Danny Park @dannyjpark.bsky.social

I use genomics to study the evolution and spread of human pathogens and lead pathogen analytics at the Broad. @[email protected] @dannyjpark.bsky.social

[Christin H. @chanigan]

Just wrapped up meetings with @CDC_AMD state public health and academic partners doing awesome work in pathogen genomic sequencing and bioinformatics! So much awesome work being done and so much more for us to do! @APHL

[Danny Park @dannyjpark.bsky.social @DannyJPark]

@DSI_Africa events this week are well covered on the Twittersphere. But who shall carry the burden of tooting this meeting to the federated mastodonverse?
I, @[email protected], I shall take up my phone and live toot! Follow me, and we shall bring science fomo to your feed!

[Brian Nosek (@[email protected]) @BrianNosek]

Everyone moving from twitter to mastodon is very likely to fail because it is a collective action problem, benefits depend on others actions.

Here's how it can succeed. It will require your commitment for 1 month to do a few things. Read and retweet if you commit to do them.

[Danny Park @dannyjpark.bsky.social @DannyJPark]

It’s been a great start to the DS-I Africa meeting so far!

[DS-I Africa @DSI_Africa]

It's a good morning for DS-I Africa in Cape Town as the Do-athon kicks off in less than 2 hours! #DSIAfricaDoathon #DSIAfricaConsortiumMeeting #DataScience

[Danny Park @dannyjpark.bsky.social @DannyJPark]

Alright @pathogenomenick @firefoxx66 @AineToole time for some pre-dawn outbreak simulation fun

[Danny Park @dannyjpark.bsky.social @DannyJPark]

@dmaccannell Sounds like we should’ve had you come to Barcelona!

[Inês Mendes @ines_cim]

#SARSCoV2 took the world for a spin. At the time, our newly born @pha4ge Data Structures working group thought we could make a difference here. Today our efforts of two years are announced to the world in @GigaScience ⤵️
https://t.co/QUJa3nULLm

[Danny Park @dannyjpark.bsky.social @DannyJPark]

It took me seven episodes to realize that the song actually had lyrics, and the lyrics were his name.
FETT! Boba boba boom, boba boba boba FETT!

[Danny Park @dannyjpark.bsky.social @DannyJPark]

It's worth saying that much of the lab techniques and practices in our viral genomics lab were strongly shaped by Adrianne over the past decade. Plus I love that my kids get to see her videos every time we visit the Museum of Science.

[Pardis Sabeti @PardisSabeti]

For 8 years Adrianne Gladden-Young elevated @sabeti_lab viral genomics and inspired us all. Here is a brief history celebrating the brilliant mind & powerful voice of @agladdenyoung #BlackHistoryMonth 1/16

[ACEGID @acegid_igh]

Hearty congratulations to the duo of Idowu Olawoye @idowuolawoye & Paul Oluniyi @pauloluniyi for their successful post-field seminar (internal defense) yesterday.

#Bioinformatics #PhD

[Russ Corbett @RussCorbett]

I am very pleased to see this analysis posted (+preprint soon!). With tons of fantastic collaborators, @TheSchneiderPhD and @mishmash_su show that pango lineage assignment with pUShER is more stable than pangoLEARN.

[Danny Park @dannyjpark.bsky.social @DannyJPark]

ISO-8601 forever

[Randall Munroe @xkcd]

Formatting Meeting https://t.co/XzuJuct18a

[Danny Park @dannyjpark.bsky.social @DannyJPark]

@akislyuk Aw thanks Andrey!

[Danny Park @dannyjpark.bsky.social @DannyJPark]

My group at the Broad Institute is hiring two computational full-time positions to work in computational methods, analytics, and cloud pipelines for viral genomics in public health!

BS/MS: https://t.co/SAy4c9A4Nz

PhD/MD: https://t.co/iAMBtu1xSj

[Danny Park @dannyjpark.bsky.social @DannyJPark]

@drensber I think folks paying attention were not surprised that it would be quick. I think we were still a bit surprised to see it come even faster than we thought. Once we saw the 8% day, we knew there were only a couple days left.

[Danny Park @dannyjpark.bsky.social @DannyJPark]

The CDC predicts we are already majority omicron in the US based on its nowcast projection from genomic surveillance data from earlier this month. These models are great: it's essential to make decisions based on now & future, not a snapshot 2 weeks ago. https://t.co/xutoKRhmFj

[Danny Park @dannyjpark.bsky.social @DannyJPark]

@drensber That was based on the CDC’s Nowcast models they run every weekend which is a logistic regression on the most recent surveillance data from 1-2wks ago projected to today. Which fits the more recent observed data surprisingly well. https://t.co/yGOYxh0aUA

[Danny Park @dannyjpark.bsky.social @DannyJPark]

@CurtisKapsak We've seen enough of these to know not to make promises about the future! But if only everyone would apply their critical updates and sanitize their inputs properly with an N95 or better, maybe we won't have to deal with the next exploit!

[Danny Park @dannyjpark.bsky.social @DannyJPark]

The CDC considers your server fully patched two weeks after your second zero-day log4j hotfix.

[Danny Park @dannyjpark.bsky.social @DannyJPark]

The blue line will soon fill the gap and probably confirm/overlap the red lines, but the value of a rapid glimpse at current trends (especially real measurements, not extrapolated) cannot be overstated. And the inflection point is brief--if you miss a week, it's already over!

[Danny Park @dannyjpark.bsky.social @DannyJPark]

At the request of @MassDPH, @NicoleLWelch & team applied this assay to >1400 recent clinical specimens from the Broad testing catchment to report this picture. The blue line is all the sequencing data we finished this weekend. The red line she just painted over the past two days.