220 related articles for article (PubMed ID: 29028988)
1. QuASAR-MPRA: accurate allele-specific analysis for massively parallel reporter assays.
Kalita CA; Moyerbrailean GA; Brown C; Wen X; Luca F; Pique-Regi R
Bioinformatics; 2018 Mar; 34(5):787-794. PubMed ID: 29028988
[TBL] [Abstract][Full Text] [Related]
2. QuASAR: quantitative allele-specific analysis of reads.
Harvey CT; Moyerbrailean GA; Davis GO; Wen X; Luca F; Pique-Regi R
Bioinformatics; 2015 Apr; 31(8):1235-42. PubMed ID: 25480375
[TBL] [Abstract][Full Text] [Related]
3. Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays.
Movva R; Greenside P; Marinov GK; Nair S; Shrikumar A; Kundaje A
PLoS One; 2019; 14(6):e0218073. PubMed ID: 31206543
[TBL] [Abstract][Full Text] [Related]
4. Statistical considerations for the analysis of massively parallel reporter assays data.
Qiao D; Zigler CM; Cho MH; Silverman EK; Zhou X; Castaldi PJ; Laird NH
Genet Epidemiol; 2020 Oct; 44(7):785-794. PubMed ID: 32681690
[TBL] [Abstract][Full Text] [Related]
5. Design tools for MPRA experiments.
Ghazi AR; Chen ES; Henke DM; Madan N; Edelstein LC; Shaw CA
Bioinformatics; 2018 Aug; 34(15):2682-2683. PubMed ID: 30052913
[TBL] [Abstract][Full Text] [Related]
6. Meta-analysis of massively parallel reporter assays enables prediction of regulatory function across cell types.
Kreimer A; Yan Z; Ahituv N; Yosef N
Hum Mutat; 2019 Sep; 40(9):1299-1313. PubMed ID: 31131957
[TBL] [Abstract][Full Text] [Related]
7. Deep learning-assisted genome-wide characterization of massively parallel reporter assays.
Lu F; Sossin A; Abell N; Montgomery SB; He Z
Nucleic Acids Res; 2022 Nov; 50(20):11442-11454. PubMed ID: 36350674
[TBL] [Abstract][Full Text] [Related]
8. MPRAscore: robust and non-parametric analysis of massively parallel reporter assays.
Niroula A; Ajore R; Nilsson B
Bioinformatics; 2019 Dec; 35(24):5351-5353. PubMed ID: 31359027
[TBL] [Abstract][Full Text] [Related]
9. Bayesian modelling of high-throughput sequencing assays with malacoda.
Ghazi AR; Kong X; Chen ES; Edelstein LC; Shaw CA
PLoS Comput Biol; 2020 Jul; 16(7):e1007504. PubMed ID: 32692749
[TBL] [Abstract][Full Text] [Related]
10. Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation.
Guzman C; Duttke S; Zhu Y; De Arruda Saldanha C; Downes NL; Benner C; Heinz S
Nucleic Acids Res; 2023 Aug; 51(15):e80. PubMed ID: 37403796
[TBL] [Abstract][Full Text] [Related]
11. Deciphering regulatory architectures from synthetic single-cell expression patterns.
Pan RW; Röschinger T; Faizi K; Garcia H; Phillips R
bioRxiv; 2024 Jun; ():. PubMed ID: 38352569
[TBL] [Abstract][Full Text] [Related]
12. MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments.
Georgakopoulos-Soares I; Jain N; Gray JM; Hemberg M
Bioinformatics; 2017 Jan; 33(1):137-138. PubMed ID: 27605100
[TBL] [Abstract][Full Text] [Related]
13. Focus on your locus with a massively parallel reporter assay.
McAfee JC; Bell JL; Krupa O; Matoba N; Stein JL; Won H
J Neurodev Disord; 2022 Sep; 14(1):50. PubMed ID: 36085003
[TBL] [Abstract][Full Text] [Related]
14. Massively parallel reporter assays and mouse transgenic assays provide complementary information about neuronal enhancer activity.
Kosicki M; Cintrón DL; Page NF; Georgakopoulos-Soares I; Akiyama JA; Plajzer-Frick I; Novak CS; Kato M; Hunter RD; von Maydell K; Barton S; Godfrey P; Beckman E; Sanders SJ; Pennacchio LA; Ahituv N
bioRxiv; 2024 Apr; ():. PubMed ID: 38712228
[TBL] [Abstract][Full Text] [Related]
15. Sequence-based correction of barcode bias in massively parallel reporter assays.
Lee D; Kapoor A; Lee C; Mudgett M; Beer MA; Chakravarti A
Genome Res; 2021 Sep; 31(9):1638-1645. PubMed ID: 34285053
[TBL] [Abstract][Full Text] [Related]
16. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions.
Ernst J; Melnikov A; Zhang X; Wang L; Rogov P; Mikkelsen TS; Kellis M
Nat Biotechnol; 2016 Nov; 34(11):1180-1190. PubMed ID: 27701403
[TBL] [Abstract][Full Text] [Related]
17. Massively parallel reporter assay: a novel technique for analyzing the regulation of gene expression.
Yuan M; Li H; Wang SZ
Yi Chuan; 2023 Oct; 45(10):859-873. PubMed ID: 37872110
[TBL] [Abstract][Full Text] [Related]
18. A systematic evaluation of the design and context dependencies of massively parallel reporter assays.
Klein JC; Agarwal V; Inoue F; Keith A; Martin B; Kircher M; Ahituv N; Shendure J
Nat Methods; 2020 Nov; 17(11):1083-1091. PubMed ID: 33046894
[TBL] [Abstract][Full Text] [Related]
19. Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.
Degner JF; Marioni JC; Pai AA; Pickrell JK; Nkadori E; Gilad Y; Pritchard JK
Bioinformatics; 2009 Dec; 25(24):3207-12. PubMed ID: 19808877
[TBL] [Abstract][Full Text] [Related]
20. Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing.
Heap GA; Yang JH; Downes K; Healy BC; Hunt KA; Bockett N; Franke L; Dubois PC; Mein CA; Dobson RJ; Albert TJ; Rodesch MJ; Clayton DG; Todd JA; van Heel DA; Plagnol V
Hum Mol Genet; 2010 Jan; 19(1):122-34. PubMed ID: 19825846
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]