Author

Karl D. Gaisser

Institute for Systems BiologyORCID 0009-0002-8035-5137Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Genomics· 1 Microbiology· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Assay:scRNA-seq· 3 Research Focus:cell type annotation· 2 Research Focus:differential expression· 2 Approach:experimental assay· 2 Research Focus:gene regulatory network inference· 2 Organism:bacteria (other)· 1 Research Focus:clustering· 1 Research Focus:database / resource· 1

Frequent Co-Authors

Anna KuchinaiD· 3 shared Dmitry A. SutorminiD· 3 shared Georg SeeligiD· 2 shared Alex V. CarriD· 1 shared Alexander Robertson· 1 shared Anika GuptaiD· 1 shared Anjana PunniamoorthyiD· 1 shared Christian DieneriD· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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3 shared papersMicrobiology

Anna KuchinaORCID

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3 papers

Recent·Most cited

Phenotypic heterogeneity in the human gut microbiome revealed by subspecies-resolution single-cell transcriptomics

Dmitry A. Sutormin, Karl D. Gaisser, Jacqueline Haring, Anjana Punniamoorthy, Theinmozhi Arulraj, Crystal Perez, Christian Diener, Katherine Ramos Sarmiento, Alex V. Carr, Noa Rappaport, Sean M. Gibbons, Anna Kuchina

The paper develops metaSPLiT, a single-cell RNA sequencing method, to reveal sub-species functional specialization in the human gut microbiome.

bioRxiv · Jul 31, 2026 · PreprintMicrobiology

Pooled single-cell CRISPRa/i screens for functional genomics in bacteria at scale

Jacob Brandner, Quoc Tran, Yujia Huang, Dmitry A. Sutormin, Karl D. Gaisser, Georg Seelig, Jesse G. Zalatan, James M. Carothers, Anna Kuchina

The paper introduces mapSPLiT, a pooled CRISPRa/i screening platform for bacteria, linking perturbations to single-cell transcriptomes and expanding regulatory networks in E. coli and P. putida.

bioRxiv · Dec 22, 2025 · PreprintGenomics

Combinatorial phenotypic landscape enables bacterial resistance to phage infection

Anika Gupta, Norma M. Morella, Dmitry A. Sutormin, Naisi Li, Karl D. Gaisser, Alexander Robertson, Yaroslav Ispolatov, Georg Seelig, Neelendu Dey, Anna Kuchina

The paper profiles single-cell transcriptomes of Bacteroides fragilis infected with a phage, revealing combinatorial phase-variable expression of defense systems that enable super-resistant cells to avoid phage infection without mutations.

bioRxiv · Jan 13, 2025 · PreprintSystems Biology