Global mapping of cancers: The Cancer Genome Atlas and beyond

Diverse approaches to predicting drug-induced liver injury using gene-expression profiles

(2020) G. Rex Sumsion et al.   Biology Direct

Predictability of drug-induced liver injury by machine learning

(2020) Marco Chierici et al.   Biology Direct

Saga of Mcl-1: regulation from transcription to degradation

(2020) Viacheslav V. Senichkin et al.   CELL DEATH AND DIFFERENTIATION

Technology-driven research for radiotherapy innovation

(2020) Claudio Fiorino et al.   Molecular Oncology

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

(2020) Esther Rheinbay et al.   NATURE

Genomic basis for RNA alterations in cancer

(2020) Claudia Calabrese et al.   NATURE

Pan-cancer analysis of whole genomes

(2020)   NATURE

The evolutionary history of 2,658 cancers

(2020) Moritz Gerstung et al.   NATURE

The repertoire of mutational signatures in human cancer

(2020) Ludmil B. Alexandrov et al.   NATURE

Patterns of somatic structural variation in human cancer genomes

(2020) Yilong Li et al.   NATURE

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

(2020) Isidro Cortés-Ciriano et al.   NATURE GENETICS

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

(2020) Kadir C. Akdemir et al.   NATURE GENETICS

The landscape of viral associations in human cancers

(2020) Marc Zapatka et al.   NATURE GENETICS

High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations

(2020) Yiqun Zhang et al.   Nature Communications

Progesterone and Breast Cancer: an NCI Workshop Report

(2020) Neeraja Sathyamoorthy et al.   Hormones & Cancer

Progesterone Receptor Gene Variants in Metastatic Estrogen Receptor Positive Breast Cancer

(2020) Amy M. Fowler et al.   Hormones & Cancer

Origin of the nuclear proteome on the basis of pre-existing nuclear localization signals in prokaryotic proteins

(2020) Olga M. Lisitsyna et al.   Biology Direct

The genome-wide landscape of C:G > T:A polymorphism at the CpG contexts in the human population

(2020) Jeonghwan Youk et al.   BMC GENOMICS

Inhibitor of apoptosis-stimulating protein of p53 inhibits ferroptosis and alleviates intestinal ischemia/reperfusion-induced acute lung injury

(2020) Yingchuan Li et al.   CELL DEATH AND DIFFERENTIATION

Arginine hypomethylation-mediated proteasomal degradation of histone H4—an early biomarker of cellular senescence

(2020) Cong Lin et al.   CELL DEATH AND DIFFERENTIATION

Genome-scale screening of deubiquitinase subfamily identifies USP3 as a stabilizer of Cdc25A regulating cell cycle in cancer

(2020) Soumyadip Das et al.   CELL DEATH AND DIFFERENTIATION

Cell type‐specific transcriptomics of esophageal adenocarcinoma as a scalable alternative for single cell transcriptomics

(2020) Max Krämer et al.   Molecular Oncology

Genomic landscape of platinum resistant and sensitive testicular cancers

(2020) Chey Loveday et al.   Nature Communications

Computational identification and characterization of glioma candidate biomarkers through multi-omics integrative profiling

(2020) Lin Liu et al.   Biology Direct

Long non-coding RNA LINC00426 contributes to doxorubicin resistance by sponging miR-4319 in osteosarcoma

(2020) Lulin Wang et al.   Biology Direct

RBMX is required for activation of ATR on repetitive DNAs to maintain genome stability

(2020) Tian Zheng et al.   CELL DEATH AND DIFFERENTIATION

Molecular Origins of APOBEC-Associated Mutations in Cancer

(2020) Mia Petljak et al.   DNA REPAIR

Estimating the effects of copy‐number variants on intelligence using hierarchical Bayesian models

(2020) Lai Jiang et al.   GENETIC EPIDEMIOLOGY

The benefits of smoking cessation on survival in cancer patients by integrative analysis of multi‐omics data

(2020) Sheng Yang et al.   Molecular Oncology

TERTpromoter mutation determines apoptotic and therapeutic responses ofBRAF-mutant cancers to BRAF and MEK inhibitors: Achilles Heel

