Author: Xun Xu

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Preprints

Plasma cell-free DNA promise disease monitoring and tissue injury assessment of COVID-19

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Metagenome-genome-wide association studies reveal human genetic impact on the oral microbiome

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Large field of view-spatially resolved transcriptomics at nanoscale resolution

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  • Site-wide: 1,200
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  • Site-wide: 215
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  • Site-wide: 512

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

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  • Site-wide: 1,800
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  • Site-wide: 18,252
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  • Site-wide: 23,099

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

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  • Site-wide: 2,327
  • In cell biology: 37
• Year to date:
  • Site-wide: 4,347
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  • Site-wide: 6,754

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

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  • Site-wide: 2,370
  • In genomics: 235
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  • Site-wide: 8,124
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  • Site-wide: 9,618

Construction of the third generation Zea mays haplotype map

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  • Site-wide: 2,786
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  • Site-wide: 41,930
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  • Site-wide: 66,270

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

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  • Site-wide: 3,032
  • In genomics: 318
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  • Site-wide: 6,634
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  • Site-wide: 7,049

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

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  • Site-wide: 4,876
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  • Site-wide: 29,446
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  • Site-wide: 50,661

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

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  • Site-wide: 5,995
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  • Site-wide: 107,291
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  • Site-wide: 72,154

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

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  • Site-wide: 6,620
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  • Site-wide: 4,902
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  • Site-wide: 10,301

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

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  • Site-wide: 7,307
  • In cell biology: 159
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  • Site-wide: 17,103
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  • Site-wide: 19,698

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

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  • Site-wide: 8,066
  • In pathology: 45
• Year to date:
  • Site-wide: 7,046
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  • Site-wide: 9,229

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

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  • Site-wide: 9,093
  • In microbiology: 535
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  • Site-wide: 29,132
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  • Site-wide: 37,063

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

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  • Site-wide: 9,314
  • In cell biology: 222
• Year to date:
  • Site-wide: 7,730
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  • Site-wide: 19,909

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

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  • In genomics: 1,008
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Reliable Multiplex Sequencing with Rare Index Mis-Assignment on DNB-Based NGS Platform

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  • Site-wide: 10,142
  • In genomics: 1,058
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  • Site-wide: 67,724

Initial Study of Human Genetic Contribution to COVID-19 Severity and Susceptibility

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  • Site-wide: 10,870
  • In genetic and genomic medicine: 44
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  • Site-wide: 16,035
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  • Site-wide: 27,092

PIRD: Pan immune repertoire database

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  • Site-wide: 11,819
  • In immunology: 372
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  • Site-wide: 16,954
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  • Site-wide: 18,312

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

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  • Site-wide: 12,333
  • In evolutionary biology: 398
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  • Site-wide: 14,729
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  • Site-wide: 18,934

Single-cell RNA-seq reveals dynamic transcriptome profiling in human early neural differentiation

• Downloaded 1,547 times
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  • Site-wide: 12,396
  • In developmental biology: 180
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  • Site-wide: 34,298
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  • Site-wide: 43,637

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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  • Site-wide: 13,760
  • In molecular biology: 376
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  • Site-wide: 13,604
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  • Site-wide: 7,815

The Trans-omics Landscape of COVID-19

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  • Site-wide: 14,977
  • In infectious diseases: 1,627
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  • Site-wide: 19,349
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  • Site-wide: 19,641

Circularization of genes and chromosome by CRISPR in human cells

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  • Site-wide: 15,556
  • In genomics: 1,570
• Year to date:
  • Site-wide: 74,584
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  • Site-wide: 67,951

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

• Downloaded 1,260 times
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  • Site-wide: 16,921
  • In genomics: 1,671
• Year to date:
  • Site-wide: 39,229
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  • Site-wide: 24,274

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

• Downloaded 1,233 times
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  • Site-wide: 17,471
  • In microbiology: 1,014
• Year to date:
  • Site-wide: 95,430
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  • Site-wide: 146,975

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

• Downloaded 1,222 times
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  • Site-wide: 17,690
  • In infectious diseases: 1,765
• Year to date:
  • Site-wide: 17,357
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  • Site-wide: 17,269

Life history recorded in the vagino-cervical microbiome

• Downloaded 1,220 times
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  • Site-wide: 17,743
  • In microbiology: 1,026
• Year to date:
  • Site-wide: 51,284
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  • Site-wide: 39,198

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

• Downloaded 1,218 times
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  • Site-wide: 17,799
  • In bioinformatics: 2,069
• Year to date:
  • Site-wide: 16,171
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  • Site-wide: 88,529

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

• Downloaded 1,209 times
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  • Site-wide: 17,989
  • In microbiology: 1,047
• Year to date:
  • Site-wide: 30,370
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  • Site-wide: 33,717

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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  • Site-wide: 18,068
  • In epidemiology: 1,144
• Year to date:
  • Site-wide: 55,112
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  • Site-wide: 44,945

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

• Downloaded 1,148 times
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  • Site-wide: 19,433
  • In systems biology: 378
• Year to date:
  • Site-wide: 32,271
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  • Site-wide: 30,811

