Ruth E. Timme
@ruthtimme.bsky.social
Public health scientist in pathogen genomic surveillance . twin mama . botanist by training . birder . (tweets are my own)
Pinned
Ruth E. Timme
@ruthtimme.bsky.social
· Nov 19
journals.lww.com
📣 New Manuscript from #FDA and #APHL 📣
The human health and broad economic benefits of funding genomic surveillance for foodborne pathogens are clear, yet significant challenges remain to sustaining and advancing this critical public health work in the US.
journals.lww.com/jphmp/fullte...
The human health and broad economic benefits of funding genomic surveillance for foodborne pathogens are clear, yet significant challenges remain to sustaining and advancing this critical public health work in the US.
journals.lww.com/jphmp/fullte...
Reposted by Ruth E. Timme
So glad this is finally out. The method has been instrumental in allowing us to compress the AllTheBacteria data - ~2 million bacterial genomes shrink from 3Terabytes (gzipped) to 100Gb using phylogenetic compression. Great work by @brinda.eu
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
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rdcu.be/eg4OA
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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 10:27 PM
So glad this is finally out. The method has been instrumental in allowing us to compress the AllTheBacteria data - ~2 million bacterial genomes shrink from 3Terabytes (gzipped) to 100Gb using phylogenetic compression. Great work by @brinda.eu
🚨 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
Reposted by Ruth E. Timme
Suffice to say - if you are a local philanthropist and would like to see infectious disease surveillance continue here in San Diego County, please reach out.
Without continued support, we'll lose our eyes on infectious diseases in our county, just as they're likely to surge.
Email on website 👇.
Without continued support, we'll lose our eyes on infectious diseases in our county, just as they're likely to surge.
Email on website 👇.
We were just notified that our contract to UCSD and Scripps Research to support wastewater surveillance in San Diego (searchcovid.info) was terminated immediately for the same reasons 👇.
That means no more genomic wastewater surveillance, and our proposed extensions to measles, Hep A, others, gone.
That means no more genomic wastewater surveillance, and our proposed extensions to measles, Hep A, others, gone.
April 7, 2025 at 4:31 PM
Suffice to say - if you are a local philanthropist and would like to see infectious disease surveillance continue here in San Diego County, please reach out.
Without continued support, we'll lose our eyes on infectious diseases in our county, just as they're likely to surge.
Email on website 👇.
Without continued support, we'll lose our eyes on infectious diseases in our county, just as they're likely to surge.
Email on website 👇.
@fda.gov's #GenomeTrakr is in the news! This program collects genomic data from foodborne pathogens to rapidly stop outbreaks and support long-term prevention strategies to ensure a safer U.S. food supply.
www.the-scientist.com/a-critical-f... #FoodSafety🧬🦠
www.the-scientist.com/a-critical-f... #FoodSafety🧬🦠
A Critical FDA Program Has Helped Solve Thousands of Foodborne Outbreaks
For over a decade, GenomeTrakr has helped scientists trace contaminants from Salmonella to E. coli in the food system.
www.the-scientist.com
March 10, 2025 at 5:54 PM
@fda.gov's #GenomeTrakr is in the news! This program collects genomic data from foodborne pathogens to rapidly stop outbreaks and support long-term prevention strategies to ensure a safer U.S. food supply.
www.the-scientist.com/a-critical-f... #FoodSafety🧬🦠
www.the-scientist.com/a-critical-f... #FoodSafety🧬🦠
Reposted by Ruth E. Timme
Today Pathoplexus announces the inclusion of a new viral pathogen: mpox (previously known as monkeypox).
Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response.
1/7
Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response.
1/7
December 9, 2024 at 7:15 PM
Today Pathoplexus announces the inclusion of a new viral pathogen: mpox (previously known as monkeypox).
Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response.
1/7
Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response.
1/7
Reposted by Ruth E. Timme
Our new commentary out today in @asm.org AAC: "Pathogen genomics in healthcare: overcoming barriers to proactive surveillance"!
Here, my colleagues and I discuss the promises, barriers, and potential solutions for genomic surveillance in healthcare 🦠
#IDSky #PublicHealth
doi.org/10.1128/aac....
Here, my colleagues and I discuss the promises, barriers, and potential solutions for genomic surveillance in healthcare 🦠
#IDSky #PublicHealth
doi.org/10.1128/aac....
December 5, 2024 at 2:19 PM
Our new commentary out today in @asm.org AAC: "Pathogen genomics in healthcare: overcoming barriers to proactive surveillance"!
Here, my colleagues and I discuss the promises, barriers, and potential solutions for genomic surveillance in healthcare 🦠
#IDSky #PublicHealth
doi.org/10.1128/aac....
