Steph N. Seifert, PhD

I'm sorry, 50 what now?

"We present a GPU implementation of kallisto for RNA-seq transcript quantification (...). For a large dataset of 295 million reads, runtime drops from 40 minutes to 50 seconds"

www.biorxiv.org/content/10.6...

Oh and if you liked this, check out this chapter, where we unpack how science gets used in negotiations - and how the pharmaceutical industry followed the fossil fuel playbook and found a way into the room through “expert engagement” bsky.app/profile/coli...

MIReVTD, a Minimum Information Standard for Reporting Vector Trait Data Abstract. Vector-borne diseases pose a persistent and increasing challenge to human, animal, and agricultural systems globally. Mathematical modeling frame

📣 Useful publication alert!
If you're collecting or sharing vector trait data 🦟🦠, this new paper from @vectorbyte.bsky.social introducing the MIReVTD (Minimum Information for Reporting Vector Trait Data) standard is for you:

doi.org/10.1093/giga...

#FAIRData #DataStandards #DataSharing #Traits

🚨 New pre-print! 🚨 In the largest study of its kind to-date, we investigate the ecological and evolutionary mechanisms driving within-patient evolution of antimicrobial resistance (AMR). Read here:
www.biorxiv.org/content/10.6... , and follow along with this thread, discussing our findings (1/21)

Graduate Students’ NSF Fellowship Applications Are Being “Returned Without Review” - Eos Graduate students applying for NSF funding have had their applications returned without review—even though their proposed research appears to fall squarely within the fields of study outlined in the p...

Students applying for NSF funding are having their applications “returned without review” for being “ineligible,” despite their proposed research falling squarely within the application guidelines. eos.org/research-and...

I am SO incredibly excited to announce the launch of a global list of Inspiring Black Scientists. You can use this list to nominate and connect with researchers. Please share and join us in highlighting these outstanding scientists for #BlackHistoryMonth and beyond!

www.wiley.com/en-us/resear...

How? With the RIFs and awarding fewer grants, and cancelling so many grants, how did they obligate almost all of the funding? Doesn't seem like grants were larger, as several of my colleagues received cuts from their requested budgets which had not been flagged in review as unreasonable.

But, as they say, there is no time like the present

[OK, maybe the 1930s if you want to nitpick]

But, with some data wrangling, my first NSF Funding Curves!

2/3

Ecology and environment predict spatially stratified risk of H5 highly pathogenic avian influenza clade 2.3.4.4b in wild birds across Europe - Scientific Reports Highly pathogenic avian influenza (HPAI) represents a threat to animal and human health, with the ongoing H5N1 outbreak within the H5 2.3.4.4b clade being one of the largest on record. However, it rem...

🦅 What’s driving the spread of highly pathogenic avian influenza (H5N1) across Europe?

Using machine learning and wild bird ecology, a new study from @L_Brierley & colleagues reveals a shift towards year-round risk in cold, low-lying regions of NW Europe.

www.nature.com/articles/s41...

Love molecular evolution, design, and/or t-shirts? JME wants your help! We seek molecular evolution themed designs for a JME T-shirt. The winner will receive a FREE T-shirt featuring their design! Submit your design here by March 31st: tinyurl.com/ypk76t6z
Please RT!

🧪

Thanks @noamross.net, I just sent to students in my orbit who had written for the GRFP this year.

NSF GRFP applicants (and mentors): Was your application Returned Without Review and deemed ineligible despite fitting in the allowed topics?
1) Write NSF
2) Write your Congressperson
3) CC us at grfp@grant-witness.us so we can compile + follow up

Details and template at grant-witness.us/grfp-letter

If you are a student whose NSF GRFP application was returned without review for vague 'eligibility' reasons:
1) Let your department chair & Graduate School know. Encourage them to contact NSF & congress
2) Write to your congressional reps.
3) Write to grfp@nsf.gov to request re-consideration;

Check out these tools to detect co-evolution in protein-protein interactions developed by postdoc @chrislbgraham.bsky.social

Very useful as a hypothesis generator, complementing protein interaction prediction from Alphafold.

www.biorxiv.org/content/10.6...

🧪 Figuring out the right way to represent interactions as a network is a really difficult task, makes a big difference on the interpretation.

In a new preprint by @tanyadoesscience.bsky.social we attempt to provide a hierarchical framework for network ecology:

ecoevorxiv.org/repository/v...

🚨New paper 🚨

Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇
1/12

Biomedical and life science articles by female researchers spend longer under review Women are underrepresented in academia, especially in STEMM fields, at top institutions, and in senior positions. This study analyzes millions of biomedical and life science articles, revealing that f...

Cost of being female lead/corresponding author in biomedical sciences: "[T]he median amount of time spent under review is 7.4%–14.6% longer for female-authored articles than for male-authored articles" even in disciplines where women well-represented. #AcademicSky

journals.plos.org/plosbiology/...

There is still time to apply! The deadline has been extended until February 3rd.

Looking for something new to integrate into an #evolution or #microbiology course? Useful for lectures, labs, homework?

Have a look at our STEPS program, which simulates bacterial evolution, including the #LTEE. Easy web-based interface & lab manual w/ exercises to help develop students' intuition.

The Women Saving America’s Climate Data Meet the network saving federal environmental data. But, as Trump enters his second year, how long can this effort last?

"For over a year now, more than a dozen groups have been working together to rescue environment and climate data—and the majority are being led by women."

Are they serious with this? New vision for NIAID by the NIH Director and they put it behind a paywall?

We estimate JCV spreads only ~30–60 km²/year, a relatively slow rate for a mosquito-borne virus. This may reflect how univoltine Aedes mosquitoes maintain the virus in restricted areas across years, while multivoltine mosquitoes drive short-term bursts of spread.

Evolutionary history of Jamestown Canyon virus disentangles complex multi-vector ecology https://www.biorxiv.org/content/10.64898/2026.01.09.698726v1

Excited to share a new study published in PNAS! @pnas.org

We reconstructed the early, cryptic spatial spread of 2009 H1N1 influenza and SARS-CoV-2 across US metropolitan areas.

Link👉https://www.pnas.org/doi/10.1073/pnas.2518051123

#PandemicPreparedness #InfectiousDisease #HumanMobility

🧪Continuity is essential to scientific discovery as shown by the many projects bearing 🥑🥝🍇🍒this year. Here is the 2025 lab recap! Intermittent, unpredictable and likely to be incomplete 1/?

The year Trump broke the federal government How DOGE and the White House carried out a once-unthinkable transformation of the nation’s sprawling bureaucracy.

Inside the federal government as Trump and DOGE pushed it past its breaking point in 2025, as told by some of the more than 1,200 federal workers @hannahnatanson.bsky.social and @merylkornfield.bsky.social have spoken to this year

I know it feels great to check things off your to-do list like submit that manuscript, IACUC protocol, or IBC amendment right before you walk out the door for two weeks.... but maybe wrap up the work then pause on submitting new requests until Jan. Your colleagues want a break, too 😅

Put a perspective piece together on how fever may have driven the evolution of antiviral genes: rupress.org/jem/article/...