Author: Xun Xu

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Preprints

Large field of view-spatially resolved transcriptomics at nanoscale resolution

• Downloaded 6,686 times
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  • Site-wide: 1,369
  • In cell biology: 17
• Year to date:
  • Site-wide: 144
• Since beginning of last month:
  • Site-wide: 412

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

• Downloaded 5,892 times
• Download rankings, all-time:
  • Site-wide: 1,645
  • In genomics: 147
• Year to date:
  • Site-wide: 16,318
• Since beginning of last month:
  • Site-wide: 15,766

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

• Downloaded 4,717 times
• Download rankings, all-time:
  • Site-wide: 2,238
  • In cell biology: 38
• Year to date:
  • Site-wide: 3,785
• Since beginning of last month:
  • Site-wide: 2,875

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

• Downloaded 4,716 times
• Download rankings, all-time:
  • Site-wide: 2,239
  • In genomics: 234
• Year to date:
  • Site-wide: 8,303
• Since beginning of last month:
  • Site-wide: 7,422

Construction of the third generation Zea mays haplotype map

• Downloaded 4,298 times
• Download rankings, all-time:
  • Site-wide: 2,543
  • In bioinformatics: 222
• Year to date:
  • Site-wide: 34,000
• Since beginning of last month:
  • Site-wide: 56,285

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

• Downloaded 3,877 times
• Download rankings, all-time:
  • Site-wide: 2,956
  • In genomics: 329
• Year to date:
  • Site-wide: 7,183
• Since beginning of last month:
  • Site-wide: 14,492

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

• Downloaded 2,879 times
• Download rankings, all-time:
  • Site-wide: 4,505
  • In genomics: 503
• Year to date:
  • Site-wide: 23,264
• Since beginning of last month:
  • Site-wide: 34,897

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

• Downloaded 2,521 times
• Download rankings, all-time:
  • Site-wide: 5,466
  • In genomics: 608
• Year to date:
  • Site-wide: 100,160
• Since beginning of last month:
  • Site-wide: 88,553

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

• Downloaded 2,192 times
• Download rankings, all-time:
  • Site-wide: 6,718
  • In genomics: 737
• Year to date:
  • Site-wide: 4,062
• Since beginning of last month:
  • Site-wide: 2,160

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

• Downloaded 2,130 times
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  • Site-wide: 7,025
  • In cell biology: 155
• Year to date:
  • Site-wide: 15,717
• Since beginning of last month:
  • Site-wide: 20,621

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

• Downloaded 1,908 times
• Download rankings, all-time:
  • Site-wide: 8,242
  • In pathology: 43
• Year to date:
  • Site-wide: 6,386
• Since beginning of last month:
  • Site-wide: 6,530

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

• Downloaded 1,866 times
• Download rankings, all-time:
  • Site-wide: 8,544
  • In microbiology: 490
• Year to date:
  • Site-wide: 22,859
• Since beginning of last month:
  • Site-wide: 23,071

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

• Downloaded 1,796 times
• Download rankings, all-time:
  • Site-wide: 9,036
  • In genomics: 975
• Year to date:
  • Site-wide: 47,840
• Since beginning of last month:
  • Site-wide: 38,683

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

• Downloaded 1,776 times
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  • Site-wide: 9,204
  • In cell biology: 225
• Year to date:
  • Site-wide: 5,755
• Since beginning of last month:
  • Site-wide: 8,182

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

• Downloaded 1,731 times
• Download rankings, all-time:
  • Site-wide: 9,578
  • In genomics: 1,035
• Year to date:
  • Site-wide: 56,440
• Since beginning of last month:
  • Site-wide: 80,247

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

• Downloaded 1,620 times
• Download rankings, all-time:
  • Site-wide: 10,535
  • In genetic and genomic medicine: 39
• Year to date:
  • Site-wide: 12,943
• Since beginning of last month:
  • Site-wide: 15,569

