Systems biology in drug discovery and development.

[1]  Yudong D. He,et al.  Functional Discovery via a Compendium of Expression Profiles , 2000, Cell.

[2]  S. Huang,et al.  Shape-dependent control of cell growth, differentiation, and apoptosis: switching between attractors in cell regulatory networks. , 2000, Experimental cell research.

[3]  Joshua M. Stuart,et al.  A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules , 2003, Science.

[4]  E. Kunkel Systems biology in drug discovery , 2004, Nature Biotechnology.

[5]  V. Thorsson,et al.  Integrated Genomic and Proteomic Analyses of Gene Expression in Mammalian Cells*S , 2004, Molecular & Cellular Proteomics.

[6]  E. Berg,et al.  An integrative biology approach for analysis of drug action in models of human vascular inflammation , 2004, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[7]  Leroy Hood,et al.  The impact of systems approaches on biological problems in drug discovery , 2004, Nature Biotechnology.

[8]  C. Hughes,et al.  Of Mice and Not Men: Differences between Mouse and Human Immunology , 2004, The Journal of Immunology.

[9]  S. Horvath,et al.  Statistical Applications in Genetics and Molecular Biology , 2011 .

[10]  E. Butcher Can cell systems biology rescue drug discovery? , 2005, Nature Reviews Drug Discovery.

[11]  E L Berg,et al.  Biological complexity and drug discovery: a practical systems biology approach. , 2005, Systems biology.

[12]  Eric J Kunkel,et al.  Characterization of compound mechanisms and secondary activities by BioMAP analysis. , 2006, Journal of pharmacological and toxicological methods.

[13]  Paul A Clemons,et al.  The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease , 2006, Science.

[14]  Chris Wiggins,et al.  ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context , 2004, BMC Bioinformatics.

[15]  S. Paik Development and clinical utility of a 21-gene recurrence score prognostic assay in patients with early breast cancer treated with tamoxifen. , 2007, The oncologist.

[16]  R. Solé,et al.  Data completeness—the Achilles heel of drug-target networks , 2008, Nature Biotechnology.

[17]  Younghoon Kim,et al.  Combining tissue transcriptomics and urine metabolomics for breast cancer biomarker identification , 2009, Bioinform..

[18]  Pooja Mittal,et al.  A novel signaling pathway impact analysis , 2009, Bioinform..

[19]  Emanuel F Petricoin,et al.  Causal reasoning identifies mechanisms of sensitivity for a novel AKT kinase inhibitor, GSK690693 , 2010, BMC Genomics.

[20]  Richard S. Judson,et al.  Profiling Bioactivity of the ToxCast Chemical Library Using BioMAP Primary Human Cell Systems , 2009, Journal of biomolecular screening.

[21]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[22]  H. Boezen,et al.  Genome-wide association studies: what do they teach us about asthma and chronic obstructive pulmonary disease? , 2009, Proceedings of the American Thoracic Society.

[23]  Brad T. Sherman,et al.  Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists , 2008, Nucleic acids research.

[24]  D. Chan,et al.  The Road from Discovery to Clinical Diagnostics: Lessons Learned from the First FDA-Cleared In Vitro Diagnostic Multivariate Index Assay of Proteomic Biomarkers , 2010, Cancer Epidemiology, Biomarkers & Prevention.

[25]  Avi Ma’ayan,et al.  Protein kinase target discovery from genome-wide messenger RNA expression profiling. , 2010, The Mount Sinai journal of medicine, New York.

[26]  A. Hubbard,et al.  Toxicogenomic profiling of chemically exposed humans in risk assessment. , 2010, Mutation research.

[27]  Xiaobo Zhou,et al.  Predicting enzyme targets for cancer drugs by profiling human Metabolic reactions in NCI-60 cell lines , 2010, BMC Bioinformatics.

[28]  Joel Dudley,et al.  Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets , 2010, PLoS Comput. Biol..

