Author: Xun Xu

Downloads per author, site-wide

Preprints

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

• Downloaded 5,809 times
• Download rankings, all-time:
  • Site-wide: 1,511
  • In genomics: 145
• Year to date:
  • Site-wide: 11,785
• Since beginning of last month:
  • Site-wide: 8,647

Large field of view-spatially resolved transcriptomics at nanoscale resolution

• Downloaded 5,059 times
• Download rankings, all-time:
  • Site-wide: 1,819
  • In cell biology: 26
• Year to date:
  • Site-wide: 87
• Since beginning of last month:
  • Site-wide: 236

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

• Downloaded 4,567 times
• Download rankings, all-time:
  • Site-wide: 2,112
  • In genomics: 232
• Year to date:
  • Site-wide: 6,869
• Since beginning of last month:
  • Site-wide: 5,485

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

• Downloaded 4,442 times
• Download rankings, all-time:
  • Site-wide: 2,196
  • In cell biology: 39
• Year to date:
  • Site-wide: 3,725
• Since beginning of last month:
  • Site-wide: 5,005

Construction of the third generation Zea mays haplotype map

• Downloaded 4,255 times
• Download rankings, all-time:
  • Site-wide: 2,332
  • In bioinformatics: 210
• Year to date:
  • Site-wide: 23,505
• Since beginning of last month:
  • Site-wide: 26,610

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

• Downloaded 3,754 times
• Download rankings, all-time:
  • Site-wide: 2,784
  • In genomics: 330
• Year to date:
  • Site-wide: 4,367
• Since beginning of last month:
  • Site-wide: 5,765

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

• Downloaded 2,830 times
• Download rankings, all-time:
  • Site-wide: 4,168
  • In genomics: 483
• Year to date:
  • Site-wide: 13,480
• Since beginning of last month:
  • Site-wide: 11,012

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

• Downloaded 2,507 times
• Download rankings, all-time:
  • Site-wide: 5,002
  • In genomics: 584
• Year to date:
  • Site-wide: 92,274
• Since beginning of last month:
  • Site-wide: 75,190

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

• Downloaded 2,047 times
• Download rankings, all-time:
  • Site-wide: 6,717
  • In cell biology: 142
• Year to date:
  • Site-wide: 11,052
• Since beginning of last month:
  • Site-wide: 10,441

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

• Downloaded 1,902 times
• Download rankings, all-time:
  • Site-wide: 7,488
  • In genomics: 830
• Year to date:
  • Site-wide: 4,812
• Since beginning of last month:
  • Site-wide: 4,399

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

• Downloaded 1,798 times
• Download rankings, all-time:
  • Site-wide: 8,154
  • In microbiology: 454
• Year to date:
  • Site-wide: 17,514
• Since beginning of last month:
  • Site-wide: 15,286

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

• Downloaded 1,755 times
• Download rankings, all-time:
  • Site-wide: 8,462
  • In genomics: 953
• Year to date:
  • Site-wide: 47,911
• Since beginning of last month:
  • Site-wide: 31,152

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

• Downloaded 1,709 times
• Download rankings, all-time:
  • Site-wide: 8,829
  • In pathology: 46
• Year to date:
  • Site-wide: 6,301
• Since beginning of last month:
  • Site-wide: 6,760

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

• Downloaded 1,709 times
• Download rankings, all-time:
  • Site-wide: 8,841
  • In genomics: 990
• Year to date:
  • Site-wide: 37,442
• Since beginning of last month:
  • Site-wide: 27,615

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

• Downloaded 1,531 times
• Download rankings, all-time:
  • Site-wide: 10,388
  • In cell biology: 275
• Year to date:
  • Site-wide: 7,613
• Since beginning of last month:
  • Site-wide: None

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

• Downloaded 1,516 times
• Download rankings, all-time:
  • Site-wide: 10,549
  • In genetic and genomic medicine: 35
• Year to date:
  • Site-wide: 10,005
• Since beginning of last month:
  • Site-wide: 9,222

