Log in

Relevant bibliographies by topics / Massively Parallel Reporter Assay / Journal articles

To see the other types of publications on this topic, follow the link: Massively Parallel Reporter Assay.

Journal articles on the topic 'Massively Parallel Reporter Assay'

Author: Grafiati

Published: 30 June 2021

Last updated: 29 July 2025

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles

Select a source type:

Consult the top 50 journal articles for your research on the topic 'Massively Parallel Reporter Assay.'

Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.

You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.

Browse journal articles on a wide variety of disciplines and organise your bibliography correctly.

1

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

Full text

APA, Harvard, Vancouver, ISO, and other styles

2

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

Full text

APA, Harvard, Vancouver, ISO, and other styles

3

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.

Full text

APA, Harvard, Vancouver, ISO, and other styles

4

Delfosse, Kate, Chiara Gerhardinger, John L. Rinn, and Philipp G. Maass. "High-throughput functional analysis of regulatory variants using a massively parallel reporter assay." STAR Protocols 4, no. 4 (2023): 102731. http://dx.doi.org/10.1016/j.xpro.2023.102731.

Full text

APA, Harvard, Vancouver, ISO, and other styles

5

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 (2016): 137–38. http://dx.doi.org/10.1093/bioinformatics/btw584.

Full text

APA, Harvard, Vancouver, ISO, and other styles

6

Easterlin, Ryder, and Nadav Ahituv. "Lineage-specific regulatory evolution: insights from massively parallel reporter assays." Current Opinion in Genetics & Development 93 (August 2025): 102372. https://doi.org/10.1016/j.gde.2025.102372.

Full text

APA, Harvard, Vancouver, ISO, and other styles

7

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 (2021): 1638–45. http://dx.doi.org/10.1101/gr.268599.120.

Full text

Abstract:

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

APA, Harvard, Vancouver, ISO, and other styles

8

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 (2018): 90–95. http://dx.doi.org/10.1038/nbt.4285.

Full text

APA, Harvard, Vancouver, ISO, and other styles

9

Tonelli, Anastasiia, Pascal Cousin, and Maria Cristina Gambetta. "Protocol for detecting genomic insulators in Drosophila using insulator-seq, a massively parallel reporter assay." STAR Protocols 5, no. 4 (2024): 103391. http://dx.doi.org/10.1016/j.xpro.2024.103391.

Full text

APA, Harvard, Vancouver, ISO, and other styles

10

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 (2018): 1520–31. http://dx.doi.org/10.1101/gr.231886.117.

Full text

APA, Harvard, Vancouver, ISO, and other styles

11

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 (2020): 1468–80. http://dx.doi.org/10.1101/gr.263228.120.

Full text

APA, Harvard, Vancouver, ISO, and other styles

12

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 (2017): 787–94. http://dx.doi.org/10.1093/bioinformatics/btx598.

Full text

APA, Harvard, Vancouver, ISO, and other styles

13

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

Full text

Abstract:

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

APA, Harvard, Vancouver, ISO, and other styles

14

Qiao, Dandi, Corwin M. Zigler, Michael H. Cho, et al. "Statistical considerations for the analysis of massively parallel reporter assays data." Genetic Epidemiology 44, no. 7 (2020): 785–94. http://dx.doi.org/10.1002/gepi.22337.

Full text

APA, Harvard, Vancouver, ISO, and other styles

15

Kreimer, Anat, Haoyang Zeng, Matthew D. Edwards, et al. "Predicting gene expression in massively parallel reporter assays: A comparative study." Human Mutation 38, no. 9 (2017): 1240–50. http://dx.doi.org/10.1002/humu.23197.

Full text

APA, Harvard, Vancouver, ISO, and other styles

16

Melnikov, Alexandre, Anand Murugan, Xiaolan Zhang, et al. "Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay." Nature Biotechnology 30, no. 3 (2012): 271–77. http://dx.doi.org/10.1038/nbt.2137.

Full text

APA, Harvard, Vancouver, ISO, and other styles

17

Kheradpour, P., J. Ernst, A. Melnikov, et al. "Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay." Genome Research 23, no. 5 (2013): 800–811. http://dx.doi.org/10.1101/gr.144899.112.