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

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  • Site-wide: 19,759
  • In neuroscience: 2,436
• Year to date:
  • Site-wide: 16,843
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  • Site-wide: 27,224

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

• Downloaded 1,105 times
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  • Site-wide: 20,546
  • In bioinformatics: 2,382
• Year to date:
  • Site-wide: 47,330
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  • Site-wide: 57,074

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

• Downloaded 1,006 times
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  • Site-wide: 23,550
  • In genomics: 2,239
• Year to date:
  • Site-wide: 47,012
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  • Site-wide: 41,458

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

• Downloaded 991 times
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  • Site-wide: 24,125
  • In bioinformatics: 2,780
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  • Site-wide: 21,700
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  • Site-wide: 28,629

Towards Practical and Robust DNA-based Data Archiving Using "Yin-Yang Codec" System

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  • Site-wide: 24,209
  • In synthetic biology: 305
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  • Site-wide: 18,430
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  • Site-wide: 14,568

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

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  • Site-wide: 25,112
  • In genetics: 1,162
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  • Site-wide: 32,551
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  • Site-wide: 43,737

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

• Downloaded 943 times
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  • Site-wide: 25,899
  • In microbiology: 1,517
• Year to date:
  • Site-wide: 38,006
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  • Site-wide: 32,205

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

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  • Site-wide: 26,524
  • In microbiology: 1,562
• Year to date:
  • Site-wide: 65,668
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  • Site-wide: 57,753

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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  • Site-wide: 27,325
  • In genomics: 2,495
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  • Site-wide: 43,780

Three genomes of Osteoglossidae shed light on ancient teleost evolution

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  • Site-wide: 28,993
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  • Site-wide: 47,667

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

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  • Site-wide: 30,804
  • In bioinformatics: 3,443
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  • Site-wide: 25,990

Intratumor Heterogeneity and Evolution of Colorectal Cancer

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  • Site-wide: 31,701
  • In genetics: 1,477
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  • Site-wide: 31,320

Age-dependent sexual dimorphism in the adult human gut microbiota

• Downloaded 790 times
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  • Site-wide: 33,172
  • In genomics: 2,872
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  • Site-wide: 85,826
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  • Site-wide: 112,990

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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  • Site-wide: 34,626
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  • Site-wide: 46,866

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

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  • Site-wide: 34,985
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  • Site-wide: 102,684
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  • Site-wide: 101,517

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

• Downloaded 738 times
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  • Site-wide: 36,442
  • In bioinformatics: 3,979
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  • Site-wide: 88,282

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

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  • Site-wide: 36,945
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  • Site-wide: 120,980
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  • Site-wide: 138,192

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

• Downloaded 729 times
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  • Site-wide: 37,048
  • In epidemiology: 1,861
• Year to date:
  • Site-wide: 38,319
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  • Site-wide: 59,500

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

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  • Site-wide: 38,488
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Sequencing of Panax notoginseng genome reveals genes involved in disease resistance and ginsenoside biosynthesis

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  • Site-wide: 41,274
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  • Site-wide: 57,461

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

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  • Site-wide: 42,201
  • In genetics: 1,924
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  • Site-wide: 51,867
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  • Site-wide: 37,103

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

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  • Site-wide: 42,446
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  • Site-wide: 101,170

Single cell chromatin accessibility of the developmental cephalochordate

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  • Site-wide: 42,637
  • In developmental biology: 938
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De novo assembly of the Mongolian gerbil genome and transcriptome

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  • Site-wide: 46,421
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  • Site-wide: 99,582
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  • Site-wide: 97,061

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

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  • Site-wide: 48,395
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  • Site-wide: 79,297

Single cell atlas of trisomy 21 cerebral cortex

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  • Site-wide: 50,994
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  • Site-wide: 33,720

The female urinary microbiota in relation to the reproductive tract microbiota

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  • Site-wide: 54,935
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  • Site-wide: 49,893
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Genomic analyses reveal the origin of domestic ducks and identify different genetic underpinnings of wild ducks

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  • Site-wide: 56,100
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  • Site-wide: 55,669

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

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  • Site-wide: 61,777
  • In immunology: 1,832
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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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  • Site-wide: 90,005

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

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

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  • Site-wide: 76,792
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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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  • Site-wide: 77,868
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  • Site-wide: 102,719

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

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  • Site-wide: 42,670

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

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  • Site-wide: 88,921
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  • Site-wide: 121,593

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

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  • Site-wide: 97,742
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Landscapes and dynamic diversifications of B-cell receptor repertoires in COVID-19 patients

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  • Site-wide: 99,356
  • In immunology: 2,921
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Draft Genomes of two Artocarpus plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis)

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  • In genomics: 6,089
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CNSA: a data repository for archiving omics data

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

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Genomic epidemiology of SARS-CoV-2 in the United Arab Emirates reveals novel virus mutation, patterns of co-infection and tissue specific host innate immune response

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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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  • In cancer biology: 3,358
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A Chinese host genetic study discovered type I interferons and causality of cholesterol levels and WBC counts on COVID-19 severity

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  • In genetic and genomic medicine: 619
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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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Sequencing of clinical samples reveals that adaptation keeps establishing during H7N9 virus infection in humans

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