Steph N. Seifert, PhD

Next question: if the money is appropriated, will NIH be able to spend it? Asking because it's nearly August in FY25 and there's some $15 billion in unspent NIH funds.

From Senator @murray.senate.gov: the Senate's proposed NIH budget would reject 40% cuts, increase funding by $400M.

"We're not going to give up the fight against cancer, Alzheimer's or rare diseases."

Message to scientists: "we support you. We need you to stay here & keep this research going."

Staff at NIH and NSF have been so amazing and so resilient during these rapid and frequent changes in funding and procedures. I am so grateful for their tireless efforts on behalf of the scientific community in the US. 🙌

The Marsupial Database: A comprehensive dataset on the ecology and life history of American and Australasian marsupials ecoevorxiv.org/repository/v...

An image showing the ARTIC and Pathoplexus logos connected by blue lines, with the text "Hiring: post-doc/software engineer" and "Global open-source pathogen tools" and "Join Swiss TPH, Work on ARTIC2 and Pathoplexus, Basel, Switzerland"

📢New job posting!📢
Are you excited by the idea of building global infrastructure to make pathogen sequencing more accessible, interpretable, and equitable? 🧑🏻‍💻🧬

My group at @swisstph.ch has an opening working with ARTIC2, @pathoplexus.org, & Loculus - read on!

1/5

A global map of travel time to access veterinarians - Nature Communications Veterinary care is unevenly distributed globally, limiting access to care. Our maps show that 93.8% of isolated animals (>1h travel time) are in low- and middle-income countries. A 5% targeted incr...

👀global mapping of veterinary care 'coldspots'
🐮access to veterinary care = zoonotic surveillance capacity
👉(i.e., many spillover events linked to domestic/farmed animals as intermediary hosts (e.g., Nipah virus 🐷))
doi.org/10.1038/s414...

We crossed the 25 million mark at VecDyn!! We now have nearly 500 datasets with over 25 million rows of data spatiotemporal data online, with more in our curatorial pipeline.
vectorbyte.crc.nd.edu/vecdyn-datas...

So proud of @ricardoriveroh.bsky.social for passing his prelim exam! Keep an eye out for the truly innovative and exciting work on viral evolution and ecology coming from Ricardo in the next couple of years as part of his thesis research and beyond 💫

A phylogenetic approach uncovers cryptic endogenous retrovirus subfamilies in the primate lineage A phylogenetic approach reveals cryptic LTR subfamilies and functional insights at nucleotide resolution in primates.

Is the annotation of viruses in the human genome accurate? We think not. Take a look at our new paper and let us know if you agree! www.science.org/doi/10.1126/...

Synchronized seasonal excretion of multiple coronaviruses coincides with high rates of coinfection in immature bats - Nature Communications Bats harbor diverse coronaviruses but temporal dynamics are less well studied. Here, the authors analyzed coronaviruses in Australian flying foxes over 3 years showing peak shedding and co-infections ...

🦇 NEW RESEARCH: Our 3-year study of Australian flying foxes identified six co-circulating coronaviruses, with highest rates of infection and co-infection in young bats, and evidence of circulating recombinants 🧪🌏 🧵

Available open access in @natcomms.nature.com

📄 www.nature.com/articles/s41...

That Borrelia animation totally changed my understanding of how spirochetes get around! So cool!

Our analysis reveals persistent gender and race imbalances in IDD research. Man-authored and White-authored publications dominate the field, with little progress in racial diversification of US and UK publications over the last two decades. Woman-authored articles have the most representative citation practices but are under cited, especially when women are senior authors. In the USA and UK, most citations feature White lead and senior authors, even when citing articles have lead or senior authors of colour.

Final paper I'm printing out this week to take home and read over the weekend, from the inimitable @bansallab.bsky.social and two amazing students in her group: really staggering results on inclusivity in infectious disease research 😷🧪 royalsocietypublishing.org/doi/epdf/10....

A complex render of flaviruses invading the midgut epithelium of the deer tick (Ixodes scapularis). Might make a good screen saver for a vector biologist.

Pathways to an Intergovernmental Panel on Pandemics: lessons from the IPCC and IPBES Colin J Carlson, Christopher H Trisos, Ben Oppenheim, Shweta Bansal, Sara E Davies, Aïda Diongue-Niang, Victoria Y Fan, John D Kraemer, Rachel Golden Kroner, Lawrence O Gostin, David T S Hayman, Marion Koopmans, Torre E Lavelle, Carlos G das Neves, Zoe O’Donoghue, Laura M Pereira, Benjamin Roche, Matiangai Sirleaf, Kayla Zamanian, Carlos Zambrana-Torrelio, Alexandra L Phelan Pandemics pose a global threat to human wellbeing, justice, economies, and ecosystems and are comparable with other planetary crises such as climate change and biodiversity loss in terms of urgency and impact. The global community would benefit from a dedicated scientific synthesis body to assess pandemic risks and solutions. In this Personal View, we explore proposals for an Intergovernmental Panel on Pandemics and assess potential pathways to its creation. Learning lessons from the Intergovernmental Panel on Climate Change (IPCC) and the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) might help national governments and international organisations to chart a course through important decisions about format, governance, operations, scientific scope and process, and ability to recommend policies that make the world safer.

So today, we're sharing two years of research on the path to an "IPCC for pandemics." It's an unflinching look at multilateralism, scientific complexity, and why global health doesn't quite work. But it's also a blueprint for the future.

