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A comparative overview of epigenomic profiling methods
, Article Frontiers in Cell and Developmental Biology ; Volume 9 , 2021 ; 2296634X (ISSN) ; Sepehri, M. H ; Nazer, N ; Norouzi, M. R ; Sharif University of Technology
Frontiers Media S. A
2021
Abstract
In the past decade, assays that profile different aspects of the epigenome have grown exponentially in number and variation. However, standard guidelines for researchers to choose between available tools depending on their needs are lacking. Here, we introduce a comprehensive collection of the most commonly used bulk and single-cell epigenomic assays and compare and contrast their strengths and weaknesses. We summarize some of the most important technical and experimental parameters that should be considered for making an appropriate decision when designing epigenomic experiments. © Copyright © 2021 Mehrmohamadi, Sepehri, Nazer and Norouzi
Capturing single-cell heterogeneity via data fusion improves image-based profiling
, Article Nature Communications ; Volume 10, Issue 1 , 2019 ; 20411723 (ISSN) ; Abbasi, H. S ; Singh, S ; Carpenter, A. E ; Sharif University of Technology
Nature Publishing Group
2019
Abstract
Single-cell resolution technologies warrant computational methods that capture cell heterogeneity while allowing efficient comparisons of populations. Here, we summarize cell populations by adding features’ dispersion and covariances to population averages, in the context of image-based profiling. We find that data fusion is critical for these metrics to improve results over the prior alternatives, providing at least ~20% better performance in predicting a compound’s mechanism of action (MoA) and a gene’s pathway. © 2019, The Author(s)