Cancer systems biology: embracing complexity to develop better anticancer therapeutic strategies

Widespread Genetic Heterogeneity in Multiple Myeloma: Implications for Targeted Therapy

(2014) Jens G. Lohr et al.   CANCER CELL

Mathematical Modeling of PDGF-Driven Glioblastoma Reveals Optimized Radiation Dosing Schedules

(2014) Kevin Leder et al.   CELL

Tumour cell heterogeneity maintained by cooperating subclones in Wnt-driven mammary cancers

(2014) Allison S. Cleary et al.   NATURE

Clinical development success rates for investigational drugs

(2014) Michael Hay et al.   NATURE BIOTECHNOLOGY

Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing

(2014) Marco Gerlinger et al.   NATURE GENETICS

Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine

(2014) Eliezer M Van Allen et al.   NATURE MEDICINE

Inference of Tumor Evolution during Chemotherapy by Computational Modeling and In Situ Analysis of Genetic and Phenotypic Cellular Diversity

(2014) Vanessa Almendro et al.   Cell Reports

Tumour-site-dependent expression profile of angiogenic factors in tumour-associated stroma of primary colorectal cancer and metastases

(2013) C Kahlert et al.   BRITISH JOURNAL OF CANCER

Macrophage Regulation of Tumor Responses to Anticancer Therapies

(2013) Michele De Palma et al.   CANCER CELL

Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia

(2013) Dan A. Landau et al.   CELL

Punctuated Evolution of Prostate Cancer Genomes

(2013) Sylvan C. Baca et al.   CELL

Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling

(2013) Ali Bashashati et al.   JOURNAL OF PATHOLOGY

Network quantification of EGFR signaling unveils potential for targeted combination therapy

(2013) B. Klinger et al.   Molecular Systems Biology

Comprehensive molecular characterization of clear cell renal cell carcinoma

(2013)   NATURE

Integrated genomic characterization of endometrial carcinoma

(2013) Gad Getz et al.   NATURE

Landscape of genomic alterations in cervical carcinomas

(2013) Akinyemi I. Ojesina et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Heterogeneity of tumor-induced gene expression changes in the human metabolic network

(2013) Jie Hu et al.   NATURE BIOTECHNOLOGY

Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing

(2013) Garrett M Frampton et al.   NATURE BIOTECHNOLOGY

Emerging landscape of oncogenic signatures across human cancers

(2013) Giovanni Ciriello et al.   NATURE GENETICS

A nanoparticle-based strategy for the imaging of a broad range of tumours by nonlinear amplification of microenvironment signals

(2013) Yiguang Wang et al.   NATURE MATERIALS

Microenvironmental regulation of tumor progression and metastasis

(2013) Daniela F Quail et al.   NATURE MEDICINE

The quest to overcome resistance to EGFR-targeted therapies in cancer

(2013) Curtis R Chong et al.   NATURE MEDICINE

Impact of deleterious passenger mutations on cancer progression

(2013) C. D. McFarland et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics

(2013) A. Sottoriva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetic Reprogramming in Cancer

(2013) M. L. Suva et al.   SCIENCE

Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of Recurrent Glioma

(2013) B. E. Johnson et al.   SCIENCE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Profiles of Basal and Stimulated Receptor Signaling Networks Predict Drug Response in Breast Cancer Lines

(2013) M. Niepel et al.   Science Signaling

Receptor Tyrosine Kinases Fall into Distinct Classes Based on Their Inferred Signaling Networks

(2013) J. P. Wagner et al.   Science Signaling

Computational Modeling of ERBB2-Amplified Breast Cancer Identifies Combined ErbB2/3 Blockade as Superior to the Combination of MEK and AKT Inhibitors

(2013) D. C. Kirouac et al.   Science Signaling

Kinase-Substrate Enrichment Analysis Provides Insights into the Heterogeneity of Signaling Pathway Activation in Leukemia Cells

(2013) P. Casado et al.   Science Signaling

Genome-Wide Mutational Signatures of Aristolochic Acid and Its Application as a Screening Tool

(2013) S. L. Poon et al.   Science Translational Medicine

Development of a Prognostic Model for Breast Cancer Survival in an Open Challenge Environment

