Sullivan Lab at OSU
We develop new ways to “see” and understand viruses in the laboratory and in nature.
- New paper published in @natcomms.nature.com! Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient doi.org/10.1038/s414... www.nature.com/collections/... @sullivan-lab.bsky.social
- Critical review for integrating viruses into ocean modelling now in Frontiers: www.frontiersin.org/journals/mar... Bringing viruses into Earth system models will sharpen predictions of carbon sequestration, nutrient retention, and climate sensitivity in the ocean.
- 🚨vConTACT3 now in Nature Biotechnology: - >95% agreement with ICTV for known viruses - Classifies both prokaryotic and eukaryotic viruses - Extends beyond genus → subfamily, family & order - Systematically assigns taxonomy to tens of thousands of previously unclassified viruses
- Read it here: www.nature.com/articles/s41...
- 🚨NEW paper: Benchmarking Hi-C for virus–host inference journals.plos.org/plosbiology/... A clear baseline for anyone mapping virus–host interactions that establishes robust, benchmarked thresholds for Hi-C linkages. Key results: 👇
- • Synthetic community (4 hosts, 9 phages) provides a ground-truth benchmark • Raw Hi-C links: ~100% sensitivity but only ~26% specificity • Z-score ≥0.5: specificity → ~99%, sensitivity → ~62%
- • In soils: broad host links recovered, but genus/species resolution remains challenging • Practical thresholds + guidance offered for applying Hi-C in complex microbiomes #Virology #HiC #VirusHost #Microbiome #Metagenomics #virusecology
- 🚨vConTACT3 preprint live!🚨(Peer Review soon...!) vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification. 🔗 Read the preprint: doi.org/10.1101/2025... Improvements details below 👇
- With vConTACT3, we rebuilt the system from the ground up: 🎯 Multi-rank hierarchical classification (genus → order) ⚙️ Scales to tens of thousands of genomes 🧬 Expands beyond dsDNA phages to include eukaryotic and RNA viruses 👇
- 📊 Machine-learning–optimized thresholds benchmarked across 6 realms 🧩 Identifies taxonomic inconsistencies and areas for ICTV revision #ViralTaxonomy #Metagenomics #ViralEcology #Bioinformatics #ICTV #PhageResearch #MachineLearning #VirusDiscovery #BioRxiv #vConTACT3
- The ocean’s got rhythm — and so do its viruses. With the Bermuda Atlantic Time-Series (BATS), we dove deep — every 4 to 12 hours — to see how viral populations swing through day and night.
-
View full threadWe found that overall virus-community diversity remains stable, but individual populations show clear diel and depth-linked shifts, with distinct viral archetypes peaking at day or night. Read the full story on BioRxiv: doi.org/10.1101/2025... Lead author: Alfonso Carrillo
- Using high-frequency metagenomics, we tracked 48,000+ viral populations and their hosts, from Prochlorococcus to SAR11.
- From tracking SARS-CoV-2 in wastewater to discovering hidden marine RNA viruses, CLAE unlocks read-level viral variant detection and fixes short-read misassemblies. ⚡ Portable, field-ready 🧬 A game-changer for epidemiology & environmental surveillance. #RNAvirus #metagenomics
- 🚨NEW VIROCELL PAPER🚨 from Cristina Howard-Varona et al: "Virocell resource manipulation under nutrient limitation". @howard-varona.bsky.social How do virocells use resources during nutrient limitation to build phages and alter the ecosystem? Check out the link! journals.asm.org/doi/10.1128/...
- Microbiome researchers! Join Dr. Shareef Dabdoub (U of Iowa) for a free webinar on multi-omics microbiome data analysis. Learn to integrate DNA, RNA, proteins, & metabolite data. April 1st, 10 am EST. go.osu.edu/2025_microbi... #microbiome #workshop
- Time's ticking, microbiome researchers! ⏰ Submit your abstract for the Midwest Microbiome Symposium at Ohio State by March 31st. Submit here: coms.osu.edu/midwest-micr... #microbiome #research #science #OhioState #CoMS
- 🚨 Microbiome researchers! The deadline to submit your abstract for the Midwest Microbiome Symposium at Ohio State is March 31st! 🚨 Don't miss this chance to share your work with leading experts. Submit here: coms.osu.edu/midwest-micr... #microbiome #microbiology #symposium #OhioState #microbiome
- 🚨Multiple positions open in Bas Duthil's group (Viral Ecology and Omics Group, Jena, Germany): - Postdoc experimental: lnkd.in/dJZ2GRUX - PhD experimental: lnkd.in/ddqQmvA9 - PhD bioinformatics: lnkd.in/d-nTJfAh Group: www.bio.uni-jena.de/en/2245/team
- New week, new microbiome webinar topic: learn the DRAM tool for annotation and curation of function for microbial and viral genomes, presented by Dr. Garrett Smith. 📅 Date: March 11, 2025 🕒 Time: 10am EST 📍 Link: go.osu.edu/2025_microbi... More details on full course: coms.osu.edu/webinars/mic...
- 🚨New paper from NSF EMERGE BII: A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry. Read here: www.nature.com/articles/s41...
- The Microbiome Informatics Webinar continues tomorrow with Dr. Dylan Cronin, teaching how to go from metagenomic data MAGs. March 4, 2025 at 10am EST Virtual Event zoom link: go.osu.edu/2025_microbi... 🔗 More details on the SP25 Microbiome Informatics series schedule: coms.osu.edu/webinars/mic...
- Summer School on Quantitative Phage-Bacteria Dynamics Across Scales -> Application date: March 21, 2025. Open to MS + PhD students + postdocs Application site: bit.ly/phageschool2...
- 🚨Spring 2025 Updated Microbiome Informatics Webinar Series starts tomorrow Feb. 25!🚨 Free to attend, join us to learn with leaders in the field. More info and registration: coms.osu.edu/webinars/mic...
- New paper from our PhD student Marissa Gittrich! In-depth characterization of 24 phages of rhizobacterium Klebsiella sp. M5al at PLOS One. Congrats Marissa and team! journals.plos.org/plosone/arti...
- Watch our latest research as a Video Byte about global ocean AMG function and distribution: www.researchsquare.com/article/rs-6...! From our lab's work in Microbiome (Tian & Wainana et al., 2024:https://doi.org/10.1186/s40168-024-01876-z)
- Upcoming wastewater virome webinar from Dr. Mike Tisza, Feb. 12! Free for everyone. More: coms.osu.edu/events/early... #virus #virome #viromics #pathogen #sequencing #microbiome #microbe #bacteria #science #microbiology #webinar
- Our 'global ocean AMGs in marine viruses' paper featured in @OhioStateNews! Congrats to Funing Tian and James Wainaina et al: "Identifying the genes that viruses ‘steal’ from ocean microbes" news.osu.edu/identifying-... #virus #phage #ecology #biogeochemistry #viromics #oceans
- 🚨VIROMICS WORKSHOP 2024🚨 Happy to announce the 7th International Viromics Workshop will take place Oct. 23-25, 2024 at Ohio State. Stay tuned for registration details. Enter our mailing list for updates: forms.gle/wAvZmRibq8rN.... #viromics #viruses #ecology #workshop
