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Assembly and Validation of Versatile Transcription Activator-Like Effector Libraries
(Nature Publishing Group, 2014-05-06)
The ability to perturb individual genes in genome-wide experiments has been instrumental in unraveling cellular and disease properties. Here we introduce, describe the assembly, and demonstrate the use of comprehensive and ...
ModuleRole: A Tool for Modulization, Role Determination and Visualization in Protein-Protein Interaction Networks
(Public Library of Science, 2014-05-01)
Rapidly increasing amounts of (physical and genetic) protein-protein interaction (PPI) data are produced by various high-throughput techniques, and interpretation of these data remains a major challenge. In order to gain ...
Distinct and Predictive Histone Lysine Acetylation Patterns at Promoters, Enhancers, and Gene Bodies
(Genetics Society America, 2014-11-01)
In eukaryotic cells, histone lysines are frequently acetylated. However, unlike modifications such as methylations, histone acetylation modifications are often considered redundant. As such, the functional roles of distinct ...
Nucleosome Eviction and Multiple Co-Factor Binding Predict Estrogen-Receptor-Alpha-Asociated Long-Range Interactions
(Oxford University Press, 2014-04-29)
Many enhancers regulate their target genes via long-distance interactions. High-throughput experiments like ChIA-PET have been developed to map such largely cell-type-specific interactions between cis-regulatory elements ...
CRISPR-Based Self-Cleaving Mechanism for Controllable Gene Delivery in Human Cells
(Oxford University Press, 2014-12-18)
Controllable gene delivery via vector-based systems remains a formidable challenge in mammalian synthetic biology and a desirable asset in gene therapy applications. Here, we introduce a methodology to control the copies ...
Quantitative liver-specific protein fingerprint in blood: A signature for hepatotoxicity
(2014-01-14)
We discuss here a new approach to detecting hepatotoxicity by employing concentration changes of liver-specific blood proteins during disease progression. These proteins are capable of assessing the behaviors of their ...
Miror: A Method for Cell-Type Specific MicroRNA Occupancy Rate Prediction
(Royal Soc Chemistry, 2014-03-13)
MicroRNA (miRNA) regulation is highly cell-type specific. It is sensitive to both the miRNA-mRNA relative abundance and the competitive endogenous RNA (ceRNA) effect. However, almost all existing miRNA target prediction ...
Genome Wide Mapping of Foxo1 Binding-Sites in Murine T Lymphocytes
(Elsevier Inc, 2014-08-01)
The Forkhead box O (Foxo) family of transcription factors has a critical role in controlling the development, differentiation, and function of T cells. However, the direct target genes of Foxo transcription factors in T ...