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GIInger predicts homologous recombination deficiency and patient response to PARPi treatment from shallow genomic profiles.
Pozzorini C, Andre G, Coletta T, Buisson A, Bieler J, Ferrer L, Kempfer R, Saintigny P, Harlé A, Vacirca D, Barberis M, Gilson P, Roma C, Saitta A, Smith E, Consales Barras F, Ripol L, Fritzsche M, Marques AC, Alkodsi A, Marin R, Normanno N, Grimm C, Müllauer L, Harter P, Pignata S, Gonzalez-Martin A, Denison U, Fujiwara K, Vergote I, Colombo N, Willig A, Pujade-Lauraine E, Just PA, Ray-Coquard I, Xu Z. Pozzorini C, et al. Among authors: kempfer r. Cell Rep Med. 2023 Dec 19;4(12):101344. doi: 10.1016/j.xcrm.2023.101344. Cell Rep Med. 2023. PMID: 38118421 Free PMC article.
Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C.
Beagrie RA, Thieme CJ, Annunziatella C, Baugher C, Zhang Y, Schueler M, Kukalev A, Kempfer R, Chiariello AM, Bianco S, Li Y, Davis T, Scialdone A, Welch LR, Nicodemi M, Pombo A. Beagrie RA, et al. Among authors: kempfer r. Nat Methods. 2023 Jul;20(7):1037-1047. doi: 10.1038/s41592-023-01903-1. Epub 2023 Jun 19. Nat Methods. 2023. PMID: 37336949 Free PMC article.
Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos.
McGarvey AC, Kopp W, Vučićević D, Mattonet K, Kempfer R, Hirsekorn A, Bilić I, Gil M, Trinks A, Merks AM, Panáková D, Pombo A, Akalin A, Junker JP, Stainier DYR, Garfield D, Ohler U, Lacadie SA. McGarvey AC, et al. Among authors: kempfer r. Cell Genom. 2022 Jan 13;2(1):100083. doi: 10.1016/j.xgen.2021.100083. eCollection 2022 Jan 12. Cell Genom. 2022. PMID: 36777038 Free PMC article.
Cell-type specialization is encoded by specific chromatin topologies.
Winick-Ng W, Kukalev A, Harabula I, Zea-Redondo L, Szabó D, Meijer M, Serebreni L, Zhang Y, Bianco S, Chiariello AM, Irastorza-Azcarate I, Thieme CJ, Sparks TM, Carvalho S, Fiorillo L, Musella F, Irani E, Torlai Triglia E, Kolodziejczyk AA, Abentung A, Apostolova G, Paul EJ, Franke V, Kempfer R, Akalin A, Teichmann SA, Dechant G, Ungless MA, Nicodemi M, Welch L, Castelo-Branco G, Pombo A. Winick-Ng W, et al. Among authors: kempfer r. Nature. 2021 Nov;599(7886):684-691. doi: 10.1038/s41586-021-04081-2. Epub 2021 Nov 17. Nature. 2021. PMID: 34789882 Free PMC article.
Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin.
Fiorillo L, Musella F, Conte M, Kempfer R, Chiariello AM, Bianco S, Kukalev A, Irastorza-Azcarate I, Esposito A, Abraham A, Prisco A, Pombo A, Nicodemi M. Fiorillo L, et al. Among authors: kempfer r. Nat Methods. 2021 May;18(5):482-490. doi: 10.1038/s41592-021-01135-1. Epub 2021 May 7. Nat Methods. 2021. PMID: 33963348 Free PMC article.
Methods for mapping 3D chromosome architecture.
Kempfer R, Pombo A. Kempfer R, et al. Nat Rev Genet. 2020 Apr;21(4):207-226. doi: 10.1038/s41576-019-0195-2. Epub 2019 Dec 17. Nat Rev Genet. 2020. PMID: 31848476 Review.
Formation of new chromatin domains determines pathogenicity of genomic duplications.
Franke M, Ibrahim DM, Andrey G, Schwarzer W, Heinrich V, Schöpflin R, Kraft K, Kempfer R, Jerković I, Chan WL, Spielmann M, Timmermann B, Wittler L, Kurth I, Cambiaso P, Zuffardi O, Houge G, Lambie L, Brancati F, Pombo A, Vingron M, Spitz F, Mundlos S. Franke M, et al. Among authors: kempfer r. Nature. 2016 Oct 13;538(7624):265-269. doi: 10.1038/nature19800. Epub 2016 Oct 5. Nature. 2016. PMID: 27706140