[29]  Sean Ekins,et al.  Chemical target and pathway toxicity mechanisms defined in primary human cell systems. , 2010, Journal of pharmacological and toxicological methods.

[30]  Hans-Werner Mewes,et al.  CORUM: the comprehensive resource of mammalian protein complexes , 2007, Nucleic Acids Res..

[31]  O. Elemento,et al.  DNA methylation signatures define molecular subtypes of diffuse large B-cell lymphoma. , 2010, Blood.

[32]  M. Imieliński,et al.  In Situ Proteomic Analysis of Human Breast Cancer Epithelial Cells Using Laser Capture Microdissection: Annotation by Protein Set Enrichment Analysis and Gene Ontology* , 2010, Molecular & Cellular Proteomics.

[33]  David Haussler,et al.  Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM , 2010, Bioinform..

[34]  J. Weinstein,et al.  mRNA and microRNA Expression Profiles of the NCI-60 Integrated with Drug Activities , 2010, Molecular Cancer Therapeutics.

[35]  Alejandra C. Ventura,et al.  Multisite Phosphorylation Provides an Effective and Flexible Mechanism for Switch-Like Protein Degradation , 2010, PloS one.

[36]  Craig D Wenger,et al.  Phosphoproteomics for the masses. , 2010, ACS chemical biology.

[37]  P. Sharp,et al.  MicroRNA functions in stress responses. , 2010, Molecular cell.

[38]  A. Barabasi,et al.  Network medicine : a network-based approach to human disease , 2010 .

[39]  Andrew P. Feinberg,et al.  Epigenomics Reveals a Functional Genome Anatomy and a New Approach to Common Disease , 2010, Nature Biotechnology.

[40]  Pankaj Agarwal,et al.  Systematic Drug Repositioning Based on Clinical Side-Effects , 2011, PloS one.

[41]  Jennifer Park,et al.  A computable cellular stress network model for non-diseased pulmonary and cardiovascular tissue , 2011, BMC Systems Biology.

[42]  F. Azuaje,et al.  Drug-target network in myocardial infarction reveals multiple side effects of unrelated drugs , 2011, Scientific reports.

[43]  F. Prinz,et al.  Believe it or not: how much can we rely on published data on potential drug targets? , 2011, Nature Reviews Drug Discovery.

[44]  Paul Bowness,et al.  Discovery of Candidate Serum Proteomic and Metabolomic Biomarkers in Ankylosing Spondylitis* , 2011, Molecular & Cellular Proteomics.

[45]  G. Daley,et al.  Induced pluripotent stem cells for modelling human diseases , 2011, Philosophical Transactions of the Royal Society B: Biological Sciences.

[46]  Chuan He,et al.  Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine , 2011, Science.

[47]  Joshua M. Stuart,et al.  Identification of aberrant pathway and network activity from high-throughput data. , 2011, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[48]  Canguo Zhao,et al.  Expression-Based In Silico Screening of Candidate Therapeutic Compounds for Lung Adenocarcinoma , 2011, PloS one.

[49]  Allegra Via,et al.  Phospho.ELM: a database of phosphorylation sites—update 2008 , 2007, Nucleic Acids Res..

[50]  Cengizhan Ozturk,et al.  Pathway analysis of high-throughput biological data within a Bayesian network framework , 2011, Bioinform..

[51]  Ana Kozomara,et al.  miRBase: integrating microRNA annotation and deep-sequencing data , 2010, Nucleic Acids Res..

[52]  D. Cutler,et al.  Genistein cooperates with the histone deacetylase inhibitor vorinostat to induce cell death in prostate cancer cells , 2012, BMC Cancer.

[53]  J. Cuzick,et al.  Risk of recurrence and chemotherapy benefit for patients with node-negative, estrogen receptor-positive breast cancer: recurrence score alone and integrated with pathologic and clinical factors. , 2011, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[54]  Sean C. Bendall,et al.  Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum , 2011, Science.