Full text

APA, Harvard, Vancouver, ISO, and other styles

18

Madan, Namrata, Andrew Ghazi, Xianguo Kong, Edward Chen, Chad Shaw, and Leonard C. Edelstein. "Identification of the Genetic Variant Responsible for Variable Platelet CD36 Expression By Massively Parallel Reporter Assay." Blood 132, Supplement 1 (2018): 520. http://dx.doi.org/10.1182/blood-2018-99-118607.

Full text

Abstract:

Abstract CD36 is a platelet membrane glycoprotein whose engagement with oxidized low density lipoprotein (oxLDL) results in platelet activation. Deletion of CD36 in mice fed a high fat diet results in attenuation of the pro-thrombotic state and platelet hyper-activity. The CD36 gene has been associated with platelet count, platelet volume, as well as lipid levels and CVD risk. Platelet CD36 expression is highly variable with 3-8% of non-white populations displaying a complete lack of expression. Platelet CD36 expression levels have been shown to be associated with both the platelet oxLDL respo

APA, Harvard, Vancouver, ISO, and other styles

19

Rabani, Michal, Lindsey Pieper, Guo-Liang Chew, and Alexander F. Schier. "A Massively Parallel Reporter Assay of 3′ UTR Sequences Identifies In Vivo Rules for mRNA Degradation." Molecular Cell 68, no. 6 (2017): 1083–94. http://dx.doi.org/10.1016/j.molcel.2017.11.014.

Full text

APA, Harvard, Vancouver, ISO, and other styles

20

Rabani, Michal, Lindsey Pieper, Guo-Liang Chew, and Alexander F. Schier. "A Massively Parallel Reporter Assay of 3′ UTR Sequences Identifies In Vivo Rules for mRNA Degradation." Molecular Cell 70, no. 3 (2018): 565. http://dx.doi.org/10.1016/j.molcel.2018.04.013.

Full text

APA, Harvard, Vancouver, ISO, and other styles

21

Wang, Kaiyu, Meng Meng, Minghong Leng, et al. "Protocol for assessing regulatory elements in murine heart using an AAV9-based massively parallel reporter assay." STAR Protocols 6, no. 2 (2025): 103782. https://doi.org/10.1016/j.xpro.2025.103782.

Full text

APA, Harvard, Vancouver, ISO, and other styles

22

Eapen, Amy, Xiaoming Lu, Carmy Forney, et al. "Massively Parallel Reporter Assays (MPRAs) Identify Allelic Transcriptional Dysregulation in Atopic Dermatitis." Journal of Allergy and Clinical Immunology 145, no. 2 (2020): AB197. http://dx.doi.org/10.1016/j.jaci.2019.12.289.

Full text

APA, Harvard, Vancouver, ISO, and other styles

23

Mulvey, Bernard, Tomás Lagunas, and Joseph D. Dougherty. "Massively Parallel Reporter Assays: Defining Functional Psychiatric Genetic Variants Across Biological Contexts." Biological Psychiatry 89, no. 1 (2021): 76–89. http://dx.doi.org/10.1016/j.biopsych.2020.06.011.

Full text

APA, Harvard, Vancouver, ISO, and other styles

24

Kinney, Justin B., and David M. McCandlish. "Massively Parallel Assays and Quantitative Sequence–Function Relationships." Annual Review of Genomics and Human Genetics 20, no. 1 (2019): 99–127. http://dx.doi.org/10.1146/annurev-genom-083118-014845.

Full text

Abstract:

Over the last decade, a rich variety of massively parallel assays have revolutionized our understanding of how biological sequences encode quantitative molecular phenotypes. These assays include deep mutational scanning, high-throughput SELEX, and massively parallel reporter assays. Here, we review these experimental methods and how the data they produce can be used to quantitatively model sequence–function relationships. In doing so, we touch on a diverse range of topics, including the identification of clinically relevant genomic variants, the modeling of transcription factor binding to DNA,

APA, Harvard, Vancouver, ISO, and other styles

25

Rhine, Christy L., Christopher Neil, Jing Wang, et al. "Massively parallel reporter assays discover de novo exonic splicing mutants in paralogs of Autism genes." PLOS Genetics 18, no. 1 (2022): e1009884. http://dx.doi.org/10.1371/journal.pgen.1009884.

