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
🧪 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
Do you want to join @epic-biodiversity.org to do research on biodiversity, disease emergence, equity in data access, or related topics?
We are looking to support one application for the Impact+ program.
🗓️ Jan. 30 (the application is ~ 1 page)
💰 120k$
epic-biodiversity.org/opportunities/
🧪🌎😷
We are looking to support one application for the Impact+ program.
🗓️ Jan. 30 (the application is ~ 1 page)
💰 120k$
epic-biodiversity.org/opportunities/
🧪🌎😷
Join us! | ÉPICBiodiversity
epic-biodiversity.org
January 22, 2026 at 3:37 PM
Do you want to join @epic-biodiversity.org to do research on biodiversity, disease emergence, equity in data access, or related topics?
We are looking to support one application for the Impact+ program.
🗓️ Jan. 30 (the application is ~ 1 page)
💰 120k$
epic-biodiversity.org/opportunities/
🧪🌎😷
We are looking to support one application for the Impact+ program.
🗓️ Jan. 30 (the application is ~ 1 page)
💰 120k$
epic-biodiversity.org/opportunities/
🧪🌎😷
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 😅
Reposted by Steph N. Seifert, PhD
Put a perspective piece together on how fever may have driven the evolution of antiviral genes: rupress.org/jem/article/...
Does fever drive the evolution of antiviral genes? | Journal of Experimental Medicine | Rockefeller University Press
Fever is an evolutionary conserved response to pathogens. In this Perspective, Langlois hypothesizes that antiviral genes are selected for their function a
rupress.org
December 15, 2025 at 3:20 PM
Put a perspective piece together on how fever may have driven the evolution of antiviral genes: rupress.org/jem/article/...
Reposted by Steph N. Seifert, PhD
In this Perspective, Ryan Langlois hypothesizes that antiviral genes are evolutionarily selected for their function at fever temperatures yet are commonly studied at basal temperatures, a potential blind spot in our understanding of antiviral gene mechanisms. rupress.org/jem/article/...
#Virology
#Virology
December 11, 2025 at 6:20 PM
In this Perspective, Ryan Langlois hypothesizes that antiviral genes are evolutionarily selected for their function at fever temperatures yet are commonly studied at basal temperatures, a potential blind spot in our understanding of antiviral gene mechanisms. rupress.org/jem/article/...
#Virology
#Virology
Reposted by Steph N. Seifert, PhD
You can do this right now:
Think of a person who wrote a paper you love, whose work influenced or helped you, or has made your professional life better.
Search up their email address. Shoot them a quick email of thanks. It means so, so much. This is a rough time of year, share some joy.
Think of a person who wrote a paper you love, whose work influenced or helped you, or has made your professional life better.
Search up their email address. Shoot them a quick email of thanks. It means so, so much. This is a rough time of year, share some joy.
December 11, 2025 at 10:08 PM
You can do this right now:
Think of a person who wrote a paper you love, whose work influenced or helped you, or has made your professional life better.
Search up their email address. Shoot them a quick email of thanks. It means so, so much. This is a rough time of year, share some joy.
Think of a person who wrote a paper you love, whose work influenced or helped you, or has made your professional life better.
Search up their email address. Shoot them a quick email of thanks. It means so, so much. This is a rough time of year, share some joy.
Reposted by Steph N. Seifert, PhD
"The only reason I don’t have this funding is because my last name is Rodriguez,” he said. “It has nothing to do with the science."
STAT on the betrayal of early-career researchers:
www.statnews.com/2025/12/08/t...
STAT on the betrayal of early-career researchers:
www.statnews.com/2025/12/08/t...
NIH shut out hundreds of young scientists from funding to start their own labs
Special Report: The NIH has shut out hundreds of young scientists from funding to start their own labs.
www.statnews.com
December 8, 2025 at 11:43 AM
"The only reason I don’t have this funding is because my last name is Rodriguez,” he said. “It has nothing to do with the science."
STAT on the betrayal of early-career researchers:
www.statnews.com/2025/12/08/t...
STAT on the betrayal of early-career researchers:
www.statnews.com/2025/12/08/t...
Reposted by Steph N. Seifert, PhD
We created a database of all published paramyxovirus detection attempts in pteropodid bats! Lots of sampling gaps and avenues for future study ⬇️ Excited to share this PhD chapter with @danjbecker.bsky.social and @viralemergence.org, out last month in @plos.org 🦇🦠🔓
journals.plos.org/plosntds/art...
journals.plos.org/plosntds/art...
