Relevant bibliographies by topics / Massively Parallel Reporter Assay

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers

Academic literature on the topic 'Massively Parallel Reporter Assay'

Author: Grafiati
Published: 30 June 2021
Last updated: 1 February 2022

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Journal articles on the topic "Massively Parallel Reporter Assay"

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Inoue, Fumitaka, and Nadav Ahituv. "Decoding enhancers using massively parallel reporter assays." Genomics 106, no. 3 (September 2015): 159–64. http://dx.doi.org/10.1016/j.ygeno.2015.06.005.

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Trauernicht, Max, Miguel Martinez-Ara, and Bas van Steensel. "Deciphering Gene Regulation Using Massively Parallel Reporter Assays." Trends in Biochemical Sciences 45, no. 1 (January 2020): 90–91. http://dx.doi.org/10.1016/j.tibs.2019.10.006.

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Avramopoulos, Dimitrios, Leslie Myint, Kasper Hansen, Ruihua Wang, Leandros Boukas, and Loyal Goff. "SA131A MASSIVELY PARALLEL REPORTER ASSAY FOR VARIANTS ASSOCIATED WITH SCHIZOPHRENIA AND ALZHEIMER'S DISEASE." European Neuropsychopharmacology 29 (2019): S1260—S1261. http://dx.doi.org/10.1016/j.euroneuro.2018.08.353.

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Georgakopoulos-Soares, Ilias, Naman Jain, Jesse M. Gray, and Martin Hemberg. "MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments." Bioinformatics 33, no. 1 (September 6, 2016): 137–38. http://dx.doi.org/10.1093/bioinformatics/btw584.

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Lee, Dongwon, Ashish Kapoor, Changhee Lee, Michael Mudgett, Michael A. Beer, and Aravinda Chakravarti. "Sequence-based correction of barcode bias in massively parallel reporter assays." Genome Research 31, no. 9 (July 20, 2021): 1638–45. http://dx.doi.org/10.1101/gr.268599.120.

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Massively 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 upstream or downstream from a reporter gene tagged by unique DNA sequences. However, tag sequences may themselves affect reporter gene expression and lead to major potential biases in the measured cis-regulatory activity. Here, we present a sequence-based method for correcting tag-sequence-specific effects and show that our method can significantly reduce this source of variation and improve the identification of functional regulatory variants by MPRAs. We also show that our model captures sequence features associated with post-transcriptional regulation of mRNA. Thus, this new method helps not only to improve detection of regulatory signals in MPRA experiments but also to design better MPRA protocols.
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Hughes, Andrew E. O., Connie A. Myers, and Joseph C. Corbo. "A massively parallel reporter assay reveals context-dependent activity of homeodomain binding sites in vivo." Genome Research 28, no. 10 (August 29, 2018): 1520–31. http://dx.doi.org/10.1101/gr.231886.117.

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Hammelman, Jennifer, Konstantin Krismer, Budhaditya Banerjee, David K. Gifford, and Richard I. Sherwood. "Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay." Genome Research 30, no. 10 (September 24, 2020): 1468–80. http://dx.doi.org/10.1101/gr.263228.120.

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Maricque, Brett B., Hemangi G. Chaudhari, and Barak A. Cohen. "A massively parallel reporter assay dissects the influence of chromatin structure on cis-regulatory activity." Nature Biotechnology 37, no. 1 (November 19, 2018): 90–95. http://dx.doi.org/10.1038/nbt.4285.

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Kalita, Cynthia A., Gregory A. Moyerbrailean, Christopher Brown, Xiaoquan Wen, Francesca Luca, and Roger Pique-Regi. "QuASAR-MPRA: accurate allele-specific analysis for massively parallel reporter assays." Bioinformatics 34, no. 5 (September 22, 2017): 787–94. http://dx.doi.org/10.1093/bioinformatics/btx598.

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Niroula, Abhishek, Ram Ajore, and Björn Nilsson. "MPRAscore: robust and non-parametric analysis of massively parallel reporter assays." Bioinformatics 35, no. 24 (July 29, 2019): 5351–53. http://dx.doi.org/10.1093/bioinformatics/btz591.

