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Author: William Stafford Noble

Rankings

  • All-time downloads: 57,995 (rank: 3,533 )
  • Categories:
    • biochemistry: 1,390 (rank: 4,758 (tie) )
    • bioinformatics: 35,844 (rank: 92 )
    • genomics: 17,787 (rank: 873 )
    • microbiology: 1,355 (rank: 14,270 (tie) )
    • molecular biology: 958 (rank: 8,386 (tie) )
    • systems biology: 661 (rank: 8,191 (tie) )

Downloads per author, site-wide

Preprints

MS1Connect: a mass spectrometry run similarity measure

bioinformatics more details view paper

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An Integrative Framework For Detecting Structural Variations In Cancer Genomes

genomics more details view paper
  • Downloaded 4,258 times
  • Download rankings, all-time:
    • Site-wide: 3,483
    • In genomics: 333
  • Year to date:
    • Site-wide: 109,128
  • Since beginning of last month:
    • Site-wide: 94,601

Multi-scale deep tensor factorization learns a latent representation of the human epigenome

bioinformatics more details view paper
  • Downloaded 3,819 times
  • Download rankings, all-time:
    • Site-wide: 4,064
    • In bioinformatics: 358
  • Year to date:
    • Site-wide: 127,865
  • Since beginning of last month:
    • Site-wide: 124,884

Gromov-Wasserstein optimal transport to align single-cell multi-omics data

bioinformatics more details view paper
  • Downloaded 3,510 times
  • Download rankings, all-time:
    • Site-wide: 4,574
    • In bioinformatics: 416
  • Year to date:
    • Site-wide: 6,755
  • Since beginning of last month:
    • Site-wide: 4,422

Jointly embedding multiple single-cell omics measurements

bioinformatics more details view paper
  • Downloaded 2,890 times
  • Download rankings, all-time:
    • Site-wide: 6,045
    • In bioinformatics: 582
  • Year to date:
    • Site-wide: 109,705
  • Since beginning of last month:
    • Site-wide: 16,555

A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types

genomics more details view paper
  • Downloaded 2,590 times
  • Download rankings, all-time:
    • Site-wide: 7,113
    • In genomics: 710
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 67,453

A pitfall for machine learning methods aiming to predict across cell types

bioinformatics more details view paper
  • Downloaded 2,454 times
  • Download rankings, all-time:
    • Site-wide: 7,680
    • In bioinformatics: 803
  • Year to date:
    • Site-wide: 128,368
  • Since beginning of last month:
    • Site-wide: 80,974

Capturing cell type-specific chromatin structural patterns by applying topic modeling to single-cell Hi-C data

genomics more details view paper
  • Downloaded 2,098 times
  • Download rankings, all-time:
    • Site-wide: 9,642
    • In genomics: 944
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 67,822

Software tools for visualizing Hi-C data

genomics more details view paper
  • Downloaded 1,742 times
  • Download rankings, all-time:
    • Site-wide: 12,723
    • In genomics: 1,243
  • Year to date:
    • Site-wide: 55,793
  • Since beginning of last month:
    • Site-wide: 80,229

A learned embedding for efficient joint analysis of millions of mass spectra

bioinformatics more details view paper
  • Downloaded 1,640 times
  • Download rankings, all-time:
    • Site-wide: 13,910
    • In bioinformatics: 1,530
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: None

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell type-specific expression

genomics more details view paper
  • Downloaded 1,512 times
  • Download rankings, all-time:
    • Site-wide: 15,819
    • In genomics: 1,517
  • Year to date:
    • Site-wide: 69,882
  • Since beginning of last month:
    • Site-wide: 30,792

Matrix-matched calibration curves for assessing analytical figures of merit in quantitative proteomics

biochemistry more details view paper
  • Downloaded 1,390 times
  • Download rankings, all-time:
    • Site-wide: 17,978
    • In biochemistry: 384
  • Year to date:
    • Site-wide: 35,515
  • Since beginning of last month:
    • Site-wide: 145,075

Predicting gene expression in the human malaria parasite Plasmodium falciparum

genomics more details view paper
  • Downloaded 1,375 times
  • Download rankings, all-time:
    • Site-wide: 18,276
    • In genomics: 1,722
  • Year to date:
    • Site-wide: 125,932
  • Since beginning of last month:
    • Site-wide: 158,600

The essential transcriptional regulator HDP1 drives expansion of the inner membrane complex during early sexual differentiation of malaria parasites.

microbiology more details view paper
  • Downloaded 1,355 times
  • Download rankings, all-time:
    • Site-wide: 18,672
    • In microbiology: 1,075
  • Year to date:
    • Site-wide: 84,375
  • Since beginning of last month:
    • Site-wide: 22,052

GenomeDISCO: A concordance score for chromosome conformation capture experiments using random walks on contact map graphs

bioinformatics more details view paper
  • Downloaded 1,322 times
  • Download rankings, all-time:
    • Site-wide: 19,405
    • In bioinformatics: 2,167
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 118,987

Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair

genomics more details view paper
  • Downloaded 1,276 times
  • Download rankings, all-time:
    • Site-wide: 20,448
    • In genomics: 1,880
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 67,311

Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy

genomics more details view paper
  • Downloaded 1,272 times
  • Download rankings, all-time:
    • Site-wide: 20,537
    • In genomics: 1,888
  • Year to date:
    • Site-wide: 52,303
  • Since beginning of last month:
    • Site-wide: 93,473

Eliminating redundancy among protein sequences using submodular optimization

bioinformatics more details view paper
  • Downloaded 1,265 times
  • Download rankings, all-time:
    • Site-wide: 20,714
    • In bioinformatics: 2,313
  • Year to date:
    • Site-wide: 117,771
  • Since beginning of last month:
    • Site-wide: 123,991

Unsupervised manifold alignment for single-cell multi-omics data

bioinformatics more details view paper
  • Downloaded 1,254 times
  • Download rankings, all-time:
    • Site-wide: 20,960
    • In bioinformatics: 2,344
  • Year to date:
    • Site-wide: 103,947
  • Since beginning of last month:
    • Site-wide: 127,793

Fast open modification spectral library searching through approximate nearest neighbor indexing

bioinformatics more details view paper
  • Downloaded 1,111 times
  • Download rankings, all-time:
    • Site-wide: 25,255
    • In bioinformatics: 2,804
  • Year to date:
    • Site-wide: 47,489
  • Since beginning of last month:
    • Site-wide: 122,249

Inferring diploid 3D chromatin structures from Hi-C data

bioinformatics more details view paper
  • Downloaded 1,026 times
  • Download rankings, all-time:
    • Site-wide: 28,448
    • In bioinformatics: 3,127
  • Year to date:
    • Site-wide: 76,737
  • Since beginning of last month:
    • Site-wide: 154,600

Extremely fast and accurate open modification spectral library searching of high-resolution mass spectra using feature hashing and graphics processing units

bioinformatics more details view paper
  • Downloaded 1,018 times
  • Download rankings, all-time:
    • Site-wide: 28,787
    • In bioinformatics: 3,171
  • Year to date:
    • Site-wide: 76,540
  • Since beginning of last month:
    • Site-wide: 116,369

PREDICTD: PaRallel Epigenomics Data Imputation With Cloud-based Tensor Decomposition

bioinformatics more details view paper
  • Downloaded 1,016 times
  • Download rankings, all-time:
    • Site-wide: 28,842
    • In bioinformatics: 3,175
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 151,226

LR-DNase: Predicting TF binding from DNase-seq data

bioinformatics more details view paper
  • Downloaded 1,016 times
  • Download rankings, all-time:
    • Site-wide: 28,860
    • In bioinformatics: 3,178
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 123,443

DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding

bioinformatics more details view paper
  • Downloaded 987 times
  • Download rankings, all-time:
    • Site-wide: 30,151
    • In bioinformatics: 3,299
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 151,040

Unsupervised embedding of single-cell Hi-C data

bioinformatics more details view paper
  • Downloaded 971 times
  • Download rankings, all-time:
    • Site-wide: 30,864
    • In bioinformatics: 3,370
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 160,338

Chromatin Fiber Folding Represses Transcription and Loop Extrusion in Quiescent Cells

molecular biology more details view paper
  • Downloaded 958 times
  • Download rankings, all-time:
    • Site-wide: 31,482
    • In molecular biology: 856
  • Year to date:
    • Site-wide: 95,982
  • Since beginning of last month:
    • Site-wide: 48,925

Choosing panels of genomics assays using submodular optimization

bioinformatics more details view paper
  • Downloaded 850 times
  • Download rankings, all-time:
    • Site-wide: 37,484
    • In bioinformatics: 3,989
  • Year to date:
    • Site-wide: 117,905
  • Since beginning of last month:
    • Site-wide: 123,883

MoMo: Discovery of post-translational modification motifs

bioinformatics more details view paper
  • Downloaded 844 times
  • Download rankings, all-time:
    • Site-wide: 37,872
    • In bioinformatics: 4,023
  • Year to date:
    • Site-wide: 119,955
  • Since beginning of last month:
    • Site-wide: 96,056

Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples

bioinformatics more details view paper
  • Downloaded 785 times
  • Download rankings, all-time:
    • Site-wide: 42,083
    • In bioinformatics: 4,396
  • Year to date:
    • Site-wide: 75,390
  • Since beginning of last month:
    • Site-wide: 147,079

Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes

genomics more details view paper
  • Downloaded 721 times
  • Download rankings, all-time:
    • Site-wide: 47,526
    • In genomics: 3,625
  • Year to date:
    • Site-wide: 29,320
  • Since beginning of last month:
    • Site-wide: 131,315

Ledidi: Designing genome edits that induce functional activity

bioinformatics more details view paper
  • Downloaded 688 times
  • Download rankings, all-time:
    • Site-wide: 50,622
    • In bioinformatics: 5,105
  • Year to date:
    • Site-wide: 63,322
  • Since beginning of last month:
    • Site-wide: 126,884

A machine learning strategy that leverages large datasets to boost statistical power in small-scale experiments

bioinformatics more details view paper
  • Downloaded 673 times
  • Download rankings, all-time:
    • Site-wide: 52,261
    • In bioinformatics: 5,213
  • Year to date:
    • Site-wide: 121,277
  • Since beginning of last month:
    • Site-wide: 137,907

Large-scale tandem mass spectrum clustering using fast nearest neighbor searching

bioinformatics more details view paper
  • Downloaded 671 times
  • Download rankings, all-time:
    • Site-wide: 52,377
    • In bioinformatics: 5,226
  • Year to date:
    • Site-wide: 57,072
  • Since beginning of last month:
    • Site-wide: 22,435

HiC-Spector: A matrix library for spectral and reproducibility analysis of Hi-C contact maps

bioinformatics more details view paper
  • Downloaded 666 times
  • Download rankings, all-time:
    • Site-wide: 52,950
    • In bioinformatics: 5,272
  • Year to date:
    • Site-wide: 69,362
  • Since beginning of last month:
    • Site-wide: 98,251

Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages

systems biology more details view paper
  • Downloaded 661 times
  • Download rankings, all-time:
    • Site-wide: 53,430
    • In systems biology: 1,124
  • Year to date:
    • Site-wide: 130,401
  • Since beginning of last month:
    • Site-wide: 142,277

Segway 2.0: Gaussian mixture models and minibatch training

bioinformatics more details view paper
  • Downloaded 613 times
  • Download rankings, all-time:
    • Site-wide: 59,138
    • In bioinformatics: 5,799
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 98,189

An averaging strategy to reduce variability in target-decoy estimates of false discovery rate

bioinformatics more details view paper
  • Downloaded 588 times
  • Download rankings, all-time:
    • Site-wide: 62,237
    • In bioinformatics: 6,036
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 144,266

Combining high resolution and exact calibration to boost statistical power: A well-calibrated score function for high-resolution MS2 data

bioinformatics more details view paper
  • Downloaded 534 times
  • Download rankings, all-time:
    • Site-wide: 70,060
    • In bioinformatics: 6,597
  • Year to date:
    • Site-wide: 123,513
  • Since beginning of last month:
    • Site-wide: 152,436

Measuring significant changes in chromatin conformation with ACCOST

genomics more details view paper
  • Downloaded 478 times
  • Download rankings, all-time:
    • Site-wide: 79,523
    • In genomics: 5,227
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 147,126

Epiphany: predicting Hi-C contact maps from 1D epigenomic signals

genomics more details view paper
  • Downloaded 465 times
  • Download rankings, all-time:
    • Site-wide: 81,849
    • In genomics: 5,341
  • Year to date:
    • Site-wide: 9,744
  • Since beginning of last month:
    • Site-wide: 660

Joint precursor elution profile inference via regression for peptide detection in data-independent acquisition mass spectra

bioinformatics more details view paper
  • Downloaded 453 times
  • Download rankings, all-time:
    • Site-wide: 84,253
    • In bioinformatics: 7,564
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 141,532

Inference of genome 3D architecture by modeling overdispersion of Hi-C data

bioinformatics more details view paper
  • Downloaded 446 times
  • Download rankings, all-time:
    • Site-wide: 85,664
    • In bioinformatics: 7,662
  • Year to date:
    • Site-wide: 18,427
  • Since beginning of last month:
    • Site-wide: 28,326

Submodular sketches of single-cell RNA-seq measurements

bioinformatics more details view paper
  • Downloaded 441 times
  • Download rankings, all-time:
    • Site-wide: 86,792
    • In bioinformatics: 7,752
  • Year to date:
    • Site-wide: 21,221
  • Since beginning of last month:
    • Site-wide: 54,463

Semi-supervised single-cell cross-modality translation using Polarbear

bioinformatics more details view paper
  • Downloaded 440 times
  • Download rankings, all-time:
    • Site-wide: 86,947
    • In bioinformatics: 7,771
  • Year to date:
    • Site-wide: 15,961
  • Since beginning of last month:
    • Site-wide: 4,311

Improving power while controlling the false discovery rate when only a subset of peptides are relevant

bioinformatics more details view paper
  • Downloaded 430 times
  • Download rankings, all-time:
    • Site-wide: 88,965
    • In bioinformatics: 7,900
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 169,657

mokapot: Fast and flexible semi-supervised learning for peptide detection

bioinformatics more details view paper
  • Downloaded 418 times
  • Download rankings, all-time:
    • Site-wide: 91,429
    • In bioinformatics: 8,049
  • Year to date:
    • Site-wide: 87,788
  • Since beginning of last month:
    • Site-wide: 113,410

Detecting modifications in proteomics experiments with Param-Medic

bioinformatics more details view paper
  • Downloaded 320 times
  • Download rankings, all-time:
    • Site-wide: 115,112
    • In bioinformatics: 9,491
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 161,658

HiCRep.py: Fast comparison of Hi-C contact matrices in Python

bioinformatics more details view paper
  • Downloaded 298 times
  • Download rankings, all-time:
    • Site-wide: 120,769
    • In bioinformatics: 9,856
  • Year to date:
    • Site-wide: 96,914
  • Since beginning of last month:
    • Site-wide: 109,490

A flexible workflow for building spectral libraries from narrow window data independent acquisition mass spectrometry data

bioinformatics more details view paper
  • Downloaded 210 times
  • Download rankings, all-time:
    • Site-wide: 144,428
    • In bioinformatics: 11,236
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 5,030

ppx: Programmatic access to proteomics data repositories

bioinformatics more details view paper
  • Downloaded 177 times
  • Download rankings, all-time:
    • Site-wide: 152,137
    • In bioinformatics: 11,620
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: 77,992

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