Full text

Abstract:

To determine the contribution of defective splicing in Autism Spectrum Disorders (ASD), the most common neurodevelopmental disorder, a high throughput Massively Parallel Splicing Assay (MaPSY) was employed and identified 42 exonic splicing mutants out of 725 coding de novo variants discovered in the sequencing of ASD families. A redesign of the minigene constructs in MaPSY revealed that upstream exons with strong 5’ splice sites increase the magnitude of skipping phenotypes observed in downstream exons. Select hits were validated by RT-PCR and amplicon sequencing in patient cell lines. Exonic

APA, Harvard, Vancouver, ISO, and other styles

26

Litterman, Adam J., Robin Kageyama, Olivier Le Tonqueze, et al. "A massively parallel 3′ UTR reporter assay reveals relationships between nucleotide content, sequence conservation, and mRNA destabilization." Genome Research 29, no. 6 (2019): 896–906. http://dx.doi.org/10.1101/gr.242552.118.

Full text

APA, Harvard, Vancouver, ISO, and other styles

27

Hudgins, Adam D., and Yousin Suh. "O4-01-03: FUNCTIONAL NON-CODING VARIANTS AFFECTING ALZHEIMER'S DISEASE RISK IDENTIFIED BY MASSIVELY PARALLEL REPORTER ASSAY." Alzheimer's & Dementia 14, no. 7S_Part_26 (2006): P1400—P1401. http://dx.doi.org/10.1016/j.jalz.2018.06.2911.

Full text

APA, Harvard, Vancouver, ISO, and other styles

28

Rykova, E. Yu, N. I. Ershov, A. O. Degtyareva, L. O. Bryzgalov, and E. L. Lushnikova. "Search for and functional analysis of genetic variants in microRNA binding sites using massively parallel reporter assay." Bulletin of Experimental Biology and Medicine 176, no. 11 (2023): 611–15. http://dx.doi.org/10.47056/0365-9615-2023-176-11-611-615.

Full text

APA, Harvard, Vancouver, ISO, and other styles

29

English, Justin, Adam M. Zahm, William S. Owens, et al. "A Massively Parallel Reporter Assay Library to Screen Short Synthetic Promoters in Mammalian Cells (Abstract ID: 159301)." Journal of Pharmacology and Experimental Therapeutics 392, no. 3 (2025): 100660. https://doi.org/10.1016/j.jpet.2024.100660.

Full text

APA, Harvard, Vancouver, ISO, and other styles

30

Zheng, Yanjiang, and Nathan J. VanDusen. "Massively Parallel Reporter Assays for High-Throughput In Vivo Analysis of Cis-Regulatory Elements." Journal of Cardiovascular Development and Disease 10, no. 4 (2023): 144. http://dx.doi.org/10.3390/jcdd10040144.

Full text

Abstract:

The rapid improvement of descriptive genomic technologies has fueled a dramatic increase in hypothesized connections between cardiovascular gene expression and phenotypes. However, in vivo testing of these hypotheses has predominantly been relegated to slow, expensive, and linear generation of genetically modified mice. In the study of genomic cis-regulatory elements, generation of mice featuring transgenic reporters or cis-regulatory element knockout remains the standard approach. While the data obtained is of high quality, the approach is insufficient to keep pace with candidate identificati

APA, Harvard, Vancouver, ISO, and other styles

31

Klein, Jason C., Vikram Agarwal, Fumitaka Inoue, et al. "A systematic evaluation of the design and context dependencies of massively parallel reporter assays." Nature Methods 17, no. 11 (2020): 1083–91. http://dx.doi.org/10.1038/s41592-020-0965-y.

Full text

APA, Harvard, Vancouver, ISO, and other styles

32

Chen, Andy B., Kriti Thapa, Hongyu Gao, et al. "38766 Massively Parallel Reporter Assay Reveals Functional Impact of 3™-UTR SNPs Associated with Neurological and Psychiatric Disorders." Journal of Clinical and Translational Science 5, s1 (2021): 95. http://dx.doi.org/10.1017/cts.2021.645.