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

• Downloaded 1,438 times
• Download rankings, all-time:
  • Site-wide: 11,375
  • In developmental biology: 171
• Year to date:
  • Site-wide: 23,553
• Since beginning of last month:
  • Site-wide: 19,962

PIRD: Pan immune repertoire database

• Downloaded 1,416 times
• Download rankings, all-time:
  • Site-wide: 11,637
  • In immunology: 317
• Year to date:
  • Site-wide: 12,253
• Since beginning of last month:
  • Site-wide: 6,846

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

• Downloaded 1,338 times
• Download rankings, all-time:
  • Site-wide: 12,700
  • In evolutionary biology: 475
• Year to date:
  • Site-wide: 11,807
• Since beginning of last month:
  • Site-wide: 9,617

Circularization of genes and chromosome by CRISPR in human cells

• Downloaded 1,282 times
• Download rankings, all-time:
  • Site-wide: 13,542
  • In genomics: 1,470
• Year to date:
  • Site-wide: 57,016
• Since beginning of last month:
  • Site-wide: 47,985

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

• Downloaded 1,228 times
• Download rankings, all-time:
  • Site-wide: 14,456
  • In molecular biology: 404
• Year to date:
  • Site-wide: 9,860
• Since beginning of last month:
  • Site-wide: 9,111

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

• Downloaded 1,213 times
• Download rankings, all-time:
  • Site-wide: 14,712
  • In microbiology: 828
• Year to date:
  • Site-wide: 40,961
• Since beginning of last month:
  • Site-wide: 35,758

The Trans-omics Landscape of COVID-19

• Downloaded 1,176 times
• Download rankings, all-time:
  • Site-wide: 15,407
  • In infectious diseases: 1,407
• Year to date:
  • Site-wide: 19,237
• Since beginning of last month:
  • Site-wide: 20,997

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

• Downloaded 1,159 times
• Download rankings, all-time:
  • Site-wide: 15,758
  • In genomics: 1,670
• Year to date:
  • Site-wide: 30,224
• Since beginning of last month:
  • Site-wide: 21,440

Life history recorded in the vagino-cervical microbiome

• Downloaded 1,145 times
• Download rankings, all-time:
  • Site-wide: 16,070
  • In microbiology: 899
• Year to date:
  • Site-wide: 35,867
• Since beginning of last month:
  • Site-wide: 50,145

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

• Downloaded 1,131 times
• Download rankings, all-time:
  • Site-wide: 16,356
  • In epidemiology: 1,005
• Year to date:
  • Site-wide: 44,165
• Since beginning of last month:
  • Site-wide: 40,186

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

• Downloaded 1,030 times
• Download rankings, all-time:
  • Site-wide: 18,874
  • In microbiology: 1,050
• Year to date:
  • Site-wide: None
• Since beginning of last month:
  • Site-wide: None

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 1,030 times
• Download rankings, all-time:
  • Site-wide: 18,876
  • In systems biology: 390
• Year to date:
  • Site-wide: 24,173
• Since beginning of last month:
  • Site-wide: 33,720

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

• Downloaded 1,028 times
• Download rankings, all-time:
  • Site-wide: 18,920
  • In bioinformatics: 2,289
• Year to date:
  • Site-wide: 29,470
• Since beginning of last month:
  • Site-wide: 18,210

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

• Downloaded 1,022 times
• Download rankings, all-time:
  • Site-wide: 19,073
  • In bioinformatics: 2,308
• Year to date:
  • Site-wide: 12,123
• Since beginning of last month:
  • Site-wide: 13,251

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

• Downloaded 991 times
• Download rankings, all-time:
  • Site-wide: 19,904
  • In infectious diseases: 1,585
• Year to date:
  • Site-wide: 27,422
• Since beginning of last month:
  • Site-wide: 28,488

