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Single-cell sequencing of individual retinal organoids reveals determinants of cell fate heterogeneity.
Tresenrider A, Sridhar A, Eldred KC, Cuschieri S, Hoffer D, Trapnell C, Reh TA. Tresenrider A, et al. Among authors: trapnell c. bioRxiv [Preprint]. 2023 Jun 3:2023.05.31.543087. doi: 10.1101/2023.05.31.543087. bioRxiv. 2023. Update in: Cell Rep Methods. 2023 Aug 09;3(8):100548. doi: 10.1016/j.crmeth.2023.100548 PMID: 37398481 Free PMC article. Updated. Preprint.
High-Capacity Sample Multiplexing for Single Cell Chromatin Accessibility Profiling.
Booth GT, Daza RM, Srivatsan SR, McFaline-Figueroa JL, Gladden RG, Furlan SN, Shendure J, Trapnell C. Booth GT, et al. Among authors: trapnell c. bioRxiv [Preprint]. 2023 Mar 6:2023.03.05.531201. doi: 10.1101/2023.03.05.531201. bioRxiv. 2023. Update in: BMC Genomics. 2023 Dec 4;24(1):737. doi: 10.1186/s12864-023-09832-1 PMID: 36945538 Free PMC article. Updated. Preprint.
Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies.
Edman NI, Redler RL, Phal A, Schlichthaerle T, Srivatsan SR, Etemadi A, An SJ, Favor A, Ehnes D, Li Z, Praetorius F, Gordon M, Yang W, Coventry B, Hicks DR, Cao L, Bethel N, Heine P, Murray A, Gerben S, Carter L, Miranda M, Negahdari B, Lee S, Trapnell C, Stewart L, Ekiert DC, Schlessinger J, Shendure J, Bhabha G, Ruohola-Baker H, Baker D. Edman NI, et al. Among authors: trapnell c. bioRxiv [Preprint]. 2023 Mar 15:2023.03.14.532666. doi: 10.1101/2023.03.14.532666. bioRxiv. 2023. Update in: Cell. 2024 Jul 11;187(14):3726-3740.e43. doi: 10.1016/j.cell.2024.05.025 PMID: 36993355 Free PMC article. Updated. Preprint.
A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup.
Qiu C, Martin BK, Welsh IC, Daza RM, Le TM, Huang X, Nichols EK, Taylor ML, Fulton O, O'Day DR, Gomes AR, Ilcisin S, Srivatsan S, Deng X, Disteche CM, Noble WS, Hamazaki N, Moens CB, Kimelman D, Cao J, Schier AF, Spielmann M, Murray SA, Trapnell C, Shendure J. Qiu C, et al. Among authors: trapnell c. bioRxiv [Preprint]. 2023 Apr 5:2023.04.05.535726. doi: 10.1101/2023.04.05.535726. bioRxiv. 2023. Update in: Nature. 2024 Feb;626(8001):1084-1093. doi: 10.1038/s41586-024-07069-w PMID: 37066300 Free PMC article. Updated. Preprint.
Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy.
McFaline-Figueroa JL, Srivatsan S, Hill AJ, Gasperini M, Jackson DL, Saunders L, Domcke S, Regalado SG, Lazarchuck P, Alvarez S, Monnat RJ Jr, Shendure J, Trapnell C. McFaline-Figueroa JL, et al. Among authors: trapnell c. bioRxiv [Preprint]. 2023 Jun 14:2023.03.10.531983. doi: 10.1101/2023.03.10.531983. bioRxiv. 2023. Update in: Cell Genom. 2024 Feb 14;4(2):100487. doi: 10.1016/j.xgen.2023.100487 PMID: 37398090 Free PMC article. Updated. Preprint.
A multiplexed, single-cell sequencing screen identifies compounds that increase neurogenic reprogramming of murine Muller glia.
Tresenrider A, Hooper M, Todd L, Kierney F, Blasdel N, Trapnell C, Reh TA. Tresenrider A, et al. Among authors: trapnell c. bioRxiv [Preprint]. 2024 Apr 12:2023.09.26.559569. doi: 10.1101/2023.09.26.559569. bioRxiv. 2024. Update in: Elife. 2024 Dec 12;12:RP92091. doi: 10.7554/eLife.92091 PMID: 37808650 Free PMC article. Updated. Preprint.
Pulmonary osteoclast-like cells in silica induced pulmonary fibrosis.
Hasegawa Y, Franks JM, Tanaka Y, Uehara Y, Read DF, Williams C, Srivatsan S, Pitstick LB, Nikolaidis NM, Shaver CM, Wu H, Gardner JC, Osterburg AR, Yu JJ, Kopras EJ, Teitelbaum SL, Wikenheiser-Brokamp KA, Trapnell C, McCormack FX. Hasegawa Y, et al. Among authors: trapnell c. bioRxiv [Preprint]. 2023 Feb 18:2023.02.17.528996. doi: 10.1101/2023.02.17.528996. bioRxiv. 2023. Update in: Sci Adv. 2024 Jul 12;10(28):eadl4913. doi: 10.1126/sciadv.adl4913 PMID: 36824953 Free PMC article. Updated. Preprint.
Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy.
McFaline-Figueroa JL, Srivatsan S, Hill AJ, Gasperini M, Jackson DL, Saunders L, Domcke S, Regalado SG, Lazarchuck P, Alvarez S, Monnat RJ Jr, Shendure J, Trapnell C. McFaline-Figueroa JL, et al. Among authors: trapnell c. Cell Genom. 2024 Feb 14;4(2):100487. doi: 10.1016/j.xgen.2023.100487. Epub 2024 Jan 25. Cell Genom. 2024. PMID: 38278156 Free PMC article.
An attractor state zone precedes neural crest fate in melanoma initiation.
McConnell AM, Chassé MH, Noonan HR, Mito JK, Barbano J, Weiskopf E, Gosselink IF, Prasad M, Yang S, Abarzua P, Lian CG, Murphy GF, Trapnell C, Zon LI. McConnell AM, et al. Among authors: trapnell c. bioRxiv [Preprint]. 2024 Oct 25:2024.10.22.618007. doi: 10.1101/2024.10.22.618007. bioRxiv. 2024. PMID: 39484503 Free PMC article. Preprint.
146 results