Steph N. Seifert, PhD
@stephseifertphd.bsky.social
PI of the Molecular Ecology of Zoonotic and Animal Pathogens Lab
Co-PI, Viral Emergence Research Institute
Interested in virology, evolution, ecology, and still cares about diversity and equity in STEM
she/her
Co-PI, Viral Emergence Research Institute
Interested in virology, evolution, ecology, and still cares about diversity and equity in STEM
she/her
Pinned
TATAT: a containerized software for generating annotated coding transcriptomes from raw RNA-seq data
Motivation: Many transcriptome creation workflows are not standardized, are difficult to install or share, prone to breaking as dependencies update or cease to be maintained and are resource intensive...
www.biorxiv.org
🚨 Our team just released a reproducible Docker pipeline for RNAseq assembly and annotation designed for nonmodel organisms!
We're using it to explore how bats manage viral infections, but it's built for broad utility in wildlife transcriptomics. @viralemergence.org
www.biorxiv.org/content/10.1...
We're using it to explore how bats manage viral infections, but it's built for broad utility in wildlife transcriptomics. @viralemergence.org
www.biorxiv.org/content/10.1...
Reposted by Steph N. Seifert, PhD
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...
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...
eos.org
February 6, 2026 at 8:58 PM
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...
Reposted by Steph N. Seifert, PhD
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...
www.wiley.com/en-us/resear...
February 5, 2026 at 5:36 PM
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...
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.
February 5, 2026 at 4:58 PM
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.
Reposted by Steph N. Seifert, PhD
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
[OK, maybe the 1930s if you want to nitpick]
But, with some data wrangling, my first NSF Funding Curves!
2/3
February 5, 2026 at 1:58 PM
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
[OK, maybe the 1930s if you want to nitpick]
But, with some data wrangling, my first NSF Funding Curves!
2/3
Reposted by Steph N. Seifert, PhD
🦅 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...
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...
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...
www.nature.com
February 4, 2026 at 11:32 AM
🦅 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...
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...
Reposted by Steph N. Seifert, PhD
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!
Please RT!
tinyurl.com
February 2, 2026 at 3:55 PM
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!
Please RT!
Reposted by Steph N. Seifert, PhD
🧪
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
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
February 2, 2026 at 6:52 PM
🧪
Thanks @noamross.net, I just sent to students in my orbit who had written for the GRFP this year.
February 2, 2026 at 7:19 PM
Thanks @noamross.net, I just sent to students in my orbit who had written for the GRFP this year.
Reposted by Steph N. Seifert, PhD
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
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
February 2, 2026 at 5:58 PM
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
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
Reposted by Steph N. Seifert, PhD
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;
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;
January 30, 2026 at 5:15 PM
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;
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;
Reposted by Steph N. Seifert, PhD
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...
Very useful as a hypothesis generator, complementing protein interaction prediction from Alphafold.
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 27, 2026 at 8:55 AM
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...
Very useful as a hypothesis generator, complementing protein interaction prediction from Alphafold.
www.biorxiv.org/content/10.6...
Reposted by Steph N. Seifert, PhD
🧪 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...
In a new preprint by @tanyadoesscience.bsky.social we attempt to provide a hierarchical framework for network ecology:
ecoevorxiv.org/repository/v...
Scaling from Metawebs to Realised Webs: A Hierarchical Approach to Network Ecology
ecoevorxiv.org
January 22, 2026 at 1:51 PM
🧪 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...
In a new preprint by @tanyadoesscience.bsky.social we attempt to provide a hierarchical framework for network ecology:
ecoevorxiv.org/repository/v...
Reposted by Steph N. Seifert, PhD
🚨New paper 🚨
Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇
1/12
Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇
1/12
August 17, 2025 at 3:42 AM
🚨New paper 🚨
Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇
1/12
Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇
1/12
Reposted by Steph N. Seifert, PhD
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/...
journals.plos.org/plosbiology/...
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...
journals.plos.org
January 21, 2026 at 2:38 PM
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/...
journals.plos.org/plosbiology/...
Reposted by Steph N. Seifert, PhD
There is still time to apply! The deadline has been extended until February 3rd.
Have thoughts for a special symposium at the Virtual Evolution meeting (May 20-22, 2026)? The @asn-amnat.bsky.social is looking for proposals! Click here to pitch your idea or find out more: www.amnat.org/announcement... #Evol2026
Call for Symposium Proposals for Evolution 2026
<p><strong>Due January 15, 2026:</strong> The ASN invites proposals for a special symposium at Evolution 2026! Have an idea? We want to hear it!</p><br/>
www.amnat.org
January 20, 2026 at 3:15 PM
There is still time to apply! The deadline has been extended until February 3rd.
Reposted by Steph N. Seifert, PhD
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.
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.
Excited to share new #program, STEPS, which can simulate #dynamics of the E. coli Long-Term Evolution Experiment (#LTEE) or other microbes in serial transfer regime.
telliamedrevisited.wordpress.com/2025/08/12/s...
STEPS developed by @devinmlake.bsky.social, Zachary Matson, Minako Izutsu, and me.
telliamedrevisited.wordpress.com/2025/08/12/s...
STEPS developed by @devinmlake.bsky.social, Zachary Matson, Minako Izutsu, and me.
STEPS To It
Announcing a new program, called STEPS, to simulate the dynamics of evolving microbial populations.
telliamedrevisited.wordpress.com
January 20, 2026 at 4:12 PM
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.
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.
Reposted by Steph N. Seifert, PhD
"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."
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?
time.com
January 17, 2026 at 1:49 AM
"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 recognize that much of the American public lost trust in the NIAID, the National Institutes of Health (NIH; of which the NIAID is a part), and in the greater scientific community."
Factually incorrect statement on trust in Nature Medicine via NIH Director + co.
🧵
www.nature.com/articles/s41...
Factually incorrect statement on trust in Nature Medicine via NIH Director + co.
🧵
www.nature.com/articles/s41...
The new vision from the National Institute of Allergy and Infectious Diseases (NIAID) - Nature Medicine
Preparing for tomorrow’s threats by enhancing our ability to help patients today.
www.nature.com
January 16, 2026 at 5:27 PM
Are they serious with this? New vision for NIAID by the NIH Director and they put it behind a paywall?
Reposted by Steph N. Seifert, PhD
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.
January 12, 2026 at 11:20 AM
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.
Reposted by Steph N. Seifert, PhD
Evolutionary history of Jamestown Canyon virus disentangles complex multi-vector ecology https://www.biorxiv.org/content/10.64898/2026.01.09.698726v1
January 11, 2026 at 1:31 AM
Evolutionary history of Jamestown Canyon virus disentangles complex multi-vector ecology https://www.biorxiv.org/content/10.64898/2026.01.09.698726v1
Reposted by Steph N. Seifert, PhD
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
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
January 6, 2026 at 7:41 PM
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
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
Reposted by Steph N. Seifert, PhD
🧪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/?
December 31, 2025 at 4:38 PM
🧪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/?
Reposted by Steph N. Seifert, PhD
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
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.
www.washingtonpost.com
December 21, 2025 at 2:45 PM
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 😅
December 20, 2025 at 1:31 AM
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 😅