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Abstract Motivation Massively parallel reporter assays (MPRA) enable systematic screening of DNA sequence variants for effects on transcriptional activity. However, convenient analysis tools are still needed. Results We introduce MPRAscore, a novel tool to infer allele-specific effects on transcription from MPRA data. MPRAscore uses a weighted, variance-regularized method to calculate variant effect sizes robustly, and a permutation approach to test for significance without assuming normality or independence. Availability and implementation Source code (C++), precompiled binaries and data used in the paper at https://github.com/abhisheknrl/MPRAscore and https://www.ncbi.nlm.nih.gov/bioproject/PRJNA554195. Supplementary information Supplementary data are available at Bioinformatics online.
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Dissertations / Theses on the topic "Massively Parallel Reporter Assay"

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Samenuk, Thomas. "Incorporation of Organ-Specific MicroRNA Target Sequences to Improve Gene Therapy Specificity:." Thesis, Boston College, 2021. http://hdl.handle.net/2345/bc-ir:109174.

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Thesis advisor: Vassilios Bezzerides
The aim of this study was to utilize a massively parallel reporter assay (MPRA) to identify organ-specific microRNA (miRNA) target sequences to refine the timing and expression of transgene expression for gene therapy. We previously had developed a cardiac gene therapy for Catecholaminergic Polymorphic Ventricular Tachycardia (CPVT) using a systemically delivered adeno-associated virus (AAV9) vector. We hypothesized that incorporation of organ specific miRNA target sites into our vector construct could improve our therapy’s tissue specificity due to the ability of miRNAs to silence transgene expression. Initially, we attempted to incorporate mir-124 target sequences into our vector to detarget the brain. Although these initial attempts were unsuccessful, the study allowed us to develop a protocol to test the effectiveness of miRNA target sequences. Thereafter, we developed a method to screen thousands of putative miRNA target sequences simultaneously. In this study, target sequences of miRNAs specific to the heart, brain and liver were incorporated into a plasmid library. This plasmid library was subsequently made into AAV and injected into mice from a CPVT transgenic line. Total DNA and RNA was later extracted from the target organs, converted into genomic DNA (gDNA) and complementary DNA (cDNA) libraries respectively, and sent for amplicon sequencing. We analyzed the results using Comparative Microbiome Analysis 2.0 software (CoMA) and a custom python script to count the occurrence of each specified barcode per sample. In doing so, we showed that the miRNA suppression mechanism is not only effective but also organ specific. Furthermore, we developed a second script to create a combinatorial library from a set list of miRNA target sequences enabling us to efficiently test thousands of target sequence combinations at once. In doing so, we will be able to identify effective miRNA target sequence combinations to further improve gene therapy specificity
Thesis (BS) — Boston College, 2021
Submitted to: Boston College. College of Arts and Sciences
Discipline: Departmental Honors
Discipline: Biology
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FitzPatrick, Vincent Drury. "Predicting Autonomous Promoter Activity Based on Genome-wide Modeling of Massively Parallel Reporter Data." Thesis, 2020. https://doi.org/10.7916/d8-qct0-z873.

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Existing methods to systematically characterize sequence-intrinsic activity of promoters are limited by relatively low throughput and the length of sequences that could be tested. Here we present Survey of Regulatory Elements (SuRE), a method to assay more than a billion DNA fragments in parallel for their ability to drive transcription autonomously. In SuRE, a plasmid library is constructed of random genomic fragments upstream of a barcode and decoded by paired-end sequencing. This library is transfected into cells and transcribed barcodes are quantified in the RNA by high-throughput sequencing. By computationally analyzing the resulting data using generalized linear models, we succeed in delineating subregions within promoters that are relevant for their activity on a genomic scale, and making accurate predictions of expression levels that can be used to inform minimal promoter reporter construct design. We also show how our approach can be extended to analyze the differential impact of single-nucleotide polymorphisms (SNPs) on gene expression.
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Book chapters on the topic "Massively Parallel Reporter Assay"

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Oh, Inez Y., and Shiming Chen. "High-Throughput Analysis of Retinal Cis-Regulatory Networks by Massively Parallel Reporter Assays." In Retinal Degenerative Diseases, 359–64. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-27378-1_59.

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Conference papers on the topic "Massively Parallel Reporter Assay"

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Choi, Jiyeon, Tongwu Zhang, Michael Kovacs, Mai Xu, Nghi Lam, Leandro Colli, and Kevin Brown. "Abstract 1317: Simultaneous identification of candidate melanoma risk variants using massively parallel reporter assay." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-1317.

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Journal articles
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