Looks useful: github.com/nf-core/path...
June 27, 2025 at 6:20 PM
Looks useful: github.com/nf-core/path...
PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification www.biorxiv.org/content/10.1...
Code: github.com/nf-core/path...
Nextflow nf-core pipeline: nf-co.re/pathogensurv...
Code: github.com/nf-core/path...
Nextflow nf-core pipeline: nf-co.re/pathogensurv...
November 2, 2025 at 9:58 PM
PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification www.biorxiv.org/content/10.1...
Code: github.com/nf-core/path...
Nextflow nf-core pipeline: nf-co.re/pathogensurv...
Code: github.com/nf-core/path...
Nextflow nf-core pipeline: nf-co.re/pathogensurv...
PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification. #PathogenSurveillance #Nextflow #Bioinformatics #WGS #PathogenIdentification @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
November 9, 2025 at 5:49 PM
PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification. #PathogenSurveillance #Nextflow #Bioinformatics #WGS #PathogenIdentification @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Smarter #PathogenSurveillance could transform disease response.
Genomics, #MultiOmics and #AI can improve pathogen tracking, transmission prediction and resistance profiling while addressing data quality, bias and privacy challenges.
#OpenAccess #DIT_Journal: doi.org/10.1016/j.dc...
Genomics, #MultiOmics and #AI can improve pathogen tracking, transmission prediction and resistance profiling while addressing data quality, bias and privacy challenges.
#OpenAccess #DIT_Journal: doi.org/10.1016/j.dc...
September 26, 2026 at 8:01 AM
Smarter #PathogenSurveillance could transform disease response.
Genomics, #MultiOmics and #AI can improve pathogen tracking, transmission prediction and resistance profiling while addressing data quality, bias and privacy challenges.
#OpenAccess #DIT_Journal: doi.org/10.1016/j.dc...
Genomics, #MultiOmics and #AI can improve pathogen tracking, transmission prediction and resistance profiling while addressing data quality, bias and privacy challenges.
#OpenAccess #DIT_Journal: doi.org/10.1016/j.dc...
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...
Great to hear from @nisbetalice.bsky.social who shared new insights into how Salmonella Paratyphi A adapts during long-term, asymptomatic carriage 👀
#MicrobialGenomics #PathogenSurveillance #PublicHealth #Microbiology #EntericFever #Salmonella #ECR #MNGPopUp @quadraminstitute.bsky.social
#MicrobialGenomics #PathogenSurveillance #PublicHealth #Microbiology #EntericFever #Salmonella #ECR #MNGPopUp @quadraminstitute.bsky.social
July 3, 2025 at 2:25 PM
Great to hear from @nisbetalice.bsky.social who shared new insights into how Salmonella Paratyphi A adapts during long-term, asymptomatic carriage 👀
#MicrobialGenomics #PathogenSurveillance #PublicHealth #Microbiology #EntericFever #Salmonella #ECR #MNGPopUp @quadraminstitute.bsky.social
#MicrobialGenomics #PathogenSurveillance #PublicHealth #Microbiology #EntericFever #Salmonella #ECR #MNGPopUp @quadraminstitute.bsky.social
Highlight of #SHiMR2025: an insightful keynote from Nabil-Fareed Alikhan on #EntericPathogens, #COVID19 genomics, and how #bioinformatics, large-scale #genomics and open software are shaping global #PublicHealth responses.
#COGUK #PathogenSurveillance #NTU_Metabolic #BigData #NTU #NTU_Metabolic
#COGUK #PathogenSurveillance #NTU_Metabolic #BigData #NTU #NTU_Metabolic
July 2, 2025 at 10:45 PM
Highlight of #SHiMR2025: an insightful keynote from Nabil-Fareed Alikhan on #EntericPathogens, #COVID19 genomics, and how #bioinformatics, large-scale #genomics and open software are shaping global #PublicHealth responses.
#COGUK #PathogenSurveillance #NTU_Metabolic #BigData #NTU #NTU_Metabolic
#COGUK #PathogenSurveillance #NTU_Metabolic #BigData #NTU #NTU_Metabolic
Pipeline release! nf-core/pathogensurveillance v1.0.0 - 1.0.0!