Full text

Abstract:

ABSTRACT IMPACT: Screening the effect of thousands of non-coding genetic variants will help identify variants important in the etiology of diseases OBJECTIVES/GOALS: Massively parallel reporter assays (MPRAs) can experimentally evaluate the impact of genetic variants on gene expression. In this study, our objective was to systematically evaluate the functional activity of 3’-UTR SNPs associated with neurological disorders and use those results to help understand their contributions to disease etiology. METHODS/STUDY POPULATION: To choose variants to evaluate with the MPRA, we first gathered SN

APA, Harvard, Vancouver, ISO, and other styles

33

Poon, Kok-Siong, Lily Chiu, and Karen Mei-Ling Tan. "Laboratory Verification of a BRCA1 and BRCA2 Massively Parallel Sequencing Assay from Wet Bench to Bioinformatics for Germline DNA Analysis." Global Medical Genetics 08, no. 02 (2021): 062–68. http://dx.doi.org/10.1055/s-0041-1726338.

Full text

Abstract:

Abstract Introduction A robust genetic test for BRCA1 and BRCA2 genes is necessary for the diagnosis, prognosis, and treatment of patients with hereditary breast and ovarian cancer. We evaluated a commercial amplicon-based massively parallel sequencing (MPS) assay, BRCA MASTR Plus on the MiSeq platform, for germline BRCA genetic testing. Methods This study was performed on 31 DNA from cell lines and proficiency testing samples to establish the accuracy of the assay. A reference cell line DNA, NA12878 was used to determine the reproducibility of the assay. Discordant MPS result was resolved ort

APA, Harvard, Vancouver, ISO, and other styles

34

Koesterich, Justin, Joon-Yong An, Fumitaka Inoue, et al. "Characterization of De Novo Promoter Variants in Autism Spectrum Disorder with Massively Parallel Reporter Assays." International Journal of Molecular Sciences 24, no. 4 (2023): 3509. http://dx.doi.org/10.3390/ijms24043509.

Full text

Abstract:

Autism spectrum disorder (ASD) is a common, complex, and highly heritable condition with contributions from both common and rare genetic variations. While disruptive, rare variants in protein-coding regions clearly contribute to symptoms, the role of rare non-coding remains unclear. Variants in these regions, including promoters, can alter downstream RNA and protein quantity; however, the functional impacts of specific variants observed in ASD cohorts remain largely uncharacterized. Here, we analyzed 3600 de novo mutations in promoter regions previously identified by whole-genome sequencing of

APA, Harvard, Vancouver, ISO, and other styles

35

Kreimer, Anat, Zhongxia Yan, Nadav Ahituv, and Nir Yosef. "Meta‐analysis of massively parallel reporter assays enables prediction of regulatory function across cell types." Human Mutation 40, no. 9 (2019): 1299–313. http://dx.doi.org/10.1002/humu.23820.

Full text

APA, Harvard, Vancouver, ISO, and other styles

36

Abell, Nathan S., Marianne K. DeGorter, Michael J. Gloudemans, et al. "Multiple causal variants underlie genetic associations in humans." Science 375, no. 6586 (2022): 1247–54. http://dx.doi.org/10.1126/science.abj5117.

Full text

Abstract:

Associations between genetic variation and traits are often in noncoding regions with strong linkage disequilibrium (LD), where a single causal variant is assumed to underlie the association. We applied a massively parallel reporter assay (MPRA) to functionally evaluate genetic variants in high, local LD for independent cis-expression quantitative trait loci (eQTL). We found that 17.7% of eQTLs exhibit more than one major allelic effect in tight LD. The detected regulatory variants were highly and specifically enriched for activating chromatin structures and allelic transcription factor bindin

APA, Harvard, Vancouver, ISO, and other styles

37

Nuytemans, Karen, Derek J. van Booven, Natalia K. Hofmann, et al. "P2-143: USING MASSIVELY PARALLEL REPORTER ASSAYS TO IDENTIFY PROTECTIVE FUNCTIONAL VARIANTS IN THE APOE REGION." Alzheimer's & Dementia 15 (July 2019): P628. http://dx.doi.org/10.1016/j.jalz.2019.06.2550.

