Integrative computational biology for cancer research

Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology

(2010) Keith A. Baggerly et al.   Annals of Applied Statistics

Standards Affecting the Consistency of Gene Expression Arrays in Clinical Applications

(2010) S. A. Enkemann   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Prognostic Gene Expression Signature for Squamous Cell Carcinoma of Lung

(2010) C.-Q. Zhu et al.   CLINICAL CANCER RESEARCH

The FlowVizMenu and Parallel Scatterplot Matrix: Hybrid Multidimensional Visualizations for Network Exploration

(2010) C Viau et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Prognostic and Predictive Gene Signature for Adjuvant Chemotherapy in Resected Non–Small-Cell Lung Cancer

(2010) Chang-Qi Zhu et al.   JOURNAL OF CLINICAL ONCOLOGY

Primary Tumor Xenografts of Human Lung Adeno and Squamous Cell Carcinoma Express Distinct Proteomic Signatures

(2010) Yuhong Wei et al.   JOURNAL OF PROTEOME RESEARCH

Cancer Biomarkers: Can We Turn Recent Failures into Success?

(2010) E. P. Diamandis   JNCI-Journal of the National Cancer Institute

Programmed cell death 4 loss increases tumor cell invasion and is regulated by miR-21 in oral squamous cell carcinoma

(2010) Patricia P Reis et al.   Molecular Cancer

Differential roles of cyclin D1 and D3 in pancreatic ductal adenocarcinoma

(2010) Nikolina Radulovich et al.   Molecular Cancer

Big science: The cancer genome challenge

(2010) Heidi Ledford   NATURE

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

PROMISCUOUS: a database for network-based drug-repositioning

(2010) J. von Eichborn et al.   NUCLEIC ACIDS RESEARCH

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

In Silico Ascription of Gene Expression Differences to Tumor and Stromal Cells in a Model to Study Impact on Breast Cancer Outcome

(2010) Simen Myhre et al.   PLoS One

Implementing Data Standards: A report on the HUPOPSI Workshop September 2009, Toronto, Canada

(2010) Sandra Orchard et al.   PROTEOMICS

An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer

(2010) Rod K. Nibbe et al.   PLoS Computational Biology

Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging

(2010) Kristen Fortney et al.   GENOME BIOLOGY

Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I2D

(2009) Yun Niu et al.   BIOINFORMATICS

An active registry for bioinformatics web services

(2009) S. Pettifer et al.   BIOINFORMATICS

NAViGaTOR: Network Analysis, Visualization and Graphing Toronto

(2009) Kevin R. Brown et al.   BIOINFORMATICS

The development of a comparison approach for Illumina bead chips unravels unexpected challenges applying newest generation microarrays

(2009) Daniela Eggle et al.   BMC BIOINFORMATICS

The pitfalls of platform comparison: DNA copy number array technologies assessed

(2009) Christina Curtis et al.   BMC GENOMICS

Discovering cancer genes by integrating network and functional properties

(2009) Li Li et al.   BMC Medical Genomics

Gene Networks and microRNAs Implicated in Aggressive Prostate Cancer

(2009) L. Wang et al.   CANCER RESEARCH

Integrative Analysis of Cyclin Protein Levels Identifies Cyclin B1 as a Classifier and Predictor of Outcomes in Breast Cancer

(2009) R. Agarwal et al.   CLINICAL CANCER RESEARCH

Understanding Prognostic Gene Expression Signatures in Lung Cancer

(2009) Chang-Qi Zhu et al.   Clinical Lung Cancer

Identification of a microRNA signature associated with progression of leukoplakia to oral carcinoma

(2009) Nilva K. Cervigne et al.   HUMAN MOLECULAR GENETICS

Interaction Techniques for Selecting and Manipulating Subgraphs in Network Visualizations

(2009) M.J. McGuffin et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

A comprehensive catalogue of functional genetic variations in the EGFR pathway: Protein-protein interaction analysis reveals novel genes and polymorphisms important for cancer research

(2009) Sevtap Savas et al.   INTERNATIONAL JOURNAL OF CANCER

Assessment of tumour hypoxia for prediction of response to therapy and cancer prognosis

(2009) Adrian M. Jubb et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

Alterations in the TOP2A and HER2 Genes: Association With Adjuvant Anthracycline Sensitivity in Human Breast Cancers