[55]  Fuchu He,et al.  A Systems Biology-Based Classifier for Hepatocellular Carcinoma Diagnosis , 2011, PloS one.

[56]  John W Haycock,et al.  3D cell culture: a review of current approaches and techniques. , 2011, Methods in molecular biology.

[57]  Teresa M. Przytycka,et al.  Identifying Causal Genes and Dysregulated Pathways in Complex Diseases , 2011, PLoS Comput. Biol..

[58]  F. Staedtler,et al.  Integrated Epigenetics of Human Breast Cancer: Synoptic Investigation of Targeted Genes, MicroRNAs and Proteins upon Demethylation Treatment , 2011, PloS one.

[59]  F. Pammolli,et al.  The productivity crisis in pharmaceutical R&D , 2011, Nature Reviews Drug Discovery.

[60]  D. Swinney,et al.  How were new medicines discovered? , 2011, Nature Reviews Drug Discovery.

[61]  Julio Saez-Rodriguez,et al.  Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli , 2011, PLoS Comput. Biol..

[62]  S. Turner,et al.  Going beyond five bases in DNA sequencing. , 2012, Current opinion in structural biology.

[63]  Jason H. Moore,et al.  Chapter 11: Genome-Wide Association Studies , 2012, PLoS Comput. Biol..

[64]  Edwin K Silverman,et al.  Network medicine approaches to the genetics of complex diseases. , 2012, Discovery medicine.

[65]  A. Bordbar,et al.  Using the reconstructed genome‐scale human metabolic network to study physiology and pathology , 2012, Journal of internal medicine.

[66]  Shahab Asgharzadeh,et al.  TARGETgene: A Tool for Identification of Potential Therapeutic Targets in Cancer , 2012, PloS one.

[67]  Rondi A. Butler,et al.  Peripheral blood DNA methylation profiles are indicative of head and neck squamous cell carcinoma: An epigenome-wide association study , 2012, Epigenetics.

[68]  R. Aebersold,et al.  Mass spectrometry-based proteomics and network biology. , 2012, Annual review of biochemistry.

[69]  Deepak K Rajpal,et al.  Applications of Connectivity Map in drug discovery and development. , 2012, Drug discovery today.

[70]  Long Gao,et al.  Multi-Analyte Network Markers for Tumor Prognosis , 2012, PloS one.

[71]  Courtney Corley,et al.  Topological analysis of protein co-abundance networks identifies novel host targets important for HCV infection and pathogenesis , 2012, BMC Systems Biology.

[72]  Katsuhiko Murakami,et al.  PCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from H-Invitational protein-protein interactions integrative dataset , 2012, BMC Systems Biology.

[73]  Yuanhua Liu,et al.  Multilevel omic data integration in cancer cell lines: advanced annotation and emergent properties , 2013, BMC Systems Biology.

[74]  Glyn Stacey,et al.  Current developments in cell culture technology. , 2012, Advances in experimental medicine and biology.

[75]  S. Volinia,et al.  MicroRNA Expression Signatures in Solid Malignancies , 2012, Cancer journal.

[76]  Susumu Goto,et al.  KEGG for integration and interpretation of large-scale molecular data sets , 2011, Nucleic Acids Res..

[77]  Thomas Lengauer,et al.  Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues , 2012, Epigenetics.

[78]  Yoshihiro Yamanishi,et al.  Relating drug–protein interaction network with drug side effects , 2012, Bioinform..

[79]  P. Visscher,et al.  Five years of GWAS discovery. , 2012, American journal of human genetics.

[80]  Bin Zhang,et al.  PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse , 2011, Nucleic Acids Res..

[81]  Kenny Q. Ye,et al.  An integrated map of genetic variation from 1,092 human genomes , 2012, Nature.

[82]  Aldert H Piersma,et al.  Next-generation text-mining mediated generation of chemical response-specific gene sets for interpretation of gene expression data , 2013, BMC Medical Genomics.

