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stephseifertphd.bsky.social
Steph N. Seifert, PhD
@stephseifertphd.bsky.social
1.7K followers 400 following 40 posts
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
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stephseifertphd.bsky.social
Steph N. Seifert, PhD @stephseifertphd.bsky.social · Jul 14
🚨 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...
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
Reposted by Steph N. Seifert, PhD
ecography.bsky.social
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
Reposted by Steph N. Seifert, PhD
plosbiology.org
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
Graphic representation of the recombination events in the Sugarlandvirus I and J variants. Top left: Representation of the variants isolates in the different strains in the three lines. Genome fragments of each parent are represented in a different color. Regions with the most abundant recombination events are marked and associated with a schematic representation of the functional annotation and intergenomic similarity between the two parental phages. Bottom left: 3D folding of the RBPγ. The consensus recombinant region, which is associated with the infection of the K-type 47, is represented in light orange. Variable positions detected in the protein sequence alignment of the variants are represented as hot pink spheres. The table indicates the percentage of identity of the parental protein sequences in three protein regions limited by the amino acids indicated. Right: Transmission electron microscopy (TEM) image of Klebsiella myoviruses artificially coloured, showing their characteristic contractile tails and icosahedral capsids. Image acquired by the Environmental and Biomedical Virology group (Institute for Integrative Systems Biology, Universitat de València-CSIC).
November 28, 2025 at 1:58 PM
Reposted by Steph N. Seifert, PhD
liambrierley.bsky.social
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!
November 28, 2025 at 2:34 PM
Reposted by Steph N. Seifert, PhD
stephenturner.us
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
Reposted by Steph N. Seifert, PhD
lhmoncla.bsky.social
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
Reposted by Steph N. Seifert, PhD
colincarlson.bsky.social
NEW! 🦠🦧 We revisited a perplexing paradox: do wildlife really pose less of a risk to human health as they become more endangered? Turns out, it's sampling bias all the way down: conservation risks correlate with disease surveillance blindspots. 🔓 esajournals.onlinelibrary.wiley.com/doi/full/10....
Viral diversity and zoonotic risk in endangered species
A growing body of evidence links zoonotic disease risk, including pandemic threats, to biodiversity loss and other upstream anthropogenic impacts on ecosystem health. However, there is little current...
esajournals.onlinelibrary.wiley.com
November 25, 2025 at 1:25 PM
Reposted by Steph N. Seifert, PhD
gsimpson.bsky.social
A new release of the mgcv #RStats 📦 is out on CRAN and Simon Wood (U Edinburgh) has added some significant new features despite the small bump in version number:

🌟 scasm() for estimating GAMs with shape constrained smooths. Can be used with any family & smoothness selection is via the EFS method
Model is: b3 <- scasm( y ~ s(x0, bs = "bs", k= k) + s(x1, bs = "sc", xt = "m+", k = k) + s(x2, bs = "bs", k = k) + s(x3, bs = "bs", k = k), family=poisson, bs=200 ) The second smooth `s(x1) is a shape constrained smooth with a positive monotonicity constraint (xt = "m+"). The `bs = 200` arguments uses 200 boostrap samples, which generates bootstrap distributions for each coefficient in the model. These bootstrap samples respect the shape constraints, while the usual +/- 2 SE credible intervals may not. The uncertainty in the partial effects is shown by two credible interval bands; a dark blue central band is a 68% Bayesian credible interval, while the lighter blue outer interval is a 95% Bayesian credible interval. The background of each panel is light grey with white grid lines, in a similar style to ggplot2's default theme.
November 12, 2025 at 11:28 AM
Reposted by Steph N. Seifert, PhD
baym.lol
PSA for people with NIH grant periods starting January 1st (including most NIGMS MIRAs): your RPPR is due Saturday, but they haven’t sent out the usual automated reminders, presumably due to the shutdown
November 11, 2025 at 1:20 AM
Reposted by Steph N. Seifert, PhD
plosbiology.org
What are the #antiviral barriers to cross-species transmission of #zoonotic #influenza A viruses? @jordanbeckerphd.bsky.social @langloislab.bsky.social &co show that CpG-enriched avian #viruses are restricted by several mammalian proteins, including ZAP & KHNYN @plosbiology.org 🧪 plos.io/47fkMVp
Prenylated human ZAP and mammalian KHNYN can independently restrict naturally CpG-enriched ROSV. Top: CpG content of retroviruses (ROSV in black, ROSV-mCherry reporter virus in pink dashed line, MLV in orange, and HIV-1 in blue) calculated as # CpG per 100 nucleotides over a sliding window (graph). Schematic of retrovirus open reading frame (ORF) organization (top). Bottom left: Retroviral assembly and single-cycle infectivity results of human ZAP-L, ZAP-S, and mutants effects on ROSV showing relative percent ROSV infected cells (% mCherry-positive; % mCh+) as determined by flow cytometry. DF-1 cells transfected with increasing plasmid amounts of indicated host proteins (100, 200, or 400 ng), 1,500 ng ROSV, and 200 ng VSV-G. Infectivity is relative to backbone pcDNA3.2 transfections (Mock). Below, western blots detecting ROSV cleaved Gagp19 in supernatant virions as well as full-length ROSV GagPr76, ZAP proteins, and ACTIN loading controls from cellular lysates. Bottom right: Retroviral assembly and single-cycle infectivity results of human KHNYN, mutants, and mammalian KHNYN homologs (from pig, dog, and platypus) on ROSV infectivity. Below, western blots detecting ROSV cleaved Gagp19 in supernatant virions as well as full-length ROSV GagPr76, human KHNYN proteins, and ACTIN loading controls from cellular lysates. Note mammalian KHNYN orthologues were not detected by human KHNYN antibodies.
October 29, 2025 at 5:31 PM
Reposted by Steph N. Seifert, PhD
gfalbery.bsky.social
I'm v excited to be recruiting a PhD student to work on badger behaviour and ecology! Starting date is March 2026; see the ad here, or message me for more details: www.gregalbery.me/s/March-2026...
October 3, 2025 at 2:05 PM
Reposted by Steph N. Seifert, PhD
plosbiology.org
What are the #antiviral barriers to cross-species transmission of #zoonotic #influenza A viruses? @jordanbeckerphd.bsky.social @langloislab.bsky.social &co show that CpG-enriched avian #viruses are restricted by several mammalian proteins, including ZAP & KHNYN @plosbiology.org 🧪 plos.io/47fkMVp
Prenylated human ZAP and mammalian KHNYN can independently restrict naturally CpG-enriched ROSV. Top: CpG content of retroviruses (ROSV in black, ROSV-mCherry reporter virus in pink dashed line, MLV in orange, and HIV-1 in blue) calculated as # CpG per 100 nucleotides over a sliding window (graph). Schematic of retrovirus open reading frame (ORF) organization (top). Bottom left: Retroviral assembly and single-cycle infectivity results of human ZAP-L, ZAP-S, and mutants effects on ROSV showing relative percent ROSV infected cells (% mCherry-positive; % mCh+) as determined by flow cytometry. DF-1 cells transfected with increasing plasmid amounts of indicated host proteins (100, 200, or 400 ng), 1,500 ng ROSV, and 200 ng VSV-G. Infectivity is relative to backbone pcDNA3.2 transfections (Mock). Below, western blots detecting ROSV cleaved Gagp19 in supernatant virions as well as full-length ROSV GagPr76, ZAP proteins, and ACTIN loading controls from cellular lysates. Bottom right: Retroviral assembly and single-cycle infectivity results of human KHNYN, mutants, and mammalian KHNYN homologs (from pig, dog, and platypus) on ROSV infectivity. Below, western blots detecting ROSV cleaved Gagp19 in supernatant virions as well as full-length ROSV GagPr76, human KHNYN proteins, and ACTIN loading controls from cellular lysates. Note mammalian KHNYN orthologues were not detected by human KHNYN antibodies.
October 29, 2025 at 10:10 AM
Reposted by Steph N. Seifert, PhD
gsimpson.bsky.social
Just updated my manuscript on using #GAMs in #AnimalScience, now on arXiv: doi.org/10.48550/arX...
🐄🐖🪶

Extended examples now show how GAMs go beyond prediction, helping estimate biologically meaningful traits from data.

Code: github.com/gavinsimpson...

