Author: Katherine S. Pollard

Downloads per author, site-wide

Preprints

Direct detection of SARS-CoV-2 using CRISPR-Cas13a and a mobile phone

• Downloaded 12,665 times
• Download rankings, all-time:
  • Site-wide: 931
  • In infectious diseases: 307
• Year to date:
  • Site-wide: 8,657
• Since beginning of last month:
  • Site-wide: 7,371

Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates

• Downloaded 10,228 times
• Download rankings, all-time:
  • Site-wide: 1,227
  • In genomics: 75
• Year to date:
  • Site-wide: 13,145
• Since beginning of last month:
  • Site-wide: 9,498

Single cell epigenomic atlas of the developing human brain and organoids

• Downloaded 7,995 times
• Download rankings, all-time:
  • Site-wide: 1,665
  • In developmental biology: 10
• Year to date:
  • Site-wide: 16,363
• Since beginning of last month:
  • Site-wide: 12,020

A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome

• Downloaded 3,970 times
• Download rankings, all-time:
  • Site-wide: 4,237
  • In microbiology: 280
• Year to date:
  • Site-wide: 36,166
• Since beginning of last month:
  • Site-wide: 50,653

American Gut: an Open Platform for Citizen-Science Microbiome Research

• Downloaded 3,929 times
• Download rankings, all-time:
  • Site-wide: 4,287
  • In microbiology: 283
• Year to date:
  • Site-wide: 70,461
• Since beginning of last month:
  • Site-wide: 149,537

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

• Downloaded 3,928 times
• Download rankings, all-time:
  • Site-wide: 4,289
  • In evolutionary biology: 64
• Year to date:
  • Site-wide: 80,019
• Since beginning of last month:
  • Site-wide: 98,418

Predicting 3D genome folding from DNA sequence

• Downloaded 3,905 times
• Download rankings, all-time:
  • Site-wide: 4,321
  • In genomics: 401
• Year to date:
  • Site-wide: 45,588
• Since beginning of last month:
  • Site-wide: None

Massively parallel dissection of human accelerated regions in human and chimpanzee neural progenitors

• Downloaded 3,438 times
• Download rankings, all-time:
  • Site-wide: 5,204
  • In evolutionary biology: 95
• Year to date:
  • Site-wide: 16,526
• Since beginning of last month:
  • Site-wide: 15,132

An integrated metagenomics pipeline for strain profiling reveals novel patterns of transmission and global biogeography of bacteria

• Downloaded 3,292 times
• Download rankings, all-time:
  • Site-wide: 5,546
  • In genomics: 507
• Year to date:
  • Site-wide: 43,799
• Since beginning of last month:
  • Site-wide: 76,983

Transcription Factors Recognize DNA Shape Without Nucleotide Recognition

• Downloaded 2,771 times
• Download rankings, all-time:
  • Site-wide: 7,100
  • In systems biology: 100
• Year to date:
  • Site-wide: 141,439
• Since beginning of last month:
  • Site-wide: 102,687

Chromatin features constrain structural variation across evolutionary timescales

• Downloaded 2,673 times
• Download rankings, all-time:
  • Site-wide: 7,487
  • In genomics: 690
• Year to date:
  • Site-wide: 146,711
• Since beginning of last month:
  • Site-wide: 135,037

Accelerated RNA detection using tandem CRISPR nucleases

• Downloaded 2,333 times
• Download rankings, all-time:
  • Site-wide: 9,165
  • In infectious diseases: 1,538
• Year to date:
  • Site-wide: 11,026
• Since beginning of last month:
  • Site-wide: 7,406

Principles of Meiotic Chromosome Assembly

• Downloaded 2,076 times
• Download rankings, all-time:
  • Site-wide: 10,892
  • In molecular biology: 253
• Year to date:
  • Site-wide: 112,929
• Since beginning of last month:
  • Site-wide: 150,910

A high-resolution, chromosome-assigned Komodo dragon genome reveals adaptations in the cardiovascular, muscular, and chemosensory systems of monitor lizards

• Downloaded 2,028 times
• Download rankings, all-time:
  • Site-wide: 11,282
  • In genomics: 1,065
• Year to date:
  • Site-wide: 40,641
• Since beginning of last month:
  • Site-wide: 47,442

Molecular basis of CTCF binding polarity in genome folding

• Downloaded 1,871 times
• Download rankings, all-time:
  • Site-wide: 12,710
  • In molecular biology: 308
• Year to date:
  • Site-wide: 151,748
• Since beginning of last month:
  • Site-wide: 170,120

