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Author: Howard Y. Chang

Rankings

  • All-time downloads: 132,264 (rank: 943 )
  • Categories:
    • bioinformatics: 3,151 (rank: 5,294 (tie) )
    • cancer biology: 6,968 (rank: 454 )
    • cell biology: 11,858 (rank: 363 )
    • developmental biology: 523 (rank: 12,063 (tie) )
    • evolutionary biology: 1,673 (rank: 4,289 (tie) )
    • genetics: 2,919 (rank: 7,004 (tie) )
    • genomics: 68,894 (rank: 142 )
    • immunology: 12,817 (rank: 830 )
    • microbiology: 3,137 (rank: 5,891 (tie) )
    • molecular biology: 9,814 (rank: 290 )
    • neuroscience: 10,510 (rank: 1,590 )

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Preprints

Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH

cancer biology more details view paper

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Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

genomics more details view paper
  • Downloaded 13,558 times
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    • Site-wide: 734
    • In genomics: 42
  • Year to date:
    • Site-wide: 6,608
  • Since beginning of last month:
    • Site-wide: 12,531

Atlas of Subcellular RNA Localization Revealed by APEX-seq

cell biology more details view paper
  • Downloaded 9,217 times
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    • Site-wide: 1,197
    • In cell biology: 14
  • Year to date:
    • Site-wide: 43,374
  • Since beginning of last month:
    • Site-wide: 73,421

ArchR: An integrative and scalable software package for single-cell chromatin accessibility analysis

genomics more details view paper
  • Downloaded 6,679 times
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    • Site-wide: 1,803
    • In genomics: 138
  • Year to date:
    • Site-wide: 2,948
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    • Site-wide: 13,226

Clonal replacement of tumor-specific T cells following PD-1 blockade

immunology more details view paper
  • Downloaded 6,561 times
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    • Site-wide: 1,853
    • In immunology: 63
  • Year to date:
    • Site-wide: 26,908
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    • Site-wide: 47,013

Single-cell epigenomic identification of inherited risk loci in Alzheimer's and Parkinson's disease

genomics more details view paper
  • Downloaded 6,035 times
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    • Site-wide: 2,069
    • In genomics: 166
  • Year to date:
    • Site-wide: 5,505
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A single cell framework for multi-omic analysis of disease identifies malignant regulatory signatures in mixed phenotype acute leukemia

genomics more details view paper
  • Downloaded 5,758 times
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    • Site-wide: 2,208
    • In genomics: 182
  • Year to date:
    • Site-wide: 13,485
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    • Site-wide: 33,211

Single-cell epigenomics maps the continuous regulatory landscape of human hematopoietic differentiation

genomics more details view paper
  • Downloaded 5,733 times
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    • Site-wide: 2,221
    • In genomics: 183
  • Year to date:
    • Site-wide: 69,382
  • Since beginning of last month:
    • Site-wide: 59,896

Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution

neuroscience more details view paper
  • Downloaded 5,598 times
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    • Site-wide: 2,288
    • In neuroscience: 119
  • Year to date:
    • Site-wide: 575
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    • Site-wide: 968

Genetic determinants of co-accessible chromatin regions in T cell activation across humans

genomics more details view paper
  • Downloaded 5,169 times
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    • Site-wide: 2,564
    • In genomics: 232
  • Year to date:
    • Site-wide: 63,566
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    • Site-wide: 51,786

Coupled single-cell CRISPR screening and epigenomic profiling reveals causal gene regulatory networks

genomics more details view paper
  • Downloaded 4,630 times
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    • Site-wide: 2,980
    • In genomics: 283
  • Year to date:
    • Site-wide: 71,409
  • Since beginning of last month:
    • Site-wide: 126,822

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

genomics more details view paper
  • Downloaded 4,589 times
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    • Site-wide: 3,014
    • In genomics: 289
  • Year to date:
    • Site-wide: 41,742
  • Since beginning of last month:
    • Site-wide: 66,624

