Author: Ming Hu

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Preprints

Caution on Kidney Dysfunctions of 2019-nCoV Patients

• Downloaded 13,332 times
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  • Site-wide: 939
  • In infectious diseases: 310
• Year to date:
  • Site-wide: 5,694
• Since beginning of last month:
  • Site-wide: 8,998

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

• Downloaded 9,791 times
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  • Site-wide: 1,376
  • In genetics: 27
• Year to date:
  • Site-wide: 39,599
• Since beginning of last month:
  • Site-wide: 24,738

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

• Downloaded 3,186 times
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  • Site-wide: 6,531
  • In genetics: 246
• Year to date:
  • Site-wide: 10,839
• Since beginning of last month:
  • Site-wide: 8,232

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

• Downloaded 3,153 times
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  • Site-wide: 6,632
  • In bioinformatics: 592
• Year to date:
  • Site-wide: 94,677
• Since beginning of last month:
  • Site-wide: 96,119

Histone H3 Lysine 4 methyltransferases MLL3 and MLL4 Modulate Long-range Chromatin Interactions at Enhancers

• Downloaded 2,734 times
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  • Site-wide: 8,112
  • In genomics: 745
• Year to date:
  • Site-wide: 122,676
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  • Site-wide: 49,332

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

• Downloaded 2,414 times
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  • Site-wide: 9,769
  • In genomics: 944
• Year to date:
  • Site-wide: 19,427
• Since beginning of last month:
  • Site-wide: 15,547

HiCPlus: Resolution Enhancement of Hi-C interaction heatmap

• Downloaded 2,315 times
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  • Site-wide: 10,427
  • In bioinformatics: 1,062
• Year to date:
  • Site-wide: 124,848
• Since beginning of last month:
  • Site-wide: 69,770

CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains

• Downloaded 2,205 times
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  • Site-wide: 11,212
  • In molecular biology: 249
• Year to date:
  • Site-wide: 71,421
• Since beginning of last month:
  • Site-wide: 102,938

Removing unwanted variation between samples in Hi-C experiments

• Downloaded 2,080 times
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  • Site-wide: 12,259
  • In genomics: 1,118
• Year to date:
  • Site-wide: 13,647
• Since beginning of last month:
  • Site-wide: 30,221

CTCF Promotes Long-range Enhancer-promoter Interactions and Lineage-specific Gene Expression in Mammalian Cells

• Downloaded 2,049 times
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  • Site-wide: 12,524
  • In genomics: 1,144
• Year to date:
  • Site-wide: 58,497
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  • Site-wide: 23,005

Long-term labeling and imaging of synaptically-connected neuronal networks in vivo using nontoxic, double-deletion-mutant rabies viruses

• Downloaded 1,925 times
• Download rankings, all-time:
  • Site-wide: 13,781
  • In neuroscience: 1,406
• Year to date:
  • Site-wide: 9,563
• Since beginning of last month:
  • Site-wide: 26,984

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

• Downloaded 1,690 times
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  • Site-wide: 16,772
  • In genomics: 1,513
• Year to date:
  • Site-wide: 68,246
• Since beginning of last month:
  • Site-wide: 37,130

Reliable sensory processing in mouse visual cortex through inhibitory interactions between Somatostatin and Parvalbumin interneurons

• Downloaded 1,652 times
• Download rankings, all-time:
  • Site-wide: 17,416
  • In neuroscience: 1,928
• Year to date:
  • Site-wide: 64,725
• Since beginning of last month:
  • Site-wide: 44,254

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

• Downloaded 1,581 times
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  • Site-wide: 18,650
  • In genomics: 1,633
• Year to date:
  • Site-wide: 180,245
• Since beginning of last month:
  • Site-wide: 124,801

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

• Downloaded 1,405 times
• Download rankings, all-time:
  • Site-wide: 22,534
  • In bioinformatics: 2,412
• Year to date:
  • Site-wide: 84,326
• Since beginning of last month:
  • Site-wide: 68,267

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

• Downloaded 1,149 times
• Download rankings, all-time:
  • Site-wide: 30,996
  • In genomics: 2,544
• Year to date:
  • Site-wide: 38,951
• Since beginning of last month:
  • Site-wide: 85,322

Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues

• Downloaded 978 times
• Download rankings, all-time:
  • Site-wide: 39,668
  • In developmental biology: 884
• Year to date:
  • Site-wide: 3,501
• Since beginning of last month:
  • Site-wide: 17,221

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

• Downloaded 925 times
• Download rankings, all-time:
  • Site-wide: 43,182
  • In bioinformatics: 4,363
• Year to date:
  • Site-wide: 106,892
• Since beginning of last month:
  • Site-wide: 175,429

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

• Downloaded 891 times
• Download rankings, all-time:
  • Site-wide: 45,668
  • In genomics: 3,419
• Year to date:
  • Site-wide: 93,283
• Since beginning of last month:
  • Site-wide: 129,134

In V4, pair-wise synchrony and correlations depend on the structure of the population code

• Downloaded 866 times
• Download rankings, all-time:
  • Site-wide: 47,770
  • In neuroscience: 6,232
• Year to date:
  • Site-wide: 122,550
• Since beginning of last month:
  • Site-wide: 49,464

Learning from invariants predicts upcoming behavioral choice from spiking activity in monkey V1

• Downloaded 818 times
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  • Site-wide: 52,056
  • In neuroscience: 6,849
• Year to date:
  • Site-wide: 44,066
• Since beginning of last month:
  • Site-wide: 141,708

