Author: Xun Xu

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Preprints

Efficient long single molecule sequencing for cost effective and accurate sequencing, haplotyping, and de novo assembly

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A portable and cost-effective microfluidic system for massively parallel single-cell transcriptome profiling

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Construction of the third generation Zea mays haplotype map

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Single-cell atlas of a non-human primate reveals new pathogenic mechanisms of COVID-19

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CoolMPS™: Advanced massively parallel sequencing using antibodies specific to each natural nucleobase

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Multiple approaches for massively parallel sequencing of HCoV-19 (SARS-CoV-2) genomes directly from clinical samples

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Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity

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Single-cell screening of SARS-CoV-2 target cells in pets, livestock, poultry and wildlife

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Single-cell Transcriptomic Landscape of Nucleated Cells in Umbilical Cord Blood

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A multi-omic cohort as a reference point for promoting a healthy human gut microbiome

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Reliable Multiplex Sequencing with Rare Index Mis-Assignment on DNB-Based NGS Platform

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Advanced Whole Genome Sequencing Using an Entirely PCR-free Massively Parallel Sequencing Workflow

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Single-Cell Analysis Reveals Macrophage-Driven T Cell Dysfunction in Severe COVID-19 Patients

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  • In pathology: 49 out of 699
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Single-cell RNA-seq reveals dynamic transcriptome profiling in human early neural differentiation

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Integrated profiling of single cell epigenomic and transcriptomic landscape of Parkinson's disease mouse brain

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PIRD: Pan immune repertoire database

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  • In immunology: 292 out of 3,339
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Initial Study of Human Genetic Contribution to COVID-19 Severity and Susceptibility

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  • In genetic and genomic medicine: 29 out of 493
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Circularization of genes and chromosome by CRISPR in human cells

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Recent origin of an XX/XY sex-determination system in the ancient plant lineage Ginkgo biloba

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A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment

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3′ Branch Ligation: A Novel Method to Ligate Non-Complementary DNA to Recessed or Internal 3′ OH Ends in DNA or RNA

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Life history recorded in the vagino-cervical microbiome

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Initial data release and announcement of the Fish10K: Fish 10,000 Genomes Project

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Effect of large-scale testing platform in prevention and control of the COVID-19 pandemic: an empirical study with a novel numerical model

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The Trans-omics Landscape of COVID-19

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Over 50000 metagenomically assembled draft genomes for the human oral microbiome reveal new taxa

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Massively parallel quantification of CRISPR editing in cells by TRAP-seq enables better design of Cas9, ABE, CBE gRNAs of high efficiency and accuracy

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LFMD: detecting low-frequency mutations in high-depth genome sequencing data without molecular tags

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Characterization of Microbial Co-infections in the Respiratory Tract of hospitalized COVID-19 patients

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TGS-GapCloser: fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads

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Intra-host Variation and Evolutionary Dynamics of SARS-CoV-2 Population in COVID-19 Patients

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Integration of gut microbiome, host biomarkers, and urine metabolome data reveals networks of interactions associated with distinct clinical phenotypes

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Three genomes of Osteoglossidae shed light on ancient teleost evolution

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Development of Coupling Controlled Polymerizations by Adapter-ligation in Mate-pair Sequencing for Detection of Various Genomic Variants in One Single Assay

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Identification of gut microbiome markers for schizophrenia delineates a potential role of Streptococcus

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Enhance genome editing efficiency and specificity by a quick CRISPR/Cas9 system

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Single-cell regulatory landscape and disease vulnerability map of adult Macaque cortex

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Age-dependent sexual dimorphism in the adult human gut microbiota

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Single cell atlas of domestic pig brain illuminates the conservation and divergence of cell types at spatial and species levels

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A chromosome-level genome of black rockfish, Sebastes schlegelii, provides insights into the evolution of live birth

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Towards Practical and Robust DNA-based Data Archiving by Codec System Named ‘Yin-Yang’

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Draft genome sequence of the Solanum aethiopicum provides insights into disease resistance, drought tolerance and the evolution of the genome

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Haplotype-Resolved Assembly for Synthetic Long Reads Using a Trio-Binning Strategy

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SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme

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Dynamic chromosome rearrangements of the white-spotted bamboo shark shed light on cartilaginous fish diversification mechanisms

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Sequencing of Panax notoginseng genome reveals genes involved in disease resistance and ginsenoside biosynthesis

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Intratumor Heterogeneity and Evolution of Colorectal Cancer

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PALM-Seq: simultaneous sequencing of cell-free long RNA and small RNA

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Population Bottlenecks and Intra-host Evolution during Human-to-Human Transmission of SARS-CoV-2Population Bottlenecks and Intra-host Evolution during Human-to-Human Transmission of SARS-CoV-2

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De novo assembly of the Mongolian gerbil genome and transcriptome

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Time-series plasma cell-free DNA analysis reveals disease severity of COVID-19 patients

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Nationwide population genetic screening improves outcomes of newborn screening for hearing loss in China

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Single cell chromatin accessibility of the developmental cephalochordate

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M-GWAS for the gut microbiome in Chinese adults illuminates on complex diseases

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Integrated multi-omics analysis to study the effects of simulated weightlessness on rhesus macaques (Macaca mulatta)

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Single cell atlas of trisomy 21 cerebral cortex

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Genomic analyses reveal the origin of domestic ducks and identify different genetic underpinnings of wild ducks

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DNB-Based On-Chip Motif Finding (DocMF): a High-Throughput Method to Profile Different Types of Protein-DNA Interactions

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The female urinary microbiota in relation to the reproductive tract microbiota

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Distinct gut metagenomics and metaproteomics signatures in prediabetics and treatment-naïve type 2 diabetics

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Sequencing of the MHC region defines HLA-DQA1 as the major independent risk for anti-citrullinated protein antibodies (ACPA)-positive rheumatoid arthritis in Han population

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New genetic variants associated with major adverse cardiovascular events in patients with acute coronary syndromes and treated with clopidogrel and aspirin

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Sequencing and comparative analysis of three Chlorella genomes provide insights into strain-specific adaptation to wastewater

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Complete chloroplast genomes of 14 mangroves: phylogenetic and genomic comparative analyses

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Slicing the genome of star-fruit (Averrhoa carambola L.)

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Recovered and dead outcome patients caused by influenza A (H7N9) virus infection show different pro-inflammatory cytokine dynamics during disease progress and its application in real-time prognosis

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Draft Genomes of two Artocarpus plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis)

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Inter-determination of blood metabolite levels and gut microbiome supported by Mendelian randomization

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stLFRsv: a germline SV analysis pipeline using co-barcoded reads

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Genome sequencing combining prenatal ultrasound in the evaluation of fetal CNS structural anomalies

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CNSA: a data repository for archiving omics data

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Comparative analysis of clonal evolution among patients with right-sided colon cancer, left-sided colon cancer and rectal cancer

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Personalized vagino-cervical microbiome dynamics after oral probiotics

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Independent domestications shape the genetic pattern of a reproductive isolation system in rice

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