Niklaus Grunwald
@grunwald.bsky.social
Genomic epidemiology, population genomics, plant pathology, pathogen emergence, #Oomycetes, #Phytophthora, #SuddenOakDeath. Opinions are my own. 🧬🦠🧪🖥️
Pinned
PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification
Whole genome sequencing (WGS) offers a comprehensive, organism-agnostic method that effectively meets the need for efficient, reliable, and standardized responses to emerging threats from pathogens an...
www.biorxiv.org
Our PathogenSurveillance pipeline is out in bioRxiv. PathogenSurveillance is an open-source and automated Nextflow pipeline for population genomic analyses of WGS data. It is flexible, using both short and long read data, mixed samples of prokaryotes and eukaryotes.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Niklaus Grunwald
Understanding bioRxiv/medRxiv DOIs. How openRxiv assigns them, a changing prefix, and the embedded priority date in citations openrxiv.org/dois-for-pre...
Understanding DOIs for preprints: how openRxiv assigns and manages persistent identifiers - openRxiv
Digital object identifiers (DOIs) are a class of persistent identifier (PID) assigned to an object to ensure that it can always be uniquely identified and, ideally, accessed reliably. Each DOI is a un...
openrxiv.org
November 19, 2025 at 7:40 PM
Understanding bioRxiv/medRxiv DOIs. How openRxiv assigns them, a changing prefix, and the embedded priority date in citations openrxiv.org/dois-for-pre...
Great satire: www.nature.com/articles/d41...
Introducing the j-metric: a true measure of what matters in academia
Science has become obsessed with publishing numbers. With this new satirical proposal, have we reached peak metric?
www.nature.com
November 19, 2025 at 8:44 PM
Great satire: www.nature.com/articles/d41...
Our PathogenSurveillance pipeline is out in bioRxiv. PathogenSurveillance is an open-source and automated Nextflow pipeline for population genomic analyses of WGS data. It is flexible, using both short and long read data, mixed samples of prokaryotes and eukaryotes.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification
Whole genome sequencing (WGS) offers a comprehensive, organism-agnostic method that effectively meets the need for efficient, reliable, and standardized responses to emerging threats from pathogens an...
www.biorxiv.org
November 3, 2025 at 6:52 PM
Our PathogenSurveillance pipeline is out in bioRxiv. PathogenSurveillance is an open-source and automated Nextflow pipeline for population genomic analyses of WGS data. It is flexible, using both short and long read data, mixed samples of prokaryotes and eukaryotes.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
A one-of-a-kind repeated natural experiment. Population Genomic Analysis of Two Independent Clonal Invasions of the Sudden Oak Death Pathogen into One Forest | Phytopathology® apsjournals.apsnet.org/doi/10.1094/...
Population Genomic Analysis of Two Independent Clonal Invasions of the Sudden Oak Death Pathogen into One Forest | Phytopathology®
Upon introduction, clonal pathogen populations are expected to go through a genetic bottleneck followed by gradual clonal divergence. Two distinct and purely clonal lineages of the sudden oak death pa...
apsjournals.apsnet.org
October 23, 2025 at 3:22 PM
A one-of-a-kind repeated natural experiment. Population Genomic Analysis of Two Independent Clonal Invasions of the Sudden Oak Death Pathogen into One Forest | Phytopathology® apsjournals.apsnet.org/doi/10.1094/...
If you admix barcodes in your Illumina library, use Demulticoder: An R Package for the Simultaneous Analysis of Multiplexed Metabarcodes | Phytopathology® apsjournals.apsnet.org/doi/10.1094/...
Demulticoder: An R Package for the Simultaneous Analysis of Multiplexed Metabarcodes | Phytopathology®
Metabarcoding is a widely used approach relying on short DNA sequences to identify organisms present in a community. Although established workflows exist for analysis of single metabarcodes, these are...
apsjournals.apsnet.org
October 22, 2025 at 8:43 PM
If you admix barcodes in your Illumina library, use Demulticoder: An R Package for the Simultaneous Analysis of Multiplexed Metabarcodes | Phytopathology® apsjournals.apsnet.org/doi/10.1094/...
