Searching journal content for articles similar to Mogno et al. 23 (11): 1908.

Displaying results 1-10 of 62

For checked items

view abstracts
download to citation manager

Select this article
Resource: MPRAbase a Massively Parallel Reporter Assay database
- Jingjing Zhao,
- Fotis A Baltoumas,
- Maxwell A Konnaris,
- Ioannis Mouratidis,
- Zhe Liu,
- Jasmine Sims,
- Vikram Agarwal,
- Georgios A Pavlopoulos,
- Ilias Georgakopoulos-Soares,
- and Nadav Ahituv
Genome Res. April 22, 2025 gr.280387.124; Published in Advance April 22, 2025, doi:10.1101/gr.280387.124
...RNA Center of Excellence, Sanofi Pasteur Inc., Waltham, MA, USA. ♱Corresponding authors: izg5139@psu.edu, nadav.ahituv@ucsf.edu Abstract Massively parallel reporter assays (MPRAs) represent a set of high-throughput technologies that measure the functional effects of thousands of sequences/variants on gene...
- Abstract
- Full Text (PDF)
OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
Select this article
Method: Iterative improvement of deep learning models using synthetic regulatory genomics
- André M. Ribeiro-dos-Santos and
- Matthew T. Maurano
Genome Res. November 2025 35: 2539-2549; Published in Advance October 22, 2025, doi:10.1101/gr.280540.125
...the reference, such as disease- and trait-associated variants or engineered sequences. Recent work has applied synthetic regulatory genomics to characterized dozens of deletions, inversions, and rearrangements of DNase I hypersensitive sites (DHSs). Here, we use the state-of-the-art model Enformer to predict...
Select this article
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
..., Cohen BA. 2013. Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants. Genome Res 23: 1908–1915. doi:10.1101/gr.157891.113 ↵Mullokandov G, Baccarini A, Ruzo A, Jayaprakash AD, Tung N, Israelow B, Evans MJ, Sachidanandam R, Brown BD. 2012. High...
Select this article
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...
Select this article
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
Select this article
Perspective: Challenges and considerations for reproducibility of STARR-seq assays
- Maitreya Das,
- Ayaan Hossain,
- Deepro Banerjee,
- Craig Alan Praul,
- and Santhosh Girirajan
Genome Res. April 2023 33: 479-495; Published in Advance May 2, 2023, doi:10.1101/gr.277204.122
...-seq), like other episomal massively parallel reporter assays (MPRAs) (Melnikov et al. 2012; Patwardhan et al. 2012), directly quantifies enhancer activity by relying on transcription factors within a host cell system, thereby removing any chromatin-associated biases (Arnold et al. 2013). STARR-seq takes...
Select this article
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...
Select this article
Research: Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors
- James L. Shepherdson,
- Ryan Z. Friedman,
- Yiqiao Zheng,
- Chi Sun,
- Inez Y. Oh,
- David M. Granas,
- Barak A. Cohen,
- Shiming Chen,
- and Michael A. White
Genome Res. February 2024 34: 243-255; Published in Advance February 14, 2024, doi:10.1101/gr.278133.123
...-regulatory function by deploying massively parallel reporter assays (MPRAs) in mouse retina explants carrying knock-ins of two variants, one in the DNA-binding domain (p.R90W) and the other in the transcriptional effector domain (p.E168d2). The degree of reporter gene dysregulation in these mutant Crx retinas...
OPEN ACCESS ARTICLE
Select this article
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
...assays (Nord et al. 2013; Visel et al. 2013), never before has massively parallel cis-regulatory analysis been conducted in the mammalian CNS in vivo. Here, we sought to overcome current technological hurdles by developing a “capture-and-clone” approach for synthesizing CRE-seq libraries...
Select this article
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
...elements by synthetic saturation mutagenesis. Nat Biotechnol 27: 1173–1175. ↵Patwardhan RP, Hiatt JB, Witten DM, Kim MJ, Smith RP, May D, Lee C, Andrie JM, Lee SI, Cooper GM, et al. 2012. Massively parallel functional dissection of mammalian enhancers in vivo. Nat...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Mogno et al. 23 (11): 1908.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: