Author: Ken Chen

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Preprints

Multi-platform discovery of haplotype-resolved structural variation in human genomes

• Downloaded 8,640 times
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  • Site-wide: 1,664
  • In genomics: 117
• Year to date:
  • Site-wide: 19,183
• Since beginning of last month:
  • Site-wide: 90,395

A robust benchmark for germline structural variant detection

• Downloaded 7,114 times
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  • Site-wide: 2,161
  • In genomics: 159
• Year to date:
  • Site-wide: 5,174
• Since beginning of last month:
  • Site-wide: 10,802

Pan-cancer analysis of whole genomes reveals driver rearrangements promoted by LINE-1 retrotransposition in human tumours

• Downloaded 3,873 times
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  • Site-wide: 5,028
  • In genomics: 464
• Year to date:
  • Site-wide: 73,694
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  • Site-wide: 142,992

Unbiased integration of single cell multi-omics data

• Downloaded 3,176 times
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  • Site-wide: 6,740
  • In bioinformatics: 626
• Year to date:
  • Site-wide: 11,936
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  • Site-wide: 29,240

Spatial drivers and pre-cancer populations collaborate with the microenvironment in untreated and chemo-resistant pancreatic cancer

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  • Site-wide: 9,248
  • In cancer biology: 166
• Year to date:
  • Site-wide: 8,853
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  • Site-wide: 15,837

Spatial charting of single cell transcriptomes in tissues

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  • Site-wide: 11,667
  • In genomics: 1,125
• Year to date:
  • Site-wide: 5,322
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  • Site-wide: 3,372

SiFit: A Method for Inferring Tumor Trees from Single-Cell Sequencing Data under Finite-site Models

• Downloaded 1,553 times
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  • Site-wide: 19,928
  • In bioinformatics: 2,188
• Year to date:
  • Site-wide: 165,803
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  • Site-wide: 117,888

CIS checkpoint deletion enhances the fitness of cord blood derived natural killer cells transduced with a chimeric antigen receptor

• Downloaded 1,360 times
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  • Site-wide: 24,670
  • In immunology: 908
• Year to date:
  • Site-wide: 47,142
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  • Site-wide: 30,079

Inhibition of the av integrin-TGF-b axis improves natural killer cell function against glioblastoma stem cells

• Downloaded 1,354 times
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  • Site-wide: 24,863
  • In immunology: 915
• Year to date:
  • Site-wide: 67,108
• Since beginning of last month:
  • Site-wide: 65,991

SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data

• Downloaded 1,183 times
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  • Site-wide: 30,744
  • In genomics: 2,551
• Year to date:
  • Site-wide: 173,071
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  • Site-wide: 142,472

Single-cell copy number lineage tracing enabling gene discovery

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  • Site-wide: 32,617
  • In bioinformatics: 3,501
• Year to date:
  • Site-wide: None
• Since beginning of last month:
  • Site-wide: 190,396

Single-Cell Manifold Preserving Feature Selection (SCMER)

• Downloaded 1,105 times
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  • Site-wide: 34,183
  • In bioinformatics: 3,601
• Year to date:
  • Site-wide: None
• Since beginning of last month:
  • Site-wide: 136,546

Generation of glucocorticoid resistant SARS-CoV-2 T-cells for adoptive cell therapy

• Downloaded 1,036 times
• Download rankings, all-time:
  • Site-wide: 37,761
  • In immunology: 1,354
• Year to date:
  • Site-wide: 85,568
• Since beginning of last month:
  • Site-wide: 65,842

Combining accurate tumour genome simulation with crowd-sourcing to benchmark somatic structural variant detection

• Downloaded 1,022 times
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  • Site-wide: 38,574
  • In bioinformatics: 4,028
• Year to date:
  • Site-wide: 195,176
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  • Site-wide: 92,418

SCMarker: ab initio marker selection for single cell transcriptome profiling

• Downloaded 1,008 times
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  • Site-wide: 39,359
  • In bioinformatics: 4,106
• Year to date:
  • Site-wide: 194,916
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  • Site-wide: 120,004

Relative Abundance of SARS-CoV-2 Entry Genes in the Enterocytes of the Lower Gastrointestinal Tract

• Downloaded 954 times
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  • Site-wide: 42,898
  • In bioinformatics: 4,447
• Year to date:
  • Site-wide: 87,414
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  • Site-wide: 102,190

HySA: A Hybrid Structural variant Assembly approach using next generation and single-molecule sequencing technologies

• Downloaded 931 times
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  • Site-wide: 44,517
  • In bioinformatics: 4,571
• Year to date:
  • Site-wide: 97,944
• Since beginning of last month:
  • Site-wide: 142,004

Latent periodic process inference from single-cell RNA-seq data

• Downloaded 711 times
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  • Site-wide: 66,740
  • In bioinformatics: 6,334
• Year to date:
  • Site-wide: 98,876
• Since beginning of last month:
  • Site-wide: 94,237

Occult polyclonality of preclinical pancreatic cancer models drives in vitro evolution.