Super-resolution Imaging Reveals 3D Structure and Organizing Mechanism of Accessible Chromatin

molecular biology more details view paper
  • Downloaded 3,691 times
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    • Site-wide: 4,078
    • In molecular biology: 84
  • Year to date:
    • Site-wide: 29,762
  • Since beginning of last month:
    • Site-wide: 47,446

EcDNA hubs drive cooperative intermolecular oncogene expression

cancer biology more details view paper
  • Downloaded 3,538 times
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    • Site-wide: 4,333
    • In cancer biology: 59
  • Year to date:
    • Site-wide: 1,539
  • Since beginning of last month:
    • Site-wide: 1,508

Transient "rest" induces functional reinvigoration and epigenetic remodeling in exhausted CAR-T cells

immunology more details view paper
  • Downloaded 3,390 times
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    • Site-wide: 4,621
    • In immunology: 163
  • Year to date:
    • Site-wide: 6,094
  • Since beginning of last month:
    • Site-wide: 29,701

Enhancer connectome in primary human cells reveals target genes of disease-associated DNA elements

genomics more details view paper
  • Downloaded 3,261 times
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    • Site-wide: 4,878
    • In genomics: 479
  • Year to date:
    • Site-wide: 83,762
  • Since beginning of last month:
    • Site-wide: 77,512

Systematic discovery and functional interrogation of SARS-CoV-2 viral RNA-host protein interactions during infection

microbiology more details view paper
  • Downloaded 3,137 times
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    • Site-wide: 5,157
    • In microbiology: 344
  • Year to date:
    • Site-wide: 4,059
  • Since beginning of last month:
    • Site-wide: 14,791

HiChIP: Efficient and sensitive analysis of protein-directed genome architecture

genomics more details view paper
  • Downloaded 2,744 times
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    • Site-wide: 6,257
    • In genomics: 628
  • Year to date:
    • Site-wide: 103,732
  • Since beginning of last month:
    • Site-wide: 95,008

Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity

genomics more details view paper
  • Downloaded 2,648 times
  • Download rankings, all-time:
    • Site-wide: 6,584
    • In genomics: 662
  • Year to date:
    • Site-wide: 78,635
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    • Site-wide: 137,011

B cell-specific XIST complex enforces X-inactivation and restrains atypical B cells

genomics more details view paper
  • Downloaded 2,417 times
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    • Site-wide: 7,562
    • In genomics: 768
  • Year to date:
    • Site-wide: 1,563
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    • Site-wide: 6,636

Cerebellar nuclei evolved by repeatedly duplicating a conserved cell type set

neuroscience more details view paper
  • Downloaded 2,333 times
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    • Site-wide: 7,972
    • In neuroscience: 749
  • Year to date:
    • Site-wide: 12,796
  • Since beginning of last month:
    • Site-wide: 13,704

Dynamic Regulation of RNA Structure in Mammalian Cells

molecular biology more details view paper
  • Downloaded 2,211 times
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    • Site-wide: 8,630
    • In molecular biology: 208
  • Year to date:
    • Site-wide: 64,949
  • Since beginning of last month:
    • Site-wide: 66,167

The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation

genomics more details view paper
  • Downloaded 2,001 times
  • Download rankings, all-time:
    • Site-wide: 10,012
    • In genomics: 983
  • Year to date:
    • Site-wide: 5,079
  • Since beginning of last month:
    • Site-wide: 11,190

Single-cell lineage tracing by endogenous mutations enriched in transposase accessible mitochondrial DNA

genomics more details view paper
  • Downloaded 1,984 times
  • Download rankings, all-time:
    • Site-wide: 10,120
    • In genomics: 994
  • Year to date:
    • Site-wide: 98,089
  • Since beginning of last month:
    • Site-wide: 42,998

Frequent extrachromosomal oncogene amplification drives aggressive tumors

cancer biology more details view paper
  • Downloaded 1,978 times
  • Download rankings, all-time:
    • Site-wide: 10,168
    • In cancer biology: 184
  • Year to date:
    • Site-wide: 25,388
  • Since beginning of last month:
    • Site-wide: 40,228