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

• Downloaded 984 times
• Download rankings, all-time:
  • Site-wide: 20,098
  • In neuroscience: 2,580
• Year to date:
  • Site-wide: 8,005
• Since beginning of last month:
  • Site-wide: 9,418

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

• Downloaded 934 times
• Download rankings, all-time:
  • Site-wide: 21,652
  • In genomics: 2,162
• Year to date:
  • Site-wide: 26,132
• Since beginning of last month:
  • Site-wide: 25,508

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

• Downloaded 858 times
• Download rankings, all-time:
  • Site-wide: 24,497
  • In microbiology: 1,408
• Year to date:
  • Site-wide: 78,402
• Since beginning of last month:
  • Site-wide: 95,106

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

• Downloaded 844 times
• Download rankings, all-time:
  • Site-wide: 25,069
  • In genetics: 1,241
• Year to date:
  • Site-wide: 25,830
• Since beginning of last month:
  • Site-wide: 21,733

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

• Downloaded 838 times
• Download rankings, all-time:
  • Site-wide: 25,299
  • In microbiology: 1,463
• Year to date:
  • Site-wide: 30,264
• Since beginning of last month:
  • Site-wide: 52,151

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

• Downloaded 829 times
• Download rankings, all-time:
  • Site-wide: 25,706
  • In bioinformatics: 3,043
• Year to date:
  • Site-wide: 16,915
• Since beginning of last month:
  • Site-wide: 13,227

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

• Downloaded 816 times
• Download rankings, all-time:
  • Site-wide: 26,247
  • In genomics: 2,485
• Year to date:
  • Site-wide: 46,874
• Since beginning of last month:
  • Site-wide: 41,139

Three genomes of Osteoglossidae shed light on ancient teleost evolution

• Downloaded 814 times
• Download rankings, all-time:
  • Site-wide: 26,367
  • In genomics: 2,490
• Year to date:
  • Site-wide: 71,770
• Since beginning of last month:
  • Site-wide: 54,019

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

• Downloaded 774 times
• Download rankings, all-time:
  • Site-wide: 28,246
  • In synthetic biology: 364
• Year to date:
  • Site-wide: 24,509
• Since beginning of last month:
  • Site-wide: 14,066

Age-dependent sexual dimorphism in the adult human gut microbiota

• Downloaded 751 times
• Download rankings, all-time:
  • Site-wide: 29,484
  • In genomics: 2,707
• Year to date:
  • Site-wide: 60,510
• Since beginning of last month:
  • Site-wide: 32,013

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

• Downloaded 740 times
• Download rankings, all-time:
  • Site-wide: 30,075
  • In genomics: 2,743
• Year to date:
  • Site-wide: 50,439
• Since beginning of last month:
  • Site-wide: 40,568

Intratumor Heterogeneity and Evolution of Colorectal Cancer

• Downloaded 729 times
• Download rankings, all-time:
  • Site-wide: 30,702
  • In genetics: 1,526
• Year to date:
  • Site-wide: 22,658
• Since beginning of last month:
  • Site-wide: 21,486

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

• Downloaded 705 times
• Download rankings, all-time:
  • Site-wide: 32,142
  • In genomics: 2,881
• Year to date:
  • Site-wide: 111,860
• Since beginning of last month:
  • Site-wide: 82,490

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

• Downloaded 704 times
• Download rankings, all-time:
  • Site-wide: 32,221
  • In bioinformatics: 3,655
• Year to date:
  • Site-wide: 27,315
• Since beginning of last month:
  • Site-wide: 20,227

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

• Downloaded 668 times
• Download rankings, all-time:
  • Site-wide: 34,574
  • In bioinformatics: 3,880
• Year to date:
  • Site-wide: 38,525
• Since beginning of last month:
  • Site-wide: 31,550

