Author: Yun Li

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Preprints

Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression

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  • Site-wide: 894
  • In genetics: 26
• Year to date:
  • Site-wide: 34,573
• Since beginning of last month:
  • Site-wide: 45,224

An epigenetic biomarker of aging for lifespan and healthspan

• Downloaded 2,944 times
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  • Site-wide: 4,359
  • In epidemiology: 396
• Year to date:
  • Site-wide: 38,313
• Since beginning of last month:
  • Site-wide: 51,424

The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions

• Downloaded 2,933 times
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  • Site-wide: 4,388
  • In bioinformatics: 451
• Year to date:
  • Site-wide: 70,632
• Since beginning of last month:
  • Site-wide: 127,157

Multi-epitope vaccine design using an immunoinformatics approach for 2019 novel coronavirus (SARS-CoV-2)

• Downloaded 2,912 times
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  • Site-wide: 4,428
  • In bioinformatics: 453
• Year to date:
  • Site-wide: 13,432
• Since beginning of last month:
  • Site-wide: 19,538

SAFE-clustering: Single-cell Aggregated (From Ensemble) Clustering for Single-cell RNA-seq Data

• Downloaded 2,864 times
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  • Site-wide: 4,534
  • In bioinformatics: 470
• Year to date:
  • Site-wide: 32,379
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  • Site-wide: 57,620

Trans-ethnic and ancestry-specific blood-cell genetics in 746,667 individuals from 5 global populations

• Downloaded 2,458 times
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  • Site-wide: 5,706
  • In genetics: 262
• Year to date:
  • Site-wide: 5,304
• Since beginning of last month:
  • Site-wide: 6,955

Using three-dimensional regulatory chromatin interactions from adult and fetal cortex to interpret genetic results for psychiatric disorders and cognitive traits

• Downloaded 2,295 times
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  • Site-wide: 6,298
  • In genetics: 297
• Year to date:
  • Site-wide: 9,563
• Since beginning of last month:
  • Site-wide: 14,051

The Polygenic and Monogenic Basis of Blood Traits and Diseases

• Downloaded 2,020 times
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  • Site-wide: 7,567
  • In genetic and genomic medicine: 28
• Year to date:
  • Site-wide: 25,402
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  • Site-wide: 44,783

3D Epigenomic Characterization Reveals Insights Into Gene Regulation and Lineage Specification During Corticogenesis

• Downloaded 1,755 times
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  • Site-wide: 9,369
  • In genomics: 1,013
• Year to date:
  • Site-wide: 10,254
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  • Site-wide: 6,648

Large-scale GWAS reveals genetic architecture of brain white matter microstructure and genetic overlap with cognitive and mental health traits (n=17,706)

• Downloaded 1,699 times
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  • Site-wide: 9,844
  • In genetics: 461
• Year to date:
  • Site-wide: 51,893
• Since beginning of last month:
  • Site-wide: 38,409

Common DNA sequence variation influences 3-dimensional conformation of the human genome

• Downloaded 1,490 times
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  • Site-wide: 11,883
  • In genomics: 1,285
• Year to date:
  • Site-wide: 112,257
• Since beginning of last month:
  • Site-wide: 71,903

SCDC: Bulk Gene Expression Deconvolution by Multiple Single-Cell RNA Sequencing References

• Downloaded 1,353 times
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  • Site-wide: 13,780
  • In bioinformatics: 1,659
• Year to date:
  • Site-wide: 39,627
• Since beginning of last month:
  • Site-wide: 51,074

Robust Hi-C chromatin loop maps in human neurogenesis and brain tissues at high-resolution

• Downloaded 1,331 times
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  • Site-wide: 14,136
  • In genomics: 1,485
• Year to date:
  • Site-wide: 14,146
• Since beginning of last month:
  • Site-wide: 23,217

SMNN: Batch Effect Correction for Single-cell RNA-seq data via Supervised Mutual Nearest Neighbor Detection

• Downloaded 1,245 times
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  • Site-wide: 15,647
  • In bioinformatics: 1,886
• Year to date:
  • Site-wide: 37,645
• Since beginning of last month:
  • Site-wide: 83,439

The intestinal microbiota programs diurnal rhythms in host metabolism through histone deacetylase 3

• Downloaded 1,226 times
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  • Site-wide: 15,988
  • In microbiology: 923
• Year to date:
  • Site-wide: 76,931
• Since beginning of last month:
  • Site-wide: 56,726