[83]  Claudio Altafini,et al.  Predicting and characterizing selective multiple drug treatments for metabolic diseases and cancer , 2012, BMC Systems Biology.

[84]  R. Tibshirani,et al.  Coronary risk assessment among intermediate risk patients using a clinical and biomarker based algorithm developed and validated in two population cohorts , 2012, Current medical research and opinion.

[85]  Tyler J Moss,et al.  The glucose-deprivation network counteracts lapatinib-induced toxicity in resistant ErbB2-positive breast cancer cells , 2012, Molecular systems biology.

[86]  Xing-Ming Zhao,et al.  Exploring drug combinations in genetic interaction network , 2012, BMC Bioinformatics.

[87]  Carlo M. Croce,et al.  Causes and Consequences of MicroRNA Dysregulation , 2012, Cancer journal.

[88]  Michael J. Keiser,et al.  Large Scale Prediction and Testing of Drug Activity on Side-Effect Targets , 2012, Nature.

[89]  J. Kirkwood,et al.  Whole genome methylation profiles as independent markers of survival in stage IIIC melanoma patients , 2012, Journal of Translational Medicine.

[90]  Karen Sachs,et al.  Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators , 2012, Nature Biotechnology.

[91]  R. Aebersold,et al.  Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions , 2012, Nature Methods.

[92]  R. Stallings,et al.  Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers , 2012, Genome Biology.

[93]  R. Iyengar,et al.  Systems pharmacology: network analysis to identify multiscale mechanisms of drug action. , 2012, Annual review of pharmacology and toxicology.

[94]  Hugo Y. K. Lam,et al.  Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes , 2012, Cell.

[95]  Steven J. M. Jones,et al.  Comprehensive molecular portraits of human breast tumors , 2012, Nature.

[96]  Pora Kim,et al.  A High-Dimensional, Deep-Sequencing Study of Lung Adenocarcinoma in Female Never-Smokers , 2013, PloS one.

[97]  Martin J. Aryee,et al.  Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in Rheumatoid Arthritis , 2013, Nature Biotechnology.

[98]  E. Berg,et al.  Building Predictive Models for Mechanism-of-Action Classification from Phenotypic Assay Data Sets , 2013, Journal of biomolecular screening.

[99]  Manuel C. Peitsch,et al.  A Modular Cell-Type Focused Inflammatory Process Network Model for Non-Diseased Pulmonary Tissue , 2013, Bioinformatics and biology insights.

[100]  E. Berg,et al.  Neoclassic Drug Discovery , 2013, Journal of biomolecular screening.

[101]  M. Peng,et al.  Toward a comprehensive characterization of a human cancer cell phosphoproteome. , 2013, Journal of proteome research.

[102]  R. Gamelli,et al.  Genomic responses in mouse models poorly mimic human inflammatory diseases , 2013, Proceedings of the National Academy of Sciences.

[103]  N. Perrimon,et al.  Protein Complex–Based Analysis Framework for High-Throughput Data Sets , 2013, Science Signaling.

[104]  David S. Wishart,et al.  HMDB 3.0—The Human Metabolome Database in 2013 , 2012, Nucleic Acids Res..

[105]  Sarah R. Langley,et al.  Proteomics: from single molecules to biological pathways , 2012, Cardiovascular research.

[106]  I. Tomlinson,et al.  Whole-genome methylation analysis of benign and malignant colorectal tumours , 2013, The Journal of pathology.

[107]  S. Carr,et al.  Proteomic Mapping of Mitochondria in Living Cells via Spatially Restricted Enzymatic Tagging , 2013, Science.

[108]  Peer Bork,et al.  PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins , 2012, Nucleic Acids Res..

[109]  Benjamin Meder,et al.  Alterations in cardiac DNA methylation in human dilated cardiomyopathy , 2013, EMBO molecular medicine.

[110]  Ronan M. T. Fleming,et al.  A community-driven global reconstruction of human metabolism , 2013, Nature Biotechnology.