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Research in our lab aims to develop technologies to investigate the mechanisms by which gene networks control the self-organization of cells into complex 3-D tissues during development, as well as the modifications to this organization that take place in disease. This includes approaches to collect new types of data as well as algorithms to analyze these data. The techniques we use include gene editing (CRISPR), spatial transcriptomics, single cell RNA sequencing, microscopy, and computational methods for image analysis and statistics. We develop our tools in tissues like the brain or tumors.
The specific research areas in the laboratory include:
Binan L, Danquah S, Valakh V, Simonton B, Bezney J, Nehme R, Cleary B, Farhi SL. bioRxiv [Preprint]. 2023 Dec 1:2023.11.30.569494. doi: 10.1101/2023.11.30.569494. Update in: Cell. 2025 Apr 17;188(8):2141-2158.e18. doi: 10.1016/j.cell.2025.02.012. PMID: 38076932; PMCID: PMC10705493.
Yao D, Binan L, Bezney J, Simonton B, Freedman J, Frangieh CJ, Dey K, Geiger-Schuller K, Eraslan B, Gusev A, Regev A, Cleary B. Nat Biotechnol. 2024 Aug;42(8):1282-1295. doi: 10.1038/s41587-023-01964-9. Epub 2023 Oct 23. PMID: 37872410; PMCID: PMC11035494.
Stogsdill JA, Kim K, Binan L, Farhi SL, Levin JZ, Arlotta P. Nature. 2022 Aug;608(7924):750-756. doi: 10.1038/s41586-022-05056-7. Epub 2022 Aug 10. PMID: 35948630; PMCID: PMC10502800.
Favuzzi E, Huang S, Saldi GA, Binan L, Ibrahim LA, Fernández-Otero M, Cao Y, Zeine A, Sefah A, Zheng K, Xu Q, Khlestova E, Farhi SL, Bonneau R, Datta SR, Stevens B, Fishell G. Cell. 2021 Jul 22;184(15):4048-4063.e32. doi: 10.1016/j.cell.2021.06.018. Epub 2021 Jul 6. Erratum in: Cell. 2021 Oct 28;184(22):5686. doi: 10.1016/j.cell.2021.10.009. PMID: 34233165; PMCID: PMC9122259.
Binan L, Mazzaferri J, Choquet K, Lorenzo LE, Wang YC, Affar EB, De Koninck Y, Ragoussis J, Kleinman CL, Costantino S. Nat Commun. 2016 May 20;7:11636. doi: 10.1038/ncomms11636. PMID: 27198043; PMCID: PMC4876456.
