👾 Karthik

Postdoc @UCLA | PhD @scrippsresearch | | 🐘@[email protected]

[Angie Hinrichs @AngieSHinrichs]

Got milk virus genomes?  (or any H5N1?)  Throw them at https://t.co/Carfmuc0N1 and see where they land in per-segment trees of tens of thousands of public Influenza A H5N1 sequences!

[Michael Worobey @MichaelWorobey]

For a report on our analyses of #H5N1 in cattle, see
worobey bsky social

[Michael Worobey @MichaelWorobey]

My colleagues and I have just posted a
"Note about availability of #H5N1 2.3.4.4b consensus sequences from cattle and other species" @virological_org.

Consensus genomes and metadata.

https://t.co/ggfgW4FPYa

[European Virus Bioinformatics Center @EVirusBioinfC]

#GPUalgorithms achieve significant speedup in statistical #phylogenetics, exemplified by estimating West Nile virus introduction timing from 104 genomes using BEAGLE v4.0.0 in BEAST. [co-authored by EVBC members @LemeyLab @suchard_group] https://t.co/sa5ACZfaSW

[👾 Karthik @xrayfoo]

@ScienceStanley @DiseaseOutbreak @GISAID Glad you find it useful!

[👾 Karthik @xrayfoo]

We've been working hard to enable quicker and easier ⚡️ access to simple but key SC2 variant statistics 📉📈 on @DiseaseOutbreak

Our R package now lets any user with @GISAID credentials to quickly access these stats for surveillance efforts 🔍 & complex downstream analyses 🤓

[Martin Enserink @martinenserink]

In a @VanityFair story, @KatherineEban oddly misrepresented an investigation into @GISAID and Peter Bogner by @sciencecohen and me; suggested our story was a volley in the lab leak debate; and let Bogner dismiss it as a "hit piece." Here's our response. https://t.co/v8FMgeHz2L

[Martin Enserink @martinenserink]

My colleague @sciencecohen and I spent months investigating @GISAID and the mysterious man behind it, Peter Bogner. Here's what we found. https://t.co/FVfswDnAD5

[👾 Karthik @xrayfoo]

Great to see these API connections!

[Theo Sanderson @theosanderson]

Had a good week participating in the NCBI Beyond Phylogenies codeathon. One of the things our team achieved was to add links between tools used for viral phylogenetics

You can now:
- load @nextstrain trees in Taxonium
- export out NS subtrees
- get clade stats with @GenSpectrum

[Chrispin Chaguza @ChrispinChaguza]

🧵for our latest preprint on the intrahost evolution of SARS-CoV-2 virus in an immunocompromised individual (60s) with a history of cancer chronically infected for at least 471 days (ongoing) with consistently replicating viruses at a high viral load. 1/n

https://t.co/qBNEjXTqMt

[👾 Karthik @xrayfoo]

@TWenseleers @RobLanfear @flaneuseks @K_G_Andersen I’m not aware of such an R package but might be worth connecting with GISAID regarding their api feeds through which they provide programmatic access.

[👾 Karthik @xrayfoo]

@TWenseleers @RobLanfear @flaneuseks @K_G_Andersen Sorry but the API can only be used to access the aggregated metrics on our database. The direct downloads are accessible only via GISAID.

[👾 Karthik @xrayfoo]

@RobLanfear @flaneuseks @K_G_Andersen We have vignettes but we should document this usage for sure 😅

[👾 Karthik @xrayfoo]

@flaneuseks @RobLanfear @K_G_Andersen In the meantime, we actually have this endpoint that can be access in a hacky way thru R pkg.

url <- "https://t.co/1pLMFwgI2C"
df <- getGenomicsResponse(url)[[1]]

[👾 Karthik @xrayfoo]

@malkuzweny @GISAID @TAlexPerkins Yes, let’s go with that 😉

[👾 Karthik @xrayfoo]

This was a big team effort only made possible by global 🗺️ sequencing efforts and the team at @GISAID!

In particular, I wanted to highlight @malkuzweny's work in building the R package. She has gone on to doing more exciting work as a PhD student in @TAlexPerkins's group!

[👾 Karthik @xrayfoo]

We've also described the technical details on https://t.co/33nZjrFuEy in these preprints,

Genomic reports
https://t.co/R1OfknTYHy

Research Library
https://t.co/n0092l4YKw