MAPS: model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments

• Downloaded 1,155 times
• Download rankings, all-time:
  • Site-wide: 17,483
  • In bioinformatics: 2,093
• Year to date:
  • Site-wide: 100,150
• Since beginning of last month:
  • Site-wide: 62,832

The Big Five, Self-efficacy, and Self-control in Boxers

• Downloaded 1,150 times
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  • Site-wide: 17,576
  • In scientific communication and education: 143
• Year to date:
  • Site-wide: 24,363
• Since beginning of last month:
  • Site-wide: 35,733

Common genetic variation influencing human white matter microstructure

• Downloaded 1,021 times
• Download rankings, all-time:
  • Site-wide: 20,961
  • In genetics: 1,000
• Year to date:
  • Site-wide: 11,811
• Since beginning of last month:
  • Site-wide: 6,958

A Possible Role Of Microglia In Zika Virus Infection Of The Fetal Human Brain

• Downloaded 1,019 times
• Download rankings, all-time:
  • Site-wide: 20,995
  • In neuroscience: 2,651
• Year to date:
  • Site-wide: 102,803
• Since beginning of last month:
  • Site-wide: 107,884

MOSTWAS: Multi-Omic Strategies for Transcriptome-Wide Association Studies

• Downloaded 990 times
• Download rankings, all-time:
  • Site-wide: 21,857
  • In genetics: 1,040
• Year to date:
  • Site-wide: 34,791
• Since beginning of last month:
  • Site-wide: 86,662

Neuronal and glial 3D chromatin architecture illustrates cellular etiology of brain disorders

• Downloaded 971 times
• Download rankings, all-time:
  • Site-wide: 22,476
  • In neuroscience: 2,875
• Year to date:
  • Site-wide: 21,314
• Since beginning of last month:
  • Site-wide: 21,250

GWAS of 19,629 individuals identifies novel genetic variants for regional brain volumes and refines their genetic co-architecture with cognitive and mental health traits

• Downloaded 895 times
• Download rankings, all-time:
  • Site-wide: 25,362
  • In genetics: 1,212
• Year to date:
  • Site-wide: 68,717
• Since beginning of last month:
  • Site-wide: 68,509

Transcriptome-wide association analysis of 211 neuroimaging traits identifies new genes for brain structures and yields insights into the gene-level pleiotropy with other complex traits

• Downloaded 854 times
• Download rankings, all-time:
  • Site-wide: 27,039
  • In genetics: 1,294
• Year to date:
  • Site-wide: 22,417
• Since beginning of last month:
  • Site-wide: 24,110

GWAS of epigenetic ageing rates in blood reveals a critical role for TERT

• Downloaded 821 times
• Download rankings, all-time:
  • Site-wide: 28,552
  • In genetics: 1,375
• Year to date:
  • Site-wide: 125,152
• Since beginning of last month:
  • Site-wide: 94,089

Heritability of regional brain volumes in large-scale neuroimaging and genetic studies

• Downloaded 820 times
• Download rankings, all-time:
  • Site-wide: 28,628
  • In genetics: 1,379
• Year to date:
  • Site-wide: 94,990
• Since beginning of last month:
  • Site-wide: 93,892

MRLocus: identifying causal genes mediating a trait through Bayesian estimation of allelic heterogeneity

• Downloaded 768 times
• Download rankings, all-time:
  • Site-wide: 31,422
  • In bioinformatics: 3,536
• Year to date:
  • Site-wide: 16,526
• Since beginning of last month:
  • Site-wide: 9,190

HUGIn: Hi-C Unifying Genomic Interrogator

• Downloaded 734 times
• Download rankings, all-time:
  • Site-wide: 33,459
  • In genetics: 1,600
• Year to date:
  • Site-wide: 122,462
• Since beginning of last month:
  • Site-wide: 124,282

Use of >100,000 NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium whole genome sequences improves imputation quality and detection of rare variant associations in admixed African and Hispanic/Latino populations

• Downloaded 669 times
• Download rankings, all-time:
  • Site-wide: 37,870
  • In genomics: 3,186
• Year to date:
  • Site-wide: 84,001
• Since beginning of last month:
  • Site-wide: 121,257

Multi-SNP Mediation Intersection-Union Test

• Downloaded 642 times
• Download rankings, all-time:
  • Site-wide: 39,947
  • In genetics: 1,885
• Year to date:
  • Site-wide: 66,746
• Since beginning of last month:
  • Site-wide: 82,311

SAME-clustering: Single-cell Aggregated Clustering via Mixture Model Ensemble

• Downloaded 621 times
• Download rankings, all-time:
  • Site-wide: 41,674
  • In bioinformatics: 4,485
• Year to date:
  • Site-wide: 128,558
• Since beginning of last month:
  • Site-wide: 120,604