Average genome size estimation enables accurate quantification of gene family abundance and sheds light on the functional ecology of the human microbiome

• Downloaded 1,786 times
• Download rankings, all-time:
  • Site-wide: 13,570
  • In bioinformatics: 1,389
• Year to date:
  • Site-wide: 160,688
• Since beginning of last month:
  • Site-wide: 167,626

Topical Silver Diamine Fluoride For Dental Caries Arrest In Preschool Children: A Randomized Controlled Trial

• Downloaded 1,733 times
• Download rankings, all-time:
  • Site-wide: 14,226
  • In clinical trials: 28
• Year to date:
  • Site-wide: 85,607
• Since beginning of last month:
  • Site-wide: 52,008

Phylogeny-corrected identification of microbial gene families relevant to human gut colonization

• Downloaded 1,620 times
• Download rankings, all-time:
  • Site-wide: 15,698
  • In bioinformatics: 1,618
• Year to date:
  • Site-wide: 156,760
• Since beginning of last month:
  • Site-wide: 134,828

Proteobacteria drive significant functional variability in the human gut microbiome

• Downloaded 1,518 times
• Download rankings, all-time:
  • Site-wide: 17,377
  • In bioinformatics: 1,837
• Year to date:
  • Site-wide: 112,736
• Since beginning of last month:
  • Site-wide: 98,725

Most regulatory interactions are not in linkage disequilibrium

• Downloaded 1,505 times
• Download rankings, all-time:
  • Site-wide: 17,594
  • In genomics: 1,576
• Year to date:
  • Site-wide: 127,857
• Since beginning of last month:
  • Site-wide: 167,094

Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment

• Downloaded 1,505 times
• Download rankings, all-time:
  • Site-wide: 17,603
  • In microbiology: 992
• Year to date:
  • Site-wide: 54,064
• Since beginning of last month:
  • Site-wide: 136,270

A Chromatin Accessibility Atlas of the Developing Human Telencephalon

• Downloaded 1,419 times
• Download rankings, all-time:
  • Site-wide: 19,237
  • In neuroscience: 2,139
• Year to date:
  • Site-wide: 52,734
• Since beginning of last month:
  • Site-wide: 143,356

Genomic analyses for age at menarche identify 389 independent signals and indicate BMI-independent effects of puberty timing on cancer susceptibility

• Downloaded 1,360 times
• Download rankings, all-time:
  • Site-wide: 20,524
  • In genomics: 1,797
• Year to date:
  • Site-wide: 92,637
• Since beginning of last month:
  • Site-wide: 146,057

An atlas of lamina-associated chromatin across twelve human cell types revealsan intermediate chromatin subtype

• Downloaded 1,356 times
• Download rankings, all-time:
  • Site-wide: 20,618
  • In developmental biology: 353
• Year to date:
  • Site-wide: 11,392
• Since beginning of last month:
  • Site-wide: 16,079

Protein binding and methylation on looping chromatin accurately predict distal regulatory interactions

• Downloaded 1,344 times
• Download rankings, all-time:
  • Site-wide: 20,891
  • In bioinformatics: 2,208
• Year to date:
  • Site-wide: 155,658
• Since beginning of last month:
  • Site-wide: 127,325

Development of Inflammatory Bowel Disease is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice

• Downloaded 1,324 times
• Download rankings, all-time:
  • Site-wide: 21,372
  • In microbiology: 1,190
• Year to date:
  • Site-wide: 142,539
• Since beginning of last month:
  • Site-wide: 113,238

A Transcriptional Switch Governing Fibroblast Plasticity Underlies Reversibility of Chronic Heart Disease

• Downloaded 1,317 times
• Download rankings, all-time:
  • Site-wide: 21,552
  • In molecular biology: 550
• Year to date:
  • Site-wide: 86,461
• Since beginning of last month:
  • Site-wide: 67,715

Reconstructing the 3D genome organization of Neanderthals reveals that chromatin folding shaped phenotypic and sequence divergence

• Downloaded 1,216 times
• Download rankings, all-time:
  • Site-wide: 24,445
  • In evolutionary biology: 1,683
• Year to date:
  • Site-wide: 952
• Since beginning of last month:
  • Site-wide: 4,249

Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing

• Downloaded 1,207 times
• Download rankings, all-time:
  • Site-wide: 24,726
  • In bioinformatics: 2,667
• Year to date:
  • Site-wide: 56,625
• Since beginning of last month:
  • Site-wide: 64,278