PIRD: Pan immune repertoire database

• Downloaded 1,508 times
• Download rankings, all-time:
  • Site-wide: 11,648
  • In immunology: 334
• Year to date:
  • Site-wide: 15,641
• Since beginning of last month:
  • Site-wide: 11,638

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

• Downloaded 1,493 times
• Download rankings, all-time:
  • Site-wide: 11,843
  • In developmental biology: 174
• Year to date:
  • Site-wide: 30,050
• Since beginning of last month:
  • Site-wide: 32,881

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

• Downloaded 1,458 times
• Download rankings, all-time:
  • Site-wide: 12,281
  • In evolutionary biology: 419
• Year to date:
  • Site-wide: 12,793
• Since beginning of last month:
  • Site-wide: 17,241

Circularization of genes and chromosome by CRISPR in human cells

• Downloaded 1,302 times
• Download rankings, all-time:
  • Site-wide: 14,596
  • In genomics: 1,528
• Year to date:
  • Site-wide: 70,424
• Since beginning of last month:
  • Site-wide: 89,423

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

• Downloaded 1,289 times
• Download rankings, all-time:
  • Site-wide: 14,832
  • In molecular biology: 406
• Year to date:
  • Site-wide: 17,246
• Since beginning of last month:
  • Site-wide: 33,049

The Trans-omics Landscape of COVID-19

• Downloaded 1,283 times
• Download rankings, all-time:
  • Site-wide: 14,937
  • In infectious diseases: 1,500
• Year to date:
  • Site-wide: 17,436
• Since beginning of last month:
  • Site-wide: 13,319

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

• Downloaded 1,226 times
• Download rankings, all-time:
  • Site-wide: 15,993
  • In microbiology: 924
• Year to date:
  • Site-wide: 68,408
• Since beginning of last month:
  • Site-wide: 89,969

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

• Downloaded 1,200 times
• Download rankings, all-time:
  • Site-wide: 16,538
  • In genomics: 1,681
• Year to date:
  • Site-wide: 39,378
• Since beginning of last month:
  • Site-wide: 32,049

Life history recorded in the vagino-cervical microbiome

• Downloaded 1,182 times
• Download rankings, all-time:
  • Site-wide: 16,892
  • In microbiology: 966
• Year to date:
  • Site-wide: 44,917
• Since beginning of last month:
  • Site-wide: 38,585

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

• Downloaded 1,166 times
• Download rankings, all-time:
  • Site-wide: 17,234
  • In epidemiology: 1,078
• Year to date:
  • Site-wide: 50,812
• Since beginning of last month:
  • Site-wide: 39,895

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

• Downloaded 1,145 times
• Download rankings, all-time:
  • Site-wide: 17,680
  • In microbiology: 1,003
• Year to date:
  • Site-wide: 28,077
• Since beginning of last month:
  • Site-wide: 35,265

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

• Downloaded 1,140 times
• Download rankings, all-time:
  • Site-wide: 17,772
  • In bioinformatics: 2,118
• Year to date:
  • Site-wide: 13,147
• Since beginning of last month:
  • Site-wide: 18,574

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

• Downloaded 1,111 times
• Download rankings, all-time:
  • Site-wide: 18,514
  • In infectious diseases: 1,676
• Year to date:
  • Site-wide: 18,129
• Since beginning of last month:
  • Site-wide: 21,514

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 1,092 times
• Download rankings, all-time:
  • Site-wide: 18,987
  • In systems biology: 380
• Year to date:
  • Site-wide: 28,505
• Since beginning of last month:
  • Site-wide: 23,693

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

• Downloaded 1,063 times
• Download rankings, all-time:
  • Site-wide: 19,742
  • In bioinformatics: 2,334
• Year to date:
  • Site-wide: 41,689
• Since beginning of last month:
  • Site-wide: 38,035