🧪 #RStats #mgcv #Statistics #OpenScience
Results of model fitting to the average daily fat content data from @Henderson1990-bd. a) observed average daily fat content (points) and estimated lactation curves from Wood's [-@Wood1967-re] model, a Tweedie GLM, and a Tweedie GAM (lines) with associated 95% confidence (Wood's model) or 95% credible intervals (GLM and GAM). Response residuals for Wood's model (b), Tweedie GLM (c), and Tweedie GAM (d), plus scatter plot smoothers (lines) and 95% credible intervals (shaded ribbons). The fitted lactation curves are like an inverted U, with an extended longer tail to the right (later in lactation). The GAM curve fits the data well, but the fitted curves from Wood's model and the GLM equivalent do not provide good fits to the data, and over predict the amount of fat produced at the peak of lactation, and only grossly capture the decline in fat production later in lactation. The remaining panels show the raw response residuals for the three models, drawing attention to the poor fit; for Wood's model and the GLM there is significant pattern in the residuals, while for the GAM no residual pattern is observed. Quantities of interest derived from Wood's model, a Tweedie GLM, and a Tweedie GAM fitted to the lactation data example: a) the estimated week of peak average daily fat content, b) the estimated average daily fat content at the peak, and c) the rate of change (first derivative) of the lactation curve estimated at a point that is midway between the peak fat content and the end of lacation. The points are the estimated values and the lines are a 95% uncertainty interval. The uncertainty interval is based on the 0.025 and 0.975 percentiles of the bootstrap distribution of model coefficient estimates (Wood's model) or of the posterior distribution (GLM and GAM). Each panel shows three point estimates and an uncertainty range. The three points are the estimates from a GAM, a GLM, and Wood's lactation model. The first panel shows the estimated timing of the peak of lactation, with the GAM capturing the fact that the peak in the data occurs much later in lactation (~ week 11) while the other two models confidently estimate that the peak is in week ~8-9. The GAM estimate has a much wider credible interval, which does include the estimates of Wood's model & the GLM at the extreme end. This reflects the uncertainty in the estimation of the peak timing arising from the data having a wide flat peak. The other panels show the estimates of fat content at the peak, which are broadly similar at ~ 0.7 kg fat per day. The final panel showing the persistency estimate shows the GAM estimate diverging from those of the GLM and Wood's model. Again, the latter two models are overly confident in their estimation of this biologically relevant parameter, despite the fited lactation curve not really following the lactation data. a) Estimated daily growth rate on November 15^th^, 2021 and 95% Bayesian credible interval for the 18 pigs in the pig growth example. b) Posterior distribution of daily growth rate on November 15^th^, 2021, for three pigs (numbers 2, 13, and 17), for whom weight observations ceased before November 1^st^, 2021. In b), the shaded region is the posterior distribution, the point, and thick and thin bars are the posterior median, and 66% and 95% posterior intervals respectively. With the fitted growth curves, we can estimate for any day what the growth rate of each pig was. In this figure I'm showing the estimated growth rate of each pig in the example on November 21st. This growth rate is the first derivative of the fitted growth curve (smooth function). I used posterior sampling to produce the posterior distribution of the growth rate for each pig. These are summarised as a point estimate (median) and ccredible interval in the first panel with most pigs growin at ~1-1.5 kg per day by November 21st, with uncertainties on the order of +/- 0.5 kg per day. The second panel shows the entire posterior distribution of the estimated growth rate for three pigs (2, 13, and 17) for whom there were no weight estimates after November 1st. Here, the model is drawing power from the other pigs to help extrapolate the growth curves for these three pigs, but pig-specific details remain, with the posterior distribution for pig 17 being much more diffuse (wider) than for either pigs 2 or 13, reflecting greater uncertainty for the former animal.
October 29, 2025 at 10:45 AM
Reposted by Steph N. Seifert, PhD
spyroslytras.bsky.social
New preprint alert!! 🚨🚨🚨in collaboration with the Letko @fviromics.bsky.social and Baric labs!

Just in case you're tired of sarbecoviruses, this time we looked at ACE2-using merbecoviruses! specifically the first HKU5r-CoVs detected in mink a couple of years ago.

www.biorxiv.org/content/10.1...
Structural and phenotypic plasticity of the RBD loop2 region is a key determinant for HKU5r-CoVs’ emergence in mink
The emergence of novel coronaviruses from animal reservoirs continues to pose a significant zoonotic threat. Here, we investigate the evolutionary origins and virological properties of a recently repo...
www.biorxiv.org
October 28, 2025 at 5:07 AM
Reposted by Steph N. Seifert, PhD
blackinmicro.bsky.social
🔬 Microbiology job seekers 🧫 go to BMA Job Board to view open positions! Have a vacancy to fill? Posting instructions also available (scroll to bottom). blackinmicrobiology....
Webpage screenshot of the Black Microbiologists Association job board. The page lists five academic job postings with institution names, locations, and posting dates. Listings include Hofstra University, NYU Langone Health, University of Chicago, Rice University, and University of British Columbia. The interface features a yellow and blue theme with top navigation links labeled About Us, Membership, Directory, Events, and Newsroom. Buttons for Donate, Contact Us, and Job Board are located in the upper right corner.
October 15, 2025 at 9:33 PM
Reposted by Steph N. Seifert, PhD
blackinmicro.bsky.social
Friendly reminder: 🎉 Pre-register today & get ready to join our FREE online celebration. Everyone is welcome. To keep #BlackInMicro alive Donate: tinyurl.com/GiveBiM and Register to attend: linktr.ee/BlackInMicro (see links in bio) #BiMWeek2025
The summarised schedule of Black in Micro Week 2025, October 14-16. All times are in Eastern Standard Time. Mon 14: Pathways for Change. Welcome and Keynote Address 12pm. Marian Johnson-Thompson, PhD. Panel Discussion: Finding Black Spaces in STEM, 1:15-2:15 PM. Weds 15, Careers & Research: ECR Symposium 9-12 PM. Panel discussion: Navigating Careers in Microbiology 2-3 PM. Thurs 16, Community: Panel Discussion - Empowering Your Science 12-1:15 PM. Workshop: Science in Action
October 7, 2025 at 9:45 PM
Reposted by Steph N. Seifert, PhD
noamross.net
I have the privilege of working with fed agency folks. They've been jerked around, forced to move, had offices taken, lost resources, put on leave, fired, re-hired, *shot at*, and now furloughed. Still they return each day to help make America a bit more informed, healthier, and safer.
October 1, 2025 at 1:48 PM
Reposted by Steph N. Seifert, PhD
raw937.bsky.social
Multiomic analysis of the only megaphage in culture. In press today.

