A5040704785- Genomics and Phylogenetic Studies
- Nanopore and Nanochannel Transport Studies
- Microfluidic and Capillary Electrophoresis Applications
- Advanced biosensing and bioanalysis techniques
- DNA and Nucleic Acid Chemistry
- Animal Virus Infections Studies
- Genomic variations and chromosomal abnormalities
- RNA and protein synthesis mechanisms
- Chromosomal and Genetic Variations
- Sodium Intake and Health
- Advanced Fluorescence Microscopy Techniques
- MicroRNA in disease regulation
- Cancer-related molecular mechanisms research
- Molecular Biology Techniques and Applications
- Herpesvirus Infections and Treatments
- Genetic Associations and Epidemiology
- CRISPR and Genetic Engineering
- SARS-CoV-2 and COVID-19 Research
- RNA modifications and cancer
- Microfluidic and Bio-sensing Technologies
- Bioinformatics and Genomic Networks
- Analytical Chemistry and Sensors
- Genomics and Rare Diseases
- Blood Pressure and Hypertension Studies
- Circular RNAs in diseases
Chinese Academy of Medical Sciences & Peking Union Medical College
2014-2025
Yangzhou University
2025
Chongqing Medical University
2024-2025
Children's Hospital of Chongqing Medical University
2024-2025
Ruijin Hospital
2023-2025
Shanghai Zhabei District Shibei Hospital
2025
Central South University
2025
Ministry of Education of the People's Republic of China
2025
Shandong University
2025
Shanghai Jiao Tong University
2022-2024
The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies human genetic diversity and disease association. Here, we apply a suite long-read, short-read, strand-specific technologies, optical mapping, variant discovery algorithms to comprehensively analyze three trios define the full spectrum variation in haplotype-resolved manner. We identify 818,054 indel (<50 bp) 27,622 SVs (≥50 per genome. also discover 156 inversions genome 58 intersect...
Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of developing tools to fight them has been slowed by lack a high-quality genome assembly. Here we combine diverse technologies produce markedly improved, fully re-annotated AaegL5 assembly, demonstrate how it accelerates mosquito science. We anchored physical cytogenetic maps, doubled number...
Abstract Salamanders serve as important tetrapod models for developmental, regeneration and evolutionary studies. An extensive molecular toolkit makes the Mexican axolotl ( Ambystoma mexicanum ) a key representative salamander investigations. Here we report sequencing assembly of 32-gigabase-pair genome using an approach that combined long-read sequencing, optical mapping development new assembler (MARVEL). We observed size expansion introns intergenic regions, largely attributable to...
We show that genomic-length DNA molecules imaged in nanochannels have an extension along the channel scales linearly with contour length of polymer, agreement scaling arguments developed by de Gennes for self-avoiding confined polymers. This fundamental relationship allows us to measure directly single channels, and statistical analysis dynamics polymer nanochannel compute SD mean extension. λ multimers a 130-nm 1 min.
A spotlight on great ape genomes Most nonhuman primate generated to date have been “humanized” owing their many gaps and the reliance guidance by reference human genome. To remove this humanizing effect, Kronenberg et al. assembled long-read of a chimpanzee, an orangutan, two humans compared them with previously gorilla This analysis recognized genomic structural variation specific particular lineages. Comparisons between chimpanzee cerebral organoids showed down-regulation expression genes...
De novo assembly and phasing of the genome an individual from Korea using a combination different sequencing approaches provides useful population-specific reference represents most contiguous human so far. Jeong-Sun Seo colleagues report de PacBio long-read sequencing, Illumina short-read 10X Genomics linked reads, bacterial artificial chromosome (BAC) BioNano optical mapping. This to date. The authors use this close gaps in map structural variation. Advances provide opportunity investigate...
Abstract Large structural variants (SVs) in the human genome are difficult to detect and study by conventional sequencing technologies. With long-range analysis platforms, such as optical mapping, one can identify large SVs (>2 kb) across experiment. Analyzing maps of 154 individuals from 26 populations sequenced 1000 Genomes Project, we find that phylogenetic population patterns similar those single nucleotide variations 86% genome, while ~2% has high complexity. We able characterize...
