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Author: Julio Saez-Rodriguez

  • ORCiD: http://orcid.org/0000-0002-8552-8976
  • Most recently observed institution: Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Heidelberg, Germany

Rankings

  • All-time downloads: 80,761 (rank: 1,866 )
  • Categories:
    • bioinformatics: 30,960 (rank: 96 )
    • cancer biology: 13,336 (rank: 138 )
    • cardiovascular medicine: 839 (rank: 642 (tie) )
    • genetics: 1,493 (rank: 12,296 (tie) )
    • genomics: 1,331 (rank: 18,477 (tie) )
    • pathology: 1,227 (rank: 1,073 (tie) )
    • pharmacology and toxicology: 227 (rank: 6,015 (tie) )
    • systems biology: 31,348 (rank: 130 )

Downloads per author, site-wide

Preprints

Prioritisation of oncology therapeutic targets using CRISPR-Cas9 screening

cancer biology more details view paper
  • Downloaded 4,514 times
  • Download rankings, all-time:
    • Site-wide: 2,637
    • In cancer biology: 33
  • Year to date:
    • Site-wide: 6,637
  • Since beginning of last month:
    • Site-wide: 6,231

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

bioinformatics more details view paper
  • Downloaded 4,190 times
  • Download rankings, all-time:
    • Site-wide: 2,942
    • In bioinformatics: 249
  • Year to date:
    • Site-wide: 46,270
  • Since beginning of last month:
    • Site-wide: 36,648

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

bioinformatics more details view paper
  • Downloaded 3,709 times
  • Download rankings, all-time:
    • Site-wide: 3,507
    • In bioinformatics: 329
  • Year to date:
    • Site-wide: 45,088
  • Since beginning of last month:
    • Site-wide: 30,147

Assessment of network module identification across complex diseases

bioinformatics more details view paper
  • Downloaded 3,261 times
  • Download rankings, all-time:
    • Site-wide: 4,189
    • In bioinformatics: 407
  • Year to date:
    • Site-wide: 46,171
  • Since beginning of last month:
    • Site-wide: 52,069

Spatial multi-omic map of human myocardial infarction

systems biology more details view paper
  • Downloaded 3,249 times
  • Download rankings, all-time:
    • Site-wide: 4,212
    • In systems biology: 66
  • Year to date:
    • Site-wide: 1,110
  • Since beginning of last month:
    • Site-wide: 1,635

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

systems biology more details view paper
  • Downloaded 3,164 times
  • Download rankings, all-time:
    • Site-wide: 4,394
    • In systems biology: 70
  • Year to date:
    • Site-wide: 1,723
  • Since beginning of last month:
    • Site-wide: 6,102

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

systems biology more details view paper
  • Downloaded 2,732 times
  • Download rankings, all-time:
    • Site-wide: 5,391
    • In systems biology: 86
  • Year to date:
    • Site-wide: 18,312
  • Since beginning of last month:
    • Site-wide: 34,784

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

bioinformatics more details view paper
  • Downloaded 2,435 times
  • Download rankings, all-time:
    • Site-wide: 6,401
    • In bioinformatics: 697
  • Year to date:
    • Site-wide: 54,675
  • Since beginning of last month:
    • Site-wide: 81,083

Transcription factor activities enhance markers of drug response in cancer

cancer biology more details view paper
  • Downloaded 1,999 times
  • Download rankings, all-time:
    • Site-wide: 8,525
    • In cancer biology: 144
  • Year to date:
    • Site-wide: 77,889
  • Since beginning of last month:
    • Site-wide: 68,364

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

bioinformatics more details view paper
  • Downloaded 1,987 times
  • Download rankings, all-time:
    • Site-wide: 8,616
    • In bioinformatics: 1,004
  • Year to date:
    • Site-wide: 49,108
  • Since beginning of last month:
    • Site-wide: 43,085

CELLector: Genomics Guided Selection of Cancer in vitro Models

bioinformatics more details view paper
  • Downloaded 1,981 times
  • Download rankings, all-time:
    • Site-wide: 8,662
    • In bioinformatics: 1,009
  • Year to date:
    • Site-wide: 81,808
  • Since beginning of last month:
    • Site-wide: 118,575

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

bioinformatics more details view paper
  • Downloaded 1,870 times
  • Download rankings, all-time:
    • Site-wide: 9,441
    • In bioinformatics: 1,103
  • Year to date:
    • Site-wide: 54,679
  • Since beginning of last month:
    • Site-wide: 94,386