Here, my colleagues and I discuss the promises, barriers, and potential solutions for genomic surveillance in healthcare 🦠
#IDSky #PublicHealth
doi.org/10.1128/aac....
Reposted by Ruth E. Timme
About the detection of bird flu virus in raw milk in CA:
CDC, others warn against drinking raw milk.
CDFA routinely tests raw milk in bulk tanks.
This batch discovered because Santa Clara County health staff buy and test raw milk from retail stores for another line of defense.
Public health, y’all.
CDC, others warn against drinking raw milk.
CDFA routinely tests raw milk in bulk tanks.
This batch discovered because Santa Clara County health staff buy and test raw milk from retail stores for another line of defense.
Public health, y’all.
.@capublichealth.bsky.social reports finding #H5N1 #birdflu virus in raw milk. The producer, Raw Farm LLC of Fresno County, has agreed to recall a batch of a whole milk product called "cream top."
Milk from infected cows contains staggering levels of virus. www.statnews.com/2024/04/29/b...
Milk from infected cows contains staggering levels of virus. www.statnews.com/2024/04/29/b...
November 25, 2024 at 1:41 AM
About the detection of bird flu virus in raw milk in CA:
CDC, others warn against drinking raw milk.
CDFA routinely tests raw milk in bulk tanks.
This batch discovered because Santa Clara County health staff buy and test raw milk from retail stores for another line of defense.
Public health, y’all.
CDC, others warn against drinking raw milk.
CDFA routinely tests raw milk in bulk tanks.
This batch discovered because Santa Clara County health staff buy and test raw milk from retail stores for another line of defense.
Public health, y’all.
Reposted by Ruth E. Timme
Big congrats to the @who.int IPSN for coordinating a substantial collection of tools for enhancing the development of pathogen surveillance & organising a great Global Partners Forum. This complements the work of PHA4GE & of course many others. Lots of "homework" for us all & see you next year!!
November 22, 2024 at 1:06 PM
Big congrats to the @who.int IPSN for coordinating a substantial collection of tools for enhancing the development of pathogen surveillance & organising a great Global Partners Forum. This complements the work of PHA4GE & of course many others. Lots of "homework" for us all & see you next year!!
📣 New Manuscript from #FDA and #APHL 📣
The human health and broad economic benefits of funding genomic surveillance for foodborne pathogens are clear, yet significant challenges remain to sustaining and advancing this critical public health work in the US.
journals.lww.com/jphmp/fullte...
The human health and broad economic benefits of funding genomic surveillance for foodborne pathogens are clear, yet significant challenges remain to sustaining and advancing this critical public health work in the US.
journals.lww.com/jphmp/fullte...
journals.lww.com
November 19, 2024 at 5:26 PM
📣 New Manuscript from #FDA and #APHL 📣
The human health and broad economic benefits of funding genomic surveillance for foodborne pathogens are clear, yet significant challenges remain to sustaining and advancing this critical public health work in the US.
journals.lww.com/jphmp/fullte...
The human health and broad economic benefits of funding genomic surveillance for foodborne pathogens are clear, yet significant challenges remain to sustaining and advancing this critical public health work in the US.
journals.lww.com/jphmp/fullte...
Reposted by Ruth E. Timme
Seq data of varying quality can be used for different public health applications (analysis, training, more). @pha4ge standardized QC tags help users share, triage, and identify a wider array of data in public repos. For more info, see: shorturl.at/1yaCw hot off the presses!
PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training
As public health laboratories expand their genomic sequencing and bioinformatics capacity for the surveillance of different pathogens, labs must carry out robust validation, training, and optimization...
shorturl.at
June 11, 2024 at 4:44 PM
Seq data of varying quality can be used for different public health applications (analysis, training, more). @pha4ge standardized QC tags help users share, triage, and identify a wider array of data in public repos. For more info, see: shorturl.at/1yaCw hot off the presses!
First post on the sky app!
Our local paper, #Oaklandside, joined our Christmas bird count team this year 🐦🦆📈:
oaklandside.org/2023/12/21/h...
Our local paper, #Oaklandside, joined our Christmas bird count team this year 🐦🦆📈:
oaklandside.org/2023/12/21/h...
December 22, 2023 at 2:26 PM
First post on the sky app!
Our local paper, #Oaklandside, joined our Christmas bird count team this year 🐦🦆📈:
oaklandside.org/2023/12/21/h...
Our local paper, #Oaklandside, joined our Christmas bird count team this year 🐦🦆📈:
oaklandside.org/2023/12/21/h...