(2020) Jie Tan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A user guide for the online exploration and visualization of PCAWG data

(2020) Mary J. Goldman et al.   Nature Communications

An integrative multi-omics analysis to identify candidate DNA methylation biomarkers related to prostate cancer risk

(2020) Lang Wu et al.   Nature Communications

Correlates of clinical benefit from immunotherapy and targeted therapy in metastatic renal cell carcinoma: comprehensive genomic and transcriptomic analysis

(2020) Nazli Dizman et al.   Journal for ImmunoTherapy of Cancer

Hot Spot TERT Promoter Mutations Are Rare in Sporadic Pancreatic Neuroendocrine Neoplasms and Associated with Telomere Length and Epigenetic Expression Patterns

(2020) Alexandra Posch et al.   Cancers

A comparative pharmaco-metabolomic study of glutaminase inhibitors in glioma stem-like cells confirms biological effectiveness but reveals differences in target-specificity

(2020) Katharina Koch et al.   Cell Death Discovery

On the definition of a self-sustaining chemical reaction system and its role in heredity

(2020) Yu Liu   Biology Direct

Cancer predictive studies

(2020) Ivano Amelio et al.   Biology Direct

Integrated Omics of Metastatic Colorectal Cancer

(2020) Chen Li et al.   CANCER CELL

TRF2 recruits nucleolar protein TCOF1 to coordinate telomere transcription and replication

(2020) Xin Nie et al.   CELL DEATH AND DIFFERENTIATION

Computational Analysis of Phosphoproteomics Data in Multi‐Omics Cancer Studies

(2020) Giulia Mantini et al.   PROTEOMICS

Multi-omics analysis identifies FoxO1 as a regulator of macrophage function through metabolic reprogramming

(2020) Kai Yan et al.   Cell Death & Disease

Pathogenic impact of transcript isoform switching in 1,209 cancer samples covering 27 cancer types using an isoform-specific interaction network

(2020) Abdullah Kahraman et al.   Scientific Reports

The Janus-like role of proline metabolism in cancer

(2020) Lynsey Burke et al.   Cell Death Discovery

Systematic evaluation of supervised machine learning for sample origin prediction using metagenomic sequencing data

(2020) Julie Chih-yu Chen et al.   Biology Direct

Commensal microbes and p53 in cancer progression

(2020) Ivana Celardo et al.   Biology Direct

The power of randomization by sex in multilocus genetic evolution

(2020) Liudmyla Vasylenko et al.   Biology Direct

A machine learning framework to determine geolocations from metagenomic profiling

(2020) Lihong Huang et al.   Biology Direct

Identification and functional characterization of new missense SNPs in the coding region of the TP53 gene

(2020) Flora Doffe et al.   CELL DEATH AND DIFFERENTIATION

Identification of a survival-related signature for sarcoma patients through integrated transcriptomic and proteomic profiling analyses

(2020) Biyu Zhang et al.   GENE

Telomeric injury by KML001 in human T cells induces mitochondrial dysfunction through the p53-PGC-1α pathway

(2020) Madison Schank et al.   Cell Death & Disease

Liquid biopsies and cancer omics

(2020) Ivano Amelio et al.   Cell Death Discovery

Molecular evidence of field cancerization initiated by diabetes in colon cancer patients

(2019) Laura Del Puerto-Nevado et al.   Molecular Oncology

The Combination of RET, BRAF and Demographic Data Identifies Subsets of Patients with Aggressive Papillary Thyroid Cancer

(2019) Jose R. W. Martínez et al.   Hormones & Cancer

Autophagy and cancer stem cells: molecular mechanisms and therapeutic applications

(2019) Francesca Nazio et al.   CELL DEATH AND DIFFERENTIATION

Long noncoding RNA LINC00336 inhibits ferroptosis in lung cancer by functioning as a competing endogenous RNA

(2019) Min Wang et al.   CELL DEATH AND DIFFERENTIATION

Thymidylate synthase maintains the de-differentiated state of triple negative breast cancers