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

systems biology more details view paper
  • Downloaded 1,834 times
  • Download rankings, all-time:
    • Site-wide: 9,706
    • In systems biology: 176
  • Year to date:
    • Site-wide: 16,224
  • Since beginning of last month:
    • Site-wide: 57,954

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

systems biology more details view paper
  • Downloaded 1,800 times
  • Download rankings, all-time:
    • Site-wide: 9,974
    • In systems biology: 179
  • Year to date:
    • Site-wide: 61,924
  • Since beginning of last month:
    • Site-wide: 64,148

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

systems biology more details view paper
  • Downloaded 1,748 times
  • Download rankings, all-time:
    • Site-wide: 10,421
    • In systems biology: 190
  • Year to date:
    • Site-wide: 7,963
  • Since beginning of last month:
    • Site-wide: None

Integrated intra- and intercellular signaling knowledge for multicellular omics analysis

systems biology more details view paper
  • Downloaded 1,652 times
  • Download rankings, all-time:
    • Site-wide: 11,322
    • In systems biology: 200
  • Year to date:
    • Site-wide: 5,455
  • Since beginning of last month:
    • Site-wide: 28,713

Phosphoproteomics-based Profiling of Kinase Activities in Cancer Cells

bioinformatics more details view paper
  • Downloaded 1,633 times
  • Download rankings, all-time:
    • Site-wide: 11,524
    • In bioinformatics: 1,357
  • Year to date:
    • Site-wide: 85,416
  • Since beginning of last month:
    • Site-wide: 137,856

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

bioinformatics more details view paper
  • Downloaded 1,620 times
  • Download rankings, all-time:
    • Site-wide: 11,653
    • In bioinformatics: 1,371
  • Year to date:
    • Site-wide: 1,424
  • Since beginning of last month:
    • Site-wide: 876

Perturbation-response genes reveal signaling footprints in cancer gene expression

bioinformatics more details view paper
  • Downloaded 1,585 times
  • Download rankings, all-time:
    • Site-wide: 12,012
    • In bioinformatics: 1,404
  • Year to date:
    • Site-wide: 68,696
  • Since beginning of last month:
    • Site-wide: 82,837

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

cancer biology more details view paper
  • Downloaded 1,530 times
  • Download rankings, all-time:
    • Site-wide: 12,601
    • In cancer biology: 260
  • Year to date:
    • Site-wide: 104,618
  • Since beginning of last month:
    • Site-wide: 81,478

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

systems biology more details view paper
  • Downloaded 1,510 times
  • Download rankings, all-time:
    • Site-wide: 12,848
    • In systems biology: 230
  • Year to date:
    • Site-wide: 65,640
  • Since beginning of last month:
    • Site-wide: 68,513

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

genetics more details view paper
  • Downloaded 1,493 times
  • Download rankings, all-time:
    • Site-wide: 13,095
    • In genetics: 605
  • Year to date:
    • Site-wide: 61,913
  • Since beginning of last month:
    • Site-wide: 88,719

Why do pathway methods work better than they should?

systems biology more details view paper
  • Downloaded 1,474 times
  • Download rankings, all-time:
    • Site-wide: 13,353
    • In systems biology: 238
  • Year to date:
    • Site-wide: 34,169
  • Since beginning of last month:
    • Site-wide: 26,563

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

bioinformatics more details view paper
  • Downloaded 1,456 times
  • Download rankings, all-time:
    • Site-wide: 13,625
    • In bioinformatics: 1,588
  • Year to date:
    • Site-wide: 21,357
  • Since beginning of last month:
    • Site-wide: 78,963

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

systems biology more details view paper
  • Downloaded 1,396 times
  • Download rankings, all-time:
    • Site-wide: 14,519
    • In systems biology: 262
  • Year to date:
    • Site-wide: 86,402
  • Since beginning of last month:
    • Site-wide: 82,129

Chromosomal rearrangements are commonly post-transcriptionally attenuated in cancer

genomics more details view paper
  • Downloaded 1,331 times
  • Download rankings, all-time:
    • Site-wide: 15,590
    • In genomics: 1,574
  • Year to date:
    • Site-wide: 108,426
  • Since beginning of last month:
    • Site-wide: 80,354

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

bioinformatics more details view paper
  • Downloaded 1,282 times
  • Download rankings, all-time:
    • Site-wide: 16,532
    • In bioinformatics: 1,944
  • Year to date:
    • Site-wide: 65,871
  • Since beginning of last month:
    • Site-wide: 80,254

