Author: Michael M. Hoffman

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Preprints

Opportunities And Obstacles For Deep Learning In Biology And Medicine

• Downloaded 56,991 times
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  • Site-wide: 159
  • In bioinformatics: 3
• Year to date:
  • Site-wide: 2,770
• Since beginning of last month:
  • Site-wide: 2,484

Virtual ChIP-seq: Predicting transcription factor binding by learning from the transcriptome

• Downloaded 6,539 times
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  • Site-wide: 2,204
  • In bioinformatics: 129
• Year to date:
  • Site-wide: 14,287
• Since beginning of last month:
  • Site-wide: 6,863

Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping

• Downloaded 2,904 times
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  • Site-wide: 6,815
  • In genomics: 625
• Year to date:
  • Site-wide: 69,650
• Since beginning of last month:
  • Site-wide: 56,882

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

• Downloaded 2,634 times
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  • Site-wide: 7,882
  • In genomics: 725
• Year to date:
  • Site-wide: 96,066
• Since beginning of last month:
  • Site-wide: 111,701

Semi-automated genome annotation using epigenomic data and Segway

• Downloaded 2,353 times
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  • Site-wide: 9,289
  • In bioinformatics: 949
• Year to date:
  • Site-wide: 55,375
• Since beginning of last month:
  • Site-wide: 61,287

Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet

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  • Site-wide: 9,874
  • In bioinformatics: 986
• Year to date:
  • Site-wide: 109,451
• Since beginning of last month:
  • Site-wide: 147,644

DNAmod: the DNA modification database

• Downloaded 1,718 times
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  • Site-wide: 14,830
  • In bioinformatics: 1,515
• Year to date:
  • Site-wide: 100,515
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  • Site-wide: 76,322

Human papillomavirus integration transforms chromatin to drive oncogenesis

• Downloaded 1,665 times
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  • Site-wide: 15,528
  • In cancer biology: 400
• Year to date:
  • Site-wide: 9,755
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  • Site-wide: 16,689

Umap and Bismap: quantifying genome and methylome mappability

• Downloaded 1,596 times
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  • Site-wide: 16,577
  • In genomics: 1,506
• Year to date:
  • Site-wide: 69,828
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  • Site-wide: 65,205

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

• Downloaded 1,556 times
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  • Site-wide: 17,260
  • In genomics: 1,525
• Year to date:
  • Site-wide: 95,377
• Since beginning of last month:
  • Site-wide: 113,410

BEHST: genomic set enrichment analysis enhanced through integration of chromatin long-range interactions

• Downloaded 1,530 times
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  • Site-wide: 17,718
  • In bioinformatics: 1,848
• Year to date:
  • Site-wide: 91,178
• Since beginning of last month:
  • Site-wide: 56,856

Functional annotation of human long noncoding RNAs using chromatin conformation data

• Downloaded 1,523 times
• Download rankings, all-time:
  • Site-wide: 17,833
  • In genomics: 1,678
• Year to date:
  • Site-wide: 29,437
• Since beginning of last month:
  • Site-wide: 15,763

Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls

• Downloaded 1,474 times
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  • Site-wide: 18,711
  • In genomics: 1,895
• Year to date:
  • Site-wide: 11,493
• Since beginning of last month:
  • Site-wide: 13,835

Motif elucidation in ChIP-seq datasets with a knockout control

• Downloaded 1,083 times
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  • Site-wide: 30,153
  • In bioinformatics: 3,456
• Year to date:
  • Site-wide: 17,625
• Since beginning of last month:
  • Site-wide: 19,519

Assessing and assuring interoperability of a genomics file format

• Downloaded 722 times
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  • Site-wide: 54,679
  • In bioinformatics: 6,093
• Year to date:
  • Site-wide: 2,815
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  • Site-wide: 22,268

Semi-supervised segmentation and genome annotation

• Downloaded 647 times
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  • Site-wide: 63,643
  • In bioinformatics: 6,102
• Year to date:
  • Site-wide: 61,195
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  • Site-wide: 62,712

Segway 2.0: Gaussian mixture models and minibatch training

• Downloaded 630 times
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  • Site-wide: 65,875
  • In bioinformatics: 5,952
• Year to date:
  • Site-wide: 168,885
• Since beginning of last month:
  • Site-wide: 169,039

Unsupervised analysis of multi-experiment transcriptomic patterns with SegRNA identifies unannotated transcripts

• Downloaded 488 times
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  • Site-wide: 89,872
  • In bioinformatics: 8,131
• Year to date:
  • Site-wide: 44,789
• Since beginning of last month:
  • Site-wide: 42,548

Automated identification of cell-type-specific genes and alternative promoters

• Downloaded 254 times
• Download rankings, all-time:
  • Site-wide: 151,837
  • In bioinformatics: 11,987
• Year to date:
  • Site-wide: 40,535
• Since beginning of last month:
  • Site-wide: 51,368