Please see the changelog: https://github.com/nf-core/pathogensurveillance/releases/tag/1.0.0
Please see the changelog: https://github.com/nf-core/pathogensurveillance/releases/tag/1.0.0
June 27, 2025 at 5:50 PM
Pipeline release! nf-core/pathogensurveillance v1.0.0 - 1.0.0!
Please see the changelog: https://github.com/nf-core/pathogensurveillance/releases/tag/1.0.0
Please see the changelog: https://github.com/nf-core/pathogensurveillance/releases/tag/1.0.0
🚨 Tomorrow! 🧬NCBI Pathogen Detection is hosting a public seminar showcasing how their open data resource is being used by researchers and public health professionals.
📅 April 11 | 🕒 12:00 p.m.–1:00p.m. ET
datascience.nih.gov/news/april-2...
#PathogenSurveillance #DataSharing #RadicalTransparency
📅 April 11 | 🕒 12:00 p.m.–1:00p.m. ET
datascience.nih.gov/news/april-2...
#PathogenSurveillance #DataSharing #RadicalTransparency
April Data Sharing and Reuse Seminar | Data Science at NIH
datascience.nih.gov
April 10, 2025 at 3:17 PM
🚨 Tomorrow! 🧬NCBI Pathogen Detection is hosting a public seminar showcasing how their open data resource is being used by researchers and public health professionals.
📅 April 11 | 🕒 12:00 p.m.–1:00p.m. ET
datascience.nih.gov/news/april-2...
#PathogenSurveillance #DataSharing #RadicalTransparency
📅 April 11 | 🕒 12:00 p.m.–1:00p.m. ET
datascience.nih.gov/news/april-2...
#PathogenSurveillance #DataSharing #RadicalTransparency
Stephen Stockdale is at the Human Biology Building, University of Galway for #VIBEICBG2024 until 4pm. This symposium, led by SFI CRT PhD students, highlights advances in #GenomicsDataScience, #CancerGenomics, #Agrigenomics, and #PathogenSurveillance. #NGSExperts #GenomicsResearch #UniversityOfGalway
December 5, 2024 at 12:26 PM
Stephen Stockdale is at the Human Biology Building, University of Galway for #VIBEICBG2024 until 4pm. This symposium, led by SFI CRT PhD students, highlights advances in #GenomicsDataScience, #CancerGenomics, #Agrigenomics, and #PathogenSurveillance. #NGSExperts #GenomicsResearch #UniversityOfGalway
This review shows how #multiomics with #AI transforms #PathogenSurveillance, enabling biomarker discovery, outbreak prediction, and precision care, while tackling data bias, ethics, and advancing #OneHealth collaboration.
#OpenAccess: doi.org/10.1016/j.dc...
#MedSky #PublicHealth #Genomics
#OpenAccess: doi.org/10.1016/j.dc...
#MedSky #PublicHealth #Genomics
March 11, 2026 at 12:25 PM
This review shows how #multiomics with #AI transforms #PathogenSurveillance, enabling biomarker discovery, outbreak prediction, and precision care, while tackling data bias, ethics, and advancing #OneHealth collaboration.
#OpenAccess: doi.org/10.1016/j.dc...
#MedSky #PublicHealth #Genomics
#OpenAccess: doi.org/10.1016/j.dc...
#MedSky #PublicHealth #Genomics
PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification https://www.biorxiv.org/content/10.1101/2025.10.31.685798v1
November 1, 2025 at 6:46 AM
PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification https://www.biorxiv.org/content/10.1101/2025.10.31.685798v1
PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification https://www.biorxiv.org/content/10.1101/2025.10.31.685798v1
November 1, 2025 at 6:46 AM
PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification https://www.biorxiv.org/content/10.1101/2025.10.31.685798v1
Head of Pest & #PathogenSurveillance - #AFBI Newforge
#AgriFood and #Biosciences Institute #Applynow
shorturl.at/QFA4r
*Join Premium WhatsApp Channel
shorturl.at/dRnFn
*Join Telegram t.me/jobnewstimes...