Polycomb-mediated Genome Architecture Enables Long-range Spreading of H3K27 methylation

genetics more details view paper
  • Downloaded 1,679 times
  • Download rankings, all-time:
    • Site-wide: 12,990
    • In genetics: 561
  • Year to date:
    • Site-wide: 8,617
  • Since beginning of last month:
    • Site-wide: 12,052

Evolutionary dynamics of roX lncRNA function and genomic occupancy

evolutionary biology more details view paper
  • Downloaded 1,673 times
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    • Site-wide: 13,057
    • In evolutionary biology: 385
  • Year to date:
    • Site-wide: 142,583
  • Since beginning of last month:
    • Site-wide: 139,343

RNA-GPS Predicts SARS-CoV-2 RNA Localization to Host Mitochondria and Nucleolus

bioinformatics more details view paper
  • Downloaded 1,590 times
  • Download rankings, all-time:
    • Site-wide: 14,043
    • In bioinformatics: 1,562
  • Year to date:
    • Site-wide: 40,315
  • Since beginning of last month:
    • Site-wide: 126,244

Principles of ecDNA random inheritance drive rapid genome change and therapy resistance in human cancers

cancer biology more details view paper
  • Downloaded 1,452 times
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    • Site-wide: 16,279
    • In cancer biology: 350
  • Year to date:
    • Site-wide: 3,141
  • Since beginning of last month:
    • Site-wide: 3,671

Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2

immunology more details view paper
  • Downloaded 1,379 times
  • Download rankings, all-time:
    • Site-wide: 17,617
    • In immunology: 615
  • Year to date:
    • Site-wide: 40,930
  • Since beginning of last month:
    • Site-wide: 135,841

Structural modularity of the XIST ribonucleoprotein complex

molecular biology more details view paper
  • Downloaded 1,319 times
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    • Site-wide: 18,840
    • In molecular biology: 506
  • Year to date:
    • Site-wide: 64,309
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    • Site-wide: 84,211

Functional classification of noncoding RNAs associated with distinct histone modifications by PIRCh-seq

cell biology more details view paper
  • Downloaded 1,140 times
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    • Site-wide: 23,459
    • In cell biology: 810
  • Year to date:
    • Site-wide: 78,025
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    • Site-wide: 104,507

Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons

neuroscience more details view paper
  • Downloaded 1,062 times
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    • Site-wide: 26,203
    • In neuroscience: 3,265
  • Year to date:
    • Site-wide: 123,698
  • Since beginning of last month:
    • Site-wide: 123,965

Feedback Regulation between Initiation and Maturation Networks Orchestrates the Chromatin Dynamics of Epidermal Lineage Commitment

cell biology more details view paper
  • Downloaded 904 times
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    • Site-wide: 33,195
    • In cell biology: 1,272
  • Year to date:
    • Site-wide: 111,895
  • Since beginning of last month:
    • Site-wide: 95,582

PEPATAC: An optimized pipeline for ATAC-seq data analysis with serial alignments

genomics more details view paper
  • Downloaded 884 times
  • Download rankings, all-time:
    • Site-wide: 34,288
    • In genomics: 2,875
  • Year to date:
    • Site-wide: 9,803
  • Since beginning of last month:
    • Site-wide: 4,079

A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis

neuroscience more details view paper
  • Downloaded 867 times
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    • Site-wide: 35,187
    • In neuroscience: 4,642
  • Year to date:
    • Site-wide: 20,652
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    • Site-wide: 18,405

CRISPRpic: Fast and precise analysis for CRISPR-induced mutations via prefixed index counting

bioinformatics more details view paper
  • Downloaded 831 times
  • Download rankings, all-time:
    • Site-wide: 37,508
    • In bioinformatics: 4,026
  • Year to date:
    • Site-wide: 137,881
  • Since beginning of last month:
    • Site-wide: 146,105

Satb1 integrates DNA sequence, shape, motif density and torsional stress to differentially bind targets in nucleosome-dense regions.