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

• Downloaded 1,062 times
• Download rankings, all-time:
  • Site-wide: 19,756
  • In neuroscience: 2,478
• Year to date:
  • Site-wide: 13,403
• Since beginning of last month:
  • Site-wide: 21,231

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

• Downloaded 974 times
• Download rankings, all-time:
  • Site-wide: 22,395
  • In genomics: 2,181
• Year to date:
  • Site-wide: 37,226
• Since beginning of last month:
  • Site-wide: 60,860

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

• Downloaded 922 times
• Download rankings, all-time:
  • Site-wide: 24,307
  • In genetics: 1,167
• Year to date:
  • Site-wide: 25,074
• Since beginning of last month:
  • Site-wide: 20,820

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

• Downloaded 918 times
• Download rankings, all-time:
  • Site-wide: 24,459
  • In bioinformatics: 2,861
• Year to date:
  • Site-wide: 18,828
• Since beginning of last month:
  • Site-wide: 13,402

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

• Downloaded 882 times
• Download rankings, all-time:
  • Site-wide: 25,851
  • In microbiology: 1,505
• Year to date:
  • Site-wide: 74,490
• Since beginning of last month:
  • Site-wide: 82,602

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

• Downloaded 874 times
• Download rankings, all-time:
  • Site-wide: 26,161
  • In microbiology: 1,527
• Year to date:
  • Site-wide: 41,895
• Since beginning of last month:
  • Site-wide: 74,422

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

• Downloaded 874 times
• Download rankings, all-time:
  • Site-wide: 26,160
  • In synthetic biology: 343
• Year to date:
  • Site-wide: 20,486
• Since beginning of last month:
  • Site-wide: 7,976

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

• Downloaded 850 times
• Download rankings, all-time:
  • Site-wide: 27,206
  • In genomics: 2,522
• Year to date:
  • Site-wide: 52,021
• Since beginning of last month:
  • Site-wide: 35,756

Three genomes of Osteoglossidae shed light on ancient teleost evolution

• Downloaded 834 times
• Download rankings, all-time:
  • Site-wide: 27,923
  • In genomics: 2,569
• Year to date:
  • Site-wide: 79,796
• Since beginning of last month:
  • Site-wide: 58,762

Age-dependent sexual dimorphism in the adult human gut microbiota

• Downloaded 775 times
• Download rankings, all-time:
  • Site-wide: 30,992
  • In genomics: 2,778
• Year to date:
  • Site-wide: 68,558
• Since beginning of last month:
  • Site-wide: 33,377

Intratumor Heterogeneity and Evolution of Colorectal Cancer

• Downloaded 760 times
• Download rankings, all-time:
  • Site-wide: 31,865
  • In genetics: 1,525
• Year to date:
  • Site-wide: 37,914
• Since beginning of last month:
  • Site-wide: 44,409

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

• Downloaded 747 times
• Download rankings, all-time:
  • Site-wide: 32,600
  • In genomics: 2,869
• Year to date:
  • Site-wide: 86,839
• Since beginning of last month:
  • Site-wide: 118,709

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

• Downloaded 746 times
• Download rankings, all-time:
  • Site-wide: 32,639
  • In bioinformatics: 3,657
• Year to date:
  • Site-wide: 37,234
• Since beginning of last month:
  • Site-wide: 30,288

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 737 times
• Download rankings, all-time:
  • Site-wide: 33,219
  • In genetics: 1,590
• Year to date:
  • Site-wide: 23,562
• Since beginning of last month:
  • Site-wide: 26,349

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

• Downloaded 721 times
• Download rankings, all-time:
  • Site-wide: 34,237
  • In genomics: 2,971
• Year to date:
  • Site-wide: 105,736
• Since beginning of last month:
  • Site-wide: 68,709

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

• Downloaded 706 times
• Download rankings, all-time:
  • Site-wide: 35,282
  • In bioinformatics: 3,919
• Year to date:
  • Site-wide: 45,465
• Since beginning of last month:
  • Site-wide: 34,890

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

• Downloaded 693 times
• Download rankings, all-time:
  • Site-wide: 36,170
  • In epidemiology: 1,776
• Year to date:
  • Site-wide: 29,505
• Since beginning of last month:
  • Site-wide: 22,783

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

• Downloaded 676 times
• Download rankings, all-time:
  • Site-wide: 37,353
  • In molecular biology: 1,045
• Year to date:
  • Site-wide: 52,755
• Since beginning of last month:
  • Site-wide: 38,621

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

• Downloaded 647 times
• Download rankings, all-time:
  • Site-wide: 39,586
  • In genomics: 3,293
• Year to date:
  • Site-wide: 76,498
• Since beginning of last month:
  • Site-wide: 83,072

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

• Downloaded 647 times
• Download rankings, all-time:
  • Site-wide: 39,593
  • In genomics: 3,291
• Year to date:
  • Site-wide: 65,712
• Since beginning of last month:
  • Site-wide: 57,442

Single cell chromatin accessibility of the developmental cephalochordate

• Downloaded 617 times
• Download rankings, all-time:
  • Site-wide: 41,988
  • In developmental biology: 940
• Year to date:
  • Site-wide: 45,402
• Since beginning of last month:
  • Site-wide: 34,916

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

• Downloaded 611 times
• Download rankings, all-time:
  • Site-wide: 42,589
  • In genetics: 1,993
• Year to date:
  • Site-wide: 54,161
• Since beginning of last month:
  • Site-wide: None

De novo assembly of the Mongolian gerbil genome and transcriptome

• Downloaded 599 times
• Download rankings, all-time:
  • Site-wide: 43,674
  • In genomics: 3,530
• Year to date:
  • Site-wide: 86,501
• Since beginning of last month:
  • Site-wide: 82,672

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

• Downloaded 574 times
• Download rankings, all-time:
  • Site-wide: 45,929
  • In genetics: 2,144
• Year to date:
  • Site-wide: 87,672
• Since beginning of last month:
  • Site-wide: 72,175

Single cell atlas of trisomy 21 cerebral cortex

• Downloaded 524 times
• Download rankings, all-time:
  • Site-wide: 51,261
  • In neuroscience: 7,498
• Year to date:
  • Site-wide: 56,881
• Since beginning of last month:
  • Site-wide: 61,140

The female urinary microbiota in relation to the reproductive tract microbiota

• Downloaded 493 times
• Download rankings, all-time:
  • Site-wide: 55,116
  • In microbiology: 3,525
• Year to date:
  • Site-wide: 45,847
• Since beginning of last month:
  • Site-wide: 28,771

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

• Downloaded 481 times
• Download rankings, all-time:
  • Site-wide: 56,758
  • In genomics: 4,257
• Year to date:
  • Site-wide: 55,941
• Since beginning of last month:
  • Site-wide: 34,719

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

• Downloaded 470 times
• Download rankings, all-time:
  • Site-wide: 58,125
  • In immunology: 1,638
• Year to date:
  • Site-wide: 89,670
• Since beginning of last month:
  • Site-wide: 64,094

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

• Downloaded 425 times
• Download rankings, all-time:
  • Site-wide: 64,462
  • In molecular biology: 1,842
• Year to date:
  • Site-wide: 94,652
• Since beginning of last month:
  • Site-wide: 103,780

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

• Downloaded 386 times
• Download rankings, all-time:
  • Site-wide: 70,851
  • In microbiology: 4,777
• Year to date:
  • Site-wide: 121,122
• Since beginning of last month:
  • Site-wide: 106,811

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

• Downloaded 370 times
• Download rankings, all-time:
  • Site-wide: 73,722
  • In genomics: 5,024
• Year to date:
  • Site-wide: 71,947
• Since beginning of last month:
  • Site-wide: 99,385