Full text

APA, Harvard, Vancouver, ISO, and other styles

38

Davis, Jessica E., Kimberly D. Insigne, Eric M. Jones, Quinn A. Hastings, W. Clifford Boldridge, and Sriram Kosuri. "Dissection of c-AMP Response Element Architecture by Using Genomic and Episomal Massively Parallel Reporter Assays." Cell Systems 11, no. 1 (2020): 75–85. http://dx.doi.org/10.1016/j.cels.2020.05.011.

Full text

APA, Harvard, Vancouver, ISO, and other styles

39

Karollus, Alexander, Žiga Avsec, and Julien Gagneur. "Predicting mean ribosome load for 5’UTR of any length using deep learning." PLOS Computational Biology 17, no. 5 (2021): e1008982. http://dx.doi.org/10.1371/journal.pcbi.1008982.

Full text

Abstract:

The 5’ untranslated region plays a key role in regulating mRNA translation and consequently protein abundance. Therefore, accurate modeling of 5’UTR regulatory sequences shall provide insights into translational control mechanisms and help interpret genetic variants. Recently, a model was trained on a massively parallel reporter assay to predict mean ribosome load (MRL)—a proxy for translation rate—directly from 5’UTR sequence with a high degree of accuracy. However, this model is restricted to sequence lengths investigated in the reporter assay and therefore cannot be applied to the majority

APA, Harvard, Vancouver, ISO, and other styles

40

Movva, Rajiv, Peyton Greenside, Georgi K. Marinov, Surag Nair, Avanti Shrikumar, and Anshul Kundaje. "Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays." PLOS ONE 14, no. 6 (2019): e0218073. http://dx.doi.org/10.1371/journal.pone.0218073.

Full text

APA, Harvard, Vancouver, ISO, and other styles

41

Omelina, Evgeniya S., Anna E. Letiagina, Lidiya V. Boldyreva, et al. "Slight Variations in the Sequence Downstream of the Polyadenylation Signal Significantly Increase Transgene Expression in HEK293T and CHO Cells." International Journal of Molecular Sciences 23, no. 24 (2022): 15485. http://dx.doi.org/10.3390/ijms232415485.

Full text

Abstract:

Compared to transcription initiation, much less is known about transcription termination. In particular, large-scale mutagenesis studies have, so far, primarily concentrated on promoter and enhancer, but not terminator sequences. Here, we used a massively parallel reporter assay (MPRA) to systematically analyze the influence of short (8 bp) sequence variants (mutations) located downstream of the polyadenylation signal (PAS) on the steady-state mRNA level of the upstream gene, employing an eGFP reporter and human HEK293T cells as a model system. In total, we evaluated 227,755 mutations located

APA, Harvard, Vancouver, ISO, and other styles

42

White, Michael A. "Understanding how cis -regulatory function is encoded in DNA sequence using massively parallel reporter assays and designed sequences." Genomics 106, no. 3 (2015): 165–70. http://dx.doi.org/10.1016/j.ygeno.2015.06.003.

Full text

APA, Harvard, Vancouver, ISO, and other styles

43

Ferreira, Leonardo, Torsten Meissner, Tarjei Mikkelsen, et al. "Long-range chromatin interactions control trophoblast-restricted HLA-G expression during pregnancy (IRM6P.657)." Journal of Immunology 194, no. 1_Supplement (2015): 60.7. http://dx.doi.org/10.4049/jimmunol.194.supp.60.7.

Full text

Abstract:

Abstract Human pregnancy poses an immunological paradox: at the fetal-maternal interface, semi-allogeneic fetal extravillous trophoblasts (EVT) invade the uterine mucosa without being rejected by the maternal immune system. HLA-G is a nonclassical MHC class I molecule specifically expressed on the surface of EVT and is believed to be a key to fetus-induced immune tolerance. However, the EVT-specific expression of HLA-G is still poorly understood. A novel enhancer more than 10 kb upstream of HLA-G, Enhancer L, was discovered via dissection of the HLA-G locus using a Massively Parallel Reporter

APA, Harvard, Vancouver, ISO, and other styles

44

Zhao, Jingjing, Fotis A. Baltoumas, Maxwell A. Konnaris, et al. "MPRAbase a Massively Parallel Reporter Assay database." Genome Research, April 22, 2025, gr.280387.124. https://doi.org/10.1101/gr.280387.124.

