Author: Yun Li

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Preprints

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

• Downloaded 9,438 times
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  • Site-wide: 983
  • In genetics: 26
• Year to date:
  • Site-wide: 43,437
• Since beginning of last month:
  • Site-wide: 61,631

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

• Downloaded 3,043 times
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  • Site-wide: 4,611
  • In bioinformatics: 455
• Year to date:
  • Site-wide: 13,003
• Since beginning of last month:
  • Site-wide: 14,601

An epigenetic biomarker of aging for lifespan and healthspan

• Downloaded 2,987 times
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  • Site-wide: 4,735
  • In epidemiology: 443
• Year to date:
  • Site-wide: 43,986
• Since beginning of last month:
  • Site-wide: 39,038

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

• Downloaded 2,975 times
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  • Site-wide: 4,760
  • In bioinformatics: 475
• Year to date:
  • Site-wide: 65,711
• Since beginning of last month:
  • Site-wide: 77,552

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

• Downloaded 2,906 times
• Download rankings, all-time:
  • Site-wide: 4,919
  • In bioinformatics: 489
• Year to date:
  • Site-wide: 39,143
• Since beginning of last month:
  • Site-wide: 43,600

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

• Downloaded 2,686 times
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  • Site-wide: 5,515
  • In genetics: 237
• Year to date:
  • Site-wide: 5,300
• Since beginning of last month:
  • Site-wide: 7,565

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

• Downloaded 2,449 times
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  • Site-wide: 6,343
  • In genetics: 281
• Year to date:
  • Site-wide: 9,588
• Since beginning of last month:
  • Site-wide: 7,668

The Polygenic and Monogenic Basis of Blood Traits and Diseases

• Downloaded 2,062 times
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  • Site-wide: 8,119
  • In genetic and genomic medicine: 35
• Year to date:
  • Site-wide: 32,654
• Since beginning of last month:
  • Site-wide: 47,321

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

• Downloaded 1,838 times
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  • Site-wide: 9,647
  • In genomics: 995
• Year to date:
  • Site-wide: 13,098
• Since beginning of last month:
  • Site-wide: 17,380

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

• Downloaded 1,724 times
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  • Site-wide: 10,601
  • In genetics: 477
• Year to date:
  • Site-wide: 63,865
• Since beginning of last month:
  • Site-wide: 65,915

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

• Downloaded 1,499 times
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  • Site-wide: 12,988
  • In genomics: 1,352
• Year to date:
  • Site-wide: 126,374
• Since beginning of last month:
  • Site-wide: 104,377

Common genetic variation influencing human white matter microstructure

• Downloaded 1,497 times
• Download rankings, all-time:
  • Site-wide: 13,014
  • In genetics: 600
• Year to date:
  • Site-wide: 4,510
• Since beginning of last month:
  • Site-wide: 1,213

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

• Downloaded 1,395 times
• Download rankings, all-time:
  • Site-wide: 14,510
  • In bioinformatics: 1,692
• Year to date:
  • Site-wide: 45,083
• Since beginning of last month:
  • Site-wide: 53,220

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

• Downloaded 1,390 times
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  • Site-wide: 14,588
  • In genomics: 1,487
• Year to date:
  • Site-wide: 18,803
• Since beginning of last month:
  • Site-wide: 32,040

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

• Downloaded 1,292 times
• Download rankings, all-time:
  • Site-wide: 16,297
  • In bioinformatics: 1,915
• Year to date:
  • Site-wide: 41,976
• Since beginning of last month:
  • Site-wide: 46,693

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

• Downloaded 1,248 times
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  • Site-wide: 17,142
  • In scientific communication and education: 138
• Year to date:
  • Site-wide: 22,400
• Since beginning of last month:
  • Site-wide: 26,832

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

• Downloaded 1,247 times
• Download rankings, all-time:
  • Site-wide: 17,171
  • In microbiology: 999
• Year to date:
  • Site-wide: 86,025
• Since beginning of last month:
  • Site-wide: 72,626

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

• Downloaded 1,173 times
• Download rankings, all-time:
  • Site-wide: 18,813
  • In bioinformatics: 2,184
• Year to date:
  • Site-wide: 105,254
• Since beginning of last month:
  • Site-wide: 79,178

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

• Downloaded 1,052 times
• Download rankings, all-time:
  • Site-wide: 22,071
  • In neuroscience: 2,748
• Year to date:
  • Site-wide: 22,604
• Since beginning of last month:
  • Site-wide: 24,300

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

• Downloaded 1,038 times
• Download rankings, all-time:
  • Site-wide: 22,556
  • In neuroscience: 2,808
• Year to date:
  • Site-wide: 105,013
• Since beginning of last month:
  • Site-wide: 77,833