(2019) Aarif Siddiqui et al.   CELL DEATH AND DIFFERENTIATION

Genome and pan-genome analysis to classify emerging bacteria

(2019) Aurélia Caputo et al.   Biology Direct

Integrative analysis based on survival associated co-expression gene modules for predicting Neuroblastoma patients’ survival time

(2019) Yatong Han et al.   Biology Direct

Robust pathway-based multi-omics data integration using directed random walks for survival prediction in multiple cancer studies

(2019) So Yeon Kim et al.   Biology Direct

Associating expression and genomic data using co-occurrence measures

(2019) Maarten Larmuseau et al.   Biology Direct

Bok regulates mitochondrial fusion and morphology

(2019) Jacqualyn J. Schulman et al.   CELL DEATH AND DIFFERENTIATION

Genomic signatures defining responsiveness to allopurinol and combination therapy for lung cancer identified by systems therapeutics analyses

(2019) Iman Tavassoly et al.   Molecular Oncology

A 17 gene panel for non‐small‐cell lung cancer prognosis identified through integrative epigenomic‐transcriptomic analyses of hypoxia‐induced epithelial–mesenchymal transition

(2019) Yue‐Lei Chen et al.   Molecular Oncology

Exploratory Analysis of Plasma Neurotensin as a Novel Biomarker for Early Detection of Colorectal Polyp and Cancer

(2019) Shengyang Qiu et al.   Hormones & Cancer

Massive metagenomic data analysis using abundance-based machine learning

(2019) Zachary N. Harris et al.   Biology Direct

Novel secretome-to-transcriptome integrated or secreto-transcriptomic approach to reveal liquid biopsy biomarkers for predicting individualized prognosis of breast cancer patients

(2019) J. Astor Ankney et al.   BMC Medical Genomics

Multi-omics profiling of calcium-induced human keratinocytes differentiation reveals modulation of unfolded protein response signaling pathways

(2019) Michaletti Anna et al.   CELL CYCLE

Kinome screen of ferroptosis reveals a novel role of ATM in regulating iron metabolism

(2019) Po-Han Chen et al.   CELL DEATH AND DIFFERENTIATION

Why the Gold Standard Approach by Mammography Demands Extension by Multiomics? Application of Liquid Biopsy miRNA Profiles to Breast Cancer Disease Management

(2019) Pavol Zubor et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Clinical update on head and neck cancer: molecular biology and ongoing challenges

(2019) Elham Alsahafi et al.   Cell Death & Disease

Integration of molecular features with clinical information for predicting outcomes for neuroblastoma patients

(2019) Yatong Han et al.   Biology Direct

Application of machine learning techniques for creating urban microbial fingerprints

(2019) Feargal Joseph Ryan   Biology Direct

Gene connectivity and enzyme evolution in the human metabolic network

(2019) Begoña Dobon et al.   Biology Direct

HUWE1 controls MCL1 stability to unleash AMBRA1-induced mitophagy

(2019) Flavie Strappazzon et al.   CELL DEATH AND DIFFERENTIATION

Metabolomic, transcriptomic and genetic integrative analysis reveals important roles of adenosine diphosphate in haemostasis and platelet activation in non‐small‐cell lung cancer

(2019) Long T. Hoang et al.   Molecular Oncology

Differentially expressed tRFs in CD5 positive relapsed & refractory diffuse large B cell lymphoma and the bioinformatic analysis for their potential clinical use

(2019) Qingyuan Qu et al.   Biology Direct

mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation

(2019) Johannes Werner et al.   Biology Direct

A novel framework for horizontal and vertical data integration in cancer studies with application to survival time prediction models

(2019) Iliyan Mihaylov et al.   Biology Direct

Epigenetic regulation of the Warburg effect by H2B monoubiquitination

(2019) Yuan-Ya Jing et al.   CELL DEATH AND DIFFERENTIATION

Histotype influences emergency presentation and prognosis in colon cancer surgery

(2019) Simone Sibio et al.   LANGENBECKS ARCHIVES OF SURGERY

RNA‐sequence‐based microRNA expression signature in breast cancer: tumor‐suppressive miR‐101‐5p regulates molecular pathogenesis

