Matthew Croxen
@mcroxen.bsky.social
public health 🦠 genomics | associate professor | personal account (opinions my own) | 🎸⚽📷♨️🥷 he/him. 🇨🇦 ✊🏿✊🏾✊🏽.
Reposted by Matthew Croxen
New in @plosone.org : Amplicon sequencing of pasteurized retail dairy reveals H5N1 avian influenza virus in U.S. cattle milk. Tiled-amplicon NGS achieved >90% genome coverage from pasteurized milk samples, enabling genomic surveillance of H5N1 spillover in cattle. journals.plos.org/plosone/arti...
Amplicon sequencing of pasteurized retail dairy enables genomic surveillance of H5N1 avian influenza virus in United States cattle
Highly pathogenic avian influenza (HPAI) viruses with H5 hemagglutinin (HA) genes (clade 2.3.4.4b) are causing an ongoing panzootic in wild birds. Circulation of these viruses is associated with spill...
journals.plos.org
June 15, 2025 at 12:09 AM
New in @plosone.org : Amplicon sequencing of pasteurized retail dairy reveals H5N1 avian influenza virus in U.S. cattle milk. Tiled-amplicon NGS achieved >90% genome coverage from pasteurized milk samples, enabling genomic surveillance of H5N1 spillover in cattle. journals.plos.org/plosone/arti...
Reposted by Matthew Croxen
It’s Black Inclusion Week this week. If you are a Black microbiologist we would recommend connecting with the Black Microbiologists Association. They are working hard to increase visibility and facilitate connections: blackinmicrobiology.org #BlackInMicro #BIW2025
Black Microbiologists Association
Moving Microbiology Forward
blackinmicrobiology.org
May 12, 2025 at 9:02 AM
It’s Black Inclusion Week this week. If you are a Black microbiologist we would recommend connecting with the Black Microbiologists Association. They are working hard to increase visibility and facilitate connections: blackinmicrobiology.org #BlackInMicro #BIW2025
Reposted by Matthew Croxen
A new version of our Mtb pangenome preprint is out! Expanded analysis of the full pangenome data and answering all those questions the reviewers asked for ;). Great working with
@mabi-behruznia.bsky.social @danwhiley.bsky.social @blackpassiflora.bsky.social and others
www.biorxiv.org/content/10.1...
@mabi-behruznia.bsky.social @danwhiley.bsky.social @blackpassiflora.bsky.social and others
www.biorxiv.org/content/10.1...
The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference
The Mycobacterium tuberculosis complex (MTBC) is a group of bacteria causing tuberculosis (TB) in humans and animals. Understanding MTBC genetic diversity is crucial for insights into its adaptation a...
www.biorxiv.org
March 31, 2025 at 7:50 PM
A new version of our Mtb pangenome preprint is out! Expanded analysis of the full pangenome data and answering all those questions the reviewers asked for ;). Great working with
@mabi-behruznia.bsky.social @danwhiley.bsky.social @blackpassiflora.bsky.social and others
www.biorxiv.org/content/10.1...
@mabi-behruznia.bsky.social @danwhiley.bsky.social @blackpassiflora.bsky.social and others
www.biorxiv.org/content/10.1...
Reposted by Matthew Croxen
Mathew effect
“…early funding success introduces a growing rift, with winners just above the funding threshold accumulating more than twice as much research funding (€180,000) during the following eight years as nonwinners just below it.”
www.pnas.org/doi/10.1073/...
“…early funding success introduces a growing rift, with winners just above the funding threshold accumulating more than twice as much research funding (€180,000) during the following eight years as nonwinners just below it.”
www.pnas.org/doi/10.1073/...
The Matthew effect in science funding | PNAS
A classic thesis is that scientific achievement exhibits a “Matthew effect”: Scientists
who have previously been successful are more likely to succ...
www.pnas.org
January 17, 2025 at 2:44 AM
Mathew effect
“…early funding success introduces a growing rift, with winners just above the funding threshold accumulating more than twice as much research funding (€180,000) during the following eight years as nonwinners just below it.”
www.pnas.org/doi/10.1073/...
“…early funding success introduces a growing rift, with winners just above the funding threshold accumulating more than twice as much research funding (€180,000) during the following eight years as nonwinners just below it.”
www.pnas.org/doi/10.1073/...
Reposted by Matthew Croxen
Global genomic epidemiology of bla GES-5 carbapenemase-associated integrons. Published #OpenAccess and fee-free in #MGen using a #PublishAndRead agreement: https://doi.org/10.1099/mgen.0.001312
January 17, 2025 at 8:00 AM
Global genomic epidemiology of bla GES-5 carbapenemase-associated integrons. Published #OpenAccess and fee-free in #MGen using a #PublishAndRead agreement: https://doi.org/10.1099/mgen.0.001312
Reposted by Matthew Croxen
New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
Home
A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler
github.com
December 31, 2024 at 11:43 PM
New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)
Reposted by Matthew Croxen
One of the reasons I've been quiet on Bluesky for a few months is because I've been working on something big - something I'm really happy to share now! Pathoplexus.org
A new, open-source database for pathogen sequence sharing. 👐🧬🌎
1/12
A new, open-source database for pathogen sequence sharing. 👐🧬🌎
1/12
Pathoplexus| Home
Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.
Pathoplexus.org
August 27, 2024 at 9:11 PM
One of the reasons I've been quiet on Bluesky for a few months is because I've been working on something big - something I'm really happy to share now! Pathoplexus.org
A new, open-source database for pathogen sequence sharing. 👐🧬🌎
1/12
A new, open-source database for pathogen sequence sharing. 👐🧬🌎
1/12
Reposted by Matthew Croxen
This is v impressive from @pathogenomenick.bsky.social and Co. Trap mosquitoes with CO2 (dry ice), and by sequencing them+bloodmeal+viruses, you get information on host, vector and arboviruses. Piloted in Sao Paolo.
www.microbiologyresearch.org/content/jour...
www.microbiologyresearch.org/content/jour...
Tracking arboviruses, their transmission vectors and potential hosts by nanopore sequencing of mosqu...
The risk to human health from mosquito-borne viruses such as dengue, chikungunya and yellow fever is increasing due to increased human expansion, deforestation and climate change. To anticipate and pr...
www.microbiologyresearch.org
January 20, 2024 at 6:26 AM
This is v impressive from @pathogenomenick.bsky.social and Co. Trap mosquitoes with CO2 (dry ice), and by sequencing them+bloodmeal+viruses, you get information on host, vector and arboviruses. Piloted in Sao Paolo.
www.microbiologyresearch.org/content/jour...
www.microbiologyresearch.org/content/jour...
Reposted by Matthew Croxen
1. Canadian researchers publish the first estimates of 2023-24 #flu vaccine effectiveness that I've seen to date, in Eurosurveillance. The VE is pretty good — 61% overall against H1N1, which was responsible for the vast majority of cases.
#EpiSky www.eurosurveillance.org/content/10.2...
#EpiSky www.eurosurveillance.org/content/10.2...
January 11, 2024 at 7:14 PM
1. Canadian researchers publish the first estimates of 2023-24 #flu vaccine effectiveness that I've seen to date, in Eurosurveillance. The VE is pretty good — 61% overall against H1N1, which was responsible for the vast majority of cases.
#EpiSky www.eurosurveillance.org/content/10.2...
#EpiSky www.eurosurveillance.org/content/10.2...