An argument for mechanism-based statistical inference in cancer

Demystifying Disease, Democratizing Health Care

(2014) L. Hood et al.   Science Translational Medicine

Systematic Review: Gene Expression Profiling Assays in Early-Stage Breast Cancer

(2013) Luigi Marchionni et al.   ANNALS OF INTERNAL MEDICINE

Identification of direction in gene networks from expression and methylation

(2013) David M Simcha et al.   BMC Systems Biology

Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci

(2013) Qiyuan Li et al.   CELL

Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem

(2013) Nurcan Tuncbag et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

(2013) R. Levy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Half or more of the somatic mutations in cancers of self-renewing tissues originate prior to tumor initiation

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

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

A Blood-Based Proteomic Classifier for the Molecular Characterization of Pulmonary Nodules

(2013) X.-j. Li et al.   Science Translational Medicine

Integrated network analyses for functional genomic studies in cancer

(2013) Jennifer L. Wilson et al.   SEMINARS IN CANCER BIOLOGY

Mathematics of the Integrative Cancer Biology Program

(2013) A. R. A. Anderson et al.   Interface Focus

Multi-study Integration of Brain Cancer Transcriptomes Reveals Organ-Level Molecular Signatures

(2013) Jaeyun Sung et al.   PLoS Computational Biology

Metabolic Constraint-Based Refinement of Transcriptional Regulatory Networks

(2013) Sriram Chandrasekaran et al.   PLoS Computational Biology

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

(2012) Sam Ng et al.   BIOINFORMATICS

Molecular signatures from omics data: From chaos to consensus

(2012) Jaeyun Sung et al.   Biotechnology Journal

Identifying dysregulated pathways in cancers from pathway interaction networks

(2012) Ke-Qin Liu et al.   BMC BIOINFORMATICS

Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases

(2012) Yu Liu et al.   BMC Systems Biology

Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE

(2012) Yuliang Wang et al.   BMC Systems Biology

Why Your New Cancer Biomarker May Never Work: Recurrent Patterns and Remarkable Diversity in Biomarker Failures

(2012) S. E. Kern   CANCER RESEARCH

Predicting Drug Targets and Biomarkers of Cancer via Genome-Scale Metabolic Modeling

(2012) L. Jerby et al.   CLINICAL CANCER RESEARCH

Translational Bioinformatics: Linking the Molecular World to the Clinical World

(2012) R B Altman   CLINICAL PHARMACOLOGY & THERAPEUTICS

The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers

(2012) Luis A. Diaz Jr et al.   NATURE

A Critical Evaluation of Network and Pathway-Based Classifiers for Outcome Prediction in Breast Cancer

(2012) Christine Staiger et al.   PLoS One

Computational Medicine: Translating Models to Clinical Care

(2012) R. L. Winslow et al.   Science Translational Medicine

NEW: Network-Enabled Wisdom in Biology, Medicine, and Health Care

(2012) E. E. Schadt et al.   Science Translational Medicine

Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT

(2012) Rasmus Agren et al.   PLoS Computational Biology

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

Leveraging external knowledge on molecular interactions in classification methods for risk prediction of patients

(2011) Christine Porzelius et al.   BIOMETRICAL JOURNAL

Kinase inhibitors can produce off-target effects and activate linked pathways by retroactivity

(2011) Michelle L Wynn et al.   BMC Systems Biology

Is gene array testing to be considered routine now?

(2011) Soonmyung Paik   BREAST

Added predictive value of high-throughput molecular data to clinical data and its validation

(2011) A.-L. Boulesteix et al.   BRIEFINGS IN BIOINFORMATICS

Principles and Strategies for Developing Network Models in Cancer

(2011) Dana Pe'er et al.   CELL

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

The Integration of Biological Pathway Knowledge in Cancer Genomics: A review of existing computational approaches

(2011) Vinay Varadan et al.   IEEE SIGNAL PROCESSING MAGAZINE

State of the art in computational modelling of cancer

(2011) K. A. Rejniak et al.   MATHEMATICAL MEDICINE AND BIOLOGY-A JOURNAL OF THE IMA

Predicting selective drug targets in cancer through metabolic networks

(2011) O. Folger et al.   Molecular Systems Biology

Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase

(2011) Christian Frezza et al.   NATURE

Deflating the Genomic Bubble

(2011) J. P. Evans et al.   SCIENCE

Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect

(2011) Tomer Shlomi et al.   PLoS Computational Biology

Identifying Causal Genes and Dysregulated Pathways in Complex Diseases

(2011) Yoo-Ah Kim et al.   PLoS Computational Biology

Integration of pathway knowledge into a reweighted recursive feature elimination approach for risk stratification of cancer patients