• Downloaded 698 times
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  • Site-wide: 68,490
  • In cancer biology: 2,022
• Year to date:
  • Site-wide: 23,290
• Since beginning of last month:
  • Site-wide: 86,457

OmicPioneer-sc: an integrated, interactive visualization environment for single-cell sequencing data

• Downloaded 550 times
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  • Site-wide: 93,364
  • In bioinformatics: 8,307
• Year to date:
  • Site-wide: 127,036
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  • Site-wide: 76,788

Stratified Test Accurately Identifies Differentially Expressed Genes Under Batch Effects in Single-Cell Data

• Downloaded 534 times
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  • Site-wide: 96,582
  • In bioinformatics: 8,574
• Year to date:
  • Site-wide: 103,833
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  • Site-wide: 37,356

Characterizing metabolism from bulk and single-cell RNA-seq data using METAFlux

• Downloaded 521 times
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  • Site-wide: 99,376
  • In bioinformatics: 8,983
• Year to date:
  • Site-wide: 61,936
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  • Site-wide: 10,206

Spatially Interacting Phosphorylation Sites and Mutations in Cancer

• Downloaded 517 times
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  • Site-wide: 100,461
  • In bioinformatics: 8,645
• Year to date:
  • Site-wide: 186,822
• Since beginning of last month:
  • Site-wide: 137,811

Capturing large genomic contexts for accurately predicting enhancer-promoter interactions

• Downloaded 482 times
• Download rankings, all-time:
  • Site-wide: 108,566
  • In bioinformatics: 9,481
• Year to date:
  • Site-wide: 180,208
• Since beginning of last month:
  • Site-wide: 19,951

Batch-Corrected Distance Mitigates Temporal and Spatial Variability for Clustering and Visualization of Single-Cell Gene Expression Data

• Downloaded 468 times
• Download rankings, all-time:
  • Site-wide: 111,932
  • In bioinformatics: 9,535
• Year to date:
  • Site-wide: 154,021
• Since beginning of last month:
  • Site-wide: 65,860

Sensei: How many samples to tell evolution in single-cell studies?

• Downloaded 466 times
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  • Site-wide: 112,407
  • In bioinformatics: 9,485
• Year to date:
  • Site-wide: None
• Since beginning of last month:
  • Site-wide: 128,484

Ab initio Spillover Compensation in CyTOF Data

• Downloaded 397 times
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  • Site-wide: 130,882
  • In bioinformatics: 10,632
• Year to date:
  • Site-wide: 91,698
• Since beginning of last month:
  • Site-wide: 66,251

Targeting uncoupling of copy number and gene expression in cancers

• Downloaded 340 times
• Download rankings, all-time:
  • Site-wide: 147,956
  • In cancer biology: 4,541
• Year to date:
  • Site-wide: 88,209
• Since beginning of last month:
  • Site-wide: 132,280

A role for KIF9 in male fertility

• Downloaded 307 times
• Download rankings, all-time:
  • Site-wide: 157,792
  • In developmental biology: 4,207
• Year to date:
  • Site-wide: 69,034
• Since beginning of last month:
  • Site-wide: 121,663

ANTIBODY-INDEPENDENT ANTITUMOR EFFECTS OF CD32A-CHIMERIC RECEPTOR T CELLS: IMPLICATIONS FOR BREAST CANCER PROGNOSIS AND TREATMENT.

• Downloaded 295 times
• Download rankings, all-time:
  • Site-wide: 161,600
  • In immunology: 5,139
• Year to date:
  • Site-wide: 43,371
• Since beginning of last month:
  • Site-wide: 107,827

Characterizing transition cells in developmental processes from scRNA-seq data

• Downloaded 215 times
• Download rankings, all-time:
  • Site-wide: 183,853
  • In bioinformatics: 13,810
• Year to date:
  • Site-wide: 180,055
• Since beginning of last month:
  • Site-wide: 67,235

Monopogen: single nucleotide variant calling from single cell sequencing

• Downloaded 211 times
• Download rankings, all-time:
  • Site-wide: 184,939
  • In bioinformatics: None
• Year to date:
  • Site-wide: 14,318
• Since beginning of last month:
  • Site-wide: 810

Integrated single-cell functional and molecular profiling of extracellular vesicle secretion in metastatic breast cancer

• Downloaded 145 times
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  • Site-wide: 199,249
  • In cancer biology: 6,198
• Year to date:
  • Site-wide: 133,339
• Since beginning of last month:
  • Site-wide: 46,873

novoRNABreak: local assembly for novel splice junction and fusion transcript detection from RNA-seq data

• Downloaded 130 times
• Download rankings, all-time:
  • Site-wide: 202,067
  • In bioinformatics: None
• Year to date:
  • Site-wide: 8,317
• Since beginning of last month:
  • Site-wide: 2,150