#Phd #postdoc #JobnewsTimes
#ResearchJob
#AgriFood and #Biosciences Institute #Applynow
shorturl.at/QFA4r
*Join Premium WhatsApp Channel
shorturl.at/dRnFn
*Join Telegram t.me/jobnewstimes...
#Phd #postdoc #JobnewsTimes
#ResearchJob
March 25, 2025 at 4:22 AM
Head of Pest & #PathogenSurveillance - #AFBI Newforge
#AgriFood and #Biosciences Institute #Applynow
shorturl.at/QFA4r
*Join Premium WhatsApp Channel
shorturl.at/dRnFn
*Join Telegram t.me/jobnewstimes...
#Phd #postdoc #JobnewsTimes
#ResearchJob
#AgriFood and #Biosciences Institute #Applynow
shorturl.at/QFA4r
*Join Premium WhatsApp Channel
shorturl.at/dRnFn
*Join Telegram t.me/jobnewstimes...
#Phd #postdoc #JobnewsTimes
#ResearchJob
First release of our @nextflow.io #PathogenBiosurveillance population genomic pipeline that can identify known and unknown pathogen & pests as well as variants.
nf-co.re/pathogensurv.... 🧬🖥️🦠🔬🧪
nf-co.re/pathogensurv.... 🧬🖥️🦠🔬🧪
July 8, 2025 at 3:20 PM
First release of our @nextflow.io #PathogenBiosurveillance population genomic pipeline that can identify known and unknown pathogen & pests as well as variants.
nf-co.re/pathogensurv.... 🧬🖥️🦠🔬🧪
nf-co.re/pathogensurv.... 🧬🖥️🦠🔬🧪
ganon2 offers scalable, up-to-date #metagenomic classification with fast incremental indexing and accurate taxonomic binning, designed to keep pace with exploding public sequence repositories. #PathogenSurveillance #Bioinformatics 🚀🧬🔎
📄https://doi.org/10.1093/nargab/lqaf094
👤EVBC: Knut Reinert
📄https://doi.org/10.1093/nargab/lqaf094
👤EVBC: Knut Reinert
doi.org
September 29, 2025 at 8:29 AM
ganon2 offers scalable, up-to-date #metagenomic classification with fast incremental indexing and accurate taxonomic binning, designed to keep pace with exploding public sequence repositories. #PathogenSurveillance #Bioinformatics 🚀🧬🔎
📄https://doi.org/10.1093/nargab/lqaf094
👤EVBC: Knut Reinert
📄https://doi.org/10.1093/nargab/lqaf094
👤EVBC: Knut Reinert
This review highlights how integrating #NextGenSequencing, #multiomics, and #AI transforms #PathogenSurveillance, enabling #outbreak prediction and #biomarker discovery while addressing challenges of bias, ethics, and global collaboration. #MedSky
#OpenAccess: doi.org/10.1016/j.dc...
#OpenAccess: doi.org/10.1016/j.dc...
January 11, 2026 at 1:20 PM
This review highlights how integrating #NextGenSequencing, #multiomics, and #AI transforms #PathogenSurveillance, enabling #outbreak prediction and #biomarker discovery while addressing challenges of bias, ethics, and global collaboration. #MedSky
#OpenAccess: doi.org/10.1016/j.dc...
#OpenAccess: doi.org/10.1016/j.dc...