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

• Downloaded 644 times
• Download rankings, all-time:
  • Site-wide: 36,283
  • In genetics: 1,779
• Year to date:
  • Site-wide: 30,883
• Since beginning of last month:
  • Site-wide: None

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

• Downloaded 641 times
• Download rankings, all-time:
  • Site-wide: 36,546
  • In molecular biology: 1,030
• Year to date:
  • Site-wide: 50,598
• Since beginning of last month:
  • Site-wide: 42,571

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

• Downloaded 633 times
• Download rankings, all-time:
  • Site-wide: 37,104
  • In epidemiology: 1,773
• Year to date:
  • Site-wide: 25,400
• Since beginning of last month:
  • Site-wide: 26,361

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

• Downloaded 632 times
• Download rankings, all-time:
  • Site-wide: 37,202
  • In genomics: 3,200
• Year to date:
  • Site-wide: 53,078
• Since beginning of last month:
  • Site-wide: 41,394

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

• Downloaded 616 times
• Download rankings, all-time:
  • Site-wide: 38,454
  • In genomics: 3,271
• Year to date:
  • Site-wide: 77,087
• Since beginning of last month:
  • Site-wide: 79,165

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

• Downloaded 599 times
• Download rankings, all-time:
  • Site-wide: 39,803
  • In genetics: 1,930
• Year to date:
  • Site-wide: 27,551
• Since beginning of last month:
  • Site-wide: 16,755

De novo assembly of the Mongolian gerbil genome and transcriptome

• Downloaded 577 times
• Download rankings, all-time:
  • Site-wide: 41,734
  • In genomics: 3,447
• Year to date:
  • Site-wide: 100,764
• Since beginning of last month:
  • Site-wide: None

Single cell chromatin accessibility of the developmental cephalochordate

• Downloaded 571 times
• Download rankings, all-time:
  • Site-wide: 42,227
  • In developmental biology: 987
• Year to date:
  • Site-wide: 49,776
• Since beginning of last month:
  • Site-wide: 39,819

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

• Downloaded 560 times
• Download rankings, all-time:
  • Site-wide: 43,332
  • In genetics: 2,090
• Year to date:
  • Site-wide: 68,724
• Since beginning of last month:
  • Site-wide: 64,675

Single cell atlas of trisomy 21 cerebral cortex

• Downloaded 484 times
• Download rankings, all-time:
  • Site-wide: 51,486
  • In neuroscience: 7,678
• Year to date:
  • Site-wide: 76,330
• Since beginning of last month:
  • Site-wide: 78,046

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

• Downloaded 456 times
• Download rankings, all-time:
  • Site-wide: 54,968
  • In immunology: 1,490
• Year to date:
  • Site-wide: 74,381
• Since beginning of last month:
  • Site-wide: 50,016

The female urinary microbiota in relation to the reproductive tract microbiota

• Downloaded 454 times
• Download rankings, all-time:
  • Site-wide: 55,269
  • In microbiology: 3,590
• Year to date:
  • Site-wide: 38,945
• Since beginning of last month:
  • Site-wide: 35,525

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

• Downloaded 446 times
• Download rankings, all-time:
  • Site-wide: 56,383
  • In genomics: 4,281
• Year to date:
  • Site-wide: 57,705
• Since beginning of last month:
  • Site-wide: 37,284

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

• Downloaded 416 times
• Download rankings, all-time:
  • Site-wide: 60,628
  • In molecular biology: 1,744
• Year to date:
  • Site-wide: 62,551
• Since beginning of last month:
  • Site-wide: 49,537

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

• Downloaded 380 times
• Download rankings, all-time:
  • Site-wide: 66,077
  • In microbiology: 4,454
• Year to date:
  • Site-wide: 94,448
• Since beginning of last month:
  • Site-wide: 50,851

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

• Downloaded 354 times
• Download rankings, all-time:
  • Site-wide: 70,504
  • In genomics: 4,905
• Year to date:
  • Site-wide: 50,670
• Since beginning of last month:
  • Site-wide: 43,203

