Chongwei Bi
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View article: Prevalent integration of genomic repetitive and regulatory elements and donor sequences at CRISPR-Cas9-induced breaks
Prevalent integration of genomic repetitive and regulatory elements and donor sequences at CRISPR-Cas9-induced breaks Open
View article: NanoRanger enables rapid single-base-pair resolution of genomic disorders
NanoRanger enables rapid single-base-pair resolution of genomic disorders Open
View article: Modulation of the microhomology-mediated end joining pathway suppresses large deletions and enhances homology-directed repair following CRISPR-Cas9-induced DNA breaks
Modulation of the microhomology-mediated end joining pathway suppresses large deletions and enhances homology-directed repair following CRISPR-Cas9-induced DNA breaks Open
Background CRISPR-Cas9 genome editing often induces unintended, large genomic rearrangements, posing potential safety risks. However, there are no methods for mitigating these risks. Results Using long-read individual-molecule sequencing (…
View article: An open-source, automated, and cost-effective platform for COVID-19 diagnosis and rapid portable genomic surveillance using nanopore sequencing
An open-source, automated, and cost-effective platform for COVID-19 diagnosis and rapid portable genomic surveillance using nanopore sequencing Open
The COVID-19 pandemic, caused by SARS-CoV-2, has emphasized the necessity for scalable diagnostic workflows using locally produced reagents and basic laboratory equipment with minimal dependence on global supply chains. We introduce an ope…
View article: NanoRanger enables rapid single base-pair resolution of genomic disorders
NanoRanger enables rapid single base-pair resolution of genomic disorders Open
Rare diseases affect around 350 million individuals globally, yet at least half of those with suspected Mendelian disorders remain without a precise molecular diagnosis despite advanced genetic testing using short read sequencing (SRS). Lo…
View article: Quantification of Genetic Heterogeneity Using Long‐Read Targeted Individual DNA Molecule Sequencing
Quantification of Genetic Heterogeneity Using Long‐Read Targeted Individual DNA Molecule Sequencing Open
Understanding genetic heterogeneity is of paramount importance in unraveling the intricate functioning of biological systems, as it contributes to the diversity of phenotypes of gene‐environment interactions. We have developed a method ter…
View article: Wiskott-Aldrich Syndrome Protein Regulates Nucleolar Organization and Function in Innate Immune Response
Wiskott-Aldrich Syndrome Protein Regulates Nucleolar Organization and Function in Innate Immune Response Open
Wiskott-Aldrich syndrome (WAS) is a primary immunodeficiency disorder caused by the dysfunction of the WAS protein (WASP). Using an isogenic macrophage model derived from genome edited induced pluripotent stem cells we demonstrated that WA…
View article: Quantitative haplotype-resolved analysis of mitochondrial DNA heteroplasmy in Human single oocytes, blastoids, and pluripotent stem cells
Quantitative haplotype-resolved analysis of mitochondrial DNA heteroplasmy in Human single oocytes, blastoids, and pluripotent stem cells Open
Maternal mitochondria are the sole source of mtDNA for every cell of the offspring. Heteroplasmic mtDNA mutations inherited from the oocyte are a common cause of metabolic diseases and associated with late-onset diseases. However, the orig…
View article: Single-cell individual full-length mtDNA sequencing by iMiGseq uncovers unexpected heteroplasmy shifts in mtDNA editing
Single-cell individual full-length mtDNA sequencing by iMiGseq uncovers unexpected heteroplasmy shifts in mtDNA editing Open
The ontogeny and dynamics of mtDNA heteroplasmy remain unclear due to limitations of current mtDNA sequencing methods. We developed individual Mitochondrial Genome sequencing (iMiGseq) of full-length mtDNA for ultra-sensitive variant detec…
View article: Modulation of the microhomology-mediated end joining pathway suppresses large deletions and enhances homology-directed repair following CRISPR-Cas9-induced DNA breaks
Modulation of the microhomology-mediated end joining pathway suppresses large deletions and enhances homology-directed repair following CRISPR-Cas9-induced DNA breaks Open
CRISPR-Cas9, an efficient genome editing tool, has been widely used in research and holds great promise in the clinic. However, large unintended rearrangements of the genome occur frequently after CRISPR-Cas9 editing and their potential ri…
View article: Author Correction: Wiskott-Aldrich syndrome protein forms nuclear condensates and regulates alternative splicing
Author Correction: Wiskott-Aldrich syndrome protein forms nuclear condensates and regulates alternative splicing Open
View article: Wiskott-Aldrich syndrome protein forms nuclear condensates and regulates alternative splicing
Wiskott-Aldrich syndrome protein forms nuclear condensates and regulates alternative splicing Open
The diverse functions of WASP, the deficiency of which causes Wiskott-Aldrich syndrome (WAS), remain poorly defined. We generated three isogenic WAS models using patient induced pluripotent stem cells and genome editing. These models recap…
View article: Altered expression profile of long non-coding RNAs during heart aging in mice
Altered expression profile of long non-coding RNAs during heart aging in mice Open
Objective Long noncoding RNAs (lncRNAs) play an important role in regulating the occurrence and development of cardiovascular diseases. However, the role of lncRNAs in heart aging remains poorly understood. The objective of this study was …
View article: Simultaneous detection and mutation surveillance of SARS-CoV-2 and multiple respiratory viruses by rapid field-deployable sequencing
Simultaneous detection and mutation surveillance of SARS-CoV-2 and multiple respiratory viruses by rapid field-deployable sequencing Open
View article: Long Read Based Individual Molecule Sequencing and Real-time Pathogen Detection
Long Read Based Individual Molecule Sequencing and Real-time Pathogen Detection Open
With the ability to produce reads with hundreds of kilobases in length, long-read sequencing technology is emerging as a powerful tool to decode complex genetic sequences that are previously inaccessible for short reads. Though the sequenc…
View article: Single-cell Individual Complete mtDNA Sequencing Uncovers Hidden Mitochondrial Heterogeneity in Human and Mouse Oocytes
Single-cell Individual Complete mtDNA Sequencing Uncovers Hidden Mitochondrial Heterogeneity in Human and Mouse Oocytes Open
The ontogeny and dynamics of mtDNA heteroplasmy remain unclear due to limitations of current mtDNA sequencing methods. We developed individual Mi tochondrial G enome seq uencing (iMiGseq) of full-length mtDNA for ultra-sensitive variant de…
View article: Long-read individual-molecule sequencing reveals CRISPR-induced genetic heterogeneity in human ESCs
Long-read individual-molecule sequencing reveals CRISPR-induced genetic heterogeneity in human ESCs Open
Quantifying the genetic heterogeneity of a cell population is essential to understanding of biological systems. We develop a universal method to label individual DNA molecules for single-base-resolution haplotype-resolved quantitative char…
View article: Variant Analysis with UMI for Long-read Technology (VAULT)
Variant Analysis with UMI for Long-read Technology (VAULT) Open
VAULT is a tool for analyzing UMI-labeled reads, works for both error-prone long reads and accurate single-end/paired-end short reads. VAULT is a part of IDMseq. More detail can be found in our publication "Long-read individual-mol…
View article: Simultaneous Detection and Mutation Surveillance of SARS-CoV-2 and co-infections of multiple respiratory viruses by Rapid field-deployable sequencing
Simultaneous Detection and Mutation Surveillance of SARS-CoV-2 and co-infections of multiple respiratory viruses by Rapid field-deployable sequencing Open
Strategies for monitoring the COVID-19 infection are crucial for combating the pandemic. Here we describe a method for multiplex isothermal amplification-based sequencing and real-time analysis of multiple viral genomes. It can simultaneou…
View article: Long-read Individual-molecule Sequencing Reveals CRISPR-induced Genetic Heterogeneity in Human ESCs
Long-read Individual-molecule Sequencing Reveals CRISPR-induced Genetic Heterogeneity in Human ESCs Open
Accurately quantifying the genetic heterogeneity of a cell population is essential to understanding of biological systems. We develop a universal method to label individual DNA molecules for analyzing diverse types of rare genetic variants…
View article: DeepSimulator1.5: a more powerful, quicker and lighter simulator for Nanopore sequencing
DeepSimulator1.5: a more powerful, quicker and lighter simulator for Nanopore sequencing Open
Motivation Nanopore sequencing is one of the leading third-generation sequencing technologies. A number of computational tools have been developed to facilitate the processing and analysis of the Nanopore data. Previously, we have develope…
View article: By Targeting Atg7 MicroRNA-143 Mediates Oxidative Stress-Induced Autophagy of c-Kit+ Mouse Cardiac Progenitor Cells
By Targeting Atg7 MicroRNA-143 Mediates Oxidative Stress-Induced Autophagy of c-Kit+ Mouse Cardiac Progenitor Cells Open
Therapeutic efficiency of cardiac progenitor cells (CPCs) transplantation is limited by its low survival and retention in infarcted myocardium. Autophagy plays a critical role in regulating cell death and apoptosis, but the role of microRN…
View article: DeepSimulator: a deep simulator for Nanopore sequencing
DeepSimulator: a deep simulator for Nanopore sequencing Open
Motivation Oxford Nanopore sequencing is a rapidly developed sequencing technology in recent years. To keep pace with the explosion of the downstream data analytical tools, a versatile Nanopore sequencing simulator is needed to complement …
View article: Pre-Treatment with Melatonin Enhances Therapeutic Efficacy of Cardiac Progenitor Cells for Myocardial Infarction
Pre-Treatment with Melatonin Enhances Therapeutic Efficacy of Cardiac Progenitor Cells for Myocardial Infarction Open
Background/Aims: Melatonin possesses many biological activities such as antioxidant and anti-aging. Cardiac progenitor cells (CPCs) have emerged as a promising therapeutic strategy for myocardial infarction (MI). However, the low survival …
View article: Wiskott-Aldrich Syndrome Protein Regulates Nuclear Organization, Alternative Splicing and Cell Proliferation
Wiskott-Aldrich Syndrome Protein Regulates Nuclear Organization, Alternative Splicing and Cell Proliferation Open
View article: DeepSimulator: a deep simulator for Nanopore sequencing
DeepSimulator: a deep simulator for Nanopore sequencing Open
Motivation Oxford Nanopore sequencing is a rapidly developed sequencing technology in recent years. To keep pace with the explosion of the downstream data analytical tools, a versatile Nanopore sequencing simulator is needed to complement …
View article: Attenuation of Low Ambient Temperature-Induced Myocardial Hypertrophy by Atorvastatin via Promoting Bcl-2 Expression
Attenuation of Low Ambient Temperature-Induced Myocardial Hypertrophy by Atorvastatin via Promoting Bcl-2 Expression Open
Background/Aims: It is well documented that myocardial hypertrophy is associated with low ambient temperature. Atorvastatin (Atv) has been shown to protect against atherosclerosis, cardiac fibrosis, ischemia/reperfusion injury, etc. In thi…
View article: Acacetin Protects Mice from Staphylococcus aureus Bloodstream Infection by Inhibiting the Activity of Sortase A
Acacetin Protects Mice from Staphylococcus aureus Bloodstream Infection by Inhibiting the Activity of Sortase A Open
Staphylococcus aureus (S. aureus) is a major cause of infection in hospitals and communities. Widespread dissemination of multi-drug resistant S. aureus is a serious threat to the health of humans and animals. An anti-virulence strategy ha…
View article: Physiological and pathological implications of 5-hydroxymethylcytosine in diseases
Physiological and pathological implications of 5-hydroxymethylcytosine in diseases Open
Gene expression is the prerequisite of proteins. Diverse stimuli result in alteration of gene expression profile by base substitution for quite a long time. However, during the past decades, accumulating studies proved that bases modificat…
View article: Astragalus Polysaccharide Attenuated Iron Overload-Induced Dysfunction of Mesenchymal Stem Cells via Suppressing Mitochondrial ROS
Astragalus Polysaccharide Attenuated Iron Overload-Induced Dysfunction of Mesenchymal Stem Cells via Suppressing Mitochondrial ROS Open
Background/Aims: Bone marrow-derived mesenchymal stem cells (BMSCs) have the ability to differentiate into multilineage cells such as osteoblasts, chondrocytes, and cardiomyocytes. Dysfunction of BMSCs in response to pathological stimuli p…