Links 7/5/25
Links for you. Science: nf-core/pathogensurveillance is a population genomics pipeline for pathogen identification, variant detection, and biosurveillance Genome synthesis in plants Stone Age farmers’ households passed from mother to daughter All childhood vaccines in question after…
Links for you. Science: nf-core/pathogensurveillance is a population genomics pipeline for pathogen identification, variant detection, and biosurveillance Genome synthesis in plants Stone Age farmers’ households passed from mother to daughter All childhood vaccines in question after…
Links 7/5/25
Links for you. Science: nf-core/pathogensurveillance is a population genomics pipeline for pathogen identification, variant detection, and biosurveillance Genome synthesis in plants Stone Age farmers’ households passed from mother to daughter All childhood vaccines in question after first meeting of RFK Jr.’s vaccine panel ‘I’m Not Quite Sure How to Respond to This Presentation’: The discomfiting spectacle of RFK Jr.’s new vaccine-advisory committee…
mikethemadbiologist.com
July 5, 2025 at 8:44 PM
Links 7/5/25
Links for you. Science: nf-core/pathogensurveillance is a population genomics pipeline for pathogen identification, variant detection, and biosurveillance Genome synthesis in plants Stone Age farmers’ households passed from mother to daughter All childhood vaccines in question after…
Links for you. Science: nf-core/pathogensurveillance is a population genomics pipeline for pathogen identification, variant detection, and biosurveillance Genome synthesis in plants Stone Age farmers’ households passed from mother to daughter All childhood vaccines in question after…
Pipeline release! nf-core/pathogensurveillance v1.1.0 - 1.1.0!
Please see the changelog: https://github.com/nf-core/pathogensurveillance/releases/tag/1.1.0
Please see the changelog: https://github.com/nf-core/pathogensurveillance/releases/tag/1.1.0
Release 1.1.0 · nf-core/pathogensurveillance
Added
--max_parallel_downloads parameter to control how many downloads can occur in parallel. This can be used in HPC/cloud contexts to raise the default maximum that is process-specific and gener...
github.com
February 13, 2026 at 10:26 PM
Pipeline release! nf-core/pathogensurveillance v1.1.0 - 1.1.0!
Please see the changelog: https://github.com/nf-core/pathogensurveillance/releases/tag/1.1.0
Please see the changelog: https://github.com/nf-core/pathogensurveillance/releases/tag/1.1.0
A deep amplicon sequencing approach for detection of filarial nematodes in mosquitoes. This paper also discusses potential applications as a molecular xenomonitoring tool for public health and veterinary medicine. www.biorxiv.org/content/10.1...
#nanopore #pathogensurveillance #filariasis #NTD
#nanopore #pathogensurveillance #filariasis #NTD
July 31, 2025 at 6:28 PM
A deep amplicon sequencing approach for detection of filarial nematodes in mosquitoes. This paper also discusses potential applications as a molecular xenomonitoring tool for public health and veterinary medicine. www.biorxiv.org/content/10.1...
#nanopore #pathogensurveillance #filariasis #NTD
#nanopore #pathogensurveillance #filariasis #NTD
Paracoccus yeei detected using real-time, long read metagenome sequencing of cirrhotic ascites from a patient diagnosed with spontaneous bacterial peritonitis.
#nanopore #metagenomics #pathogensurveillance
#nanopore #metagenomics #pathogensurveillance
Detection of Paracoccus yeei in Spontaneous Bacterial Peritonitis using Rapid, Long Read Sequencing
Ascites is a common complication in patients with decompensated liver cirrhosis. Spontaneous bacterial peritonitis (SBP) is the most frequent infection, affecting up to 30% of hospitalized patients…
www.biorxiv.org
April 4, 2025 at 7:24 PM
Paracoccus yeei detected using real-time, long read metagenome sequencing of cirrhotic ascites from a patient diagnosed with spontaneous bacterial peritonitis.
#nanopore #metagenomics #pathogensurveillance
#nanopore #metagenomics #pathogensurveillance
If you want to learn how to sequence pathogens and quickly analyzed their genomes using our nextflow pipeline led by @weisbergaj sign up for the #PlantHealth2024 meeting in Memphis for 'Nanopore Sequencing and Genome Assembly and Annotation with nf-core/pathogensurveillance'
November 16, 2024 at 9:00 AM
If you want to learn how to sequence pathogens and quickly analyzed their genomes using our nextflow pipeline led by @weisbergaj sign up for the #PlantHealth2024 meeting in Memphis for 'Nanopore Sequencing and Genome Assembly and Annotation with nf-core/pathogensurveillance'
PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification https://www.biorxiv.org/content/10.1101/2025.10.31.685798v1
November 1, 2025 at 11:53 PM
PathogenSurveillance: an automated pipeline for population genomic analyses and pathogen identification https://www.biorxiv.org/content/10.1101/2025.10.31.685798v1