(2019) Hiroko Toda et al.   Molecular Oncology

Pan-cancer whole-genome analyses of metastatic solid tumours

(2019) Peter Priestley et al.   NATURE

Downregulation of miR-196-5p Induced by Hypoxia Drives Tumorigenesis and Metastasis in Hepatocellular Carcinoma

(2019) Hao Zheng et al.   Hormones & Cancer

Introducing a panel for early detection of lung adenocarcinoma by using data integration of genomics, epigenomics, transcriptomics and proteomics

(2019) Niloofar Haghjoo et al.   EXPERIMENTAL AND MOLECULAR PATHOLOGY

Do Mutations Turn p53 into an Oncogene?

(2019) Consuelo Pitolli et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A Computational Statistics Approach to Evaluate Blood Biomarkers for Breast Cancer Risk Stratification

(2019) Kaan Oktay et al.   Hormones & Cancer

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

(2018) Jianfang Liu et al.   CELL

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

(2018) Li Ding et al.   CELL

Oncogenic Signaling Pathways in The Cancer Genome Atlas

(2018) Francisco Sanchez-Vega et al.   CELL

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

(2018) Tathiane M. Malta et al.   CELL

TP53 gain-of-function mutation promotes inflammation in glioblastoma

(2018) Seok Won Ham et al.   CELL DEATH AND DIFFERENTIATION

The UbL-UBA Ubiquilin4 protein functions as a tumor suppressor in gastric cancer by p53-dependent and p53-independent regulation of p21

(2018) Shengkai Huang et al.   CELL DEATH AND DIFFERENTIATION

A complex of the ubiquitin ligase TRIM32 and the deubiquitinase USP7 balances the level of c-Myc ubiquitination and thereby determines neural stem cell fate specification

(2018) Sarah Nicklas et al.   CELL DEATH AND DIFFERENTIATION

Utility of circulating tumor DNA in cancer diagnostics with emphasis on early detection

(2018) Clare Fiala et al.   BMC Medicine

The Multifaceted Role of Chromosomal Instability in Cancer and Its Microenvironment

(2018) Samuel F. Bakhoum et al.   CELL

Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours

(2018) Xiaotu Ma et al.   NATURE

A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily

(2018) Anil Korkut et al.   Cell Systems

Mutant p53-dependent mitochondrial metabolic alterations in a mesenchymal stem cell-based model of progressive malignancy

(2018) Giuseppe Lonetto et al.   CELL DEATH AND DIFFERENTIATION

Comparing the effects of different cell death programs in tumor progression and immunotherapy

(2018) Michelle N. Messmer et al.   CELL DEATH AND DIFFERENTIATION

Autophagy-dependent cell death

(2018) Donna Denton et al.   CELL DEATH AND DIFFERENTIATION

A DHX9-lncRNA-MDM2 interaction regulates cell invasion and angiogenesis of cervical cancer

(2018) Xiangya Ding et al.   CELL DEATH AND DIFFERENTIATION

Mutant p53 as a guardian of the cancer cell

(2018) Fiamma Mantovani et al.   CELL DEATH AND DIFFERENTIATION

German Cancer Consortium (DKTK) - A national consortium for translational cancer research

(2018) Stefan Joos et al.   Molecular Oncology

The expression signature of cancer-associated KRAB-ZNF factors identified in TCGA pan-cancer transcriptomic data

(2018) Marta Gładych et al.   Molecular Oncology

Multi-Omics Profiling of the Tumor Microenvironment: Paving the Way to Precision Immuno-Oncology

(2018) Francesca Finotello et al.   Frontiers in Oncology

APOBEC signature mutation generates an oncogenic enhancer that drives LMO1 expression in T-ALL

(2017) Z Li et al.   LEUKEMIA

Integrated genomic and molecular characterization of cervical cancer

(2017)   NATURE

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

Antigen receptor repertoire profiling from RNA-seq data

(2017) Dmitriy A Bolotin et al.   NATURE BIOTECHNOLOGY

Use of CRISPR-modified human stem cell organoids to study the origin of mutational signatures in cancer

