Author: Chris Sander

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Preprints

Comparing cancer cell lines and tumor samples by genomic profiles

• Downloaded 6,388 times
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  • Site-wide: 1,418
  • In cancer biology: 16
• Year to date:
  • Site-wide: 7,649
• Since beginning of last month:
  • Site-wide: 8,979

Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes

• Downloaded 5,473 times
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  • Site-wide: 1,762
  • In genomics: 168
• Year to date:
  • Site-wide: 18,428
• Since beginning of last month:
  • Site-wide: 17,415

Mitochondrial DNA Copy Number Variation Across Human Cancers

• Downloaded 4,942 times
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  • Site-wide: 2,010
  • In genomics: 201
• Year to date:
  • Site-wide: 41,020
• Since beginning of last month:
  • Site-wide: 43,998

EVfold.org: Evolutionary Couplings and Protein 3D Structure Prediction

• Downloaded 4,226 times
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  • Site-wide: 2,525
  • In bioinformatics: 224
• Year to date:
  • Site-wide: 9,741
• Since beginning of last month:
  • Site-wide: 13,115

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

• Downloaded 2,819 times
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  • Site-wide: 4,515
  • In systems biology: 75
• Year to date:
  • Site-wide: 1,040
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  • Site-wide: 1,226

MatchMiner: An open source computational platform for real-time matching of cancer patients to precision medicine clinical trials using genomic and clinical criteria

• Downloaded 2,441 times
• Download rankings, all-time:
  • Site-wide: 5,597
  • In bioinformatics: 631
• Year to date:
  • Site-wide: 26,183
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  • Site-wide: 25,322

Sequence co-evolution gives 3D contacts and structures of protein complexes

• Downloaded 2,317 times
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  • Site-wide: 6,041
  • In bioinformatics: 687
• Year to date:
  • Site-wide: 61,874
• Since beginning of last month:
  • Site-wide: 92,029

Interpretable Machine Learning for Perturbation Biology

• Downloaded 2,273 times
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  • Site-wide: 6,206
  • In systems biology: 107
• Year to date:
  • Site-wide: 15,463
• Since beginning of last month:
  • Site-wide: 19,165

Causal interactions from proteomic profiles: molecular data meets pathway knowledge

• Downloaded 1,891 times
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  • Site-wide: 8,133
  • In systems biology: 143
• Year to date:
  • Site-wide: 12,867
• Since beginning of last month:
  • Site-wide: 12,782

Rapid proteotyping reveals cancer biology and drug response determinants in the NCI-60 cells

• Downloaded 1,757 times
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  • Site-wide: 9,097
  • In systems biology: 174
• Year to date:
  • Site-wide: 54,645
• Since beginning of last month:
  • Site-wide: 61,588

Protein Domain Hotspots Reveal Functional Mutations across Genes in Cancer

• Downloaded 1,704 times
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  • Site-wide: 9,532
  • In genomics: 1,041
• Year to date:
  • Site-wide: 78,255
• Since beginning of last month:
  • Site-wide: 63,470

3D protein structure from genetic epistasis experiments

• Downloaded 1,542 times
• Download rankings, all-time:
  • Site-wide: 11,019
  • In systems biology: 208
• Year to date:
  • Site-wide: 42,814
• Since beginning of last month:
  • Site-wide: 41,787

Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations

• Downloaded 1,440 times
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  • Site-wide: 12,159
  • In cancer biology: 258
• Year to date:
  • Site-wide: 69,862
• Since beginning of last month:
  • Site-wide: 61,669

Protein structure from experimental evolution

• Downloaded 1,431 times
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  • Site-wide: 12,286
  • In evolutionary biology: 429
• Year to date:
  • Site-wide: 70,756
• Since beginning of last month:
  • Site-wide: 67,093

Perturbation biology models predict c-Myc as an effective co-target in RAF inhibitor resistant melanoma cells

• Downloaded 1,414 times
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  • Site-wide: 12,527
  • In cancer biology: 266
• Year to date:
  • Site-wide: 62,218
• Since beginning of last month:
  • Site-wide: 87,010

Extensive Decoupling of Metabolic Genes in Cancer

• Downloaded 1,372 times
• Download rankings, all-time:
  • Site-wide: 13,109
  • In systems biology: 250
• Year to date:
  • Site-wide: 87,670
• Since beginning of last month:
  • Site-wide: 87,782

Cancer-associated recurrent mutations in RNase III domains of DICER1

• Downloaded 1,138 times
• Download rankings, all-time:
  • Site-wide: 17,363
  • In cancer biology: 396
• Year to date:
  • Site-wide: 86,875
• Since beginning of last month:
  • Site-wide: 96,392

Integrative analysis of pharmacogenomics in major cancer cell line databases using CellMinerCDB

• Downloaded 1,028 times
• Download rankings, all-time:
  • Site-wide: 20,193
  • In bioinformatics: 2,410
• Year to date:
  • Site-wide: 81,743
• Since beginning of last month:
  • Site-wide: 75,441

Protein Profiling In Cancer Cell Lines And Tumor Tissue Using Reverse Phase Protein Arrays

• Downloaded 1,006 times
• Download rankings, all-time:
  • Site-wide: 20,828
  • In systems biology: 424
• Year to date:
  • Site-wide: 58,205
• Since beginning of last month:
  • Site-wide: 62,783

Perturbation biology links temporal protein changes to drug responses in a melanoma cell line

• Downloaded 938 times
• Download rankings, all-time:
  • Site-wide: 23,057
  • In systems biology: 476
• Year to date:
  • Site-wide: 118,602
• Since beginning of last month:
  • Site-wide: 121,852

The EVcouplings Python framework for coevolutionary sequence analysis

• Downloaded 832 times
• Download rankings, all-time:
  • Site-wide: 27,311
  • In bioinformatics: 3,174
• Year to date:
  • Site-wide: 88,576
• Since beginning of last month:
  • Site-wide: 67,057

Accurate prediction of transmembrane β-barrel proteins from sequences

• Downloaded 799 times
• Download rankings, all-time:
  • Site-wide: 28,913
  • In bioinformatics: 3,318
• Year to date:
  • Site-wide: 111,222
• Since beginning of last month:
  • Site-wide: 112,082

Adaptive response to BET inhibition induces therapeutic vulnerability to MCL1 inhibitors in breast cancer

• Downloaded 672 times
• Download rankings, all-time:
  • Site-wide: 36,658
  • In cancer biology: 984
• Year to date:
  • Site-wide: 44,832
• Since beginning of last month:
  • Site-wide: 41,462

PaxtoolsR: Pathway Analysis in R Using Pathway Commons

• Downloaded 660 times
• Download rankings, all-time:
  • Site-wide: 37,570
  • In bioinformatics: 4,136
• Year to date:
  • Site-wide: 111,239
• Since beginning of last month:
  • Site-wide: 129,712

AlignmentViewer: Sequence Analysis of Large Protein Families

• Downloaded 622 times
• Download rankings, all-time:
  • Site-wide: 40,496
  • In bioinformatics: 4,389
• Year to date:
  • Site-wide: 43,003
• Since beginning of last month:
  • Site-wide: 47,058

3D RNA from evolutionary couplings

• Downloaded 498 times
• Download rankings, all-time:
  • Site-wide: 53,107
  • In bioinformatics: 5,415
• Year to date:
  • Site-wide: 91,008
• Since beginning of last month:
  • Site-wide: 107,302

PredictProtein - Predicting Protein Structure and Function for 29 Years

• Downloaded 368 times
• Download rankings, all-time:
  • Site-wide: 72,270
  • In bioinformatics: 6,820
• Year to date:
  • Site-wide: 4,593
• Since beginning of last month:
  • Site-wide: 2,913

Precision combination therapies based on recurrent oncogenic co-alterations

• Downloaded 345 times
• Download rankings, all-time:
  • Site-wide: 76,288
  • In cancer biology: 2,248
• Year to date:
  • Site-wide: 67,741
• Since beginning of last month:
  • Site-wide: 58,649

Disulfiram associated with lower risk of Covid-19: a retrospective cohort study

• Downloaded 340 times
• Download rankings, all-time:
  • Site-wide: 77,229
  • In epidemiology: 3,225
• Year to date:
  • Site-wide: 5,215
• Since beginning of last month:
  • Site-wide: 1,510

Pathway Commons: 2019 Update

• Downloaded 275 times
• Download rankings, all-time:
  • Site-wide: 90,600
  • In bioinformatics: 7,995
• Year to date:
  • Site-wide: 108,962
• Since beginning of last month:
  • Site-wide: 123,464

NetBoxR: Automated Discovery of Biological Process Modules by Network Analysis in R

• Downloaded 196 times
• Download rankings, all-time:
  • Site-wide: 108,171
  • In bioinformatics: 9,054
• Year to date:
  • Site-wide: 106,234
• Since beginning of last month:
  • Site-wide: 132,898

Capturing scientific knowledge in computable form

• Downloaded 172 times
• Download rankings, all-time:
  • Site-wide: 113,244
  • In bioinformatics: 9,365
• Year to date:
  • Site-wide: 13,500
• Since beginning of last month:
  • Site-wide: 3,951