molecular biology more details view paper
  • Downloaded 815 times
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    • Site-wide: 38,574
    • In molecular biology: 1,073
  • Year to date:
    • Site-wide: 121,963
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    • Site-wide: 94,817

Exploring the role of Polycomb recruitment in Xist-mediated silencing of the X chromosome in ES cells

genetics more details view paper
  • Downloaded 809 times
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    • Site-wide: 38,987
    • In genetics: 1,689
  • Year to date:
    • Site-wide: 88,937
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    • Site-wide: 105,981

Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation

genomics more details view paper
  • Downloaded 804 times
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    • Site-wide: 39,335
    • In genomics: 3,181
  • Year to date:
    • Site-wide: 87,548
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    • Site-wide: 26,580

KLF4 Recruits SWI/SNF to Increase Chromatin Accessibility and Reprogram the Endothelial Enhancer Landscape under Laminar Shear Stress

molecular biology more details view paper
  • Downloaded 791 times
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    • Site-wide: 40,270
    • In molecular biology: 1,118
  • Year to date:
    • Site-wide: 20,061
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    • Site-wide: 24,976

Macrophage inflammatory and regenerative response periodicity is programmed by cell cycle and chromatin state

immunology more details view paper
  • Downloaded 750 times
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    • Site-wide: 43,471
    • In immunology: 1,397
  • Year to date:
    • Site-wide: 8,544
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    • Site-wide: 12,398

Integrative analysis of single cell genomics data by coupled nonnegative matrix factorizations

bioinformatics more details view paper
  • Downloaded 730 times
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    • Site-wide: 45,173
    • In bioinformatics: 4,714
  • Year to date:
    • Site-wide: 159,991
  • Since beginning of last month:
    • Site-wide: 163,889

The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders

neuroscience more details view paper
  • Downloaded 650 times
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    • Site-wide: 52,971
    • In neuroscience: 7,484
  • Year to date:
    • Site-wide: 110,308
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    • Site-wide: 63,257

RNA-BINDING PROTEINS DIRECT MYOGENIC CELL FATE DECISIONS

molecular biology more details view paper
  • Downloaded 603 times
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    • Site-wide: 58,467
    • In molecular biology: 1,658
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    • Site-wide: 12,060
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    • Site-wide: 39,859

The Autism Risk Factor CHD8 Is a Chromatin Activator and Functionally Dependent on the ERK-MAPK Pathway Effector ELK1

cell biology more details view paper
  • Downloaded 597 times
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    • Site-wide: 59,163
    • In cell biology: 2,595
  • Year to date:
    • Site-wide: 19,270
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    • Site-wide: 44,676

Clonal inactivation of telomerase promotes accelerated stem cell differentiation

developmental biology more details view paper
  • Downloaded 523 times
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    • Site-wide: 69,527
    • In developmental biology: 1,740
  • Year to date:
    • Site-wide: 15,000
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    • Site-wide: 2,622

Morphogen-Lineage Selector Interactions During Surface Epithelial Commitment

genetics more details view paper
  • Downloaded 431 times
  • Download rankings, all-time:
    • Site-wide: 85,973
    • In genetics: 3,604
  • Year to date:
    • Site-wide: 143,107
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    • Site-wide: 115,324

Distinct T cell chromatin landscapes in scleroderma subtypes

immunology more details view paper
  • Downloaded 396 times
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    • Site-wide: 93,417
    • In immunology: 2,824
  • Year to date:
    • Site-wide: 23,078
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    • Site-wide: 49,989

Locus specific epigenetic modalities of random allelic expression imbalance

molecular biology more details view paper
  • Downloaded 384 times
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    • Site-wide: 96,126
    • In molecular biology: 2,844
  • Year to date:
    • Site-wide: 24,226
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    • Site-wide: 55,210

Integrative profiling of early host chromatin accessibility responses in human neutrophils with sensitive pathogen detection.

immunology more details view paper
  • Downloaded 341 times
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    • Site-wide: 106,308
    • In immunology: 3,186
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