(Q28914768)

Jüri Reimand

2

0 references

Tatsuhiro Shibata

5

Tatsuhiro Shibata

0 references

Miguel Vazquez

Miguel Vazquez

6

0 references

Ville Mustonen

Ville Mustonen

7

0 references

Abel Gonzalez-Perez

Abel Gonzalez-Perez

8

0 references

John Pearson

9

John Pearson

0 references

Chris Sander

10

Chris Sander

0 references

Benjamin J. Raphael

11

Benjamin J Raphael

0 references

Debora Marks

12

Debora S Marks

0 references

B. F. Francis Ouellette

13

B F Francis Ouellette

0 references

Alfonso Valencia

Alfonso Valencia

14

0 references

Gary D. Bader

Gary D Bader

15

0 references

Paul C. Boutros

Paul C Boutros

16

0 references

Joshua M Stuart

17

Joshua M Stuart

0 references

Núria López-Bigas

Nuria Lopez-Bigas

19

0 references

Lincoln Stein

20

Lincoln D Stein

0 references

author name string

Syed Haider

3

0 references

Guanming Wu

4

0 references

Rune Linding

describes a project that uses

18

0 references

language of work or name

English

0 references

publication date

July 2015

0 references

published in

Nature Methods

0 references

volume

12

0 references

issue

7

0 references

page(s)

615-21

0 references

Cytoscape

1 reference

Europe PubMed Central

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

based on heuristic

inferred from PubMed Central ID database lookup

cites work

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Direct reversal of glucocorticoid resistance by AKT inhibition in acute lymphoblastic leukemia

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16 March 2017

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Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes

16 March 2017

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16 March 2017

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Leveraging models of cell regulation and GWAS data in integrative network-based association studies

16 March 2017

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16 March 2017

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16 March 2017

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16 March 2017

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16 March 2017

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A human MAP kinase interactome

16 March 2017

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16 March 2017

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Comprehensive genomic characterization defines human glioblastoma genes and core pathways

16 March 2017

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Integration of biological networks and gene expression data using Cytoscape

16 March 2017

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DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists

16 March 2017

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ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context

16 March 2017

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16 March 2017

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Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

16 March 2017

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KEGG for integration and interpretation of large-scale molecular data sets

16 March 2017

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ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing

7 April 2017

1 reference

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STRING v9.1: protein-protein interaction networks, with increased coverage and integration

7 April 2017

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The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

7 April 2017

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Network-based classification of breast cancer metastasis

7 April 2017

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An integrative genomics approach to infer causal associations between gene expression and disease

7 April 2017

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Delivery of a clinical genomics service

7 April 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

ReactomeFIViz: a Cytoscape app for pathway and network-based data analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

Cross-species regulatory network analysis identifies a synergistic interaction between FOXM1 and CENPF that drives prostate cancer malignancy

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

Epigenomic alterations define lethal CIMP-positive ependymomas of infancy

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

The transcriptional regulatory network of proneural glioma determines the genetic alterations selected during tumor progression.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

Drug Intervention Response Predictions with PARADIGM (DIRPP) identifies drug resistant cancer cell lines and pathway mechanisms of resistance

3 June 2018

1 reference

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Accelerated discovery via a whole-cell model

3 June 2018

1 reference

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Power calculation for overall hypothesis testing with high-dimensional commensurate outcomes

3 June 2018

1 reference

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Pan-cancer patterns of somatic copy number alteration

3 June 2018

1 reference

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Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE).

3 June 2018

1 reference

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Computational approaches to identify functional genetic variants in cancer genomes

3 June 2018

1 reference

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RHPN2 drives mesenchymal transformation in malignant glioma by triggering RhoA activation

3 June 2018

1 reference

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Simultaneous identification of multiple driver pathways in cancer

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

Pathway-based personalized analysis of cancer

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

Lessons from the cancer genome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

GSVA: gene set variation analysis for microarray and RNA-seq data.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

A network module-based method for identifying cancer prognostic signatures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

Oncogenic NRAS signaling differentially regulates survival and proliferation in melanoma

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

EnrichNet: network-based gene set enrichment analysis.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

Bayesian inference of signaling network topology in a cancer cell line

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

Sequence analysis of mutations and translocations across breast cancer subtypes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

Camera: a competitive gene set test accounting for inter-gene correlation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

Sample-level enrichment analysis unravels shared stress phenotypes among multiple cancer types

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

Mutual exclusivity analysis identifies oncogenic network modules

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

The PathOlogist: an automated tool for pathway-centric analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

Principles and strategies for developing network models in cancer

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

An integrated approach to uncover drivers of cancer.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

Enrichment map: a network-based method for gene-set enrichment visualization and interpretation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

Logic-based models for the analysis of cell signaling networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

Automated network analysis identifies core pathways in glioblastoma

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

Interaction between Ras(V12) and scribbled clones induces tumour growth and invasion

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

The transcriptional network for mesenchymal transformation of brain tumours.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

The Gene Ontology in 2010: extensions and refinements

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

A novel signaling pathway impact analysis.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

Identifying functional modules in protein-protein interaction networks: an integrated exact approach

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

Flexible informatics for linking experimental data to mathematical models via DataRail

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4717906

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.

3 June 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3440

HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3440

Algorithms for detecting significantly mutated pathways in cancer.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3440

Adaptive clinical trials: the promise and the caution

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26125594

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

IntOGen-mutations identifies cancer drivers across tumor types.

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3440

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1038/NMETH.3440

1 reference

Dimensions Publication ID

1037060648

0 references

1 reference

1 reference

PubMed publication ID

26125594

1 reference