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Exploiting the CRISPR/Cas9 PAM Constraint for Single-Nucleotide Resolution Interventions
(2016-01-20)
CRISPR/Cas9 is an enabling RNA-guided technology for genome targeting and engineering. An acute DNA binding constraint of the Cas9 protein is the Protospacer Adjacent Motif (PAM). Here we demonstrate that the PAM requirement ...
Complete Genome Analysis of Three Acinetobacter Baumannii Clinical Isolates in China for Insight into the Diversification of Drug Resistance Elements
(2013-06-24)
Background: The emergence and rapid spreading of multidrug-resistant Acinetobacter baumannii strains has become a major health threat worldwide. To better understand the genetic recombination related with the acquisition ...
Engineering Repressors with Coevolutionary Cues Facilitates Toggle Switches with a Master Reset
(Oxford University Press, 2019-04-24)
Engineering allosteric transcriptional repressors containing an environmental sensing module (ESM) and a DNA recognition module (DRM) has the potential to unlock a combinatorial set of rationally designed biological ...
Inhibiting the Integrated Stress Response Pathway Prevents Aberrant Chondrocyte Differentiation Thereby Alleviating Chondrodysplasia
The integrated stress response (ISR) is activated by diverse forms of cellular stress, including endoplasmic reticulum (ER) stress, and is associated with diseases. However, the molecular mechanism(s) whereby the ISR impacts ...
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 ...
Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells
(Oxford University Press, 2013-12-16)
DNA methylation is an important defense and regulatory mechanism. In mammals, most DNA methylation occurs at CpG sites, and asymmetric non-CpG methylation has only been detected at appreciable levels in a few cell types. ...
OLego: Fast and Sensitive Mapping of Spliced mRNA-Seq Reads Using Small Seeds
(Oxford University Press, 2013-04)
A crucial step in analyzing mRNA-Seq data is to accurately and efficiently map hundreds of millions of reads to the reference genome and exon junctions. Here we present OLego, an algorithm specifically designed for de novo ...
Transcripts for Combined Synthetic MicroRNA and Gene Delivery
(2013-06-26)
MicroRNAs (miRNAs) are a class of short noncoding RNAs which are endogenously expressed in many organisms and regulate gene expression by binding to messenger RNA (mRNA). MicroRNAs are either produced from their independent ...
Anaerobic Cysteine Degradation and Potential Metabolic Coordination in Salmonella Enterica and Escherichia Coli
(2018-08-24)
Salmonella enterica has two CyuR-activated enzymes that degrade cysteine, i.e., the aerobic CdsH and an unidentified anaerobic enzyme; Escherichia coli has only the latter. To identify the anaerobic enzyme, transcript ...
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 ...