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

systems biology more details view paper
  • Downloaded 1,243 times
  • Download rankings, all-time:
    • Site-wide: 17,278
    • In systems biology: 336
  • Year to date:
    • Site-wide: 46,415
  • Since beginning of last month:
    • Site-wide: 66,260

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

pathology more details view paper
  • Downloaded 1,227 times
  • Download rankings, all-time:
    • Site-wide: 17,618
    • In pathology: 82
  • Year to date:
    • Site-wide: 49,830
  • Since beginning of last month:
    • Site-wide: 51,278

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

cancer biology more details view paper
  • Downloaded 1,149 times
  • Download rankings, all-time:
    • Site-wide: 19,437
    • In cancer biology: 452
  • Year to date:
    • Site-wide: 100,279
  • Since beginning of last month:
    • Site-wide: 108,353

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

systems biology more details view paper
  • Downloaded 1,057 times
  • Download rankings, all-time:
    • Site-wide: 21,956
    • In systems biology: 427
  • Year to date:
    • Site-wide: 64,579
  • Since beginning of last month:
    • Site-wide: 82,043

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

systems biology more details view paper
  • Downloaded 1,001 times
  • Download rankings, all-time:
    • Site-wide: 23,747
    • In systems biology: 466
  • Year to date:
    • Site-wide: 73,058
  • Since beginning of last month:
    • Site-wide: 59,021

Genomic determinants of protein abundance variation in colorectal cancer cells

systems biology more details view paper
  • Downloaded 968 times
  • Download rankings, all-time:
    • Site-wide: 25,021
    • In systems biology: 496
  • Year to date:
    • Site-wide: 100,310
  • Since beginning of last month:
    • Site-wide: 81,993

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

systems biology more details view paper
  • Downloaded 948 times
  • Download rankings, all-time:
    • Site-wide: 25,764
    • In systems biology: 513
  • Year to date:
    • Site-wide: 103,278
  • Since beginning of last month:
    • Site-wide: 146,429

Cooperative development of logical modelling standards and tools with CoLoMoTo

systems biology more details view paper
  • Downloaded 910 times
  • Download rankings, all-time:
    • Site-wide: 27,257
    • In systems biology: 551
  • Year to date:
    • Site-wide: 129,618
  • Since beginning of last month:
    • Site-wide: 116,765

Metabolic control of tumour extracellular matrix production in cancer-associated fibroblasts

cancer biology more details view paper
  • Downloaded 894 times
  • Download rankings, all-time:
    • Site-wide: 27,937
    • In cancer biology: 706
  • Year to date:
    • Site-wide: 27,106
  • Since beginning of last month:
    • Site-wide: 24,547

GDSCTools for Mining Pharmacogenomic Interactions in Cancer

cancer biology more details view paper
  • Downloaded 876 times
  • Download rankings, all-time:
    • Site-wide: 28,813
    • In cancer biology: 734
  • Year to date:
    • Site-wide: 62,713
  • Since beginning of last month:
    • Site-wide: 69,968

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

bioinformatics more details view paper
  • Downloaded 870 times
  • Download rankings, all-time:
    • Site-wide: 29,049
    • In bioinformatics: 3,286
  • Year to date:
    • Site-wide: 3,369
  • Since beginning of last month:
    • Site-wide: 8,048

DreamAI: algorithm for the imputation of proteomics data

bioinformatics more details view paper
  • Downloaded 866 times
  • Download rankings, all-time:
    • Site-wide: 29,275
    • In bioinformatics: 3,310
  • Year to date:
    • Site-wide: 8,262
  • Since beginning of last month:
    • Site-wide: 6,985

A Consensus Transcriptional Landscape of Human End-Stage Heart Failure

cardiovascular medicine more details view paper
  • Downloaded 839 times
  • Download rankings, all-time:
    • Site-wide: 30,573
    • In cardiovascular medicine: 49
  • Year to date:
    • Site-wide: 24,086
  • Since beginning of last month:
    • Site-wide: 38,050

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

cancer biology more details view paper
  • Downloaded 814 times
  • Download rankings, all-time:
    • Site-wide: 31,850
    • In cancer biology: 849
  • Year to date:
    • Site-wide: 6,397
  • Since beginning of last month:
    • Site-wide: 12,490

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

bioinformatics more details view paper
  • Downloaded 743 times
  • Download rankings, all-time:
    • Site-wide: 36,211
    • In bioinformatics: 3,956
  • Year to date:
    • Site-wide: 142,269
  • Since beginning of last month:
    • Site-wide: 136,970

