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  1. Method: Sequence-based correction of barcode bias in massively parallel reporter assays
    • Dongwon Lee,
    • Ashish Kapoor,
    • Changhee Lee,
    • Michael Mudgett,
    • Michael A. Beer,
    • and Aravinda Chakravarti
    Genome Res. September 2021 31: 1638-1645; Published in Advance July 20, 2021, doi:10.1101/gr.268599.120
    ...'s Hospital, Boston, MA 02115, USA Corresponding author: dongwon.lee@childrens.harvard.eduAbstractMassively parallel reporter assays (MPRAs) are a high-throughput method for evaluating in vitro activities of thousands of candidate cis-regulatory elements (CREs). In these assays, candidate sequences are cloned...
  2. Research: Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands
    • Brian S. Roberts,
    • E. Christopher Partridge,
    • Bryan A. Moyers,
    • Vikram Agarwal,
    • Kimberly M. Newberry,
    • Beth K. Martin,
    • Jay Shendure,
    • Richard M. Myers,
    • and Gregory M. Cooper
    Genome Res. May 2021 31: 866-876; Published in Advance April 20, 2021, doi:10.1101/gr.270751.120
    ...Institute for Precision Medicine, University of Washington, Seattle, Washington 98195, USA Corresponding authors: rmyers@hudsonalpha.org, gcooper@hudsonalpha.orgAbstractMassively parallel reporter assays (MPRAs) are useful tools to characterize regulatory elements in human s. An aspect of MPRAs...
  3. Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
    • Lakshana Sruthi Sadu Murari,
    • Quinn Dickinson,
    • Silvia Meyer-Nava,
    • and Juan Carlos Rivera-Mulia
    Genome Res. March 19, 2026 ; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
    ...development of multiomicmethods provided tools for the assessment of cell identity and cell-to-cell heterogeneity. Multiomic, single-cell methods also inform on distinct aspects of the epi in parallel with gene expression (Cao et al. 2018; Zhu et al. 2019; Flynn et al. 2023). Approaches that map features of 3...
    OPEN ACCESS ARTICLE
  4. Method: Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay
    • Jennifer Hammelman,
    • Konstantin Krismer,
    • Budhaditya Banerjee,
    • David K. Gifford,
    • and Richard I. Sherwood
    Genome Res. October 2020 30: 1468-1480; Published in Advance September 24, 2020, doi:10.1101/gr.263228.120
    ...Identification of determinants of differential chromatin accessibility through a massively parallel -integrated reporter assay Jennifer Hammelman1,2, Konstantin Krismer2,3, Budhaditya Banerjee4, David K. Gifford2,3,5 and Richard I. Sherwood4,6 1Computational and Systems Biology, Massachusetts...
    OPEN ACCESS ARTICLE
  5. Research: A massively parallel reporter assay reveals context-dependent activity of homeodomain binding sites in vivo
    • Andrew E.O. Hughes,
    • Connie A. Myers,
    • and Joseph C. Corbo
    Genome Res. October 2018 28: 1520-1531; Published in Advance August 29, 2018, doi:10.1101/gr.231886.117
    ...monomeric and dimeric CRX binding sites promote distinct levels of transcriptional activation is not known.Recently, massively parallel reporter assays (MPRAs) have emerged as powerful tools for quantifying the regulatory activity of many CREs simultaneously. These assays work by introducing libraries...
  6. Method: The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms
    • Daffodil M. Canson,
    • Michael T. Parsons,
    • Gemma Moir-Meyer,
    • Troy Dumenil,
    • Gemma Montalban,
    • Erica Lin,
    • Terri P. McVeigh,
    • Aimee L. Davidson,
    • Shaun M. Bouckaert,
    • Matt Trau,
    • Darren Korbie,
    • and Amanda B. Spurdle
    Genome Res. September 2025 35: 2104-2115; Published in Advance August 6, 2025, doi:10.1101/gr.279557.124
    ...-throughput methods such as massively parallel splicing assay (MaPSy) (Soemedi et al. 2017), variant exon sequencing (Vex-seq) (Adamson et al. 2018), and multiplexed functional assay of splicing using Sort-seq (MFASS) (Chong et al. 2019), the SeqSplice method measured variant effect on a single exon but presented...
  7. Research: A massively parallel 3′ UTR reporter assay reveals relationships between nucleotide content, sequence conservation, and mRNA destabilization
    • Adam J. Litterman,
    • Robin Kageyama,
    • Olivier Le Tonqueze,
    • Wenxue Zhao,
    • John D. Gagnon,
    • Hani Goodarzi,
    • David J. Erle,
    • and K. Mark Ansel
    Genome Res. June 2019 29: 896-906; Published in Advance May 31, 2019, doi:10.1101/gr.242552.118
    ...expression of the sequences of more than 25,000 RNA-binding protein (RBP) binding sites in primary mouse T cells using a massively parallel reporter assay. GC-rich sequences were destabilizing of reporter mRNAs and come from more rapidly evolving regions of the . These sequences were more likely to be folded...
  8. Method: Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data
    • Li Song,
    • Gali Bai,
    • X. Shirley Liu,
    • Bo Li,
    • and Heng Li
    Genome Res. May 11, 2023 gr.277585.122; Published in Advance May 11, 2023, doi:10.1101/gr.277585.122
    ...(Zamir et al. 2022; Ruggeri et al. 2002), autoimmune diseases (Li et al. 2022) and cancer (Purdy and Campbell 2009; Naranbhai et al. 2021). Because of the importance of these polymorphic genes, researchers created the Immuno Polymorphism Database (IPD) to curate the HLA and KIR allele sequences (IPD...
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  9. Method: Massively parallel cis-regulatory analysis in the mammalian central nervous system
    • Susan Q. Shen,
    • Connie A. Myers,
    • Andrew E.O. Hughes,
    • Leah C. Byrne,
    • John G. Flannery,
    • and Joseph C. Corbo
    Genome Res. February 2016 26: 238-255; Published in Advance November 17, 2015, doi:10.1101/gr.193789.115
    ...in functionally interpreting these data. To address this issue, massively parallel reporter assays (MPRAs) have emerged, in which barcoded reporter libraries are introduced into cells, and the resulting barcoded transcripts are quantified by next-generation sequencing. Thus far, MPRAs have been largely restricted...
  10. Method: Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort
    • Christopher M. Vockley,
    • Cong Guo,
    • William H. Majoros,
    • Michael Nodzenski,
    • Denise M. Scholtens,
    • M. Geoffrey Hayes,
    • William L. Lowe, Jr.,
    • and Timothy E. Reddy
    Genome Res. August 2015 25: 1206-1214; Published in Advance June 17, 2015, doi:10.1101/gr.190090.115
    ...), and the regulatory activity of more than one million unique DNA fragments can now be assayed in a single experiment using such massively parallel reporter assays (Arnold et al. 2013).Here, we have developed a novel high-throughput approach to efficiently measure the activity of regulatory elements captured from...
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