(2017) Jarno Drost et al.   SCIENCE

APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism

(2017) Ting-Wen Chen et al.   Nature Communications

Interleukin-34 sustains pro-tumorigenic signals in colon cancer tissue

(2017) Eleonora Franzè et al.   Oncotarget

Design of a Novel Composite H2S-Releasing Hydrogel for Cardiac Tissue Repair

(2016) Arianna Mauretti et al.   MACROMOLECULAR BIOSCIENCE

H2S-releasing nanoemulsions: a new formulation to inhibit tumor cells proliferation and improve tissue repair

(2016) Matteo Ciocci et al.   Oncotarget

Nivolumab versus chemotherapy in patients with advanced melanoma who progressed after anti-CTLA-4 treatment (CheckMate 037): a randomised, controlled, open-label, phase 3 trial

(2015) Jeffrey S Weber et al.   LANCET ONCOLOGY

Activity and safety of nivolumab, an anti-PD-1 immune checkpoint inhibitor, for patients with advanced, refractory squamous non-small-cell lung cancer (CheckMate 063): a phase 2, single-arm trial

(2015) Naiyer A Rizvi et al.   LANCET ONCOLOGY

Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets

(2015) Kornelius Schulze et al.   NATURE GENETICS

Subclonal diversification of primary breast cancer revealed by multiregion sequencing

(2015) Lucy R Yates et al.   NATURE MEDICINE

Nivolumab in Previously Untreated Melanoma without BRAF Mutation

(2015) Caroline Robert et al.   NEW ENGLAND JOURNAL OF MEDICINE

Nivolumab versus Docetaxel in Advanced Squamous-Cell Non–Small-Cell Lung Cancer

(2015) Julie Brahmer et al.   NEW ENGLAND JOURNAL OF MEDICINE

Nivolumab versus Everolimus in Advanced Renal-Cell Carcinoma

(2015) Robert J. Motzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

Effect of predicted protein-truncating genetic variants on the human transcriptome

(2015) M. A. Rivas et al.   SCIENCE

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

Systemic inflammation, as measured by the neutrophil/lymphocyte ratio, may have differential prognostic impact before and during treatment with fluorouracil, irinotecan and bevacizumab in metastatic colorectal cancer patients

(2014) Vincenzo Formica et al.   MEDICAL ONCOLOGY

Comprehensive molecular characterization of gastric adenocarcinoma

(2014) Adam J. Bass et al.   NATURE

Specificity of ε and Non-ε Isoforms of Arabidopsis 14-3-3 Proteins Towards the H+-ATPase and Other Targets

(2014) Roberta Pallucca et al.   PLoS One

Polymer composite random lasers based on diatom frustules as scatterers

(2014) Francesca Romana Lamastra et al.   RSC Advances

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

The Origin and Evolution of Mutations in Acute Myeloid Leukemia

(2012) John S. Welch et al.   CELL

Recognition mechanism of p63 by the E3 ligase Itch

(2012) Alessia Bellomaria et al.   CELL CYCLE

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE

Oxidative species and S-glutathionyl conjugates in the apoptosis induction by allyl thiosulfate

(2011) Ridvan Nepravishta et al.   FEBS Journal

Skn-1a/Oct-11 and ΔNp63α exert antagonizing effects on human keratin expression

(2010) Anna Maria Lena et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Genome-wide DNA methylation profiling reveals novel epigenetically regulated genes and non-coding RNAs in human testicular cancer

(2010) H H Cheung et al.   BRITISH JOURNAL OF CANCER

Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1

(2010) Roel G.W. Verhaak et al.   CANCER CELL

A systematic approach to understand the functional consequences of non-protein coding risk regions

(2010) Gerhard A. Coetzee et al.   CELL CYCLE

Interleukin-25 production is differently regulated by TNF-α and TGF-β1 in the human gut

(2010) D Fina et al.   Mucosal Immunology

Non-codingRNA sequence variations in human chronic lymphocytic leukemia and colorectal cancer

(2009) Sylwia E. Wojcik et al.   CARCINOGENESIS

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE