Identification of aberrant pathways and network activities from high-throughput data

Cross Talk Between O-GlcNAcylation and Phosphorylation: Roles in Signaling, Transcription, and Chronic Disease

(2011) Gerald W. Hart et al.   Annual Review of Biochemistry

Generative probabilistic models for protein–protein interaction networks—the biclique perspective

(2011) Regev Schweiger et al.   BIOINFORMATICS

Identification of metabolic network models from incomplete high-throughput datasets

(2011) Sara Berthoumieux et al.   BIOINFORMATICS

Large-scale dynamic gene regulatory network inference combining differential equation models with local dynamic Bayesian network analysis

(2011) Zheng Li et al.   BIOINFORMATICS

pathClass: an R-package for integration of pathway knowledge into support vector machines for biomarker discovery

(2011) M. Johannes et al.   BIOINFORMATICS

Physical Module Networks: an integrative approach for reconstructing transcription regulation

(2011) N. Novershtern et al.   BIOINFORMATICS

Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data

(2011) Jan Krumsiek et al.   BMC Systems Biology

Correlation of Somatic Mutation and Expression Identifies Genes Important in Human Glioblastoma Progression and Survival

(2011) D. L. Masica et al.   CANCER RESEARCH

Kernel-based data fusion improves the drug–protein interaction prediction

(2011) Yong-Cui Wang et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Adeno-associated Viral Vectors for Correction of Inborn Errors of Metabolism: Progressing Towards Clinical Application

(2011) Frank Jacobs et al.   CURRENT PHARMACEUTICAL DESIGN

Building Protein-Protein Interaction Networks with Proteomics and Informatics Tools

(2011) Mihaela E. Sardiu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Fusion methodologies for biomedical data

(2011) Georgia Tsiliki et al.   Journal of Proteomics

Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data

(2011) Chia-Hung Chien et al.   NUCLEIC ACIDS RESEARCH

Computational Integration of Homolog and Pathway Gene Module Expression Reveals General Stemness Signatures

(2011) Martina Koeva et al.   PLoS One

Construction of gene regulatory networks using biclustering and bayesian networks

(2011) Fadhl M Alakwaa et al.   Theoretical Biology and Medical Modelling

Pathway discovery in metabolic networks by subgraph extraction

(2010) Karoline Faust et al.   BIOINFORMATICS

A hybrid approach to extract protein-protein interactions

(2010) Q.-C. Bui et al.   BIOINFORMATICS

PathText: a text mining integrator for biological pathway visualizations

(2010) B. Kemper et al.   BIOINFORMATICS

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

(2010) Charles J. Vaske et al.   BIOINFORMATICS

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model

(2010) K. Yizhak et al.   BIOINFORMATICS

Prediction of epigenetically regulated genes in breast cancer cell lines

(2010) Leandro A Loss et al.   BMC BIOINFORMATICS

Data integration and analysis of biological networks

(2010) Tae Yong Kim et al.   CURRENT OPINION IN BIOTECHNOLOGY

Sarcosine in Urine after Digital Rectal Examination Fails as a Marker in Prostate Cancer Detection and Identification of Aggressive Tumours

(2010) Florian Jentzmik et al.   EUROPEAN UROLOGY

Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signatures

(2010) James Chen et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Sarcosine in Prostate Cancer Tissue is Not a Differential Metabolite for Prostate Cancer Aggressiveness and Biochemical Progression

(2010) Florian Jentzmik et al.   JOURNAL OF UROLOGY

Deconstructing the molecular portraits of breast cancer

(2010) Aleix Prat et al.   Molecular Oncology

Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism

(2010) Livnat Jerby et al.   Molecular Systems Biology

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Advances in understanding cancer genomes through second-generation sequencing

(2010) Matthew Meyerson et al.   NATURE REVIEWS GENETICS

Identification and validation of the pathways and functions regulated by the orphan nuclear receptor, ROR alpha1, in skeletal muscle

(2010) S. Raichur et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: update 2011

(2010) P. A. Fujita et al.   NUCLEIC ACIDS RESEARCH

Reactome: a database of reactions, pathways and biological processes

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

Automated Network Analysis Identifies Core Pathways in Glioblastoma

(2010) Ethan Cerami et al.   PLoS One

A pathway-based classification of human breast cancer

(2010) M. L. Gatza et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive Crosstalk Between O-GlcNAcylation and Phosphorylation Regulates Cytokinesis

(2010) Z. Wang et al.   Science Signaling

Inferring Signaling Pathway Topologies from Multiple Perturbation Measurements of Specific Biochemical Species

