Niklaus Grunwald

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...

Understanding bioRxiv/medRxiv DOIs. How openRxiv assigns them, a changing prefix, and the embedded priority date in citations openrxiv.org/dois-for-pre...

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?

Great satire: www.nature.com/articles/d41...

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...

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...

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...

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/...

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...

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/...

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...

Novel insights into CAZY pathogenicity factor AA7 involved in plant immune-modulatory function: doi.org/10.1038/s414...

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

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...

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.

I love this suggestion. Both on the citizen science individual that can help and changing the behavior of those not engaged. Yes, let's stay in touch.

I am leading an effort to identify gaps in plant biosecurity? Please let me know your thoughts on what is currently missing?

Microbial phenazines: biosynthesis, structural diversity, evolution, regulation, and biological significance journals.asm.org/doi/abs/10.1... #jcampubs

"… Goodall’s … is a story of genuine scientific curiosity, determination, and respect for nature and humanity …" H. Holden Thorp, Editor-in-chief, Science journals

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

HHMI adopts Plan U journals.plos.org/plosbiology/...

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...

@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 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...

Genomic demography predicts community dynamics in a temperate montane forest | Science www.science.org/doi/10.1126/...

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 ...

Just brilliant. Also works for bureaucrats, not just deans www.mcsweeneys.net/articles/fac...

Research posts on Bluesky are more original — and get better engagement Bluesky posts about science garner more likes and reposts than similar ones on X.

www.nature.com/articles/d41...

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

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.

Out-of-pocket ACA premium payments will likely increase about 75% on average next year due to Congressional actions.

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...

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 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...

#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...

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...

Scientific Journals Can’t Keep Up With Flood of Fake Papers The source of the trouble is “paper mills,” businesses or individuals that charge fees to publish fake studies in legitimate journals.

www.wsj.com/science/scie...

Ben Hoyt conducting a population genomic analysis of the ‘bulldozer’ Phytophthora cinnamomi #planhealth2025

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! 👇

USDA reorganization will cut agricultural and forest research One of the agency’s largest and most storied research facilities will be closed along with most forest research stations

www.science.org/content/arti...

Formatted pdf now available. Over 100 authors from across the world agree to protecting the genus Phytophthora against burdensome and unnecessary taxonomic change apsjournals.apsnet.org/doi/10.1094/...

UC Irvine keeps expanding its focus on microbial ecology and microbiome science - an exciting place to work for any early-career people on the hunt for a job!

AMAPEC: accurate antimicrobial activity prediction for fungal effector proteins Fungi typically occur in environments where numerous and diverse other microbes occur as well, often resulting in fierce competition for nutrients and habitat. To support fungal fitness in these envir...

Preprint on antimicrobial prediction pipeline: www.biorxiv.org/content/10.1...