Starkly Speaking: Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes
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Hannes Stärk
Feb 8, 2026, 5:32:25 PMFeb 8
to stark...@googlegroups.com
Hi together,
I am really looking forward to tomorrows meeting about:
Speaker:
Laura Luebbert, who is a biologist and ML researcher developing methods for real-time infectious disease detection, pandemic prevention, biosecurity, and novel virus discovery. She holds both the Eric and Wendy Schmidt and FutureHouse AI-for-Science Postdoctoral Fellowships and works with Prof. Pardis Sabeti at the Broad Institute of MIT and Harvard, where she co-leads the AI branch of the $100 million MacArthur-award Sentinel Project.
Paper:
Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes https://www.nature.com/articles/s41587-025-02614-y (Laura Luebbert, Delaney K. Sullivan, Maria Carilli, Kristján Eldjárn Hjörleifsson, Alexander Viloria Winnett, Tara Chari & Lior Pachter)
The increasing use of high-throughput sequencing methods in research, agriculture and healthcare provides an opportunity for the cost-effective surveillance of viral diversity and investigation of virus–disease correlation. However, existing methods for identifying viruses in sequencing data rely on and are limited to reference genomes or cannot retain single-cell resolution through cell barcode tracking. We introduce a method that accurately and rapidly detects viral sequences in bulk and single-cell transcriptomics data based on the highly conserved RdRP protein, enabling the detection of over 100,000 RNA virus species. The analysis of viral presence and host gene expression in parallel at single-cell resolution allows for the characterization of host viromes and the identification of viral tropism and host responses. We apply our method to peripheral blood mononuclear cell data from rhesus macaques with Ebola virus disease and describe previously unknown putative viruses. Moreover, we are able to accurately predict viral presence in individual cells based on macaque gene expression.
Meeting Details:
Every Monday at 9:00 PT / 12:00 ET / 18:00 CE(S)T
https://zoom.us/j/5775722530?pwd=ZzlGTXlDNThhUDZOdU4vN2JRMm5pQT09
Laura Luebbert, who is a biologist and ML researcher developing methods for real-time infectious disease detection, pandemic prevention, biosecurity, and novel virus discovery. She holds both the Eric and Wendy Schmidt and FutureHouse AI-for-Science Postdoctoral Fellowships and works with Prof. Pardis Sabeti at the Broad Institute of MIT and Harvard, where she co-leads the AI branch of the $100 million MacArthur-award Sentinel Project.
Paper:
Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes https://www.nature.com/articles/s41587-025-02614-y (Laura Luebbert, Delaney K. Sullivan, Maria Carilli, Kristján Eldjárn Hjörleifsson, Alexander Viloria Winnett, Tara Chari & Lior Pachter)
The increasing use of high-throughput sequencing methods in research, agriculture and healthcare provides an opportunity for the cost-effective surveillance of viral diversity and investigation of virus–disease correlation. However, existing methods for identifying viruses in sequencing data rely on and are limited to reference genomes or cannot retain single-cell resolution through cell barcode tracking. We introduce a method that accurately and rapidly detects viral sequences in bulk and single-cell transcriptomics data based on the highly conserved RdRP protein, enabling the detection of over 100,000 RNA virus species. The analysis of viral presence and host gene expression in parallel at single-cell resolution allows for the characterization of host viromes and the identification of viral tropism and host responses. We apply our method to peripheral blood mononuclear cell data from rhesus macaques with Ebola virus disease and describe previously unknown putative viruses. Moreover, we are able to accurately predict viral presence in individual cells based on macaque gene expression.
Meeting Details:
Every Monday at 9:00 PT / 12:00 ET / 18:00 CE(S)T
https://zoom.us/j/5775722530?pwd=ZzlGTXlDNThhUDZOdU4vN2JRMm5pQT09
Meeting Details:
Every Monday at 9:00 PT / 12:00 ET / 18:00 CE(S)T
https://zoom.us/j/5775722530?pwd=ZzlGTXlDNThhUDZOdU4vN2JRMm5pQT09
Slack Workspace for discussion and paper voting:
https://join.slack.com/t/logag/shared_invite/zt-2zuxi7gd1-rLUgxg6gnCkhO7WlRsyElg
All information: Schedule of upcoming papers, recordings, mailing list:
https://portal.valencelabs.com/starklyspeaking
Hannes Stärk
Website: https://hannes-stark.com
PhD student at MIT
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