Novel insights into CAZY pathogenicity factor AA7 involved in plant immune-modulatory function: doi.org/10.1038/s414...
Oomycetes manipulate plant innate immunity through galacturonide oxidases - Nature Communications
The oomycete Phytophthora infestans is a damaging crop pathogen. Here, the authors show that a group of P. infestans secreted enzymes play roles in penetration and colonization of host plants by oxidi...
doi.org
October 21, 2025 at 2:24 PM
Novel insights into CAZY pathogenicity factor AA7 involved in plant immune-modulatory function: doi.org/10.1038/s414...
Reposted by Niklaus Grunwald
On this #WorldFoodDay, we celebrate the efforts of those who nourish our communities, protect our planet, and shape a better future through better food for all. Explore resources to learn more about food security and sustainability. #FAO80
https://bit.ly/4nqN3x7
https://bit.ly/4nqN3x7
October 16, 2025 at 2:14 PM
On this #WorldFoodDay, we celebrate the efforts of those who nourish our communities, protect our planet, and shape a better future through better food for all. Explore resources to learn more about food security and sustainability. #FAO80
https://bit.ly/4nqN3x7
https://bit.ly/4nqN3x7
Working on invasive organisms? Weeds, pests, pathogens or animals? Consider submitting your work to www.cabidigitallibrary.org/journal/ab/s...
CABI Agriculture and Bioscience - Special Issues: Invasive Pathogens| CABI Digital Library
An open access journal publishing multi-, inter- and transdisciplinary research that addresses global challenges in agriculture and the environment. The editors welcome research from a wide range of f...
www.cabidigitallibrary.org
October 7, 2025 at 3:42 PM
Working on invasive organisms? Weeds, pests, pathogens or animals? Consider submitting your work to www.cabidigitallibrary.org/journal/ab/s...
Australia has one of the best and most rigorous approaches and we can all learn from your experience. I like the thought of strategies to build and maintain social license and trustworthiness before, and during any outbreak and the period of response.
great Niklaus and happy to chat more ... you can see some of what we're doing in this space at plantbiosecuritycentre.edu.au/projects/ ... there are a couple of social science projects in there now and about to advertise another.
Our projects
Explore the projects have commenced in the ARC Training Centre in Plant Biosecurity
plantbiosecuritycentre.edu.au
October 3, 2025 at 2:16 PM
Australia has one of the best and most rigorous approaches and we can all learn from your experience. I like the thought of strategies to build and maintain social license and trustworthiness before, and during any outbreak and the period of response.
I am leading an effort to identify gaps in plant biosecurity? Please let me know your thoughts on what is currently missing?
October 3, 2025 at 12:00 AM
I am leading an effort to identify gaps in plant biosecurity? Please let me know your thoughts on what is currently missing?
Reposted by Niklaus Grunwald
Microbial phenazines: biosynthesis, structural diversity, evolution, regulation, and biological significance journals.asm.org/doi/abs/10.1... #jcampubs
October 2, 2025 at 2:52 PM
Microbial phenazines: biosynthesis, structural diversity, evolution, regulation, and biological significance journals.asm.org/doi/abs/10.1... #jcampubs
Reposted by Niklaus Grunwald
Jane Goodall has died at the age of 91.
In 2020, Goodall spoke with Science Editor-in-Chief H. Holden Thorp for a #ScienceEditorial reflecting on the 60th anniversary of her arrival in Gombe to study wild chimpanzees. Read more: https://scim.ag/472Chb8
In 2020, Goodall spoke with Science Editor-in-Chief H. Holden Thorp for a #ScienceEditorial reflecting on the 60th anniversary of her arrival in Gombe to study wild chimpanzees. Read more: https://scim.ag/472Chb8
October 1, 2025 at 7:13 PM
Jane Goodall has died at the age of 91.