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

• Downloaded 1,013 times
• Download rankings, all-time:
  • Site-wide: 23,308
  • In genetics: 1,078
• Year to date:
  • Site-wide: 48,268
• Since beginning of last month:
  • Site-wide: 99,508

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 923 times
• Download rankings, all-time:
  • Site-wide: 26,706
  • In genetics: 1,239
• Year to date:
  • Site-wide: 74,393
• Since beginning of last month:
  • Site-wide: 80,627

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 909 times
• Download rankings, all-time:
  • Site-wide: 27,284
  • In genetics: 1,270
• Year to date:
  • Site-wide: 27,370
• Since beginning of last month:
  • Site-wide: 58,741

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

• Downloaded 832 times
• Download rankings, all-time:
  • Site-wide: 30,876
  • In genetics: 1,439
• Year to date:
  • Site-wide: 111,025
• Since beginning of last month:
  • Site-wide: 97,341

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

• Downloaded 828 times
• Download rankings, all-time:
  • Site-wide: 31,080
  • In genetics: 1,446
• Year to date:
  • Site-wide: 137,685
• Since beginning of last month:
  • Site-wide: 135,129

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

• Downloaded 799 times
• Download rankings, all-time:
  • Site-wide: 32,666
  • In bioinformatics: 3,624
• Year to date:
  • Site-wide: 25,205
• Since beginning of last month:
  • Site-wide: 51,321

HUGIn: Hi-C Unifying Genomic Interrogator

• Downloaded 740 times
• Download rankings, all-time:
  • Site-wide: 36,380
  • In genetics: 1,677
• Year to date:
  • Site-wide: 137,610
• Since beginning of last month:
  • Site-wide: 121,149

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 681 times
• Download rankings, all-time:
  • Site-wide: 40,645
  • In genomics: 3,326
• Year to date:
  • Site-wide: 103,253
• Since beginning of last month:
  • Site-wide: 134,973

Multi-SNP Mediation Intersection-Union Test

• Downloaded 669 times
• Download rankings, all-time:
  • Site-wide: 41,634
  • In genetics: 1,895
• Year to date:
  • Site-wide: 74,475
• Since beginning of last month:
  • Site-wide: 53,059

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

• Downloaded 666 times
• Download rankings, all-time:
  • Site-wide: 41,866
  • In bioinformatics: 4,471
• Year to date:
  • Site-wide: 10,107
• Since beginning of last month:
  • Site-wide: 13,472

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

• Downloaded 657 times
• Download rankings, all-time:
  • Site-wide: 42,598
  • In hematology: 30
• Year to date:
  • Site-wide: 8,018
• Since beginning of last month:
  • Site-wide: 21,409

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

• Downloaded 651 times
• Download rankings, all-time:
  • Site-wide: 43,101
  • In genomics: 3,484
• Year to date:
  • Site-wide: 46,245
• Since beginning of last month:
  • Site-wide: 95,099

Parallel Characterization of cis-Regulatory Elements for Multiple Genes Using CRISPRpath

• Downloaded 651 times
• Download rankings, all-time:
  • Site-wide: 43,133
  • In genomics: 3,483
• Year to date:
  • Site-wide: 5,069
• Since beginning of last month:
  • Site-wide: 15,065

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

• Downloaded 631 times
• Download rankings, all-time:
  • Site-wide: 44,800
  • In bioinformatics: 4,696
• Year to date:
  • Site-wide: 135,789
• Since beginning of last month:
  • Site-wide: 133,210

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

• Downloaded 597 times
• Download rankings, all-time:
  • Site-wide: 47,974
  • In cell biology: 2,040
• Year to date:
  • Site-wide: 44,759
• Since beginning of last month:
  • Site-wide: 97,737

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

• Downloaded 593 times
• Download rankings, all-time:
  • Site-wide: 48,410
  • In genetics: 2,183
• Year to date:
  • Site-wide: 58,491
• Since beginning of last month:
  • Site-wide: 52,898

FIREcaller: Detecting Frequently Interacting Regions from Hi-C Data

• Downloaded 548 times
• Download rankings, all-time:
  • Site-wide: 53,441
  • In bioinformatics: 5,423
• Year to date:
  • Site-wide: 87,108
• Since beginning of last month:
  • Site-wide: 112,775

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

• Downloaded 477 times
• Download rankings, all-time:
  • Site-wide: 62,495
  • In genomics: 4,504
• Year to date:
  • Site-wide: 56,283
• Since beginning of last month:
  • Site-wide: 35,479

