(Q53075272)

11 May 2018

title

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. (English)

1 reference

11 May 2018

1 reference

Eduard Porta-Pardo

3

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Antonio Colaprico

Antonio Colaprico

Cancer Genome Atlas Research Network

5

0 references

35

Cancer Genome Atlas Research Network

1 reference

11 May 2018

26

Benjamin G Vincent

1 reference

PubMed ID

29625049

11 May 2018

Isidro Cortés-Ciriano

Isidro Cortés-Ciriano

11

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Alexander J. Lazar

Alexander J Lazar

32

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Gad Getz

34

Gad Getz

1 reference

11 May 2018

0 references

19

Andrew D Cherniack

1 reference

11 May 2018

Gordon B. Mills

24

Gordon B Mills

1 reference

11 May 2018

Katherine A. Hoadley

29

Katherine A Hoadley

1 reference

11 May 2018

author name string

Li Ding

1

1 reference

11 May 2018

Matthew H Bailey

2

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11 May 2018

Vesteinn Thorsson

4

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11 May 2018

Denis Bertrand

6

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11 May 2018

David L Gibbs

7

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11 May 2018

Amila Weerasinghe

8

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11 May 2018

Kuan-Lin Huang

9

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11 May 2018

Collin Tokheim

10

1 reference

11 May 2018

Reyka Jayasinghe

12

1 reference

11 May 2018

Feng Chen

13

1 reference

11 May 2018

Lihua Yu

14

1 reference

11 May 2018

Sam Sun

15

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11 May 2018

Catharina Olsen

16

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11 May 2018

Jaegil Kim

17

1 reference

11 May 2018

Alison M Taylor

18

1 reference

11 May 2018

Rehan Akbani

20

1 reference

11 May 2018

Chayaporn Suphavilai

21

1 reference

11 May 2018

Niranjan Nagarajan

22

1 reference

11 May 2018

Joshua M Stuart

23

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11 May 2018

Matthew A Wyczalkowski

25

1 reference

11 May 2018

Carolyn M Hutter

27

1 reference

11 May 2018

Jean Claude Zenklusen

28

1 reference

11 May 2018

Michael C Wendl

30

1 reference

11 May 2018

Llya Shmulevich

31

1 reference

11 May 2018

David A Wheeler

33

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11 May 2018

language of work or name

English

0 references

publication date

1 April 2018

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11 May 2018

published in

Cell

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11 May 2018

volume

173

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11 May 2018

issue

2

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11 May 2018

page(s)

305-320.e10

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11 May 2018

MIRMMR: binary classification of microsatellite instability using methylation and mutations

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1 reference

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25 August 2018

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An immunogenic personal neoantigen vaccine for patients with melanoma

25 August 2018

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A pan-cancer genome-wide analysis reveals tumour dependencies by induction of nonsense-mediated decay

25 August 2018

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Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade.

25 August 2018

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Androgen receptor inhibitor-induced "BRCAness" and PARP inhibition are synthetically lethal for castration-resistant prostate cancer.

25 August 2018

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25 August 2018

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Mutual regulation of tumour vessel normalization and immunostimulatory reprogramming.

25 August 2018

1 reference

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Isocitrate dehydrogenase mutations suppress STAT1 and CD8+ T cell accumulation in gliomas

25 August 2018

1 reference

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HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Robust stratification of breast cancer subtypes using differential patterns of transcript isoform expression

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Safety and Antitumor Activity of the Multitargeted Pan-TRK, ROS1, and ALK Inhibitor Entrectinib: Combined Results from Two Phase I Trials (ALKA-372-001 and STARTRK-1).

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Integrated proteomic and N-glycoproteomic analyses of doxorubicin sensitive and resistant ovarian cancer cells reveal glycoprotein alteration in protein abundance and glycosylation

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Evaluating the evaluation of cancer driver genes

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Association of PD-1/PD-L axis expression with cytolytic activity, mutational load, and prognosis in melanoma and other solid tumors

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Identification of a novel serum biomarker for pancreatic cancer, C4b-binding protein α-chain (C4BPA) by quantitative proteomic analysis using tandem mass tags

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

The rules and impact of nonsense-mediated mRNA decay in human cancers

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Gain- and Loss-of-Function Mutations in the Breast Cancer Gene GATA3 Result in Differential Drug Sensitivity

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

A weighted exact test for mutually exclusive mutations in cancer

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Mutation Drivers of Immunological Responses to Cancer

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Divergent viral presentation among human tumors and adjacent normal tissues.

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Functional characterization of somatic mutations in cancer using network-based inference of protein activity

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Protein-structure-guided discovery of functional mutations across 19 cancer types

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

RNA splicing factors as oncoproteins and tumour suppressors

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Recurrent activating mutations of G-protein-coupled receptor CYSLTR2 in uveal melanoma

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Impact of KRAS, BRAF, PIK3CA, TP53 status and intraindividual mutation heterogeneity on outcome after liver resection for colorectal cancer metastases

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Patterns and functional implications of rare germline variants across 12 cancer types

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Systematic discovery of complex insertions and deletions in human cancers.

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Cancer type-dependent genetic interactions between cancer driver alterations indicate plasticity of epistasis across cell types

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Tumor evolution. High burden and pervasive positive selection of somatic mutations in normal human skin

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

The proteomic landscape of triple-negative breast cancer

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Whole genomes redefine the mutational landscape of pancreatic cancer

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Molecular and genetic properties of tumors associated with local immune cytolytic activity

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles.

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

A comprehensive transcriptional portrait of human cancer cell lines

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

RADIA: RNA and DNA integrated analysis for somatic mutation detection

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

A new tumor suppressor role for the Notch pathway in bladder cancer

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

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

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

e-Driver: a novel method to identify protein regions driving cancer

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Unravelling mechanisms of p53-mediated tumour suppression

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Prognostic value of deep sequencing method for minimal residual disease detection in multiple myeloma

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Gene co-expression modules as clinically relevant hallmarks of breast cancer diversity

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Discovery and saturation analysis of cancer genes across 21 tumour types

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

MSIsensor: microsatellite instability detection using paired tumor-normal sequence data

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Hallmarks of alternative splicing in cancer

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Mutational landscape and significance across 12 major cancer types

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

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

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

MuSiC: identifying mutational significance in cancer genomes

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Absolute quantification of somatic DNA alterations in human cancer

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

SomaticSniper: identification of somatic point mutations in whole genome sequencing data

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Frequent pathway mutations of splicing machinery in myelodysplasia

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Initial genome sequencing and analysis of multiple myeloma

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

The Sequence Alignment/Map format and SAMtools

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Fast and accurate short read alignment with Burrows-Wheeler transform

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

HMGB1 as an autocrine stimulus in human T98G glioblastoma cells: role in cell growth and migration

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

Splicing in disease: disruption of the splicing code and the decoding machinery

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

The consensus coding sequences of human breast and colorectal cancers

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

An immune-active tumor microenvironment favors clinical response to ipilimumab

25 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5916814

10.1016/J.CELL.2018.03.033

2 November 2018

Identifiers

DOI

1 reference

11 May 2018

0 references

1 reference

11 May 2018