TWO-SIGMA: a novel TWO-component SInGle cell Model-based Association method for single-cell RNA-seq data

• Downloaded 607 times
• Download rankings, all-time:
  • Site-wide: 42,895
  • In genomics: 3,488
• Year to date:
  • Site-wide: 41,735
• Since beginning of last month:
  • Site-wide: 56,163

Whole genome sequencing association analysis of quantitative red blood cell phenotypes: the NHLBI TOPMed program

• Downloaded 563 times
• Download rankings, all-time:
  • Site-wide: 47,084
  • In hematology: 30
• Year to date:
  • Site-wide: 5,737
• Since beginning of last month:
  • Site-wide: 4,870

Association between ApoE polymorphism and type 2 diabetes: A meta-analysis of 59 studies

• Downloaded 562 times
• Download rankings, all-time:
  • Site-wide: 47,199
  • In genetics: 2,203
• Year to date:
  • Site-wide: 49,718
• Since beginning of last month:
  • Site-wide: 32,931

Overarching control of autophagy and DNA damage response by CHD6 revealed by modeling a rare human pathology

• Downloaded 557 times
• Download rankings, all-time:
  • Site-wide: 47,713
  • In cell biology: 2,045
• Year to date:
  • Site-wide: 37,998
• Since beginning of last month:
  • Site-wide: 54,179

FIREcaller: Detecting Frequently Interacting Regions from Hi-C Data

• Downloaded 532 times
• Download rankings, all-time:
  • Site-wide: 50,386
  • In bioinformatics: 5,201
• Year to date:
  • Site-wide: 70,514
• Since beginning of last month:
  • Site-wide: 120,207

SnapHiC: a computational pipeline to map chromatin contacts from single cell Hi-C data

• Downloaded 530 times
• Download rankings, all-time:
  • Site-wide: 50,544
  • In bioinformatics: 5,222
• Year to date:
  • Site-wide: 9,413
• Since beginning of last month:
  • Site-wide: 25,025

Methylome-Wide Association Study Of Central Adiposity Implicates Genes Involved In Immune And Endocrine Systems

• Downloaded 424 times
• Download rankings, all-time:
  • Site-wide: 64,670
  • In genomics: 4,632
• Year to date:
  • Site-wide: 64,364
• Since beginning of last month:
  • Site-wide: 41,885

Parallel Characterization of cis-Regulatory Elements for Multiple Genes UsingCRISPRpath

• Downloaded 397 times
• Download rankings, all-time:
  • Site-wide: 69,039
  • In genomics: 4,807
• Year to date:
  • Site-wide: 5,443
• Since beginning of last month:
  • Site-wide: 7,934

Generation of Cynomolgus Monkeys (Macaca fascicularis) Embryos with ICSI Based on the MII-Stage Oocytes Acquired by Personalized Superovulation Protocol

• Downloaded 370 times
• Download rankings, all-time:
  • Site-wide: 73,589
  • In developmental biology: 1,909
• Year to date:
  • Site-wide: 65,755
• Since beginning of last month:
  • Site-wide: 36,042

Integrative methylome and transcriptome analysis of Japanese flounder (Paralichthys olivaceus) skeletal muscle during development

• Downloaded 315 times
• Download rankings, all-time:
  • Site-wide: 84,197
  • In epidemiology: 3,484
• Year to date:
  • Site-wide: 102,014
• Since beginning of last month:
  • Site-wide: 72,430

The Characteristic of Auditory Function and Cochlear Pathophysiology in a Noise-exposed Cohort: A Cross-sectional Study

• Downloaded 305 times
• Download rankings, all-time:
  • Site-wide: 86,235
  • In otolaryngology: 57
• Year to date:
  • Site-wide: 24,234
• Since beginning of last month:
  • Site-wide: 47,341

Characterizing sensitivity and coverage of clinical WGS as a diagnostic test for genetic disorders

• Downloaded 292 times
• Download rankings, all-time:
  • Site-wide: 89,203
  • In genomics: 5,603
• Year to date:
  • Site-wide: 32,590
• Since beginning of last month:
  • Site-wide: 35,040

iSMNN: Batch Effect Correction for Single-cell RNA-seq data via Iterative Supervised Mutual Nearest Neighbor Refinement

• Downloaded 282 times
• Download rankings, all-time:
  • Site-wide: 91,165
  • In bioinformatics: 8,038
• Year to date:
  • Site-wide: 18,785
• Since beginning of last month:
  • Site-wide: 40,057

Generalized Multi-SNP Mediation Intersection-Union Test

• Downloaded 250 times
• Download rankings, all-time:
  • Site-wide: 98,344
  • In genetics: 4,348
• Year to date:
  • Site-wide: 111,417
• Since beginning of last month:
  • Site-wide: 78,528

From GWAS Variant to Function: a Study of ~148,000 Variants for Blood Cell Traits.