In 2020, Goodall spoke with Science Editor-in-Chief H. Holden Thorp for a #ScienceEditorial reflecting on the 60th anniversary of her arrival in Gombe to study wild chimpanzees. Read more: https://scim.ag/472Chb8
In 2020, Goodall spoke with Science Editor-in-Chief H. Holden Thorp for a #ScienceEditorial reflecting on the 60th anniversary of her arrival in Gombe to study wild chimpanzees. Read more: https://scim.ag/472Chb8
Reposted by Niklaus Grunwald
HHMI adopts Plan U journals.plos.org/plosbiology/...
September 24, 2025 at 6:08 PM
HHMI adopts Plan U journals.plos.org/plosbiology/...
@jpodwyer.bsky.social led this elegant and novel approach using genomic demography to make ecological predictions. I am excited to have played a small part in this elegant work:
Genomic demography predicts community dynamics in a temperate montane forest | Science www.science.org/doi/10.1126/...
Genomic demography predicts community dynamics in a temperate montane forest | Science www.science.org/doi/10.1126/...
Genomic demography predicts community dynamics in a temperate montane forest
Species population sizes fluctuate over time, and these temporal dynamics play a key role in governing the maintenance of biodiversity. Although modeling approaches have been developed to characterize...
www.science.org
September 18, 2025 at 8:56 PM
@jpodwyer.bsky.social led this elegant and novel approach using genomic demography to make ecological predictions. I am excited to have played a small part in this elegant work:
Genomic demography predicts community dynamics in a temperate montane forest | Science www.science.org/doi/10.1126/...
Genomic demography predicts community dynamics in a temperate montane forest | Science www.science.org/doi/10.1126/...
Genomic demography predicts community dynamics in a temperate montane forest | Science www.science.org/doi/10.1126/...
Genomic demography predicts community dynamics in a temperate montane forest
Species population sizes fluctuate over time, and these temporal dynamics play a key role in governing the maintenance of biodiversity. Although modeling approaches have been developed to characterize...
www.science.org
September 18, 2025 at 7:18 PM
Genomic demography predicts community dynamics in a temperate montane forest | Science www.science.org/doi/10.1126/...
Just brilliant. Also works for bureaucrats, not just deans www.mcsweeneys.net/articles/fac...
Faculty, Rejoice: Gmail Can Now Translate “Deanspeak”
We are thrilled to announce that Google Translate has recently added “Deanspeak” to its suite of language-detection tools. In addition to offering ...
www.mcsweeneys.net
September 5, 2025 at 1:29 AM
Just brilliant. Also works for bureaucrats, not just deans www.mcsweeneys.net/articles/fac...
Scientists are removing words like “diverse” and “disparities” from hundreds of federal grant renewals to avoid getting flagged in the Trump administration’s focus on eliminating diversity
August 24, 2025 at 10:03 AM
Scientists are removing words like “diverse” and “disparities” from hundreds of federal grant renewals to avoid getting flagged in the Trump administration’s focus on eliminating diversity
Reposted by Niklaus Grunwald
Out-of-pocket ACA premium payments will likely increase about 75% on average next year due to Congressional actions.
Liz Weston: Married couple faces likely 300% increase in their medical insurance premiums
Out-of-pocket ACA premium payments will likely increase about 75% on average next year due to Congressional actions.
www.oregonlive.com
August 16, 2025 at 2:32 PM
Out-of-pocket ACA premium payments will likely increase about 75% on average next year due to Congressional actions.
Reposted by Niklaus Grunwald
ICYMI-- I did.
A study of software developers found it took them 19% more time to do their work when they used AI tools.
At the same time, they *perceived* they had saved time. They thought they would work faster and so they falsely "believed AI had sped them up by 20%."
A study of software developers found it took them 19% more time to do their work when they used AI tools.