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 368 times
• Download rankings, all-time:
  • Site-wide: 74,052
  • In genetics: 3,358
• Year to date:
  • Site-wide: 92,807
• Since beginning of last month:
  • Site-wide: 70,118

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

• Downloaded 338 times
• Download rankings, all-time:
  • Site-wide: 79,673
  • In genetics: 3,613
• Year to date:
  • Site-wide: 100,128
• Since beginning of last month:
  • Site-wide: 89,714

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

• Downloaded 336 times
• Download rankings, all-time:
  • Site-wide: 79,962
  • In genetics: 3,623
• Year to date:
  • Site-wide: 35,494
• Since beginning of last month:
  • Site-wide: 80,016

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

• Downloaded 324 times
• Download rankings, all-time:
  • Site-wide: 82,326
  • In genomics: 5,347
• Year to date:
  • Site-wide: 115,298
• Since beginning of last month:
  • Site-wide: 114,872

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

• Downloaded 321 times
• Download rankings, all-time:
  • Site-wide: 82,992
  • In genomics: 5,373
• Year to date:
  • Site-wide: 124,284
• Since beginning of last month:
  • Site-wide: 120,427

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 319 times
• Download rankings, all-time:
  • Site-wide: 83,361
  • In immunology: 2,355
• Year to date:
  • Site-wide: 106,349
• Since beginning of last month:
  • Site-wide: 116,736

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

• Downloaded 267 times
• Download rankings, all-time:
  • Site-wide: 94,544
  • In bioinformatics: 8,246
• Year to date:
  • Site-wide: 53,458
• Since beginning of last month:
  • Site-wide: 128,405

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

• Downloaded 254 times
• Download rankings, all-time:
  • Site-wide: 97,408
  • In genomics: 5,892
• Year to date:
  • Site-wide: 125,582
• Since beginning of last month:
  • Site-wide: 79,971

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

• Downloaded 246 times
• Download rankings, all-time:
  • Site-wide: 99,125
  • In genetic and genomic medicine: 412
• Year to date:
  • Site-wide: 84,859
• Since beginning of last month:
  • Site-wide: 53,702

CNSA: a data repository for archiving omics data

• Downloaded 243 times
• Download rankings, all-time:
  • Site-wide: 99,812
  • In genomics: 5,971
• Year to date:
  • Site-wide: 58,358
• Since beginning of last month:
  • Site-wide: 59,077

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

• Downloaded 224 times
• Download rankings, all-time:
  • Site-wide: 104,092
  • In immunology: 2,986
• Year to date:
  • Site-wide: 14,415
• Since beginning of last month:
  • Site-wide: 24,964

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

• Downloaded 220 times
• Download rankings, all-time:
  • Site-wide: 105,190
  • In cancer biology: 3,174
• Year to date:
  • Site-wide: 71,869
• Since beginning of last month:
  • Site-wide: 112,734

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

• Downloaded 182 times
• Download rankings, all-time:
  • Site-wide: 113,641
  • In epidemiology: 4,675
• Year to date:
  • Site-wide: 16,088
• Since beginning of last month:
  • Site-wide: 8,068

Personalized vagino-cervical microbiome dynamics after oral probiotics

• Downloaded 176 times
• Download rankings, all-time:
  • Site-wide: 115,049
  • In microbiology: 8,605
• Year to date:
  • Site-wide: 83,324
• Since beginning of last month:
  • Site-wide: 112,487

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

• Downloaded 113 times
• Download rankings, all-time:
  • Site-wide: 127,959
  • In evolutionary biology: 6,465
• Year to date:
  • Site-wide: 135,005
• Since beginning of last month:
  • Site-wide: 130,621

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

• Downloaded 99 times
• Download rankings, all-time:
  • Site-wide: 130,488
  • In microbiology: 10,010
• Year to date:
  • Site-wide: 40,864
• Since beginning of last month:
  • Site-wide: 84,071