• Downloaded 242 times
• Download rankings, all-time:
  • Site-wide: 100,005
  • In genetics: 4,430
• Year to date:
  • Site-wide: 10,995
• Since beginning of last month:
  • Site-wide: 15,485

THUNDER: A reference-free deconvolution method to infer cell type proportions from bulk Hi-C data

• Downloaded 233 times
• Download rankings, all-time:
  • Site-wide: 102,129
  • In bioinformatics: 8,704
• Year to date:
  • Site-wide: 60,868
• Since beginning of last month:
  • Site-wide: 61,976

CUE: CpG impUtation Ensemble for DNA Methylation Levels Across the Human Methylation450 (HM450) and EPIC (HM850) BeadChip Platforms

• Downloaded 233 times
• Download rankings, all-time:
  • Site-wide: 102,143
  • In bioinformatics: 8,698
• Year to date:
  • Site-wide: 66,193
• Since beginning of last month:
  • Site-wide: 76,200

A large-scale transcriptome-wide association study (TWAS) of ten blood cell phenotypes reveals complexities of TWAS fine-mapping

• Downloaded 218 times
• Download rankings, all-time:
  • Site-wide: 105,513
  • In genetics: 4,635
• Year to date:
  • Site-wide: 12,770
• Since beginning of last month:
  • Site-wide: 20,062

HiC-ACT: Improved Detection of Chromatin Interactions from Hi-C Data via Aggregated Cauchy Test

• Downloaded 212 times
• Download rankings, all-time:
  • Site-wide: 106,963
  • In bioinformatics: 9,007
• Year to date:
  • Site-wide: 53,576
• Since beginning of last month:
  • Site-wide: 75,996

MUNIn (Multiple sample UNifying long-range chromatin Interaction detector): a statistical framework for identifying long-range chromatin interactions from multiple samples

• Downloaded 179 times
• Download rankings, all-time:
  • Site-wide: 114,344
  • In genetics: 4,934
• Year to date:
  • Site-wide: 48,083
• Since beginning of last month:
  • Site-wide: 14,444

Phased implementation of COVID-19 vaccination: rapid assessment of policy adoption, reach and effectiveness to protect the most vulnerable in the US

• Downloaded 165 times
• Download rankings, all-time:
  • Site-wide: 117,552
  • In health policy: 261
• Year to date:
  • Site-wide: 18,277
• Since beginning of last month:
  • Site-wide: 12,124

Genome engineering of Nannochloropsis with large deletions for constructing microalgal minigenomes

• Downloaded 153 times
• Download rankings, all-time:
  • Site-wide: 119,957
  • In biochemistry: 3,601
• Year to date:
  • Site-wide: 80,578
• Since beginning of last month:
  • Site-wide: 39,749

Super interactive promoters provide insight into cell type-specific regulatory networks in blood lineage cell types

• Downloaded 144 times
• Download rankings, all-time:
  • Site-wide: 121,995
  • In genetics: 5,168
• Year to date:
  • Site-wide: 21,708
• Since beginning of last month:
  • Site-wide: 15,246

eSCAN: Scan Regulatory Regions for Aggregate Association Testing using Whole Genome Sequencing Data

• Downloaded 118 times
• Download rankings, all-time:
  • Site-wide: 126,985
  • In genetics: 5,318
• Year to date:
  • Site-wide: 57,565
• Since beginning of last month:
  • Site-wide: None

HPRep: Quantifying reproducibility in HiChIP and PLAC-seq datasets

• Downloaded 112 times
• Download rankings, all-time:
  • Site-wide: 128,269
  • In genomics: 6,829
• Year to date:
  • Site-wide: 64,670
• Since beginning of last month:
  • Site-wide: 59,966

Distal mediator-enriched, placental transcriptome-wide analyses illustrate the Developmental Origins of Health and Disease

• Downloaded 89 times
• Download rankings, all-time:
  • Site-wide: 132,210
  • In genetic and genomic medicine: 664
• Year to date:
  • Site-wide: 36,873
• Since beginning of last month:
  • Site-wide: 5,932