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

• Downloaded 351 times
• Download rankings, all-time:
  • Site-wide: 70,894
  • In genetics: 3,313
• Year to date:
  • Site-wide: 91,178
• Since beginning of last month:
  • Site-wide: 79,349

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

• Downloaded 320 times
• Download rankings, all-time:
  • Site-wide: 76,471
  • In genetics: 3,549
• Year to date:
  • Site-wide: 113,278
• Since beginning of last month:
  • Site-wide: None

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

• Downloaded 315 times
• Download rankings, all-time:
  • Site-wide: 77,524
  • In genomics: 5,178
• Year to date:
  • Site-wide: 97,520
• Since beginning of last month:
  • Site-wide: 92,606

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

• Downloaded 315 times
• Download rankings, all-time:
  • Site-wide: 77,465
  • In genomics: 5,181
• Year to date:
  • Site-wide: 102,599
• Since beginning of last month:
  • Site-wide: 97,066

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

• Downloaded 313 times
• Download rankings, all-time:
  • Site-wide: 78,007
  • In immunology: 2,116
• Year to date:
  • Site-wide: 73,721
• Since beginning of last month:
  • Site-wide: 79,178

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

• Downloaded 305 times
• Download rankings, all-time:
  • Site-wide: 79,482
  • In genetics: 3,674
• Year to date:
  • Site-wide: 20,423
• Since beginning of last month:
  • Site-wide: 26,374

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

• Downloaded 249 times
• Download rankings, all-time:
  • Site-wide: 91,194
  • In bioinformatics: 8,048
• Year to date:
  • Site-wide: 31,090
• Since beginning of last month:
  • Site-wide: 32,354

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

• Downloaded 247 times
• Download rankings, all-time:
  • Site-wide: 91,601
  • In genomics: 5,695
• Year to date:
  • Site-wide: 108,767
• Since beginning of last month:
  • Site-wide: 65,500

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

• Downloaded 227 times
• Download rankings, all-time:
  • Site-wide: 95,886
  • In genetic and genomic medicine: 357
• Year to date:
  • Site-wide: 82,769
• Since beginning of last month:
  • Site-wide: 68,605

CNSA: a data repository for archiving omics data

• Downloaded 217 times
• Download rankings, all-time:
  • Site-wide: 98,047
  • In genomics: 5,907
• Year to date:
  • Site-wide: 46,268
• Since beginning of last month:
  • Site-wide: 72,972

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

• Downloaded 210 times
• Download rankings, all-time:
  • Site-wide: 99,530
  • In cancer biology: 3,039
• Year to date:
  • Site-wide: 40,568
• Since beginning of last month:
  • Site-wide: 69,505

Personalized vagino-cervical microbiome dynamics after oral probiotics

• Downloaded 160 times
• Download rankings, all-time:
  • Site-wide: 109,899
  • In microbiology: 8,291
• Year to date:
  • Site-wide: 66,365
• Since beginning of last month:
  • Site-wide: 89,144

Landscapes and dynamic diversifications of B-cell receptor repertoires in COVID-19 patients

• Downloaded 142 times
• Download rankings, all-time:
  • Site-wide: 113,510
  • In immunology: 3,175
• Year to date:
  • Site-wide: 9,417
• Since beginning of last month:
  • Site-wide: None

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

• Downloaded 112 times
• Download rankings, all-time:
  • Site-wide: 118,983
  • In evolutionary biology: 6,156
• Year to date:
  • Site-wide: 101,916
• Since beginning of last month:
  • Site-wide: 100,557

Sequencing of clinical samples reveals that adaptation keeps establishing during H7N9 virus infection in humans

• Downloaded 76 times
• Download rankings, all-time:
  • Site-wide: 124,631
  • In microbiology: 9,668
• Year to date:
  • Site-wide: 21,766
• Since beginning of last month:
  • Site-wide: 90,977