(2010) Marc Johannes et al.   BIOINFORMATICS

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

(2010) Charles J. Vaske et al.   BIOINFORMATICS

Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context

(2010) Gad Abraham et al.   BMC BIOINFORMATICS

A Comprehensive Statistical Model for Cell Signaling

(2010) E Yoruk et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

(2010) Aarash Bordbar et al.   Molecular Systems Biology

Distant metastasis occurs late during the genetic evolution of pancreatic cancer

(2010) Shinichi Yachida et al.   NATURE

Predicting causal effects in large-scale systems from observational data

(2010) Marloes H Maathuis et al.   NATURE METHODS

Pharmacogenomics: will the promise be fulfilled?

(2010) Russ B. Altman et al.   NATURE REVIEWS GENETICS

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

DEGAS: De Novo Discovery of Dysregulated Pathways in Human Diseases

(2010) Igor Ulitsky et al.   PLoS One

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis

(2010) Sriram Chandrasekaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Usefulness of the top-scoring pairs of genes for prediction of prostate cancer progression

(2010) H Zhao et al.   PROSTATE CANCER AND PROSTATIC DISEASES

An integrative pathway-based clinical–genomic model for cancer survival prediction

(2010) Xi Chen et al.   STATISTICS & PROBABILITY LETTERS

Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC)

(2010) James A. Eddy et al.   PLoS Computational Biology

Estimating high-dimensional intervention effects from observational data

(2009) Marloes H. Maathuis et al.   ANNALS OF STATISTICS

Incorporating Predictor Network in Penalized Regression with Application to Microarray Data

(2009) Wei Pan et al.   BIOMETRICS

Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology

(2009) Caroline B. Milne et al.   Biotechnology Journal

Network-based support vector machine for classification of microarray samples

(2009) Yanni Zhu et al.   BMC BIOINFORMATICS

Incorporating pathway information into boosting estimation of high-dimensional risk prediction models

(2009) Harald Binder et al.   BMC BIOINFORMATICS

Two-transcript gene expression classifiers in the diagnosis and prognosis of human diseases

(2009) Lucas B Edelman et al.   BMC GENOMICS

Evaluation of MicroRNA Expression Profiles That May Predict Recurrence of Localized Stage I Non-Small Cell Lung Cancer after Surgical Resection

(2009) S. K. Patnaik et al.   CANCER RESEARCH

Detection of Treatment-Induced Changes in Signaling Pathways in Gastrointestinal Stromal Tumors Using Transcriptomic Data

(2009) M. F. Ochs et al.   CANCER RESEARCH

Cancer systems biology: a network modeling perspective

(2009) P. K. Kreeger et al.   CARCINOGENESIS

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

Causes and consequences of microRNA dysregulation in cancer

(2009) Carlo M. Croce   NATURE REVIEWS GENETICS

Sequences and consequences

(2009) S. Brenner   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evolution of resistance and progression to disease during clonal expansion of cancer

(2009) Richard Durrett et al.   THEORETICAL POPULATION BIOLOGY

Systems medicine: the future of medical genomics and healthcare

(2009) Charles Auffray et al.   Genome Medicine

Network-constrained regularization and variable selection for analysis of genomic data

(2008) C. Li et al.   BIOINFORMATICS

Translational Bioinformatics: Coming of Age

(2008) A. J. Butte   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major

(2008) Arvind K Chavali et al.   Molecular Systems Biology

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

An interferon-related gene signature for DNA damage resistance is a predictive marker for chemotherapy and radiation for breast cancer

(2008) R. R. Weichselbaum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene Regulation by Transcription Factors and MicroRNAs

(2008) O. Hobert   SCIENCE

An Integrated Genomic Analysis of Human Glioblastoma Multiforme

(2008) D. W. Parsons et al.   SCIENCE

Concerning the Origin of Malignant Tumours by Theodor Boveri. Translated and annotated by Henry Harris

(2007) T. Boveri   JOURNAL OF CELL SCIENCE