Select Publications

Sutormin D, Gaisser K, Haring J, Punniamoorthy A, Arulraj T, Perez C, Diener C, Ramos Sarmiento K, Carr AV, Rappaport N, Gibbons SM, Kuchina A. Phenotypic heterogeneity in the human gut microbiome revealed by subspecies-resolution single-cell transcriptomics. bioRxiv [Preprint]. 2026 July 30. doi: https://doi.org/10.64898/2026.07.30.741866

Brandner J, Tran Q, Huang Y, Sutormin D, Gaisser KD, Seelig G, Zalatan JG, Carothers JM, Kuchina A. Pooled single-cell CRISPRa/i screens for functional genomics in bacteria at scale. bioRxiv [Preprint]. 2025 Dec 22. doi: 10.64898/2025.12.20.695731

Gupta A, Morella N, Sutormin D, Li N, Gaisser K, Robertson A, Ispolatov Y, Seelig G, Dey N, Kuchina A. Dynamics of phage-host interactions in Bacteroides fragilis resolved by single-cell transcriptomics. Nat Commun (2026). https://doi.org/10.1038/s41467-026-70381-8

Cyriaque V, Ibarra-Chávez R, Kuchina A, Seelig G, Nesme J, Madsen JS. Single-cell RNA sequencing reveals plasmid constrains bacterial population heterogeneity and identifies a non-conjugating subpopulation. Nat Commun. 2024 Jul 12;15(1):5853. doi: 10.1038/s41467-024-49793-x. PMID: 38997267; PMCID: PMC11245611.

Gaisser KD*, Skloss SN*, Brettner LM, Paleologu L, Roco CM, Rosenberg AB, Hirano M, DePaolo RW, Seelig G, Kuchina A. High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding. Nat Protoc. 2024 Jun 17. doi: 10.1038/s41596-024-01007-w. Epub ahead of print. PMID: 38886529.

Kuchina A*, Brettner LM*, Paleologu L, Roco CM, Rosenberg AB, Carignano A, Kibler R, Hirano M, DePaolo RW, Seelig G. Microbial single-cell RNA sequencing by split-pool barcoding. Science 17 Dec 2020: 10.1126/science.aba5257

Rosenberg AB*, Roco CM*, Muscat RA, Kuchina A, Sample P, Yao Z, Graybuck LT, Peeler DJ, Mukherjee S, Chen W, Pun SH, Sellers DL, Tasic B, Seelig G. Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding. Science 2018 Apr 13;360(6385):176-182. doi: 10.1126/science.aam8999.  Epub 2018 Mar 15.

Cuperus JT*, Groves B*, Kuchina A*, Rosenberg AB*, Jojic N, Fields S, Seelig G. Deep learning of the regulatory grammar of yeast 5′ untranslated regions from 500,000 random sequences. Genome Res. 2017 Dec;27(12):2015-2024. doi: 10.1101/gr.224964.117

Narula J*, Kuchina A*, Zhang F, Fujita M, Süel GM, Igoshin OA. Slowdown of growth controls cellular differentiation. Mol Syst Biol.12(5):871. doi: 10.15252/msb.20156691.

Narula J*, Kuchina A*, Lee DY, Fujita M, Süel GM, Igoshin OA. Chromosomal arrangement of phosphorelay genes couples sporulation and DNA replication. Cell.162(2):328-37. doi: 10.1016/j.cell.2015.06.012.

Kuchina A, Espinar L, Çağatay T, Balbin AO, Zhang F, Alvarado A, Garcia-Ojalvo J, Süel GM. Temporal competition between differentiation programs determines cell fate choice. Mol Syst Biol 7(557) doi:10.1038/msb.2011.88.

Kuchina A*, Espinar L*, Garcia-Ojalvo J, Süel GM. Reversible and noisy progression towards a commitment point enables adaptable and reliable cellular decision-making. PLoS Comput Biol 7(11): e1002273. doi:10.1371/journal.pcbi.1002273