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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 ... -
Basal Suppression of the Sonic Hedgehog Pathway by the G-Protein-Coupled Receptor Gpr161 Restricts Medulloblastoma Pathogenesis
(Cell Press, 2018-11-05)Sonic hedgehog (Shh) determines cerebellar granule cell (GC) progenitor proliferation and medulloblastoma pathogenesis. However, the pathways regulating GC progenitors during embryogenesis before Shh production by Purkinje ... -
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 ... -
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 ... -
Prediction of High-Risk Types of Human Papillomaviruses Using Statistical Model of Protein “Sequence Space”
(Hindawi Publishing Corporation, 2015-03-21)Discrimination of high-risk types of human papillomaviruses plays an important role in the diagnosis and remedy of cervical cancer. Recently, several computational methods have been proposed based on protein sequence-based ... -
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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
FastDMA: An Infinium Humanmethylation450 Beadchip Analyzer
(2013-09-05)DNA methylation is vital for many essential biological processes and human diseases. Illumina Infinium HumanMethylation450 Beadchip is a recently developed platform studying genome-wide DNA methylation state on more than ... -
Synthetic Mammalian Transgene Negative Autoregulation
(2013-06-04)Biological networks contain overrepresented small-scale topologies, typically called motifs. A frequently appearing motif is the transcriptional negative-feedback loop, where a gene product represses its own transcription. ... -
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 ... -
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 ... -
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 ... -
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. ...
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