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

• Downloaded 392 times
• Download rankings, all-time:
  • Site-wide: 76,421
  • In developmental biology: 1,941
• Year to date:
  • Site-wide: 77,476
• Since beginning of last month:
  • Site-wide: 71,447

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

• Downloaded 375 times
• Download rankings, all-time:
  • Site-wide: 79,495
  • In bioinformatics: 7,294
• Year to date:
  • Site-wide: 19,348
• Since beginning of last month:
  • Site-wide: 37,425

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

• Downloaded 349 times
• Download rankings, all-time:
  • Site-wide: 84,541
  • In otolaryngology: 57
• Year to date:
  • Site-wide: 31,173
• Since beginning of last month:
  • Site-wide: 33,338

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

• Downloaded 344 times
• Download rankings, all-time:
  • Site-wide: 85,527
  • In genomics: 5,510
• Year to date:
  • Site-wide: 36,697
• Since beginning of last month:
  • Site-wide: 42,682

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

• Downloaded 324 times
• Download rankings, all-time:
  • Site-wide: 89,879
  • In epidemiology: 3,731
• Year to date:
  • Site-wide: 120,573
• Since beginning of last month:
  • Site-wide: 117,726

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

• Downloaded 308 times
• Download rankings, all-time:
  • Site-wide: 93,333
  • In genetics: 4,065
• Year to date:
  • Site-wide: 15,022
• Since beginning of last month:
  • Site-wide: 28,774

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

• Downloaded 267 times
• Download rankings, all-time:
  • Site-wide: 102,695
  • In bioinformatics: 8,777
• Year to date:
  • Site-wide: 68,158
• Since beginning of last month:
  • Site-wide: 73,094

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

• Downloaded 262 times
• Download rankings, all-time:
  • Site-wide: 103,956
  • In bioinformatics: 8,863
• Year to date:
  • Site-wide: 68,223
• Since beginning of last month:
  • Site-wide: 68,165

Generalized Multi-SNP Mediation Intersection-Union Test

• Downloaded 261 times
• Download rankings, all-time:
  • Site-wide: 104,129
  • In genetics: 4,486
• Year to date:
  • Site-wide: 123,903
• Since beginning of last month:
  • Site-wide: 120,383

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

• Downloaded 249 times
• Download rankings, all-time:
  • Site-wide: 107,162
  • In genetics: 4,597
• Year to date:
  • Site-wide: 20,025
• Since beginning of last month:
  • Site-wide: 76,895

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

• Downloaded 235 times
• Download rankings, all-time:
  • Site-wide: 110,564
  • In bioinformatics: 9,249
• Year to date:
  • Site-wide: 67,089
• Since beginning of last month:
  • Site-wide: 63,531

Genetic control of fetal placental genomics contributes to development of health and disease

• Downloaded 210 times
• Download rankings, all-time:
  • Site-wide: 116,711
  • In genetic and genomic medicine: 601
• Year to date:
  • Site-wide: 25,096
• Since beginning of last month:
  • Site-wide: 8,958

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

• Downloaded 197 times
• Download rankings, all-time:
  • Site-wide: 119,729
  • In health policy: 275
• Year to date:
  • Site-wide: 27,144
• Since beginning of last month:
  • Site-wide: 52,181

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

• Downloaded 194 times
• Download rankings, all-time:
  • Site-wide: 120,465
  • In genetics: 5,059
• Year to date:
  • Site-wide: 66,975
• Since beginning of last month:
  • Site-wide: 108,346

Genome engineering of Nannochloropsis with large deletions for constructing microalgal minigenomes

• Downloaded 178 times
• Download rankings, all-time:
  • Site-wide: 124,394
  • In biochemistry: 3,712
• Year to date:
  • Site-wide: 84,843
• Since beginning of last month:
  • Site-wide: 54,731

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

• Downloaded 177 times
• Download rankings, all-time:
  • Site-wide: 124,585
  • In genetics: 5,171
• Year to date:
  • Site-wide: 30,833
• Since beginning of last month:
  • Site-wide: 84,520

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

• Downloaded 158 times
• Download rankings, all-time:
  • Site-wide: 128,834
  • In genetics: 5,307
• Year to date:
  • Site-wide: 59,198
• Since beginning of last month:
  • Site-wide: 101,042

HPRep: Quantifying reproducibility in HiChIP and PLAC-seq datasets

• Downloaded 140 times
• Download rankings, all-time:
  • Site-wide: 132,919
  • In genomics: 7,065
• Year to date:
  • Site-wide: 71,466
• Since beginning of last month:
  • Site-wide: 74,327