(2013) W.-Y. Cheng et al.   Science Translational Medicine

A Drug Repositioning Approach Identifies Tricyclic Antidepressants as Inhibitors of Small Cell Lung Cancer and Other Neuroendocrine Tumors

(2013) N. S. Jahchan et al.   Cancer Discovery

RNA sequencing of cancer reveals novel splicing alterations

(2013) Jeyanthy Eswaran et al.   Scientific Reports

Novel Insights into Breast Cancer Genetic Variance through RNA Sequencing

(2013) Anelia Horvath et al.   Scientific Reports

Comprehensive identification of mutational cancer driver genes across 12 tumor types

(2013) David Tamborero et al.   Scientific Reports

VEGF Inhibits Tumor Cell Invasion and Mesenchymal Transition through a MET/VEGFR2 Complex

(2012) Kan V. Lu et al.   CANCER CELL

Imaging Tumor-Stroma Interactions during Chemotherapy Reveals Contributions of the Microenvironment to Resistance

(2012) Elizabeth S. Nakasone et al.   CANCER CELL

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor

(2012) Xun Xu et al.   CELL

Single-Cell Exome Sequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm

(2012) Yong Hou et al.   CELL

Resistance to BRAF Inhibition in BRAF-Mutant Colon Cancer Can Be Overcome with PI3K Inhibition or Demethylating Agents

(2012) M. Mao et al.   CLINICAL CANCER RESEARCH

A Panel of Four miRNAs Accurately Differentiates Malignant from Benign Indeterminate Thyroid Lesions on Fine Needle Aspiration

(2012) X. M. Keutgen et al.   CLINICAL CANCER RESEARCH

Combinations of BRAF, MEK, and PI3K/mTOR Inhibitors Overcome Acquired Resistance to the BRAF Inhibitor GSK2118436 Dabrafenib, Mediated by NRAS or MEK Mutations

(2012) J. G. Greger et al.   MOLECULAR CANCER THERAPEUTICS

Exploiting Evolution To Treat Drug Resistance: Combination Therapy and the Double Bind

(2012) David Basanta et al.   MOLECULAR PHARMACEUTICS

Passenger deletions generate therapeutic vulnerabilities in cancer

(2012) Florian L. Muller et al.   NATURE

Clonal evolution in cancer

(2012) Mel Greaves et al.   NATURE

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Tumour micro-environment elicits innate resistance to RAF inhibitors through HGF secretion

(2012) Ravid Straussman et al.   NATURE

Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing

(2012) Li Ding et al.   NATURE

p53 mutations in cancer

(2012) Patricia A. J. Muller et al.   NATURE CELL BIOLOGY

Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues

(2012) Gilad Landan et al.   NATURE GENETICS

Combined BRAF and MEK Inhibition in Melanoma with BRAF V600 Mutations

(2012) Keith T. Flaherty et al.   NEW ENGLAND JOURNAL OF MEDICINE

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

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

Tumor development is associated with decrease of TET gene expression and 5-methylcytosine hydroxylation

(2012) H Yang et al.   ONCOGENE

Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution

(2012) M. J. Booth et al.   SCIENCE

Variable Clonal Repopulation Dynamics Influence Chemotherapy Response in Colorectal Cancer

(2012) A. Kreso et al.   SCIENCE

Transcriptomic landscape of breast cancers through mRNA sequencing

(2012) Jeyanthy Eswaran et al.   Scientific Reports

In silico Experimentation of Glioma Microenvironment Development and Anti-tumor Therapy

(2012) Yu Wu et al.   PLoS Computational Biology

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

(2011) Philip J. Stephens et al.   CELL

Genetic Interactions in Cancer Progression and Treatment

(2011) Alan Ashworth et al.   CELL

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

(2011) G. C. Hon et al.   GENOME RESEARCH

Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer

(2011) J. H. Kim et al.   GENOME RESEARCH

Algorithms for Detecting Significantly Mutated Pathways in Cancer

(2011) Fabio Vandin et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

RAF inhibitor resistance is mediated by dimerization of aberrantly spliced BRAF(V600E)

