Author: Yun Li

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Preprints

Uncovering Cross-Cohort Molecular Features with Multi-Omics Integration Analysis

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

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

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An epigenetic biomarker of aging for lifespan and healthspan

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  • Site-wide: 6,278
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Using three-dimensional regulatory chromatin interactions from adult and fetal cortex to interpret genetic results for psychiatric disorders and cognitive traits

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

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

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

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

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The Polygenic and Monogenic Basis of Blood Traits and Diseases

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Common genetic variation influencing human white matter microstructure

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

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  • Site-wide: 14,356
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The Big Five, Self-efficacy, and Self-control in Boxers

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

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

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

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

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

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

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Macrophages regulate gastrointestinal motility through complement component 1q

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

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  • Site-wide: 26,280
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A comprehensive comparison on cell type composition inference for spatial transcriptomics data

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  • Site-wide: 29,051
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  • Site-wide: 2,545
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MOSTWAS: Multi-Omic Strategies for Transcriptome-Wide Association Studies

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

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

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  • Site-wide: 31,904
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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

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  • Site-wide: 33,627
  • In genetics: 1,353
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  • Site-wide: 36,131

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

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  • Site-wide: 35,297
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Whole genome sequencing association analysis of quantitative red blood cell phenotypes: the NHLBI TOPMed program

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  • Site-wide: 38,655
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  • Site-wide: 106,244

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

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  • Site-wide: 41,329
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SnapHiC: a computational pipeline to map chromatin contacts from single cell Hi-C data

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  • Site-wide: 43,239
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  • Site-wide: 177,847

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

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  • Site-wide: 44,141
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  • Site-wide: 120,034

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

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  • Site-wide: 45,026
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  • Site-wide: 208,556
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  • Site-wide: 162,445

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

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  • Site-wide: 45,212
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  • Site-wide: 22,128
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  • Site-wide: 46,336

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

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  • Site-wide: 45,707
  • In genomics: 3,419
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  • Site-wide: 142,954

HUGIn: Hi-C Unifying Genomic Interrogator

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  • Site-wide: 54,236
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Multi-SNP Mediation Intersection-Union Test

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  • Site-wide: 55,935
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  • Site-wide: 208,223
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From GWAS Variant to Function: a Study of ~148,000 Variants for Blood Cell Traits.

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  • Site-wide: 58,185
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  • Site-wide: 22,103
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  • Site-wide: 97,869

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

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  • Site-wide: 58,556
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Association between ApoE polymorphism and type 2 diabetes: A meta-analysis of 59 studies

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  • Site-wide: 59,712
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Overarching control of autophagy and DNA damage response by CHD6 revealed by modeling a rare human pathology

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  • Site-wide: 60,937
  • In cell biology: 2,524
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  • Site-wide: 127,829

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

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  • Site-wide: 63,780
  • In bioinformatics: 5,908
• Year to date:
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  • Site-wide: 154,763

TWO-SIGMA-G: A New Competitive Gene Set Testing Framework for scRNA-seq Data Accounting for Inter-Gene and Cell-Cell Correlation

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  • Site-wide: 71,371
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FIREcaller: Detecting Frequently Interacting Regions from Hi-C Data

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

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

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

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Genetic influences on the intrinsic and extrinsic functional organizations of the cerebral cortex

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

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Transcriptome-wide association study in UK Biobank Europeans identifies associations with blood cell traits.

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

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Whole genome sequencing identifies common and rare structural variants contributing to hematologic traits in the NHLBI TOPMed program

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  • Site-wide: 99,857
  • In genetic and genomic medicine: 696
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  • Site-wide: 24,058

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

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  • Site-wide: 103,319
  • In bioinformatics: 8,607
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  • Site-wide: 151,708
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  • Site-wide: 188,643

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

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  • Site-wide: 106,713
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Integrative methylome and transcriptome analysis of Japanese flounder (Paralichthys olivaceus) skeletal muscle during development

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  • Site-wide: 115,798
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The efficacy and safety of bamlanivimab treatment against COVID-19: A meta-analysis

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

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  • Site-wide: 119,072
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Genetic Examination of Hematological Parameters in SARS-CoV-2 Infection and COVID-19

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  • Site-wide: 23,507

Cell type-specific Expression Quantitative Trait Loci

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

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  • Site-wide: 131,670
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Generalized Multi-SNP Mediation Intersection-Union Test

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  • Site-wide: 141,222
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  • Site-wide: 197,702
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  • Site-wide: 134,239

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

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  • Site-wide: 142,767
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eSCAN: Scan Regulatory Regions for Aggregate Association Testing using Whole Genome Sequencing Data

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  • Site-wide: 80,286

Improving polygenic risk prediction in admixed populations by explicitly modeling ancestral-specific effects via GAUDI

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  • Site-wide: 144,573
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Genome engineering of Nannochloropsis with large deletions for constructing microalgal minigenomes

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  • Site-wide: 149,321
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  • Site-wide: 131,972

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

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  • Site-wide: 153,855
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HPRep: Quantifying reproducibility in HiChIP and PLAC-seq datasets

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Brain injury accelerates the onset of a reversible age-related microglial phenotype associated with hyperphagocytosis and inflammatory neurodegeneration

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Leveraging TOPMed Imputation Server and Constructing a Cohort-Specific Imputation Reference Panel to Enhance Genotype Imputation among Cystic Fibrosis Patients

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A brain structural connectivity biomarker for diagnosis of autism spectrum disorder in early childhood

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  • Site-wide: 179,759
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SnapHiC-D: a computational pipeline to identify differential chromatin contacts from single cell Hi-C data

• Downloaded 193 times
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  • Site-wide: 183,282
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Genetic influences on the shape of brain ventricular and subcortical structures

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pVHL regulates protein stability of TCF/LEF transcription factor family via ubiquitin-independent proteasomal degradation

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A Semi-Supervised Ensemble Approach to Rank Potential Causal Variants and Their Target Genes in Microglia for Alzheimer's Disease

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  • Site-wide: 7,138