Unlocking the genomic repertoire of a cultivated megaphage | npj Viruses share.google/HgU1cjRnaHWv...

#phage #bacteriophage
Unlocking the genomic repertoire of a cultivated megaphage - npj Viruses
npj Viruses - Unlocking the genomic repertoire of a cultivated megaphage
share.google
September 30, 2025 at 1:16 PM
Reposted by Steph N. Seifert, PhD
banerjeelab.ca
www.nature.com/articles/s41...

Stunning work from the Chandran lab!
LRP8 is a receptor for tick-borne encephalitis virus - Nature
LRP8, an apolipoprotein E and reelin receptor with high expression in the brain, is a receptor for tick-borne encephalitis virus.
www.nature.com
September 25, 2025 at 2:20 AM
Reposted by Steph N. Seifert, PhD
banerjeelab.ca
www.sciencenews.org/article/bats...
Bats live with some viruses. But others can do them in
Bats can carry some deadly human pathogens without signs of illness. A new survey shows that other viruses can still be bad for bats.
www.sciencenews.org
September 23, 2025 at 12:22 PM
Reposted by Steph N. Seifert, PhD
mayajuman.bsky.social
Super excited to finally share this! #CollectionsAreEssential
September 22, 2025 at 7:50 PM
Reposted by Steph N. Seifert, PhD
banerjeelab.ca
journals.asm.org/doi/10.1128/...
MERS-CoV and SARS-CoV-2 infection in diverse human lung organoid-derived cultures | Journal of Virology
The COVID-19 pandemic heralded the upsurge in human-derived lung organoid-based studies due to their cellular heterogeneity that partly emulates the cellular complexity of the respiratory tract. A maj...
journals.asm.org
September 21, 2025 at 3:41 PM
Reposted by Steph N. Seifert, PhD
spyroslytras.bsky.social
Great to have this one published @cp-cellreports.bsky.social !! Some sarbecoviruses can use more ACE2 orthologs than others. The reason? A few sites in the RBD modulating the receptor usage of these viruses throughout their evolution! Worth a read 👇👇👇

www.cell.com/cell-reports...
Molecular basis of sarbecovirus evolution and receptor tropism in natural hosts, potential intermediate hosts, and humans
Kosugi et al. elucidate sarbecovirus evolution and ACE2 receptor tropism in natural hosts (12 Rhinolophus bat species), potential intermediate hosts (civets and raccoon dogs), and humans using a pseud...
www.cell.com
September 20, 2025 at 10:37 AM
Reposted by Steph N. Seifert, PhD
ctrlalttim.com
Our software paper on SpeciesDistributionToolkit.jl is now published in @peercomjournal.bsky.social - peercommunityjournal.org/articles/10....
A Julia toolkit for species distribution data
peercommunityjournal.org
September 18, 2025 at 3:41 PM
stephseifertphd.bsky.social
Excited to share our study reporting the first Sin Nombre virus (SNV) genome sequences from the Northwestern U.S., and the first ever from a vole host.

www.biorxiv.org/content/10.1...
First Sin Nombre virus (Orthohantavirus sinnombreense) genome sequences from the Northwestern United States
We report the first Sin Nombre virus (SNV) genome sequences from the Northwestern United States and the first SNV sequences recovered from voles. Analysis of samples collected from 189 individual rode...
www.biorxiv.org
September 17, 2025 at 3:48 PM
Reposted by Steph N. Seifert, PhD
colincarlson.bsky.social
🚨 NEW: Climate change is already causing 30,000 deaths per year - a global annual economic loss of $100-350B USD - but the true damage is probably 10x higher. Out TODAY in Nature Climate Change: the first systematic look at the science of "health impact attribution" 🔓 www.nature.com/articles/s41...
"Health losses attributed to anthropogenic climate change," a brief communication in the journal Nature Climate Change. There's a map showing regions of the world, and pie charts of relevant studies as they apply to different health impacts like "heat-related deaths" and "maternal and child health"
September 17, 2025 at 11:57 AM