Silas Tittes

Recently we're working with SNPs from whole genome assemblies to estimate ARGs. It's a pain to go from alignment files to vcf, keeping track of masked and invariant sites. So we wrote a snakemake/SLURM pipeline. Hope it's useful to others, and don't hesitate to post issues if there are problems!

It's a pretty funny criticism because

1) the data are sourced from a public database, NIH RePORTER
2) "Deranged activist" Jeremy Berg was an NIH institute director for 7 years

and most importantly
3) Thacker admits the story is totally accurate

A post from Jason Locasale quoting Paul Thacker complaining about a Nature story from Max Kozlov using data from NIH Reporter that I posted on my Bluesky account.

Apparently Jason Locasale and Paul Thacker have a problem with using publicly available data from NIH Reporter about the number of new and competitive renewal grants from fiscal year 2026 compared to previous fiscal years because I first posted it.

1/2

Screening, sorting, and the feedback cycles that imperil peer review The process of peer review is vital to contemporary science, but is also under enormous strain. This study uses mathematical models to dissect the threats to the long-term viability of peer review, su...

1. Kevin Gross and I have a new paper out today PLOS Biology.

We used economic models based around screening games and the market for unpaid labor to highlight a meltdown cycle threatening peer review.

DHS confirms ICE agent fatally shot US citizen in 2025 Ruben Ray Martinez was shot through his driver's-side window in South Padre Island, Texas.

DHS is only now admitting that one of their agents shot and killed 23-year-old Ruben Ray Martinez, a U.S. citizen, last March.

Another day, another DHS lie exposed. Congress must rein in this abusive, lawless agency.

Forecasting Genomic Change with Time Series Sequence Data | The American Naturalist: Vol 207, No 3 Abstract Humans drive species evolution in numerous ways, ranging from the deliberate interventions of domestication to the indirect but far-reaching impacts of climate change. Anticipating how specie...

This paper doi.org/10.1086/739046 by @jacksondanny.bsky.social et al, plus the rest of the hot new Am Nat special issue on genomic forecasting

Cool!

Neat! Looks like a really thoughtful design to get a clear look at cool non additive stuff!

www.biorxiv.org/content/10.6... from @quercus62.bsky.social (ok just read the intro so far, unsure when I'll get to the rest, but so far it's very cool!!)

What are you reading today evobio and popgen friends?

Can we simulate realistic evolutionary trajectories and “replay the tape of life”? In this work, we propose a flexible, generalizable deep learning framework for modeling how the entire protein sequence evolves over time while capturing complex interactions across sites. 1/n
doi.org/10.64898/202...

Time-calibrated phylogeny of the family Drosophilidae showing major species groups, surrounded by representative adult flies that highlight the remarkable morphological diversity of this model insect group. The composite image was created using Microsoft PowerPoint. Fly photographs were taken by Darren J. Obbard and are published under the Creative Commons Attribution License with permission.

The #fly community aims to achieve a comprehensive genomic study of the Drosophilidae family. @pankajd.bsky.social @bernardkim.bsky.social @petrovadmitri.bsky.social @darrenobbard.bsky.social present a comparative gene annotation for 301 #Drosophilidae species @plosbiology.org 🧪 plos.io/4c3pyrI

I read about half this book a few years ago (forgotten 200% of it now) and found it really helpful .

Code: The Hidden Language of Computer Hardware and Software share.google/JhuX7fD4azJs...

The Pain Is the Plan MAGA is actively seeking to immiserate the country in order to cement their power over the rest of us.

"One of the best takeaways those of us on the left or the center can hold is that tariffs, the annihilation of the safety net, aggressive tax cuts, and all of their other fiscal policies are not about enrichment as an end unto itself: they’re about impoverishment as a means to reinforce hierarchy."

🔊 TONIGHT! A new episode of Make Some Noise launches on Dropout at 7PM ET / 4PM PT!

Starring host Sam Reich, and guests:
📢 Jeremy Culhane
📢 Anna Garcia
📢 Geoff Ross

If Moderna is no longer bringing vaccine trials for Epstein-Barr virus (good evidence that EB causes Multiple Sclerosis), herpes, and shingles because of Trump appointees, I want prison time for those appointees.

This might be dooming millions to disease they don’t have to experience.

I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.

Agree with Josh, it all seems nefarious and evil. I’m not saying I know their whole program is designed to make a lot of people die intentionally, but such a program sure would look a lot like what they’re doing.

Congresswoman Uses Simple Math To Show How Broken ICE Is

A stunning detail the ICE chief shared in this hearing that was supposed to be a brag, except it isn't: ICE has arrested 379,000 people between Jan. 2025-Jan. 2026 -- but only 8,700 were suspected gang members or known suspected terrorists.

That's 2%! www.huffpost.com/entry/latest...

Listen to this. Not a penny more for this. Abolish and prosecute anyone who had anything to do with it.

Definitely seeing the patterns of doomerism on here more. It’s sooooo useless and self-defeating to say nothing is working and there’s no hope — to the point where I wonder if any of the doomer accounts are commenting in good faith.

🚨BREAKING: Puerto Rico has been part of the United States since 1898, and people still act confused that Puerto Ricans are American.

States that joined after Puerto Rico:
• Oklahoma — 1907
• New Mexico — 1912
• Arizona — 1912
• Alaska — 1959
• Hawaii — 1959

Yet somehow this is still news to folks.

This is insane. The land used to produce crops to make biofuels could supply us with 22x as much power if you used solar farms.

ourworldindata.org/biofuel-land...

Davis Summer Population Genomics Program Want to learn population genetics? Please fill out this form to indicate your potential interest in a 2-week intensive online summer population genetics course taught by Jeffrey Ross-Ibarra and Graham...

Fun news! @gcbias.bsky.social and I are teaching a 2-week online population genetics workshop this summer to raise money for the Center for Population Biology at UC Davis. We're trying to gauge interest -- please fill this out if you might be interested! And please share broadly!

BREAKING: The Epstein survivors are releasing this ad on this Super Bowl Sunday to send the message that they will not “move on” from the largest sex trafficking scandal in the world. #standwithsurvivors

BREAKING: The Senate just blocked a bill that would have renewed ICE's budget without real, enforceable changes.

This is a direct result of hundreds of thousands of people across the nation demanding that our Senators vote no.

This is what letting RFK jr go wild on health looks like

If this pisses you off…I’ve got something for you to do: attend a @standupforscience.bsky.social rally on March 7th!!

To learn more, volunteer, or host a rally in your town head to: standupforscience.net/march7

Turn your outrage into action with us! #standupforscience

A retired Minneapolis couple who had guns pointed at them by ICE in a church parking lot.

"They were obviously not trained at all. I've known many police officers in my life. These people were right off the streets."

"They had the professional demeanor of criminals."

ht: @paulgraham.bsky.social

A pile of valentines, including a gulper eel saying "you make my jaw drop", a grimalditeuthis saying "I find you a-LURE-ing" a whale skeleton at the bottom of the ocean with snailfish and two octopuses making heart arms under the words "I've whale-fallen for you", and an anglerfish saying "You're my light in the darkness", and then two packs of cards that are all nice and tied up

Hey cuties. Everything sucks ass. Get some valentines and send them to your friends.

I'm sad. You're sad. They're probably sad.

Send them a valentine.

It keeps Skype a Scientist running, which hey, is very good too.

squidfacts.bigcartel.com/product/deep...