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3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing.
Nguyen HQ, Chattoraj S, Castillo D, Nguyen SC, Nir G, Lioutas A, Hershberg EA, Martins NMC, Reginato PL, Hannan M, Beliveau BJ, Church GM, Daugharthy ER, Marti-Renom MA, Wu CT. Nguyen HQ, et al. Among authors: hershberg ea. Nat Methods. 2020 Aug;17(8):822-832. doi: 10.1038/s41592-020-0890-0. Epub 2020 Jul 27. Nat Methods. 2020. PMID: 32719531 Free PMC article.
Cohesin controls X chromosome structure remodeling and X-reactivation during mouse iPSC-reprogramming.
Generoso SF, Neguembor MV, Hershberg EA, Sadreyev RI, Kurimoto K, Yabuta Y, Ricci R, Audergon P, Bauer M, Saitou M, Hochedlinger K, Beliveau BJ, Cosma MP, Lee JT, Payer B. Generoso SF, et al. Among authors: hershberg ea. Proc Natl Acad Sci U S A. 2023 Jan 24;120(4):e2213810120. doi: 10.1073/pnas.2213810120. Epub 2023 Jan 20. Proc Natl Acad Sci U S A. 2023. PMID: 36669113 Free PMC article.
JBrowse 2: a modular genome browser with views of synteny and structural variation.
Diesh C, Stevens GJ, Xie P, De Jesus Martinez T, Hershberg EA, Leung A, Guo E, Dider S, Zhang J, Bridge C, Hogue G, Duncan A, Morgan M, Flores T, Bimber BN, Haw R, Cain S, Buels RM, Stein LD, Holmes IH. Diesh C, et al. Among authors: hershberg ea. Genome Biol. 2023 Apr 17;24(1):74. doi: 10.1186/s13059-023-02914-z. Genome Biol. 2023. PMID: 37069644 Free PMC article.
JBrowse Jupyter: a Python interface to JBrowse 2.
De Jesus Martinez T, Hershberg EA, Guo E, Stevens GJ, Diesh C, Xie P, Bridge C, Cain S, Haw R, Buels RM, Stein LD, Holmes IH. De Jesus Martinez T, et al. Among authors: hershberg ea. Bioinformatics. 2023 Jan 1;39(1):btad032. doi: 10.1093/bioinformatics/btad032. Bioinformatics. 2023. PMID: 36648320 Free PMC article.
JBrowseR: an R interface to the JBrowse 2 genome browser.
Hershberg EA, Stevens G, Diesh C, Xie P, De Jesus Martinez T, Buels R, Stein L, Holmes I. Hershberg EA, et al. Bioinformatics. 2021 Nov 5;37(21):3914-3915. doi: 10.1093/bioinformatics/btab459. Bioinformatics. 2021. PMID: 34196689 Free PMC article.