(2009) D. J. Slamon et al.   JNCI-Journal of the National Cancer Institute

Predicting essential genes based on network and sequence analysis

(2009) Yih-Chii Hwang et al.   Molecular BioSystems

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

A HUPO test sample study reveals common problems in mass spectrometry–based proteomics

(2009) Alexander W Bell et al.   NATURE METHODS

Applying mass spectrometry-based proteomics to genetics, genomics and network biology

(2009) Matthias Gstaiger et al.   NATURE REVIEWS GENETICS

STITCH 2: an interaction network database for small molecules and proteins

(2009) Michael Kuhn et al.   NUCLEIC ACIDS RESEARCH

GeneSigDB—a curated database of gene expression signatures

(2009) Aedín C. Culhane et al.   NUCLEIC ACIDS RESEARCH

Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes

(2009) Adnan S. Syed et al.   NUCLEIC ACIDS RESEARCH

Prognostic gene signatures for non-small-cell lung cancer

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

Systems medicine: the future of medical genomics and healthcare

(2009) Charles Auffray et al.   Genome Medicine

Biomedical Text Mining and Its Applications

(2009) Raul Rodriguez-Esteban   PLoS Computational Biology

Apparently low reproducibility of true differential expression discoveries in microarray studies

(2008) Min Zhang et al.   BIOINFORMATICS

Predicting cancer involvement of genes from heterogeneous data

(2008) Ramon Aragues et al.   BMC BIOINFORMATICS

Pooling breast cancer datasets has a synergetic effect on classification performance and improves signature stability

(2008) Martin H van Vliet et al.   BMC GENOMICS

Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates

(2008) Andre Fujita et al.   BMC Systems Biology

How Large a Training Set is Needed to Develop a Classifier for Microarray Data?

(2008) K. K. Dobbin et al.   CLINICAL CANCER RESEARCH

Meta Analysis of Gene Expression Data within and Across Species

(2008) Ana Fierro et al.   CURRENT GENOMICS

TAp73 knockout shows genomic instability with infertility and tumor suppressor functions

(2008) R. Tomasini et al.   GENES & DEVELOPMENT

Role ofKRASandEGFRAs Biomarkers of Response to Erlotinib in National Cancer Institute of Canada Clinical Trials Group Study BR.21

(2008) Chang-Qi Zhu et al.   JOURNAL OF CLINICAL ONCOLOGY

Cancer survival in five continents: a worldwide population-based study (CONCORD)

(2008) Michel P Coleman et al.   LANCET ONCOLOGY

Discovery and Scoring of Protein Interaction Subnetworks Discriminative of Late Stage Human Colon Cancer

(2008) Rod K. Nibbe et al.   MOLECULAR & CELLULAR PROTEOMICS

Identification of pathways associated with invasive behavior by ovarian cancer cells using multidimensional protein identification technology (MudPIT)

(2008) Katharine L. Sodek et al.   Molecular BioSystems

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Gene expression–based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study

(2008) Kerby Shedden et al.   NATURE MEDICINE

An experimentally derived confidence score for binary protein-protein interactions

(2008) Pascal Braun et al.   NATURE METHODS

Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies

(2008) Romina Ponzielli et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2009

(2008) T. J. P. Hubbard et al.   NUCLEIC ACIDS RESEARCH

Reactome knowledgebase of human biological pathways and processes

(2008) L. Matthews et al.   NUCLEIC ACIDS RESEARCH

Getting Started in Text Mining

(2008) K. Bretonnel Cohen et al.   PLoS Computational Biology

Estimating the size of the human interactome

(2008) M. P. H. Stumpf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Low duplicability and network fragility of cancer genes

(2008) Davide Rambaldi et al.   TRENDS IN GENETICS

In silico cancer modeling: is it ready for prime time?

(2008) Thomas S Deisboeck et al.   Nature clinical practice. Oncology

WikiPathways: Pathway Editing for the People

(2008) Alexander R Pico et al.   PLOS BIOLOGY

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

(2008) Lourdes Peña-Castillo et al.   GENOME BIOLOGY

Text mining for biology - the way forward: opinions from leading scientists

(2008) Russ B Altman et al.   GENOME BIOLOGY

A Proteome Resource of Ovarian Cancer Ascites: Integrated Proteomic and Bioinformatic Analyses To Identify Putative Biomarkers

(2007) Limor Gortzak-Uzan et al.   JOURNAL OF PROTEOME RESEARCH