(2010) T.-R. Xu et al.   Science Signaling

A human functional protein interaction network and its application to cancer data analysis

(2010) Guanming Wu et al.   GENOME BIOLOGY

Serum sarcosine is not a marker for prostate cancer

(2010) E. A. Struys et al.   ANNALS OF CLINICAL BIOCHEMISTRY

A stochastic model for the evolution of metabolic networks with neighbor dependence

(2009) Aziz Mithani et al.   BIOINFORMATICS

A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis

(2009) Andreas Keller et al.   BIOINFORMATICS

Identification of differential gene pathways with principal component analysis

(2009) Shuangge Ma et al.   BIOINFORMATICS

A Gene Expression Signature Associated with “K-Ras Addiction” Reveals Regulators of EMT and Tumor Cell Survival

(2009) Anurag Singh et al.   CANCER CELL

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

Synthetic Lethal Interaction between Oncogenic KRAS Dependency and STK33 Suppression in Human Cancer Cells

(2009) Claudia Scholl et al.   CELL

A Genome-wide RNAi Screen Identifies Multiple Synthetic Lethal Interactions with the Ras Oncogene

(2009) Ji Luo et al.   CELL

Molecular Characterization of Breast Cancer with High-Resolution Oligonucleotide Comparative Genomic Hybridization Array

(2009) F. Andre et al.   CLINICAL CANCER RESEARCH

Identifying differentially expressed pathways via a mixed integer linear programming model

(2009) Y.-Q. Qiu et al.   IET Systems Biology

Sources of Bias in Specimens for Research About Molecular Markers for Cancer

(2009) David F. Ransohoff et al.   JOURNAL OF CLINICAL ONCOLOGY

Biomarkers Predicting Clinical Outcome of Epidermal Growth Factor Receptor–Targeted Therapy in Metastatic Colorectal Cancer

(2009) Salvatore Siena et al.   JNCI-Journal of the National Cancer Institute

A Genomic Strategy to Elucidate Modules of Oncogenic Pathway Signaling Networks

(2009) Jeffrey T. Chang et al.   MOLECULAR CELL

PI3K-dependent cross-talk interactions converge with Ras as quantifiable inputs integrated by Erk

(2009) Chun-Chao Wang et al.   Molecular Systems Biology

Pathway databases and tools for their exploitation: benefits, current limitations and challenges

(2009) Anna Bauer-Mehren et al.   Molecular Systems Biology

Systems-level dynamic analyses of fate change in murine embryonic stem cells

(2009) Rong Lu et al.   NATURE

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE

Molecular networks as sensors and drivers of common human diseases

(2009) Eric E. Schadt   NATURE

Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression

(2009) Arun Sreekumar et al.   NATURE

Dynamic modularity in protein interaction networks predicts breast cancer outcome

(2009) Ian W Taylor et al.   NATURE BIOTECHNOLOGY

Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity

(2009) Esti Yeger-Lotem et al.   NATURE GENETICS

PathExpress update: the enzyme neighbourhood method of associating gene-expression data with metabolic pathways

(2009) N. Goffard et al.   NUCLEIC ACIDS RESEARCH

VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology

(2009) Zhenjun Hu et al.   NUCLEIC ACIDS RESEARCH

Positive Selection of Tyrosine Loss in Metazoan Evolution

(2009) C. S. H. Tan et al.   SCIENCE

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses

(2009) I. Amit et al.   SCIENCE

Comparative Analysis Reveals Conserved Protein Phosphorylation Networks Implicated in Multiple Diseases

(2009) C. S. H. Tan et al.   Science Signaling

Integrating Proteomic, Transcriptional, and Interactome Data Reveals Hidden Components of Signaling and Regulatory Networks

(2009) S.-s. C. Huang et al.   Science Signaling

The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data

(2009) Regina Samaga et al.   PLoS Computational Biology

Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling

(2009) Bree B. Aldridge et al.   PLoS Computational Biology

Integrated analysis of breast cancer cell lines reveals unique signaling pathways

(2009) Laura M Heiser et al.   GENOME BIOLOGY

Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism

(2008) Cong T. Trinh et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Biomolecular network motif counting and discovery by color coding

(2008) N. Alon et al.   BIOINFORMATICS

Gene regulatory network inference: Data integration in dynamic models—A review

(2008) Michael Hecker et al.   BIOSYSTEMS

Receiver-operating characteristic curve analysis in diagnostic, prognostic and predictive biomarker research

(2008) K. Soreide   JOURNAL OF CLINICAL PATHOLOGY

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH