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Author: Julio Saez-Rodriguez

Rankings

  • All-time downloads: 103,418 (rank: 1,939 )
  • Categories:
    • bioinformatics: 35,498 (rank: 123 )
    • cancer biology: 16,557 (rank: 98 )
    • cardiovascular medicine: 1,031 (rank: 749 (tie) )
    • cell biology: 249 (rank: 42,032 (tie) )
    • genetics: 1,546 (rank: 13,537 (tie) )
    • genomics: 1,367 (rank: 21,000 (tie) )
    • pathology: 1,325 (rank: 1,212 (tie) )
    • pharmacology and toxicology: 581 (rank: 3,616 (tie) )
    • systems biology: 39,591 (rank: 128 )

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Preprints

Reconstructing the functional effect of TP53 somatic mutations on its regulon using causal signalling network modelling

systems biology more details view paper

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Community assessment of methods to deconvolve cellular composition from bulk gene expression

bioinformatics more details view paper

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Spatial multi-omic map of human myocardial infarction

systems biology more details view paper
  • Downloaded 6,106 times
  • Download rankings, all-time:
    • Site-wide: 2,421
    • In systems biology: 31
  • Year to date:
    • Site-wide: 1,154
  • Since beginning of last month:
    • Site-wide: 902

Prioritisation of oncology therapeutic targets using CRISPR-Cas9 screening

cancer biology more details view paper
  • Downloaded 5,634 times
  • Download rankings, all-time:
    • Site-wide: 2,691
    • In cancer biology: 32
  • Year to date:
    • Site-wide: 3,854
  • Since beginning of last month:
    • Site-wide: 4,664

A cancer pharmacogenomic screen powering crowd-sourced advancement of drug combination prediction

bioinformatics more details view paper
  • Downloaded 4,360 times
  • Download rankings, all-time:
    • Site-wide: 3,796
    • In bioinformatics: 291
  • Year to date:
    • Site-wide: 78,422
  • Since beginning of last month:
    • Site-wide: 85,750

Modelling cell-cell interactions from spatial molecular data with spatial variance component analysis

bioinformatics more details view paper
  • Downloaded 3,918 times
  • Download rankings, all-time:
    • Site-wide: 4,409
    • In bioinformatics: 361
  • Year to date:
    • Site-wide: 70,948
  • Since beginning of last month:
    • Site-wide: 95,411

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

systems biology more details view paper
  • Downloaded 3,805 times
  • Download rankings, all-time:
    • Site-wide: 4,612
    • In systems biology: 61
  • Year to date:
    • Site-wide: 15,886
  • Since beginning of last month:
    • Site-wide: 4,972

Comparison of Resources and Methods to infer Cell-Cell Communication from Single-cell RNA Data

bioinformatics more details view paper
  • Downloaded 3,579 times
  • Download rankings, all-time:
    • Site-wide: 5,033
    • In bioinformatics: 550
  • Year to date:
    • Site-wide: 1,998
  • Since beginning of last month:
    • Site-wide: 1,474

Assessment of network module identification across complex diseases

bioinformatics more details view paper
  • Downloaded 3,420 times
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    • Site-wide: 5,392
    • In bioinformatics: 453
  • Year to date:
    • Site-wide: 62,064
  • Since beginning of last month:
    • Site-wide: 66,436

Explainable multi-view framework for dissecting inter-cellular signaling from highly multiplexed spatial data

systems biology more details view paper
  • Downloaded 3,231 times
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    • Site-wide: 5,855
    • In systems biology: 85
  • Year to date:
    • Site-wide: 5,878
  • Since beginning of last month:
    • Site-wide: 12,040

Genomic, Proteomic and Phenotypic Heterogeneity in HeLa Cells across Laboratories: Implications for Reproducibility of Research Results

systems biology more details view paper
  • Downloaded 3,065 times
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    • Site-wide: 6,328
    • In systems biology: 90
  • Year to date:
    • Site-wide: 18,642
  • Since beginning of last month:
    • Site-wide: 10,482

Pathway-based dissection of the genomic heterogeneity of cancer hallmarks' acquisition with SLAPenrich

bioinformatics more details view paper
  • Downloaded 2,548 times
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    • Site-wide: 8,292
    • In bioinformatics: 803
  • Year to date:
    • Site-wide: 68,237
  • Since beginning of last month:
    • Site-wide: 77,635

Benchmark and integration of resources for the estimation of human transcription factor activities

bioinformatics more details view paper
  • Downloaded 2,110 times
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    • Site-wide: 10,951
    • In bioinformatics: 1,107
  • Year to date:
    • Site-wide: 87,549
  • Since beginning of last month:
    • Site-wide: 78,579

The spatial transcriptomic landscape of the healing intestine following damage

systems biology more details view paper
  • Downloaded 2,094 times
  • Download rankings, all-time:
    • Site-wide: 11,098
    • In systems biology: 194
  • Year to date:
    • Site-wide: 5,195
  • Since beginning of last month:
    • Site-wide: 13,852

CELLector: Genomics Guided Selection of Cancer in vitro Models

bioinformatics more details view paper
  • Downloaded 2,077 times
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    • Site-wide: 11,230
    • In bioinformatics: 1,143
  • Year to date:
    • Site-wide: 96,443
  • Since beginning of last month:
    • Site-wide: 131,367

Transcription factor activities enhance markers of drug response in cancer

cancer biology more details view paper
  • Downloaded 2,049 times
  • Download rankings, all-time:
    • Site-wide: 11,468
    • In cancer biology: 192
  • Year to date:
    • Site-wide: 164,943
  • Since beginning of last month:
    • Site-wide: 142,672

Deciphering the Signaling Network Landscape of Breast Cancer Improves Drug Sensitivity Prediction

systems biology more details view paper
  • Downloaded 2,023 times
  • Download rankings, all-time:
    • Site-wide: 11,676
    • In systems biology: 177
  • Year to date:
    • Site-wide: 53,381
  • Since beginning of last month:
    • Site-wide: 33,538

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

systems biology more details view paper
  • Downloaded 1,948 times
  • Download rankings, all-time:
    • Site-wide: 12,348
    • In systems biology: 195
  • Year to date:
    • Site-wide: 70,978
  • Since beginning of last month:
    • Site-wide: 44,113

Linking drug target and pathway activation for effective therapy using multi-task learning

bioinformatics more details view paper
  • Downloaded 1,942 times
  • Download rankings, all-time:
    • Site-wide: 12,389
    • In bioinformatics: 1,252
  • Year to date:
    • Site-wide: 128,315
  • Since beginning of last month:
    • Site-wide: 104,842

Integrated intra- and intercellular signaling knowledge for multicellular omics analysis

systems biology more details view paper
  • Downloaded 1,912 times
  • Download rankings, all-time:
    • Site-wide: 12,682
    • In systems biology: 208
  • Year to date:
    • Site-wide: 43,682
  • Since beginning of last month:
    • Site-wide: 31,936

PYCR1-dependent proline synthesis in cancer-associated fibroblasts is required for the deposition of pro-tumorigenic extracellular matrix

cancer biology more details view paper
  • Downloaded 1,785 times
  • Download rankings, all-time:
    • Site-wide: 14,028
    • In cancer biology: 339
  • Year to date:
    • Site-wide: 7,732
  • Since beginning of last month:
    • Site-wide: 10,473

Perturbation-response genes reveal signaling footprints in cancer gene expression

bioinformatics more details view paper
  • Downloaded 1,687 times
  • Download rankings, all-time:
    • Site-wide: 15,245
    • In bioinformatics: 1,539
  • Year to date:
    • Site-wide: 107,454
  • Since beginning of last month:
    • Site-wide: 150,320

Phosphoproteomics-based Profiling of Kinase Activities in Cancer Cells

bioinformatics more details view paper
  • Downloaded 1,671 times
  • Download rankings, all-time:
    • Site-wide: 15,470
    • In bioinformatics: 1,551
  • Year to date:
    • Site-wide: 177,244
  • Since beginning of last month:
    • Site-wide: 150,093

Why do pathway methods work better than they should?

systems biology more details view paper
  • Downloaded 1,649 times
  • Download rankings, all-time:
    • Site-wide: 15,775
    • In systems biology: 253
  • Year to date:
    • Site-wide: 66,428
  • Since beginning of last month:
    • Site-wide: 43,886

Rapid identification of optimal drug combinations for personalized cancer therapy using microfluidics

cancer biology more details view paper
  • Downloaded 1,616 times
  • Download rankings, all-time:
    • Site-wide: 16,256
    • In cancer biology: 318
  • Year to date:
    • Site-wide: 147,632
  • Since beginning of last month:
    • Site-wide: 103,985

From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL

systems biology more details view paper
  • Downloaded 1,578 times
  • Download rankings, all-time:
    • Site-wide: 16,914
    • In systems biology: 262
  • Year to date:
    • Site-wide: 138,560
  • Since beginning of last month:
    • Site-wide: 173,853

Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations.

genetics more details view paper
  • Downloaded 1,569 times
  • Download rankings, all-time:
    • Site-wide: 17,069
    • In genetics: 686
  • Year to date:
    • Site-wide: 107,829
  • Since beginning of last month:
    • Site-wide: 94,683

Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses

bioinformatics more details view paper
  • Downloaded 1,529 times
  • Download rankings, all-time:
    • Site-wide: 17,761
    • In bioinformatics: 1,847
  • Year to date:
    • Site-wide: 119,891
  • Since beginning of last month:
    • Site-wide: 81,059

Analysis of the human kinome and phosphatome reveals diseased signaling networks induced by overexpression

systems biology more details view paper
  • Downloaded 1,506 times
  • Download rankings, all-time:
    • Site-wide: 18,164
    • In systems biology: 293
  • Year to date:
    • Site-wide: 121,793
  • Since beginning of last month:
    • Site-wide: 96,169

DreamAI: algorithm for the imputation of proteomics data

bioinformatics more details view paper
  • Downloaded 1,500 times
  • Download rankings, all-time:
    • Site-wide: 18,252
    • In bioinformatics: 2,299
  • Year to date:
    • Site-wide: 10,317
  • Since beginning of last month:
    • Site-wide: 14,707

Chromosomal rearrangements are commonly post-transcriptionally attenuated in cancer

genomics more details view paper
  • Downloaded 1,388 times
  • Download rankings, all-time:
    • Site-wide: 20,603
    • In genomics: 1,775
  • Year to date:
    • Site-wide: 143,650
  • Since beginning of last month:
    • Site-wide: 129,338

A functional landscape of chronic kidney disease entities from public transcriptomic data

pathology more details view paper
  • Downloaded 1,377 times
  • Download rankings, all-time:
    • Site-wide: 20,850
    • In pathology: 94
  • Year to date:
    • Site-wide: 71,019
  • Since beginning of last month:
    • Site-wide: 46,415

Robustness and applicability of functional genomics tools on scRNA-seq data

bioinformatics more details view paper
  • Downloaded 1,369 times
  • Download rankings, all-time:
    • Site-wide: 21,032
    • In bioinformatics: 2,171
  • Year to date:
    • Site-wide: 136,337
  • Since beginning of last month:
    • Site-wide: 121,430

Predicting cellular position in the Drosophila embryo from Single-Cell Transcriptomics data

systems biology more details view paper
  • Downloaded 1,366 times
  • Download rankings, all-time:
    • Site-wide: 21,096
    • In systems biology: 354
  • Year to date:
    • Site-wide: 89,111
  • Since beginning of last month:
    • Site-wide: 96,364

Cell-to-cell and type-to-type heterogeneity of signaling networks: Insights from the crowd

bioinformatics more details view paper
  • Downloaded 1,246 times
  • Download rankings, all-time:
    • Site-wide: 24,392
    • In bioinformatics: 2,678
  • Year to date:
    • Site-wide: 37,011
  • Since beginning of last month:
    • Site-wide: 21,010

decoupleR: Ensemble of computational methods to infer biological activities from omics data

bioinformatics more details view paper
  • Downloaded 1,240 times
  • Download rankings, all-time:
    • Site-wide: 24,602
    • In bioinformatics: 3,085
  • Year to date:
    • Site-wide: 6,184
  • Since beginning of last month:
    • Site-wide: 17,111

A Community Challenge for Pancancer Drug Mechanism of Action Inference from Perturbational Profile Data

cancer biology more details view paper
  • Downloaded 1,226 times
  • Download rankings, all-time:
    • Site-wide: 25,023
    • In cancer biology: 592
  • Year to date:
    • Site-wide: 31,231
  • Since beginning of last month:
    • Site-wide: 47,370

Functional linkage of gene fusions to cancer cell fitness assessed by pharmacological and CRISPR/Cas9 screening

cancer biology more details view paper
  • Downloaded 1,214 times
  • Download rankings, all-time:
    • Site-wide: 25,387
    • In cancer biology: 572
  • Year to date:
    • Site-wide: 156,545
  • Since beginning of last month:
    • Site-wide: 114,015

Signatures of cell death and proliferation in perturbation transcriptomics data - from confounding factor to effective prediction

systems biology more details view paper
  • Downloaded 1,132 times
  • Download rankings, all-time:
    • Site-wide: 28,259
    • In systems biology: 483
  • Year to date:
    • Site-wide: 149,095
  • Since beginning of last month:
    • Site-wide: 115,849

Combi-Seq: Multiplexed transcriptome-based profiling of drug combinations using 1deterministic barcoding in single-cell droplets

systems biology more details view paper
  • Downloaded 1,093 times
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    • Site-wide: 29,802
    • In systems biology: 722
  • Year to date:
    • Site-wide: 7,837
  • Since beginning of last month:
    • Site-wide: 11,228

Prediction of combination therapies based on topological modeling of the immune signaling network in Multiple Sclerosis

systems biology more details view paper
  • Downloaded 1,087 times
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    • Site-wide: 30,034
    • In systems biology: 519
  • Year to date:
    • Site-wide: 148,294
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A Consensus Transcriptional Landscape of Human End-Stage Heart Failure

cardiovascular medicine more details view paper
  • Downloaded 1,063 times
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    • Site-wide: 31,070
    • In cardiovascular medicine: 50
  • Year to date:
    • Site-wide: 69,388
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    • Site-wide: 154,541

Genomic determinants of protein abundance variation in colorectal cancer cells

systems biology more details view paper
  • Downloaded 1,021 times
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    • Site-wide: 32,989
    • In systems biology: 587
  • Year to date:
    • Site-wide: 159,528
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    • Site-wide: 161,010

System-wide quantitative proteomics of the metabolic syndrome in mice: genotypic and dietary effects

systems biology more details view paper
  • Downloaded 1,008 times
  • Download rankings, all-time:
    • Site-wide: 33,633
    • In systems biology: 605
  • Year to date:
    • Site-wide: 159,507
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    • Site-wide: 132,629

GDSCTools for Mining Pharmacogenomic Interactions in Cancer

cancer biology more details view paper
  • Downloaded 978 times
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    • Site-wide: 35,137
    • In cancer biology: 878
  • Year to date:
    • Site-wide: 96,351
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    • Site-wide: 86,243

Nitrogen partitioning between branched-chain amino acids and urea cycle enzymes sustains renal cancer progression

cancer biology more details view paper
  • Downloaded 966 times
  • Download rankings, all-time:
    • Site-wide: 35,803
    • In cancer biology: 1,045
  • Year to date:
    • Site-wide: 19,920
  • Since beginning of last month:
    • Site-wide: 21,022

Cooperative development of logical modelling standards and tools with CoLoMoTo

systems biology more details view paper
  • Downloaded 940 times
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    • Site-wide: 37,336
    • In systems biology: 679
  • Year to date:
    • Site-wide: 182,518
  • Since beginning of last month:
    • Site-wide: 149,284

Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting

bioinformatics more details view paper
  • Downloaded 792 times
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    • Site-wide: 48,071
    • In bioinformatics: 4,551
  • Year to date:
    • Site-wide: 179,463
  • Since beginning of last month:
    • Site-wide: 170,998

Patient-specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies

systems biology more details view paper
  • Downloaded 771 times
  • Download rankings, all-time:
    • Site-wide: 49,991
    • In systems biology: 954
  • Year to date:
    • Site-wide: 169,149
  • Since beginning of last month:
    • Site-wide: 184,450

Pan-Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival

cancer biology more details view paper
  • Downloaded 768 times
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    • Site-wide: 50,224
    • In cancer biology: 1,556
  • Year to date:
    • Site-wide: 30,905
  • Since beginning of last month:
    • Site-wide: 26,545

Transfer of regulatory knowledge from human to mouse for functional genomic analysis

systems biology more details view paper
  • Downloaded 733 times
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    • Site-wide: 53,694
    • In systems biology: 1,143
  • Year to date:
    • Site-wide: 51,811
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    • Site-wide: 42,216

Systematic analysis of transcriptional and post-transcriptional regulation of metabolism in yeast

systems biology more details view paper
  • Downloaded 731 times
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    • Site-wide: 53,827
    • In systems biology: 1,044
  • Year to date:
    • Site-wide: 176,761
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    • Site-wide: 148,873

A statistical framework for assessing pharmacological response and biomarkers using uncertainty estimates

cancer biology more details view paper
  • Downloaded 690 times
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    • Site-wide: 58,315
    • In cancer biology: 1,621
  • Year to date:
    • Site-wide: 89,369
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    • Site-wide: 67,743