Paramyxoviruses in Old World fruit bats (Pteropodidae): An open database and synthesis of sampling effort, viral positivity, and coevolution
Author summary Paramyxoviruses are a family of viruses that include the human measles and mumps viruses as well as emerging zoonoses like Hendra and Nipah henipaviruses. These henipaviruses spill over...
journals.plos.org
December 2, 2025 at 12:38 PM
We created a database of all published paramyxovirus detection attempts in pteropodid bats! Lots of sampling gaps and avenues for future study ⬇️ Excited to share this PhD chapter with @danjbecker.bsky.social and @viralemergence.org, out last month in @plos.org 🦇🦠🔓
journals.plos.org/plosntds/art...
journals.plos.org/plosntds/art...
Reposted by Steph N. Seifert, PhD
Applied to COVID-19 in California, the approach yields more accurate and more stable short-term forecasts than RNNs, LSTMs, GRUs, Transformers, and naïve baselines.
🔗 royalsocietypublishing.org/doi/10.1098/...
🔗 royalsocietypublishing.org/doi/10.1098/...
December 1, 2025 at 12:31 PM
Applied to COVID-19 in California, the approach yields more accurate and more stable short-term forecasts than RNNs, LSTMs, GRUs, Transformers, and naïve baselines.
🔗 royalsocietypublishing.org/doi/10.1098/...
🔗 royalsocietypublishing.org/doi/10.1098/...
Reposted by Steph N. Seifert, PhD
Species-observer link and kernel density estimation of background points allow for sampling bias correction in bird species distribution models vist.ly/4gc4n #Birds #SDM #SamplingBias
November 28, 2025 at 9:24 AM
Species-observer link and kernel density estimation of background points allow for sampling bias correction in bird species distribution models vist.ly/4gc4n #Birds #SDM #SamplingBias
Reposted by Steph N. Seifert, PhD
Capsule diversity limits #phage host range by affecting receptor-binding protein (RBP) interactions in capsulated #bacteria. @pilardomingoc.bsky.social &co show that generalist phages evolve host range via RBP mutation & recombination, but specialists remain stable @plosbiology.org 🧪 plos.io/48nvOqY
November 28, 2025 at 1:58 PM
Capsule diversity limits #phage host range by affecting receptor-binding protein (RBP) interactions in capsulated #bacteria. @pilardomingoc.bsky.social &co show that generalist phages evolve host range via RBP mutation & recombination, but specialists remain stable @plosbiology.org 🧪 plos.io/48nvOqY
Reposted by Steph N. Seifert, PhD
What makes bird flu spill over to humans? 4y funded PhD in the genomics and molecular virology behind zoonosis of avian influenza A virus, working with @tompeacock.bsky.social and others between Liverpool, Pirbright, and Uppsala!
open to applications until next week!
open to applications until next week!
November 28, 2025 at 2:34 PM
What makes bird flu spill over to humans? 4y funded PhD in the genomics and molecular virology behind zoonosis of avian influenza A virus, working with @tompeacock.bsky.social and others between Liverpool, Pirbright, and Uppsala!
open to applications until next week!
open to applications until next week!
Reposted by Steph N. Seifert, PhD
plinkQC: An Integrated Tool for Ancestry Inference, Sample Selection, and Quality Control in Population Genetics www.biorxiv.org/content/10.1... 🧬🖥️🧪 R package meyer-lab-cshl.github.io/plinkQC/ #Rstats
November 28, 2025 at 3:01 PM
plinkQC: An Integrated Tool for Ancestry Inference, Sample Selection, and Quality Control in Population Genetics www.biorxiv.org/content/10.1... 🧬🖥️🧪 R package meyer-lab-cshl.github.io/plinkQC/ #Rstats
Reposted by Steph N. Seifert, PhD
Our lab's paper describing the North American H5N1 epizootic is out now in Nature! So thrilled to have this out, and congratulations to @lambod50.bsky.social for all the fantastic work on this: www.nature.com/articles/s41...
Ecology and spread of the North American H5N1 epizootic - Nature
The panzootic of highly pathogenic H5N1 since 2021 was driven by around nine introductions into the Atlantic and Pacific flyways, followed by rapid dissemination through wild migratory birds, primaril...
www.nature.com
November 12, 2025 at 7:33 PM
Our lab's paper describing the North American H5N1 epizootic is out now in Nature! So thrilled to have this out, and congratulations to @lambod50.bsky.social for all the fantastic work on this: www.nature.com/articles/s41...