CellWalker integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues

• Downloaded 1,191 times
• Download rankings, all-time:
  • Site-wide: 25,241
  • In bioinformatics: 2,688
• Year to date:
  • Site-wide: 103,843
• Since beginning of last month:
  • Site-wide: None

Unique Transcription Factor Functions Regulate Epigenetic and Transcriptional Dynamics During Cardiac Reprogramming

• Downloaded 1,133 times
• Download rankings, all-time:
  • Site-wide: 27,221
  • In molecular biology: 686
• Year to date:
  • Site-wide: 95,490
• Since beginning of last month:
  • Site-wide: 100,778

Climate change will lead to pronounced shifts in the diversity of soil microbial communities

• Downloaded 1,124 times
• Download rankings, all-time:
  • Site-wide: 27,572
  • In ecology: 444
• Year to date:
  • Site-wide: 134,480
• Since beginning of last month:
  • Site-wide: 113,988

Ultra-rapid metagenotyping of the human gut microbiome

• Downloaded 1,065 times
• Download rankings, all-time:
  • Site-wide: 29,842
  • In bioinformatics: 3,205
• Year to date:
  • Site-wide: 47,616
• Since beginning of last month:
  • Site-wide: 76,041

A diet-dependent enzyme from the human gut microbiome promotes Th17 cell accumulation and colitis

• Downloaded 1,020 times
• Download rankings, all-time:
  • Site-wide: 31,773
  • In immunology: 1,082
• Year to date:
  • Site-wide: 40,784
• Since beginning of last month:
  • Site-wide: 38,049

A conserved enzyme found in diverse human gut bacteria interferes with anticancer drug efficacy

• Downloaded 946 times
• Download rankings, all-time:
  • Site-wide: 35,527
  • In microbiology: 1,968
• Year to date:
  • Site-wide: 97,592
• Since beginning of last month:
  • Site-wide: None

Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species

• Downloaded 918 times
• Download rankings, all-time:
  • Site-wide: 37,175
  • In evolutionary biology: 1,454
• Year to date:
  • Site-wide: 153,487
• Since beginning of last month:
  • Site-wide: 168,174

Integration of Protein Interactome Networks with Congenital Heart Disease Variants Reveals Candidate Disease Genes

• Downloaded 916 times
• Download rankings, all-time:
  • Site-wide: 37,283
  • In genetics: 1,623
• Year to date:
  • Site-wide: 33,656
• Since beginning of last month:
  • Site-wide: 84,270

Automated and accurate estimation of gene family abundance from shotgun metagenomes

• Downloaded 871 times
• Download rankings, all-time:
  • Site-wide: 40,039
  • In bioinformatics: 4,054
• Year to date:
  • Site-wide: 140,934
• Since beginning of last month:
  • Site-wide: 113,204

Features of ChIP-seq data peak calling algorithms with good operating characteristics

• Downloaded 840 times
• Download rankings, all-time:
  • Site-wide: 42,261
  • In bioinformatics: 4,253
• Year to date:
  • Site-wide: 167,841
• Since beginning of last month:
  • Site-wide: 127,268

A most wanted list of conserved protein families with no known domains

• Downloaded 836 times
• Download rankings, all-time:
  • Site-wide: 42,570
  • In genomics: 3,249
• Year to date:
  • Site-wide: 143,854
• Since beginning of last month:
  • Site-wide: 127,957

AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design

• Downloaded 809 times
• Download rankings, all-time:
  • Site-wide: 44,670
  • In bioinformatics: 4,410
• Year to date:
  • Site-wide: 168,027
• Since beginning of last month:
  • Site-wide: 164,559

Genome-wide variability in recombination activity is associated with meiotic chromatin organization

• Downloaded 705 times
• Download rankings, all-time:
  • Site-wide: 54,362
  • In genomics: 3,959
• Year to date:
  • Site-wide: 76,063
• Since beginning of last month:
  • Site-wide: 139,421

A Metagenomic Comparison of Tracheal Aspirate and Mini-Bronchial Alveolar Lavage for Assessment of Respiratory Microbiota

• Downloaded 657 times
• Download rankings, all-time:
  • Site-wide: 59,854
  • In microbiology: 3,495
• Year to date:
  • Site-wide: 167,996
• Since beginning of last month:
  • Site-wide: 159,370

phylogenize: correcting for phylogeny reveals genes associated with microbial distributions

• Downloaded 628 times
• Download rankings, all-time:
  • Site-wide: 63,474
  • In bioinformatics: 5,883
• Year to date:
  • Site-wide: 156,672
• Since beginning of last month:
  • Site-wide: 177,754

Autism risk gene POGZ promotes chromatin accessibility and expression of clustered synaptic genes

