pLS-SceI Citations (22)

Originally described in: lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements.
Gordon MG, Inoue F, Martin B, Schubach M, Agarwal V, Whalen S, Feng S, Zhao J, Ashuach T, Ziffra R, Kreimer A, Georgakopoulous-Soares I, Yosef N, Ye CJ, Pollard KS, Shendure J, Kircher M, Ahituv N Nat Protoc. 2020 Aug;15(8):2387-2412. doi: 10.1038/s41596-020-0333-5. Epub 2020 Jul 8. PubMed Journal

---

Articles Citing pLS-SceI

Articles
The cis-regulatory effects of modern human-specific variants. Weiss CV, Harshman L, Inoue F, Fraser HB, Petrov DA, Ahituv N, Gokhman D. Elife. 2021 Apr 22;10. pii: 63713. doi: 10.7554/eLife.63713. PubMed
Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation. Kreimer A, Ashuach T, Inoue F, Khodaverdian A, Deng C, Yosef N, Ahituv N. Nat Commun. 2022 Mar 21;13(1):1504. doi: 10.1038/s41467-022-28659-0. PubMed
Characterization of De Novo Promoter Variants in Autism Spectrum Disorder with Massively Parallel Reporter Assays. Koesterich J, An JY, Inoue F, Sohota A, Ahituv N, Sanders SJ, Kreimer A. Int J Mol Sci. 2023 Feb 9;24(4):3509. doi: 10.3390/ijms24043509. PubMed
Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types. Agarwal V, Inoue F, Schubach M, Martin BK, Dash PM, Zhang Z, Sohota A, Noble WS, Yardimci GG, Kircher M, Shendure J, Ahituv N. bioRxiv. 2023 Mar 6:2023.03.05.531189. doi: 10.1101/2023.03.05.531189. Preprint. PubMed
Transcription factor binding site orientation and order are major drivers of gene regulatory activity. Georgakopoulos-Soares I, Deng C, Agarwal V, Chan CSY, Zhao J, Inoue F, Ahituv N. Nat Commun. 2023 Apr 22;14(1):2333. doi: 10.1038/s41467-023-37960-5. PubMed
Characterization of enhancer activity in early human neurodevelopment using Massively parallel reporter assay (MPRA) and forebrain organoids. Capauto D, Wang Y, Wu F, Norton S, Mariani J, Inoue F, Crawford GE, Ahituv N, Abyzov A, Vaccarino FM. bioRxiv [Preprint]. 2023 Aug 14:2023.08.14.553170. doi: 10.1101/2023.08.14.553170. PubMed
Characterization of enhancer activity in early human neurodevelopment using Massively Parallel Reporter Assay (MPRA) and forebrain organoids. Capauto D, Wang Y, Wu F, Norton S, Mariani J, Inoue F, Crawford GE, Ahituv N, Abyzov A, Vaccarino FM. Sci Rep. 2024 Feb 16;14(1):3936. doi: 10.1038/s41598-024-54302-7. PubMed
Massively parallel reporter assays and mouse transgenic assays provide complementary information about neuronal enhancer activity. Kosicki M, Cintron DL, Page NF, Georgakopoulos-Soares I, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Hunter RD, von Maydell K, Barton S, Godfrey P, Beckman E, Sanders SJ, Pennacchio LA, Ahituv N. bioRxiv [Preprint]. 2024 Apr 23:2024.04.22.590634. doi: 10.1101/2024.04.22.590634. PubMed
Emergence of activation or repression in transcriptional control under a fixed molecular context. Martinez-Corral R, Friedrich D, Fromel R, Velten L, Gunawardena J, DePace AH. bioRxiv [Preprint]. 2024 Jun 2:2024.05.29.596388. doi: 10.1101/2024.05.29.596388. PubMed
Dynamic stress- and inflammatory-based regulation of psychiatric risk loci in human neurons. Retallick-Townsley KG, Lee S, Cartwright S, Cohen S, Sen A, Jia M, Young H, Dobbyn L, Deans M, Fernandez-Garcia M, Huckins LM, Brennand KJ. bioRxiv [Preprint]. 2024 Jul 9:2024.07.09.602755. doi: 10.1101/2024.07.09.602755. PubMed
Deciphering the genetics and mechanisms of predisposition to multiple myeloma. Went M, Duran-Lozano L, Halldorsson GH, Gunnell A, Ugidos-Damboriena N, Law P, Ekdahl L, Sud A, Thorleifsson G, Thodberg M, Olafsdottir T, Lamarca-Arrizabalaga A, Cafaro C, Niroula A, Ajore R, Lopez de Lapuente Portilla A, Ali Z, Pertesi M, Goldschmidt H, Stefansdottir L, Kristinsson SY, Stacey SN, Love TJ, Rognvaldsson S, Hajek R, Vodicka P, Pettersson-Kymmer U, Spath F, Schinke C, Van Rhee F, Sulem P, Ferkingstad E, Hjorleifsson Eldjarn G, Mellqvist UH, Jonsdottir I, Morgan G, Sonneveld P, Waage A, Weinhold N, Thomsen H, Forsti A, Hansson M, Juul-Vangsted A, Thorsteinsdottir U, Hemminki K, Kaiser M, Rafnar T, Stefansson K, Houlston R, Nilsson B. Nat Commun. 2024 Aug 5;15(1):6644. doi: 10.1038/s41467-024-50932-7. PubMed
Systematic prioritization of functional variants and effector genes underlying colorectal cancer risk. Law PJ, Studd J, Smith J, Vijayakrishnan J, Harris BT, Mandelia M, Mills C, Dunlop MG, Houlston RS. Nat Genet. 2024 Oct;56(10):2104-2111. doi: 10.1038/s41588-024-01900-w. Epub 2024 Sep 16. PubMed
Statistically and functionally fine-mapped blood eQTLs and pQTLs from 1,405 humans reveal distinct regulation patterns and disease relevance. Wang QS, Hasegawa T, Namkoong H, Saiki R, Edahiro R, Sonehara K, Tanaka H, Azekawa S, Chubachi S, Takahashi Y, Sakaue S, Namba S, Yamamoto K, Shiraishi Y, Chiba K, Tanaka H, Makishima H, Nannya Y, Zhang Z, Tsujikawa R, Koike R, Takano T, Ishii M, Kimura A, Inoue F, Kanai T, Fukunaga K, Ogawa S, Imoto S, Miyano S, Okada Y. Nat Genet. 2024 Oct;56(10):2054-2067. doi: 10.1038/s41588-024-01896-3. Epub 2024 Sep 24. PubMed
Functional dissection of metabolic trait-associated gene regulation in steady state and stimulated human skeletal muscle cells. Nishino K, Kitzman JO, Parker SCJ, Tovar A. bioRxiv [Preprint]. 2025 Jan 20:2024.11.28.625886. doi: 10.1101/2024.11.28.625886. PubMed
Massively parallel characterization of transcriptional regulatory elements. Agarwal V, Inoue F, Schubach M, Penzar D, Martin BK, Dash PM, Keukeleire P, Zhang Z, Sohota A, Zhao J, Georgakopoulos-Soares I, Noble WS, Yardimci GG, Kulakovskiy IV, Kircher M, Shendure J, Ahituv N. Nature. 2025 Mar;639(8054):411-420. doi: 10.1038/s41586-024-08430-9. Epub 2025 Jan 15. PubMed
Rewriting regulatory DNA to dissect and reprogram gene expression. Martyn GE, Montgomery MT, Jones H, Guo K, Doughty BR, Linder J, Bisht D, Xia F, Cai XS, Chen Z, Cochran K, Lawrence KA, Munson G, Pampari A, Fulco CP, Sahni N, Kelley DR, Lander ES, Kundaje A, Engreitz JM. Cell. 2025 Jun 12;188(12):3349-3366.e23. doi: 10.1016/j.cell.2025.03.034. Epub 2025 Apr 16. PubMed
Design principles of cell-state-specific enhancers in hematopoiesis. Fromel R, Ruhle J, Bernal Martinez A, Szu-Tu C, Pacheco Pastor F, Martinez-Corral R, Velten L. Cell. 2025 Jun 12;188(12):3202-3218.e21. doi: 10.1016/j.cell.2025.04.017. Epub 2025 May 8. PubMed
Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity. Kosicki M, Laboy Cintron D, Keukeleire P, Schubach M, Page NF, Georgakopoulos-Soares I, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Hunter RD, von Maydell K, Barton S, Godfrey P, Beckman E, Sanders SJ, Kircher M, Pennacchio LA, Ahituv N. Nat Commun. 2025 May 23;16(1):4786. doi: 10.1038/s41467-025-60064-1. PubMed
A phylogenetic approach uncovers cryptic endogenous retrovirus subfamilies in the primate lineage. Chen X, Zhang Z, Yan Y, Goubert C, Bourque G, Inoue F. Sci Adv. 2025 Jul 18;11(29):eads9164. doi: 10.1126/sciadv.ads9164. Epub 2025 Jul 18. PubMed
Interactions Between Dietary Metabolites and Regulatory Risk Variants for Human Colon Cancer. Fabo TN, Meyers RM, Padhi E, Kellman LN, Zhao Y, Kundu S, Reynolds DL, Chen Z, Yang X, Ko L, Elfaki I, Montgomery SB, Khavari PA. bioRxiv [Preprint]. 2025 Sep 8:2025.09.05.674475. doi: 10.1101/2025.09.05.674475. PubMed
Emergence of activation or repression in transcriptional control under a fixed molecular context. Martinez-Corral R, Friedrich D, Fromel R, Velten L, Gunawardena J, DePace AH. Proc Natl Acad Sci U S A. 2025 Sep 30;122(39):e2413715122. doi: 10.1073/pnas.2413715122. Epub 2025 Sep 22. PubMed
Large-scale discovery of neural enhancers for cis-regulation therapies. McDiarmid TA, Page NF, Chardon FM, Daza RM, Chen GT, Kosicki M, James LM, Nourie HC, Laboy-Cintron D, Lee AS, Vij P, Calderon D, Lalanne JB, Martin BK, Fink K, Talkowski ME, Muotri AR, Philpot BD, Pennacchio LA, Geschwind DH, Sanders SJ, Ahituv N, Shendure J. bioRxiv [Preprint]. 2025 Nov 5:2025.11.04.686611. doi: 10.1101/2025.11.04.686611. PubMed

If you have published an article using this material, please email us at to have your article added to this page.