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Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks

Molecular cell, 2020-03, Vol.77 (6), p.1307-1321.e10

2020

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Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap

Nature protocols, 2019-02, Vol.14 (2), p.482-517

2019

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In vivo CRISPR screens reveal Serpinb9 and Adam2 as regulators of immune therapy response in lung cancer

Nature communications, 2023-05, Vol.14 (1), p.3150-3150, Article 3150

2023

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g:Profiler-a web server for functional interpretation of gene lists (2016 update)

Nucleic acids research, 2016-07, Vol.44 (W1), p.W83

2016

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Notch1 regulates the initiation of metastasis and self-renewal of Group 3 medulloblastoma

Nature communications, 2018-10, Vol.9 (1), p.4121-9, Article 4121

2018

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A transcriptome-based signature of pathological angiogenesis predicts breast cancer patient survival

PLoS genetics, 2019-12, Vol.15 (12), p.e1008482-e1008482

2019

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Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma

Nature communications, 2022-12, Vol.13 (1), p.7506-7506, Article 7506

2022

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Chromatin accessibility of primary human cancers ties regional mutational processes and signatures with tissues of origin

PLoS computational biology, 2022-08, Vol.18 (8), p.e1010393-e1010393

2022

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Single allele loss-of-function mutations select and sculpt conditional cooperative networks in breast cancer

Nature communications, 2021-09, Vol.12 (1), p.1-19, Article 5238

2021

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Impact of outdated gene annotations on pathway enrichment analysis

Nature methods, 2016-08, Vol.13 (9), p.705-706

2016

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Abstract 2354: Candidate non-coding driver mutations in super-enhancers and long-range chromatin interaction networks across 1,800 whole cancer genomes

Cancer research (Chicago, Ill.), 2018-07, Vol.78 (13_Supplement), p.2354-2354

Reimand, Juri

2018

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Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers

Molecular systems biology, 2013, Vol.9 (1), p.637-n/a

2013

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g:Profiler—a web server for functional interpretation of gene lists (2011 update)

Nucleic acids research, 2011-07, Vol.39 (suppl_2), p.W307-W315

2011

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Rare Germline Variants Are Associated with Rapid Biochemical Recurrence After Radical Prostate Cancer Treatment: A Pan Prostate Cancer Group Study

European urology, 2022-08, Vol.82 (2), p.201-211

2022

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Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders

Genome Biology, 2016-08, Vol.17 (1), p.182-182, Article 182

2016

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MIMP: predicting the impact of mutations on kinase-substrate phosphorylation

Nature methods, 2015-06, Vol.12 (6), p.531-533

2015

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Functional and genetic determinants of mutation rate variability in regulatory elements of cancer genomes

Genome Biology, 2021-05, Vol.22 (1), p.133-133, Article 133

2021

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Directional integration and pathway enrichment analysis for multi-omics data

Nature communications, 2024-07, Vol.15 (1), p.5690-14, Article 5690

2024

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ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins

Nucleic acids research, 2018-01, Vol.46 (D1), p.D901-D910

2018

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Human phospho‐signaling networks of SARS‐CoV‐2 infection are rewired by population genetic variants

Molecular systems biology, 2022-05, Vol.18 (5), p.e10823-n/a

2022

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The mutational landscape of phosphorylation signaling in cancer

Scientific reports, 2013-10, Vol.3 (1), p.2651-2651, Article 2651

2013

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Pathway and network analysis of cancer genomes

Nature methods, 2015-07, Vol.12 (7), p.615-621

2015

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Functional Genomic Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance

Cell, 2016-01, Vol.164 (1-2), p.293-309

2016

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Phosphoproteome and drug-response effects mediated by the three protein phosphatase 2A inhibitor proteins CIP2A, SET, and PME-1

The Journal of biological chemistry, 2020-03, Vol.295 (13), p.4194-4211

2020

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Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity

Proceedings of the National Academy of Sciences - PNAS, 2015-01, Vol.112 (3), p.851-856

2015

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Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks

Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap

In vivo CRISPR screens reveal Serpinb9 and Adam2 as regulators of immune therapy response in lung cancer

g:Profiler-a web server for functional interpretation of gene lists (2016 update)

Notch1 regulates the initiation of metastasis and self-renewal of Group 3 medulloblastoma

A transcriptome-based signature of pathological angiogenesis predicts breast cancer patient survival

Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma

Chromatin accessibility of primary human cancers ties regional mutational processes and signatures with tissues of origin

Single allele loss-of-function mutations select and sculpt conditional cooperative networks in breast cancer

Impact of outdated gene annotations on pathway enrichment analysis

Abstract 2354: Candidate non-coding driver mutations in super-enhancers and long-range chromatin interaction networks across 1,800 whole cancer genomes

Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers

g:Profiler—a web server for functional interpretation of gene lists (2011 update)

Rare Germline Variants Are Associated with Rapid Biochemical Recurrence After Radical Prostate Cancer Treatment: A Pan Prostate Cancer Group Study

Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders

MIMP: predicting the impact of mutations on kinase-substrate phosphorylation

Functional and genetic determinants of mutation rate variability in regulatory elements of cancer genomes

Directional integration and pathway enrichment analysis for multi-omics data

ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins

Human phospho‐signaling networks of SARS‐CoV‐2 infection are rewired by population genetic variants

The mutational landscape of phosphorylation signaling in cancer

Pathway and network analysis of cancer genomes

Functional Genomic Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance

Phosphoproteome and drug-response effects mediated by the three protein phosphatase 2A inhibitor proteins CIP2A, SET, and PME-1

Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity

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