Full text

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 regulatory activity. There are several different variations of MPRA technology and they are used for numerous applications, including regulatory element discovery, variant effect measurement, saturation mutagenesis, synthetic regulatory element generation or characterization of evolutionary gene regulatory differences. Despite their many designs and uses, there is no comprehensive database that incorporates the results of thes

APA, Harvard, Vancouver, ISO, and other styles

45

McAfee, Jessica C., Jessica L. Bell, Oleh Krupa, Nana Matoba, Jason L. Stein, and Hyejung Won. "Focus on your locus with a massively parallel reporter assay." Journal of Neurodevelopmental Disorders 14, no. 1 (2022). http://dx.doi.org/10.1186/s11689-022-09461-x.

Full text

Abstract:

AbstractA growing number of variants associated with risk for neurodevelopmental disorders have been identified by genome-wide association and whole genome sequencing studies. As common risk variants often fall within large haplotype blocks covering long stretches of the noncoding genome, the causal variants within an associated locus are often unknown. Similarly, the effect of rare noncoding risk variants identified by whole genome sequencing on molecular traits is seldom known without functional assays. A massively parallel reporter assay (MPRA) is an assay that can functionally validate tho

APA, Harvard, Vancouver, ISO, and other styles

46

Zhao, Siqi, Clarice KY Hong, Connie A. Myers, et al. "A single-cell massively parallel reporter assay detects cell type specific cis-regulatory activity." February 7, 2025. https://doi.org/10.5281/zenodo.14907846.

Full text

Abstract:

Massively parallel reporter gene assays are key tools in regulatory genomics, but cannot be used to identify cell-type specific regulatory elements without performing assays serially across different cell types. To address this problem, we developed a single-cell massively parallel reporter assay (scMPRA) to measure the activity of libraries of <em>cis-regulatory</em> sequences (CRSs) across multiple cell-types simultaneously. We assayed a library of core promoters in a mixture of HEK293 and K562 cells and showed that scMPRA is a reproducible, highly parallel, single-cell reporter ge

APA, Harvard, Vancouver, ISO, and other styles

47

Melnikov, Alexandre, Xiaolan Zhang, Peter Rogov, Li Wang, and Tarjei S. Mikkelsen. "Massively Parallel Reporter Assays in Cultured Mammalian Cells." Journal of Visualized Experiments, no. 90 (August 17, 2014). http://dx.doi.org/10.3791/51719.

Full text

APA, Harvard, Vancouver, ISO, and other styles

48

Kwon, Soo Bin, and Jason Ernst. "Investigating enhancer evolution with massively parallel reporter assays." Genome Biology 19, no. 1 (2018). http://dx.doi.org/10.1186/s13059-018-1502-5.

Full text

APA, Harvard, Vancouver, ISO, and other styles

49

Ashuach, Tal, David S. Fischer, Anat Kreimer, Nadav Ahituv, Fabian J. Theis, and Nir Yosef. "MPRAnalyze: statistical framework for massively parallel reporter assays." Genome Biology 20, no. 1 (2019). http://dx.doi.org/10.1186/s13059-019-1787-z.

Full text

APA, Harvard, Vancouver, ISO, and other styles

50

Gallego Romero, Irene, and Amanda J. Lea. "Leveraging massively parallel reporter assays for evolutionary questions." Genome Biology 24, no. 1 (2023). http://dx.doi.org/10.1186/s13059-023-02856-6.

Full text

Abstract:

AbstractA long-standing goal of evolutionary biology is to decode how gene regulation contributes to organismal diversity. Doing so is challenging because it is hard to predict function from non-coding sequence and to perform molecular research with non-model taxa. Massively parallel reporter assays (MPRAs) enable the testing of thousands to millions of sequences for regulatory activity simultaneously. Here, we discuss the execution, advantages, and limitations of MPRAs, with a focus on evolutionary questions. We propose solutions for extending MPRAs to rare taxa and those with limited genomic

APA, Harvard, Vancouver, ISO, and other styles

We offer discounts on all premium plans for authors whose works are included in thematic literature selections. Contact us to get a unique promo code!