173 related articles for article (PubMed ID: 36350674)
21. Design and Analysis of Massively Parallel Reporter Assays Using FORECAST.
Gilliot PA; Gorochowski TE
Methods Mol Biol; 2023; 2553():41-56. PubMed ID: 36227538
[TBL] [Abstract][Full Text] [Related]
22. MPRAnalyze: statistical framework for massively parallel reporter assays.
Ashuach T; Fischer DS; Kreimer A; Ahituv N; Theis FJ; Yosef N
Genome Biol; 2019 Sep; 20(1):183. PubMed ID: 31477158
[TBL] [Abstract][Full Text] [Related]
23. Linear models enable powerful differential activity analysis in massively parallel reporter assays.
Myint L; Avramopoulos DG; Goff LA; Hansen KD
BMC Genomics; 2019 Mar; 20(1):209. PubMed ID: 30866806
[TBL] [Abstract][Full Text] [Related]
24. Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework.
Liu J; Ashuach T; Inoue F; Ahituv N; Yosef N; Kreimer A
Nucleic Acids Res; 2024 Feb; 52(4):1613-1627. PubMed ID: 38296821
[TBL] [Abstract][Full Text] [Related]
25. TSVM: Transfer Support Vector Machine for Predicting MPRA Validated Regulatory Variants.
Li M; Zhou S; Liu T; Liu C; Zang M; Wang Q
IEEE/ACM Trans Comput Biol Bioinform; 2024; 21(3):472-479. PubMed ID: 38451770
[TBL] [Abstract][Full Text] [Related]
26. TVAR: assessing tissue-specific functional effects of non-coding variants with deep learning.
Yang H; Chen R; Wang Q; Wei Q; Ji Y; Zhong X; Li B
Bioinformatics; 2022 Oct; 38(20):4697-4704. PubMed ID: 36063453
[TBL] [Abstract][Full Text] [Related]
27. Characterization of enhancer activity in early human neurodevelopment using Massively Parallel Reporter Assay (MPRA) and forebrain organoids.
Capauto D; Wang Y; Wu F; Norton S; Mariani J; Inoue F; Crawford GE; Ahituv N; Abyzov A; Vaccarino FM
Sci Rep; 2024 Feb; 14(1):3936. PubMed ID: 38365907
[TBL] [Abstract][Full Text] [Related]
28. Optimized PCR conditions minimizing the formation of chimeric DNA molecules from MPRA plasmid libraries.
Omelina ES; Ivankin AV; Letiagina AE; Pindyurin AV
BMC Genomics; 2019 Jul; 20(Suppl 7):536. PubMed ID: 31291895
[TBL] [Abstract][Full Text] [Related]
29. Best practices for perturbation MPRA-a computational evaluation framework of sequence design strategies.
Liu J; Ashuach T; Inoue F; Ahituv N; Yosef N; Kreimer A
bioRxiv; 2023 Sep; ():. PubMed ID: 37808807
[TBL] [Abstract][Full Text] [Related]
30. Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits.
Ulirsch JC; Nandakumar SK; Wang L; Giani FC; Zhang X; Rogov P; Melnikov A; McDonel P; Do R; Mikkelsen TS; Sankaran VG
Cell; 2016 Jun; 165(6):1530-1545. PubMed ID: 27259154
[TBL] [Abstract][Full Text] [Related]
31. Understanding how cis-regulatory function is encoded in DNA sequence using massively parallel reporter assays and designed sequences.
White MA
Genomics; 2015 Sep; 106(3):165-170. PubMed ID: 26072432
[TBL] [Abstract][Full Text] [Related]
32. Using a modular massively parallel reporter assay to discover context-specific regulatory grammars in type 2 diabetes.
Tovar A; Kyono Y; Nishino K; Bose M; Varshney A; Parker SCJ; Kitzman JO
bioRxiv; 2023 Oct; ():. PubMed ID: 37873175
[TBL] [Abstract][Full Text] [Related]
33. High-Throughput Analysis of Retinal Cis-Regulatory Networks by Massively Parallel Reporter Assays.
Oh IY; Chen S
Adv Exp Med Biol; 2019; 1185():359-364. PubMed ID: 31884638
[TBL] [Abstract][Full Text] [Related]
34. Massively Parallel Analysis of Regulatory RNA Sequences.
Rabani M
Methods Mol Biol; 2021; 2218():355-365. PubMed ID: 33606245
[TBL] [Abstract][Full Text] [Related]
35. Effective design and inference for cell sorting and sequencing based massively parallel reporter assays.
Gilliot PA; Gorochowski TE
Bioinformatics; 2023 May; 39(5):. PubMed ID: 37084251
[TBL] [Abstract][Full Text] [Related]
36. Massively Parallel Reporter Assays: Defining Functional Psychiatric Genetic Variants Across Biological Contexts.
Mulvey B; Lagunas T; Dougherty JD
Biol Psychiatry; 2021 Jan; 89(1):76-89. PubMed ID: 32843144
[TBL] [Abstract][Full Text] [Related]
37. Genome-wide prediction of cis-regulatory regions using supervised deep learning methods.
Li Y; Shi W; Wasserman WW
BMC Bioinformatics; 2018 May; 19(1):202. PubMed ID: 29855387
[TBL] [Abstract][Full Text] [Related]
38. ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation.
Umarov R; Li Y; Arakawa T; Takizawa S; Gao X; Arner E
PLoS Comput Biol; 2021 Sep; 17(9):e1009376. PubMed ID: 34491989
[TBL] [Abstract][Full Text] [Related]
39. MPRAdecoder: Processing of the Raw MPRA Data With
Letiagina AE; Omelina ES; Ivankin AV; Pindyurin AV
Front Genet; 2021; 12():618189. PubMed ID: 34046055
[TBL] [Abstract][Full Text] [Related]
40. A new computational method to predict transcriptional activity of a DNA sequence from diverse datasets of massively parallel reporter assays.
Liu Y; Irie T; Yada T; Suzuki Y
Nucleic Acids Res; 2017 Jul; 45(13):e124. PubMed ID: 28531296
[TBL] [Abstract][Full Text] [Related]
[Previous] [Next] [New Search]