• Downloaded 615 times
• Download rankings, all-time:
  • Site-wide: 65,295
  • In neuroscience: 9,719
• Year to date:
  • Site-wide: 46,784
• Since beginning of last month:
  • Site-wide: 90,370

Cell Layers: Uncovering clustering structure and knowledge in unsupervised single-cell transcriptomic analysis

• Downloaded 599 times
• Download rankings, all-time:
  • Site-wide: 67,386
  • In bioinformatics: 6,396
• Year to date:
  • Site-wide: 68,253
• Since beginning of last month:
  • Site-wide: 92,818

The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation

• Downloaded 577 times
• Download rankings, all-time:
  • Site-wide: 70,641
  • In microbiology: 4,279
• Year to date:
  • Site-wide: 153,858
• Since beginning of last month:
  • Site-wide: 113,235

Global ecotypes in the ubiquitous marine clade SAR86

• Downloaded 564 times
• Download rankings, all-time:
  • Site-wide: 72,689
  • In ecology: 1,694
• Year to date:
  • Site-wide: 167,166
• Since beginning of last month:
  • Site-wide: 147,093

Evolution of mechanisms that control mating in Drosophila males

• Downloaded 543 times
• Download rankings, all-time:
  • Site-wide: 76,113
  • In neuroscience: 10,507
• Year to date:
  • Site-wide: 170,368
• Since beginning of last month:
  • Site-wide: 158,474

The geometry of the distance-decay of similarity in ecological communities

• Downloaded 530 times
• Download rankings, all-time:
  • Site-wide: 78,450
  • In ecology: 1,910
• Year to date:
  • Site-wide: 116,780
• Since beginning of last month:
  • Site-wide: 99,465

Integrating Host Response and Unbiased Microbe Detection for Lower Respiratory Tract Infection Diagnosis in Critically Ill Adults

• Downloaded 513 times
• Download rankings, all-time:
  • Site-wide: 81,323
  • In genomics: 5,207
• Year to date:
  • Site-wide: 118,465
• Since beginning of last month:
  • Site-wide: 135,261

Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus

• Downloaded 509 times
• Download rankings, all-time:
  • Site-wide: 82,196
  • In evolutionary biology: 3,858
• Year to date:
  • Site-wide: 161,742
• Since beginning of last month:
  • Site-wide: 114,557

A computational framework for detecting signatures of accelerated somatic evolution in cancer genomes

• Downloaded 496 times
• Download rankings, all-time:
  • Site-wide: 84,543
  • In bioinformatics: 7,414
• Year to date:
  • Site-wide: 129,278
• Since beginning of last month:
  • Site-wide: 134,611

CellWalkR: An R Package for integrating single-cell and bulk data to resolve regulatory elements

• Downloaded 460 times
• Download rankings, all-time:
  • Site-wide: 92,016
  • In bioinformatics: 7,982
• Year to date:
  • Site-wide: 66,406
• Since beginning of last month:
  • Site-wide: 73,392

Developmental loci harbor clusters of accelerated regions that evolved independently in ape lineages

• Downloaded 408 times
• Download rankings, all-time:
  • Site-wide: 103,862
  • In evolutionary biology: 4,826
• Year to date:
  • Site-wide: 169,884
• Since beginning of last month:
  • Site-wide: 177,480

Scalable microbial strain inference in metagenomic data using StrainFacts

• Downloaded 407 times
• Download rankings, all-time:
  • Site-wide: 104,120
  • In bioinformatics: 8,249
• Year to date:
  • Site-wide: 4,915
• Since beginning of last month:
  • Site-wide: 6,493

Strain-resolved analysis in a randomized trial of antibiotic pretreatment and maintenance dose delivery mode with fecal microbiota transplant for ulcerative colitis

• Downloaded 402 times
• Download rankings, all-time:
  • Site-wide: 105,313
  • In gastroenterology: 149
• Year to date:
  • Site-wide: 22,456
• Since beginning of last month:
  • Site-wide: 39,102

Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community

• Downloaded 185 times
• Download rankings, all-time:
  • Site-wide: 165,170
  • In microbiology: 12,061
• Year to date:
  • Site-wide: 34,253
• Since beginning of last month:
  • Site-wide: 141,293

An oligogenic inheritance test detects risk genes and their interactions in congenital heart defects and developmental comorbidities

• Downloaded 156 times
• Download rankings, all-time:
  • Site-wide: 172,127
  • In genetics: None
• Year to date:
  • Site-wide: 19,123
• Since beginning of last month:
  • Site-wide: 3,174