Kinetic modelling of quantitative proteome data predicts metabolic reprogramming of liver cancer

systems biology more details view paper
  • Downloaded 682 times
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    • Site-wide: 59,356
    • In systems biology: 1,139
  • Year to date:
    • Site-wide: 180,019
  • Since beginning of last month:
    • Site-wide: 183,803

A Systematic Atlas of Chaperome Deregulation Topologies Across the Human Cancer Landscape

systems biology more details view paper
  • Downloaded 670 times
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    • Site-wide: 60,926
    • In systems biology: 1,196
  • Year to date:
    • Site-wide: 129,371
  • Since beginning of last month:
    • Site-wide: 185,606

Stratification and prediction of drug synergy based on target functional similarity

bioinformatics more details view paper
  • Downloaded 641 times
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    • Site-wide: 64,487
    • In bioinformatics: 5,838
  • Year to date:
    • Site-wide: 146,740
  • Since beginning of last month:
    • Site-wide: 113,631

Dissecting cancer resistance to therapies with cell-type-specific dynamic logic models

cancer biology more details view paper
  • Downloaded 628 times
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    • Site-wide: 66,270
    • In cancer biology: 1,751
  • Year to date:
    • Site-wide: 182,915
  • Since beginning of last month:
    • Site-wide: 174,820

The human hepatocyte TXG-MAPr: WGCNA transcriptomic modules to support mechanism-based risk assessment

pharmacology and toxicology more details view paper
  • Downloaded 623 times
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    • Site-wide: 67,013
    • In pharmacology and toxicology: 418
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    • Site-wide: 63,807
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    • Site-wide: 75,591

Converting networks to predictive logic models from perturbation signalling data with CellNOpt

bioinformatics more details view paper
  • Downloaded 566 times
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    • Site-wide: 75,647
    • In bioinformatics: 6,685
  • Year to date:
    • Site-wide: 150,329
  • Since beginning of last month:
    • Site-wide: 139,059

Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells

systems biology more details view paper
  • Downloaded 514 times
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    • Site-wide: 84,889
    • In systems biology: 1,745
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    • Site-wide: 149,696
  • Since beginning of last month:
    • Site-wide: 143,382

Computational drug repurposing against SARS-CoV-2 reveals plasma membrane cholesterol depletion as key factor of antiviral drug activity

systems biology more details view paper
  • Downloaded 482 times
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    • Site-wide: 91,380
    • In systems biology: 2,085
  • Year to date:
    • Site-wide: 44,284
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    • Site-wide: 63,993

Benchmarking substrate-based kinase activity inference using phosphoproteomic data

bioinformatics more details view paper
  • Downloaded 413 times
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    • Site-wide: 107,059
    • In bioinformatics: 8,475
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    • Site-wide: 186,960
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    • Site-wide: 179,112

Patient-specific Boolean models of signaling networks guide personalized treatments

systems biology more details view paper
  • Downloaded 405 times
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    • Site-wide: 109,230
    • In systems biology: 2,529
  • Year to date:
    • Site-wide: 30,883
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Reprogramming of the intestinal epithelial-immune cell interactome during SARS-CoV-2 infection

bioinformatics more details view paper
  • Downloaded 385 times
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    • Site-wide: 114,152
    • In bioinformatics: 9,768
  • Year to date:
    • Site-wide: 56,191
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    • Site-wide: 108,980

Increasing triacylglycerol formation and lipid storage by unsaturated lipids protects renal proximal tubules in diabetes

cell biology more details view paper
  • Downloaded 348 times
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    • Site-wide: 124,394
    • In cell biology: 6,489
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    • Site-wide: 34,057

Contextualization of causal regulatory networks from toxicogenomics data applied to drug-induced liver injury

systems biology more details view paper
  • Downloaded 339 times
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    • Site-wide: 126,942
    • In systems biology: 2,541
  • Year to date:
    • Site-wide: 126,659
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Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling

systems biology more details view paper
  • Downloaded 327 times
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    • Site-wide: 130,330
    • In systems biology: 2,607
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    • Site-wide: 160,474
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    • Site-wide: 167,052

Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis

biochemistry more details view paper
  • Downloaded 189 times
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    • Site-wide: 169,670
    • In biochemistry: None
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    • Site-wide: 8,762

Proteomic Dynamics of Breast Cancers Identifies Potential Therapeutic Protein Targets

systems biology more details view paper
  • Downloaded 96 times
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    • Site-wide: 186,352
    • In systems biology: None
  • Year to date:
    • Site-wide: 49,035
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    • Site-wide: 9,245

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