Cellular and Circuit Organization of the Locus Coeruleus of Adult Mice

• Downloaded 802 times
• Download rankings, all-time:
  • Site-wide: 53,549
  • In neuroscience: 8,855
• Year to date:
  • Site-wide: 4,845
• Since beginning of last month:
  • Site-wide: 11,775

HUGIn: Hi-C Unifying Genomic Interrogator

• Downloaded 796 times
• Download rankings, all-time:
  • Site-wide: 54,237
  • In genetics: 2,087
• Year to date:
  • Site-wide: 194,627
• Since beginning of last month:
  • Site-wide: 148,357

BAMM-SC: A Bayesian mixture model for clustering droplet-based single cell transcriptomic data from population studies

• Downloaded 778 times
• Download rankings, all-time:
  • Site-wide: 56,026
  • In bioinformatics: 5,398
• Year to date:
  • Site-wide: 153,221
• Since beginning of last month:
  • Site-wide: 107,517

Integrative analyses of multi-tissue Hi-C and eQTL data demonstrate close spatial proximity between eQTLs and their target genes

• Downloaded 679 times
• Download rankings, all-time:
  • Site-wide: 68,130
  • In systems biology: 1,339
• Year to date:
  • Site-wide: 150,530
• Since beginning of last month:
  • Site-wide: 149,803

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

• Downloaded 657 times
• Download rankings, all-time:
  • Site-wide: 71,345
  • In genomics: 4,831
• Year to date:
  • Site-wide: 29,228
• Since beginning of last month:
  • Site-wide: 56,553

FIREcaller: Detecting Frequently Interacting Regions from Hi-C Data

• Downloaded 656 times
• Download rankings, all-time:
  • Site-wide: 71,440
  • In bioinformatics: 6,589
• Year to date:
  • Site-wide: 160,159
• Since beginning of last month:
  • Site-wide: 127,083

Transcriptional Network Orchestrating Regional Patterning of Cortical Progenitors

• Downloaded 654 times
• Download rankings, all-time:
  • Site-wide: 71,715
  • In neuroscience: 9,733
• Year to date:
  • Site-wide: 139,579
• Since beginning of last month:
  • Site-wide: 185,606

Label-free characterization of visual cortical areas in awake mice via three-photon microscopy reveals correlations between functional maps and structural substrates

• Downloaded 635 times
• Download rankings, all-time:
  • Site-wide: 74,665
  • In neuroscience: 10,297
• Year to date:
  • Site-wide: 178,092
• Since beginning of last month:
  • Site-wide: 139,145

A Network-based Deep Learning Framework Catalyzes GWAS and Multi-Omics Findings to Biology and Drug Repurposing for Alzheimer's Disease

• Downloaded 551 times
• Download rankings, all-time:
  • Site-wide: 89,269
  • In bioinformatics: 8,519
• Year to date:
  • Site-wide: 32,585
• Since beginning of last month:
  • Site-wide: 33,534

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

• Downloaded 486 times
• Download rankings, all-time:
  • Site-wide: 103,120
  • In bioinformatics: 8,607
• Year to date:
  • Site-wide: 151,262
• Since beginning of last month:
  • Site-wide: 182,089

Reading-out task variables as a low-dimensional reconstruction of neural spike trains in single trials

• Downloaded 447 times
• Download rankings, all-time:
  • Site-wide: 112,380
  • In neuroscience: 15,894
• Year to date:
  • Site-wide: 167,182
• Since beginning of last month:
  • Site-wide: 198,860

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

• Downloaded 376 times
• Download rankings, all-time:
  • Site-wide: 131,753
  • In bioinformatics: 10,409
• Year to date:
  • Site-wide: 178,304
• Since beginning of last month:
  • Site-wide: 178,852

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

• Downloaded 338 times
• Download rankings, all-time:
  • Site-wide: 142,912
  • In genetics: 5,224
• Year to date:
  • Site-wide: 120,273
• Since beginning of last month:
  • Site-wide: 191,594

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

• Downloaded 301 times
• Download rankings, all-time:
  • Site-wide: 154,022
  • In genetics: 5,697
• Year to date:
  • Site-wide: 175,002
• Since beginning of last month:
  • Site-wide: 119,271

HPRep: Quantifying reproducibility in HiChIP and PLAC-seq datasets

• Downloaded 274 times
• Download rankings, all-time:
  • Site-wide: 161,970
  • In genomics: 8,015
• Year to date:
  • Site-wide: 200,587
• Since beginning of last month:
  • Site-wide: 182,395

Chromatin 3D interaction analysis of the STARD10 locus unveils FCHSD2 as a new regulator of insulin secretion

• Downloaded 268 times
• Download rankings, all-time:
  • Site-wide: 163,775
  • In cell biology: 7,556
• Year to date:
  • Site-wide: 143,568
• Since beginning of last month:
  • Site-wide: 59,151

Sexually dimorphic roles for the type 2 diabetes-associated C2cd4b gene in murine glucose homeostasis

• Downloaded 258 times
• Download rankings, all-time:
  • Site-wide: 166,359
  • In genetics: 6,044
• Year to date:
  • Site-wide: 151,918
• Since beginning of last month:
  • Site-wide: 143,665

SnapHiC-D: a computational pipeline to identify differential chromatin contacts from single cell Hi-C data

• Downloaded 193 times
• Download rankings, all-time:
  • Site-wide: 183,297
  • In bioinformatics: None
• Year to date:
  • Site-wide: 47,025
• Since beginning of last month:
  • Site-wide: 36,274