(2011) Poulikos I. Poulikakos et al.   NATURE

Single-cell dissection of transcriptional heterogeneity in human colon tumors

(2011) Piero Dalerba et al.   NATURE BIOTECHNOLOGY

Increased methylation variation in epigenetic domains across cancer types

(2011) Kasper Daniel Hansen et al.   NATURE GENETICS

Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina–associated domains

(2011) Benjamin P Berman et al.   NATURE GENETICS

Methodological and practical challenges for personalized cancer therapies

(2011) Ignacio I. Wistuba et al.   Nature Reviews Clinical Oncology

Improved Survival with Vemurafenib in Melanoma with BRAF V600E Mutation

(2011) Paul B. Chapman et al.   NEW ENGLAND JOURNAL OF MEDICINE

Kinome siRNA-phosphoproteomic screen identifies networks regulating AKT signaling

(2011) Y Lu et al.   ONCOGENE

Cross-species hybridization of microarrays for studying tumor transcriptome of brain metastasis

(2011) E. S. Park et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

(2011) S. C. Bendall et al.   SCIENCE

Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study

(2011) S. Roychowdhury et al.   Science Translational Medicine

Model for in vivo progression of tumors based on co-evolving cell population and vasculature

(2011) Sehyo C. Choe et al.   Scientific Reports

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

(2010) Charles J. Vaske et al.   BIOINFORMATICS

Mechanistic modelling of dynamic MRI data predicts that tumour heterogeneity decreases therapeutic response

(2010) R Venkatasubramanian et al.   BRITISH JOURNAL OF CANCER

Genetic variegation of clonal architecture and propagating cells in leukaemia

(2010) Kristina Anderson et al.   NATURE

The mutation spectrum revealed by paired genome sequences from a lung cancer patient

(2010) William Lee et al.   NATURE

The patterns and dynamics of genomic instability in metastatic pancreatic cancer

(2010) Peter J. Campbell et al.   NATURE

COT drives resistance to RAF inhibition through MAP kinase pathway reactivation

(2010) Cory M. Johannessen et al.   NATURE

The molecular pathology of cancer

(2010) Timothy J. R. Harris et al.   Nature Reviews Clinical Oncology

Genomic instability — an evolving hallmark of cancer

(2010) Simona Negrini et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Gefitinib or Chemotherapy for Non–Small-Cell Lung Cancer with Mutated EGFR

(2010) Makoto Maemondo et al.   NEW ENGLAND JOURNAL OF MEDICINE

Akt-RSK-S6 Kinase Signaling Networks Activated by Oncogenic Receptor Tyrosine Kinases

(2010) A. Moritz et al.   Science Signaling

Antiangiogenic Therapy Elicits Malignant Progression of Tumors to Increased Local Invasion and Distant Metastasis

(2009) Marta Pàez-Ribes et al.   CANCER CELL

Systems Biology Reveals New Strategies for Personalizing Cancer Medicine and Confirms the Role of PTEN in Resistance to Trastuzumab

(2009) D. Faratian et al.   CANCER RESEARCH

Predicting and controlling the reactivity of immune cell populations against cancer

(2009) Kfir Oved et al.   Molecular Systems Biology

Transcriptome sequencing to detect gene fusions in cancer

(2009) Christopher A. Maher et al.   NATURE

Genome-wide identification of post-translational modulators of transcription factor activity in human B cells

(2009) Kai Wang et al.   NATURE BIOTECHNOLOGY

Three-dimensional microscopy of the tumor microenvironment in vivo using optical frequency domain imaging

(2009) Benjamin J Vakoc et al.   NATURE MEDICINE

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

MEK1 mutations confer resistance to MEK and B-RAF inhibition

(2009) C. M. Emery et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exomic Sequencing Identifies PALB2 as a Pancreatic Cancer Susceptibility Gene

(2009) S. Jones et al.   SCIENCE

Tumor-Immune Interaction, Surgical Treatment, and Cancer Recurrence in a Mathematical Model of Melanoma

(2009) Steffen Eikenberry et al.   PLoS Computational Biology

DNA methylation profiles in diffuse large B-cell lymphoma and their relationship to gene expression status

(2008) B L Pike et al.   LEUKEMIA

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

(2008) Timothy J. Ley et al.   NATURE

Stromal gene expression predicts clinical outcome in breast cancer

(2008) Greg Finak et al.   NATURE MEDICINE

Reverse-phase protein lysate microarrays for cell signaling analysis

(2008) Brett Spurrier et al.   Nature Protocols