We made uniform arrays of nanometer scale structures using nanoimprint lithography over large areas (100 mm wafers). The nanofluidic channels were further narrowed and sealed by techniques that are based on nonuniform deposition. resulting have a cross section as small 10 nm 50 nm, great importance for confining biological molecules into ultrasmall spaces. These can be valuable fabrication tools Nanoelectromechanical Systems Micro/Nano Total Analysis Systems.
It is difficult to introduce long genomic DNA molecules into nanometer scale fluidic channels directly from the macroscale world because of steep entropic barrier caused by necessary stretching polymer. We present a very simple technique using optical lithography fabricate continuous spatial gradient structures which smoothly narrow cross section volume micron length scale, greatly reducing local nanochannel entry. This technique, diffraction lithography, can be valuable for fabrication...
Structural variants (SVs) are less common than single nucleotide polymorphisms and indels in the population, but collectively account for a significant fraction of genetic polymorphism diseases. Base pair differences arising from SVs on much higher order (>100 fold) point mutations; however, none current detection methods comprehensive, currently available methodologies incapable providing sufficient resolution unambiguous information across complex regions human genome. To address these...
An array of nano-channels was fabricated from silicon based semiconductor materials to stretch long, native dsDNA. Here we present a labeling scheme in which it is possible identify the location specific sequences along stretched DNA molecules. The proceeds by first using strand displacement activity Vent (exo-) polymerase generate single flaps on nicked These are hybridized with sequence fluorophore-labeled probes. Subsequent imaging molecules inside nano-channel device allows for...
Next-generation sequencing (NGS) technologies have enabled high-throughput and low-cost generation of sequence data; however, de novo genome assembly remains a great challenge, particularly for large genomes. NGS short reads are often insufficient to create contigs that span repeat sequences facilitate unambiguous assembly. Plant genomes notorious containing high quantities repetitive elements, which combined with huge sizes, makes accurate these complex intractable thus far. Using two-color...
Abstract Comprehensive whole-genome structural variation detection is challenging with current approaches. With diploid cells as DNA source and the presence of numerous repetitive elements, short-read sequencing cannot be used to detect efficiently. In this report, we show that genome mapping long, fluorescently labeled molecules imaged on nanochannel arrays can for without sequencing. While haplotyping not achieved, local phasing (across &gt;150-kb regions) routine, from parental...
Abstract There is concern that the stresses of inducing pluripotency may lead to deleterious DNA mutations in induced pluripotent stem cell (iPSC) lines, which would compromise their use for therapies. Here we report comparative genomic analysis nine isogenic iPSC lines generated using three reprogramming methods: integrating retroviral vectors, non-integrating Sendai virus and synthetic mRNAs. We used whole-genome sequencing de novo genome mapping identify single-nucleotide variants,...
Short tandem repeats (STRs) and variable number (VNTRs) are important sources of natural disease-causing variation, yet they have been problematic to resolve in reference genomes genotype with short-read technology. We created a framework model the evolution instability STRs VNTRs apes. phased assembled 3 ape (chimpanzee, gorilla, orangutan) using long-read 10x Genomics linked-read sequence data for 21,442 human discovered 6 haplotype-resolved assemblies Yoruban, Chinese, Puerto Rican...
Abstract The common bed bug ( Cimex lectularius ) has been a persistent pest of humans for thousands years, yet the genetic basis bug’s basic biology and adaptation to dense human environments is largely unknown. Here we report assembly, annotation phylogenetic mapping 697.9-Mb genome, with an N50 971 kb, using both long short read technologies. A RNA-seq time course across all five developmental stages male female adults generated 36,985 coding noncoding gene models. most pronounced change...
Since its emergence in December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has developed into a global pandemic within matter of months. While subunit vaccines are one the prominent options for combating disease 2019 (COVID-19), immunogenicity spike protein-based antigens remains unknown. When immunized mice, S1 domain induced much higher IgG and IgA antibody levels than receptor-binding (RBD) more efficiently neutralized SARS-CoV-2 when adjuvanted with alum. It is...