In 2012 it was a SERIOUS uphill climb convincing folks (incl. those w/in FDA) that an open genomic epidemiology model for pathogen surveillance was a good idea. 7 years later, it's the norm. Here's our roadmap for how to do it: onehealthoutlook.biomedcentr… #GenomeTrakr

So great to see such a massive turnout for #ASMNGS! @ASMicrobiology Let’s go! 🚀🧬🦠🧫 #genomics #bioinformatics #publichealth

Check out our latest blog from Dr. Inês Mendes and Dr. Bryan A. Wee, members of the Public Health Alliance for Genomic Epidemiology @pha4ge . They show how ‘bad data’ can be made more valuable by tagging them with information about their potential issues. microb.io/3Xrg9kH

Recently, @andrewjpage, @ines_cim and @rpetit3 contributed to "Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications." You can read it here: microbiologyresearch.org/con…

I am excited to win a CZI EOSS grant! This is the first grant I have ever won after 20+ years in science. It feels wonderful to finally be funded for my open-source contributions. With @wytamma we will deliver the next generation of my popular Snippy software! 🦘🦘🦘

Genomic data quality, completeness, and standards are critical to inform public health. We are very excited to collaborate with @phaa4ge and @NCBI to train data curators across the continent. @alangchris @DrSimonHarris @MastercardFdn @gatesfoundation

This will be a great meeting for scientists working in genomic data standards. See you in Tucson!

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!

Here's where we are: Asymptomatic cows shed H5N1 into the milk supply Pasteurization inactivates the virus and renders it non-infectious @US_FDA & @USDA showed inactivation by inoculating eggs with PCR+ dairy products BUT DO NOT DRINK UNPASTEURIZED MILK fda.gov/food/alerts-advisori…

Good to see our US federal public health scientists recognized at this level!!

Kindly: please retweet if you see this important notice. Today at @officialatcc, we announced a change to the access model for the ATCC Genome Portal (genomes.atcc.org). In order to maintain its long term sustainability, we are transitioning to a Supporting Membership access model on May 1st, 2024. Members, groups, or institutions who opt in to support the AGP will continue to have access to ALL our microbial genomics data, our REST-API, recieve quarterly updates as we release new authenticated genome references to the portal (~1,000 new genomes per year), and get access to new tools for assessing the quality and accuracy of existing genomics data and reference genomes. We have many such tools on the roadmap, the first of which will be Descrepency Report tool that will compare raw sequencing data provided by end-users against our reference genomes, and provide both an easy to interpret (human-readible) report (PDF) and a machine-readable JSON, BAM, BED, and VCF files. More tools, additional data types, phenotypic data, and extensive re-curation efforts are planned, but I would love to hear feedback about what sorts of things might be of most use to you. Finally, access to the entire database and tools we develop doesn't require purchasing physical materials from ATCC, only that you opt-in to be a supporting member. For ATCC customers who decide not to opt-in for supporting the ATCC Genome Portal, we will still provide them with access to authenticated reference genome assemblies for the microbes they purchase from ATCC. So, if you purchased (for example) a bacterial strain from ATCC in the past, you will be able to still access the reference genome, annotations, and metadata for that strain directly from the ATCC Genome Portal. It's extremely important that we continue to provide customers with access to verified/authenticated reference genomes for the materials they obtain from us. These data is produced by our ISO-certified genomics lab (the ATCC Sequencing & Bioinformatics Center, my group ☺️), and is not found anywhere else. The last three years has been a wild ride as we started sequencing the entire collection. About 30% of the microbes we've sequences have never been sequenced before by anyone anywhere in history. It's very cool when you think about it! ☺️ And - wow... my team has grown from 5 to 20 in that time, and both our sequencing and bioinformatics capabilities have increased by orders of magnitude. This has been, and continues to be, a major investment by ATCC into the authenticity of both our biological materials and the data associated with those organisms. I'm really looking forward to the next three years too - and beyond - as we continue to sequence all these interesting bugs. But do to this, we'll need the help of the community to continue supporting this extensive program. I'm very happy to answer questions and take suggestions from the community as well - so please feel free to send me DM via Twitter or LinkedIn (see profile for link). And thanks again to everyone for their continued support 🥰🧬 -- Jonathan #genomics #microbiology #bioinformatics #dataprovenance #science #reproducibility #bacteriology #virology #mycology genomes.atcc.org

Our Research Topic on Integration of #NGS in clinical & public health microbiology attracted fantastic papers! Especially proud of the contribution from all the #PublicHealth labs. Here is our editorial summarizing the article collection: frontiersin.org/articles/10.… @FrontiersIn

Hey, that's me! 🦆🐦‍⬛🕊️📈📉

Huge congrats to the @PHA4GE Data Structures Working Group. Another great step forward towards standardizing our field

🚨Our new manuscript details the work of the @pha4ge Data Structures working group to standardize the type & structure of metadata submitted to the INDSC - simplifying protocols across public health pathogen genomic surveillance. Great job by all, esp @DoctorRuth @griffiemma

The Pathogen DOM is out now in @MicrobioSoc! Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications - go.shr.lc/3TnjpNQ #PHA4GE