At the same time, they *perceived* they had saved time. They thought they would work faster and so they falsely "believed AI had sped them up by 20%."
Measuring the Impact of Early-2025 AI on Experienced Open-Source Developer Productivity
We conduct a randomized controlled trial to understand how early-2025 AI tools affect the productivity of experienced open-source developers working on their own repositories. Surprisingly, we find th...
metr.org
July 21, 2025 at 10:19 AM
ICYMI-- I did.
A study of software developers found it took them 19% more time to do their work when they used AI tools.
At the same time, they *perceived* they had saved time. They thought they would work faster and so they falsely "believed AI had sped them up by 20%."
A study of software developers found it took them 19% more time to do their work when they used AI tools.
At the same time, they *perceived* they had saved time. They thought they would work faster and so they falsely "believed AI had sped them up by 20%."
Reposted by Niklaus Grunwald
#NatMicroPicks
Hidden microbial world in trees🌳
Living wood hosts trillions of bacteria making trees a complex ecosystems with major roles in forest health and function.
#PlantMicro #MicroSky
www.nature.com/articles/s41...
Hidden microbial world in trees🌳
Living wood hosts trillions of bacteria making trees a complex ecosystems with major roles in forest health and function.
#PlantMicro #MicroSky
www.nature.com/articles/s41...
A diverse and distinct microbiome inside living trees - Nature
Microbiome analyses of living trees show that a single tree can host approximately one trillion bacteria, with microbial communities distinctly partitioned between heartwood and sapwood and with minim...
www.nature.com
August 8, 2025 at 2:28 PM
#NatMicroPicks
Hidden microbial world in trees🌳
Living wood hosts trillions of bacteria making trees a complex ecosystems with major roles in forest health and function.
#PlantMicro #MicroSky
www.nature.com/articles/s41...
Hidden microbial world in trees🌳
Living wood hosts trillions of bacteria making trees a complex ecosystems with major roles in forest health and function.
#PlantMicro #MicroSky
www.nature.com/articles/s41...
Reposted by Niklaus Grunwald
Wonderful (and humble) essay on mentorship by Brandon Gaut, on occasion of Brandon receiving the inaugural Mentorship Award of @genetics-gsa.bsky.social. I hope this will be widely read!
academic.oup.com/genetics/art...
academic.oup.com/genetics/art...
August 10, 2025 at 8:41 PM
Wonderful (and humble) essay on mentorship by Brandon Gaut, on occasion of Brandon receiving the inaugural Mentorship Award of @genetics-gsa.bsky.social. I hope this will be widely read!
academic.oup.com/genetics/art...
academic.oup.com/genetics/art...
Ben Hoyt conducting a population genomic analysis of the ‘bulldozer’ Phytophthora cinnamomi #planhealth2025
August 4, 2025 at 7:56 PM
Ben Hoyt conducting a population genomic analysis of the ‘bulldozer’ Phytophthora cinnamomi #planhealth2025
Reposted by Niklaus Grunwald
Happy to share that our Helixer deeplearning-based annotation of 230 superasterid genomes is now online on
@datadryad.bsky.social
💻🌱
doi.org/10.5061/drya...
Check out how we used 69 of them to study the molecular evolution of a plant immune receptor network here! 👇
@datadryad.bsky.social
💻🌱
doi.org/10.5061/drya...
Check out how we used 69 of them to study the molecular evolution of a plant immune receptor network here! 👇
May 9, 2025 at 11:19 AM
Happy to share that our Helixer deeplearning-based annotation of 230 superasterid genomes is now online on
@datadryad.bsky.social
💻🌱
doi.org/10.5061/drya...
Check out how we used 69 of them to study the molecular evolution of a plant immune receptor network here! 👇
@datadryad.bsky.social
💻🌱
doi.org/10.5061/drya...
Check out how we used 69 of them to study the molecular evolution of a plant immune receptor network here! 👇