiology
Phage–host interactions are computationally predicted using only genomic information, highlighting future research directions and enabling generation of custom phage cocktails.
www.nature.com
November 5, 2024 at 10:08 AM
Out in Nature Microbiology, we predicted phage-bacteria interactions in E. coli species using only genomic information.
Adsorption, not defense systems, is the main driver at this scale (relevant for a phage therapy context), leading to tailored cocktails!
www.nature.com/articles/s41...
🧵👇
Adsorption, not defense systems, is the main driver at this scale (relevant for a phage therapy context), leading to tailored cocktails!
www.nature.com/articles/s41...
🧵👇
Reposted by Jason Shapiro
I'm hiring a postdoc! To use substitution models to understand protein evolution and/or improve phylogenetic methods. evol.mcmaster.ca/brian/evoldi...
https://evol.mcmaster.ca/brian/evoldir/PostDocs//UArizona.AminoAcidSubstitutionModels
Postdoc position: amino acid substitution models
A postdoc position is available with PI Joanna Masel
(https://www.masellab.org/) at the University of Arizona in Tucson. Tucson
is a vibrant city of n...
evol.mcmaster.ca
November 4, 2024 at 4:37 PM
I'm hiring a postdoc! To use substitution models to understand protein evolution and/or improve phylogenetic methods. evol.mcmaster.ca/brian/evoldi...
Reposted by Jason Shapiro
New preprint up! We sequenced hundreds of samples from across one of Earth's oldest living organisms - the Pando aspen clone - to understand how mutations accumulate and spread in long-lived clonal organisms. Our results were…surprising. 1/30
October 26, 2024 at 5:45 PM
New preprint up! We sequenced hundreds of samples from across one of Earth's oldest living organisms - the Pando aspen clone - to understand how mutations accumulate and spread in long-lived clonal organisms. Our results were…surprising. 1/30
Reposted by Jason Shapiro
Tried to put together a Microbial Evolution starter pack, but there were so many great people I didn't want to leave out it turned into 3 starter packs
Comment or DM me if you were missed or would like to be added!
A thread (1/3)
go.bsky.app/6pkuYhi
Comment or DM me if you were missed or would like to be added!
A thread (1/3)
go.bsky.app/6pkuYhi
October 20, 2024 at 9:56 PM
Tried to put together a Microbial Evolution starter pack, but there were so many great people I didn't want to leave out it turned into 3 starter packs
Comment or DM me if you were missed or would like to be added!
A thread (1/3)
go.bsky.app/6pkuYhi
Comment or DM me if you were missed or would like to be added!
A thread (1/3)
go.bsky.app/6pkuYhi
Reposted by Jason Shapiro
Note - if you are interested in the amazing Lake Arrowhead Microbial Genomes meeting but cannot attend in person, there is a highly reduced cost virtual option to participate. See www.eventbrite.com/e/lake-arrow...
August 29, 2024 at 3:03 PM
Note - if you are interested in the amazing Lake Arrowhead Microbial Genomes meeting but cannot attend in person, there is a highly reduced cost virtual option to participate. See www.eventbrite.com/e/lake-arrow...
Reposted by Jason Shapiro
🚨Im looking for postdocs to join me at Montana State!
One position will focus on phage-host-microbe interactions in Lyme disease
The other will sequence phage populations recovered from ticks/mice
Interested? Send me a CV & cover letter! Job ads soon
🧫🦠🧪
One position will focus on phage-host-microbe interactions in Lyme disease
The other will sequence phage populations recovered from ticks/mice
Interested? Send me a CV & cover letter! Job ads soon
🧫🦠🧪
I am super excited to share that my lab has relocated to the Dept of Microbiology & Cell Biology at Montana State University in Bozeman, MT.
We will be looking to recruit scientists at all levels.
Get in touch if you love phages, microbes, & mountains. 🧫🧪🦠
We will be looking to recruit scientists at all levels.
Get in touch if you love phages, microbes, & mountains. 🧫🧪🦠
August 22, 2024 at 11:22 PM
🚨Im looking for postdocs to join me at Montana State!
One position will focus on phage-host-microbe interactions in Lyme disease
The other will sequence phage populations recovered from ticks/mice
Interested? Send me a CV & cover letter! Job ads soon
🧫🦠🧪
One position will focus on phage-host-microbe interactions in Lyme disease
The other will sequence phage populations recovered from ticks/mice
Interested? Send me a CV & cover letter! Job ads soon
🧫🦠🧪
Reposted by Jason Shapiro
Solving genomic puzzles: computational methods for metagenomic binning
Want to know more about finding #phage and #bacteria in #metagenomes?
💻🧬🦠#phagesky
academic.oup.com/bib/article/...
Want to know more about finding #phage and #bacteria in #metagenomes?
💻🧬🦠#phagesky
academic.oup.com/bib/article/...
Solving genomic puzzles: computational methods for metagenomic binning
Abstract. Metagenomics involves the study of genetic material obtained directly from communities of microorganisms living in natural environments. The fiel
academic.oup.com
August 1, 2024 at 2:16 AM
Solving genomic puzzles: computational methods for metagenomic binning
Want to know more about finding #phage and #bacteria in #metagenomes?
💻🧬🦠#phagesky
academic.oup.com/bib/article/...
Want to know more about finding #phage and #bacteria in #metagenomes?
💻🧬🦠#phagesky
academic.oup.com/bib/article/...
Reposted by Jason Shapiro
Glad to see this out! gcplyr is an R package that makes it easy to wrangle and analyze microbial growth curve data. In the paper, I highlight what it adds compared to other software
(a new version is up too! update to get the latest features)
#microbiomesky #MicroSky 🧬🖥️🦠🔬
doi.org/10.1186/s128...
(a new version is up too! update to get the latest features)
#microbiomesky #MicroSky 🧬🖥️🦠🔬
doi.org/10.1186/s128...
gcplyr: an R package for microbial growth curve data analysis - BMC Bioinformatics
Background Characterization of microbial growth is of both fundamental and applied interest. Modern platforms can automate collection of high-throughput microbial growth curves, necessitating the deve...
doi.org
July 9, 2024 at 7:18 PM
Glad to see this out! gcplyr is an R package that makes it easy to wrangle and analyze microbial growth curve data. In the paper, I highlight what it adds compared to other software
(a new version is up too! update to get the latest features)
#microbiomesky #MicroSky 🧬🖥️🦠🔬
doi.org/10.1186/s128...
(a new version is up too! update to get the latest features)
#microbiomesky #MicroSky 🧬🖥️🦠🔬
doi.org/10.1186/s128...
Reposted by Jason Shapiro
Job alert!! Join Integrative Biology at UC Berkeley. We are hiring an Assistant Professor in the area of global change biology with emphasis on the Ecology and Evolution of Host-Microbe Interactions (pathogens, mutualists, microbiomes).
aprecruit.berkeley.edu/JPF04476
aprecruit.berkeley.edu/JPF04476
Assistant Professor - Global Change Biology- Department of Integrative Biology
University of California, Berkeley is hiring. Apply now!
aprecruit.berkeley.edu
July 8, 2024 at 2:51 PM
Job alert!! Join Integrative Biology at UC Berkeley. We are hiring an Assistant Professor in the area of global change biology with emphasis on the Ecology and Evolution of Host-Microbe Interactions (pathogens, mutualists, microbiomes).
aprecruit.berkeley.edu/JPF04476
aprecruit.berkeley.edu/JPF04476