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

systems biology more details view paper
  • Downloaded 715 times
  • Download rankings, all-time:
    • Site-wide: 38,170
    • In systems biology: 834
  • Year to date:
    • Site-wide: 138,129
  • Since beginning of last month:
    • Site-wide: 131,605

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

systems biology more details view paper
  • Downloaded 683 times
  • Download rankings, all-time:
    • Site-wide: 40,557
    • In systems biology: 892
  • Year to date:
    • Site-wide: 124,410
  • Since beginning of last month:
    • Site-wide: 116,928

The spatial transcriptomic landscape of the healing intestine following damage

systems biology more details view paper
  • Downloaded 679 times
  • Download rankings, all-time:
    • Site-wide: 40,830
    • In systems biology: 901
  • Year to date:
    • Site-wide: 4,813
  • Since beginning of last month:
    • Site-wide: 577

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

systems biology more details view paper
  • Downloaded 639 times
  • Download rankings, all-time:
    • Site-wide: 44,142
    • In systems biology: 976
  • Year to date:
    • Site-wide: 81,960
  • Since beginning of last month:
    • Site-wide: 108,482

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

systems biology more details view paper
  • Downloaded 605 times
  • Download rankings, all-time:
    • Site-wide: 47,301
    • In systems biology: 1,049
  • Year to date:
    • Site-wide: 122,214
  • Since beginning of last month:
    • Site-wide: 132,105

Stratification and prediction of drug synergy based on target functional similarity

bioinformatics more details view paper
  • Downloaded 597 times
  • Download rankings, all-time:
    • Site-wide: 48,086
    • In bioinformatics: 4,970
  • Year to date:
    • Site-wide: 130,307
  • Since beginning of last month:
    • Site-wide: 146,425

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

cancer biology more details view paper
  • Downloaded 591 times
  • Download rankings, all-time:
    • Site-wide: 48,636
    • In cancer biology: 1,372
  • Year to date:
    • Site-wide: 133,365
  • Since beginning of last month:
    • Site-wide: 125,049

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

cancer biology more details view paper
  • Downloaded 573 times
  • Download rankings, all-time:
    • Site-wide: 50,666
    • In cancer biology: 1,422
  • Year to date:
    • Site-wide: 68,776
  • Since beginning of last month:
    • Site-wide: 104,912

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

systems biology more details view paper
  • Downloaded 515 times
  • Download rankings, all-time:
    • Site-wide: 57,625
    • In systems biology: 1,316
  • Year to date:
    • Site-wide: 80,727
  • Since beginning of last month:
    • Site-wide: 40,407

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

bioinformatics more details view paper
  • Downloaded 499 times
  • Download rankings, all-time:
    • Site-wide: 59,662
    • In bioinformatics: 5,923
  • Year to date:
    • Site-wide: 50,711
  • Since beginning of last month:
    • Site-wide: 47,160

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

systems biology more details view paper
  • Downloaded 442 times
  • Download rankings, all-time:
    • Site-wide: 68,097
    • In systems biology: 1,585
  • Year to date:
    • Site-wide: 146,118
  • Since beginning of last month:
    • Site-wide: 144,802

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

cancer biology more details view paper
  • Downloaded 396 times
  • Download rankings, all-time:
    • Site-wide: 75,767
    • In cancer biology: 2,218
  • Year to date:
    • Site-wide: 10,607
  • Since beginning of last month:
    • Site-wide: 1,222

Benchmarking substrate-based kinase activity inference using phosphoproteomic data

bioinformatics more details view paper
  • Downloaded 376 times
  • Download rankings, all-time:
    • Site-wide: 79,548
    • In bioinformatics: 7,298
  • Year to date:
    • Site-wide: 147,950
  • Since beginning of last month:
    • Site-wide: None

Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling

systems biology more details view paper
  • Downloaded 228 times
  • Download rankings, all-time:
    • Site-wide: 112,284
    • In systems biology: 2,515
  • Year to date:
    • Site-wide: 41,236
  • Since beginning of last month:
    • Site-wide: 60,557

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

pharmacology and toxicology more details view paper
  • Downloaded 227 times
  • Download rankings, all-time:
    • Site-wide: 112,667
    • In pharmacology and toxicology: 845
  • Year to date:
    • Site-wide: 22,776
  • Since beginning of last month:
    • Site-wide: 7,385

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

systems biology more details view paper
  • Downloaded 156 times
  • Download rankings, all-time:
    • Site-wide: 129,496
    • In systems biology: 2,811
  • Year to date:
    • Site-wide: 36,043
  • Since beginning of last month:
    • Site-wide: 76,682

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