👾 Karthik
@xrayfoo
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Postdoc @UCLA | PhD @scrippsresearch | https://t.co/K5wjiCFNGw | 🐘@[email protected]
La Jolla
Joined April 2010
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!
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For a report on our analyses of #H5N1 in cattle, see worobey bsky social
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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.
virological.org
On Sunday, April 21st, 2024, “in the interest of public transparency and ensuring the scientific community has access to this information as quickly as possible to encourage disease research and...
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#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]
academic.oup.com
AbstractMotivation. Advancements in high-throughput genomic sequencing are delivering genomic pathogen data at an unprecedented rate, positioning statistic
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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
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My colleague @sciencecohen and I spent months investigating @GISAID and the mysterious man behind it, Peter Bogner. Here's what we found.
science.org
GISAID offers a safe space to post viral genomes. Peter Bogner, its perplexing creator and overseer, may be jeopardizing its future
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Great to see these API connections!
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
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🧵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
medrxiv.org
The chronic infection hypothesis for novel SARS-CoV-2 variant emergence is increasingly gaining credence following the appearance of Omicron. Here we investigate intrahost evolution and genetic...
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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!
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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
biorxiv.org
To combat the ongoing COVID-19 pandemic, scientists have been conducting research at breakneck speeds, producing over 52,000 peer-reviewed articles within the first year. To address the challenge in...
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Importantly, we hope this showcases a paradigm of data accessibility 🧑💻👩💻👨💻 and reusability ♻️ for genomic surveillance 🦠💻 efforts worldwide 🗺️. The R package is available here - https://t.co/60SsWuTI06 You can read more of our thoughts here -
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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 🤓
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we're deep into Omicron's reign. does that mean we definitely need an Omicron-specific vaccine? it's complicated for at least three big reasons: timing, Omicron's weirdness, and the vagaries of virus evolution. 1/ https://t.co/0wL4tRfkBD
theatlantic.com
Experts are expected to choose a vaccine recipe for the fall, when Omicron may or may not still be the globe’s dominant variant.
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We have just released two preprints on the origin of SARS-CoV-2: 1. "The Huanan market was the epicenter of SARS-CoV-2 emergence" https://t.co/OAVNoWdezs
zenodo.org
Geographical clustering of the earliest known COVID-19 cases and the proximity of positive environmental samples to live-animal vendors suggest that the Huanan Seafood Wholesale Market in Wuhan was...
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I wrote about what's next for the pandemic—the decisions we will *have* to make, if we are to bring COVID under control. 1/ https://t.co/b1Ao4Svoq4
theatlantic.com
The virus isn’t done with us. So we need a new approach to dealing with it.
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(1/13) By the end of the Omicron wave, nearly all of us will have glimpsed spike in some form or another—injection, infection, both. I wrote about what that means... and why “widespread exposure” does not necessarily equate to “widespread protection.” https://t.co/TSj5KWx1TE
theatlantic.com
The variant is spreading widely, but won’t necessarily give us strong protection from new infections.
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