👉 Please read and share!
🔓 www.thelancet.com/journals/lan...

Low levels of H5N1 HA and NA antibodies in the human population are boosted by seasonal A/H1N1 infection but not by A/H3N2 infection or influenza vaccination An increase in the number of human cases of influenza A/H5N1 infection in the US has raised concerns about the pandemic potential of the virus. Preexisting population immunity is a key determinant for...

1/5 The lab’s first paper on bovine H5N1 looks at preexisting antibody immunity in the human population and how influenza vaccination and infection effect it. @johnshopkinsmmi.bsky.social @johnshopkinssph.bsky.social @ceirrnetwork.bsky.social www.biorxiv.org/content/10.1...

Cool opportunity for a PhD student to work on avian influenza and avian viromes in Sweden. Should be a super fun project working on an amazing 20 year sample set from Mallards.
👉 lnu.se/mot-linneuni...

OrthoFinder just dropped a major update

It’s faster, more accurate, and ready for thousands of genomes

Let’s break it down (1/10)

github.com/OrthoFinder/...
www.biorxiv.org/content/10.1...

Impact of HPAI on cattle in Ohio: clinical disease for 3 weeks in 20% of cattle. Milk losses of ~900kg per cow. Serprev of 89%. Cost was ~700K per herd.
👉 www.nature.com/articles/s41...

LoFV will be all over ASV in Montreal this year! I am giving a plenary talk Monday evening and will share an all new study that hasn’t been pre-printed. Also, look out for our talented post-doc, Victoria Jefferson, on Wednesday (P26-15) and skilled collaborator, Nick Catanzaro, on Tuesday (W13-6).

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...

🚨 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...

Program 2025 | American Society for Virology “+I5:I23+I5:I25Mastering the host: Rotavirus manipulation of the translation machinery” “From Cells to Spillover: Unraveling the Tropism and Pathogenesis of Paramyxoviruses” “Uncovering novel receptor...

Monday kicks off #ASV2025 with 4 different Satellite Symposia sessions planned by our amazing ASV councilors. Learn a little bit about the options below or on the website! #LoveVirology asv.org/asv2025/scie...

Subcommittee Markup of the Commerce, Justice, Science, and Related Agencies Appropriations Act | United States Senate Committee on Appropriations United States Senate Committee on Appropriations

🧪 BREAKING (good news): Senate subcommittee says NO! to Trump's proposed slashes to NASA & NSF funding.

Today, the subcommittee said to keep NASA + NSF funding at $33.9 billion, the same as in FY24.

See 7:15 below. Full Senate appropriations committee meets tomorrow about it.

🧵 1/3

BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference - Nature Methods BEAST X advances Bayesian phylogenetic, phylogeographic and phylodynamic analysis by incorporating a broad range of complex models and leveraging advanced algorithms and techniques to boost statistica...

BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference

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

Thanks for organizing! Would love to be added.

Bat-specific adaptations in interferon signaling and GBP1 contribute to enhanced antiviral capacity - Nature Communications Bats harbor diverse viruses but it’s less clear how they tolerate infection. Here, by characterizing innate immune responses in bat cells the authors show that IFN-beta signaling resists antagonistic ...

🚨Our new study out today in Nature Communications. Bats can asymptomatically host multiple viruses while remaining apparently healthy. Here we identify how interferon-mediated responses protect bats and identify molecular adaptations in GBP1. #LZCI
Link: www.nature.com/articles/s41...

STAGGERING: This new study of 133 countries is the first to estimate the impact of all USAID’s work. In 2 decades, it has saved *92M* lives. Current cuts, if not reversed, are forecast to cost up to *14M* lives thru 2030. www.thelancet.com/journals/lan...

Topeka scientist says NSF funds critical to infectious disease forecasting | Opinion Planned budget cuts for 2026 would deepen damage to STEM education, jobs, and public access to taxpayer-funded data.

"You have died of dysentery." A path into science shouldn't be as fraught as the Oregon Trail. Check out epidemiologist, NSF GRFP fellow, and Kansan @haileyrobertson.bsky.social's McClintock letter in the Topeka Capital-Journal! www.cjonline.com/story/opinio...

Deciphering Probabilistic Species Interaction Networks We review how probabilistic species interactions are defined at different spatial scales. These definitions are based on the distinction between the realisation of an interaction at a specific time a....

New paper from the lab: how do we make probabilistic species interaction networks more useful and robust? @francisbanville.bsky.social has some thoughts, and went through the literature to map mathematical definitions to ecological concepts.
onlinelibrary.wiley.com/doi/10.1111/...
🧪

Plot showing skewed distribution toward comp science and applied physics

The 500 additional GRFPs NSF awarded were not very evenly distributed across fields, it seems.
www.science.org/content/arti...

BMA invites abstract submissions from early career researchers for the Early Career Research Symposium on Career & Research Day! Including undergraduates, all the way up to junior faculty/managers across academic, industry and government sectors. Submit your abstract today at tinyurl.com/BIM-abstract25. Abstracts due July 8, 11.59PM EST. This will be a virtual symposium.

🚨📆⏰ ABSTRACT SUBMISSION REMINDER 🧬🦠🧫
The ECR symposium abstract call closes in TWO WEEKS!
Submit your abstract at tinyurl.com/BIM-abst... by July 8, 11.59PM EST! #BiM2025 #BlackInMicrobiology #EarlyCareerResearch