High‐Throughput Protein‐Based Technologies and Computational Models for Drug Development, Efficacy, and Toxicity

[1]  John G. Albeck,et al.  Collecting and organizing systematic sets of protein data , 2006, Nature Reviews Molecular Cell Biology.

[2]  Roger E Bumgarner,et al.  Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. , 2001, Science.

[3]  W. Koch Technology platforms for pharmacogenomic diagnostic assays , 2004, Nature Reviews Drug Discovery.

[4]  E. Oren,et al.  Potential role of pharmacogenomics in reducing adverse drug reactions: a systematic review. , 2001, JAMA.

[5]  Patricia L. Harris,et al.  Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. , 2004, The New England journal of medicine.

[6]  Péter Csermely,et al.  The efficiency of multi-target drugs: the network approach might help drug design. , 2004, Trends in pharmacological sciences.

[7]  Lili X. Peng,et al.  A High-throughput Quantitative Multiplex Kinase Assay for Monitoring Information Flow in Signaling Networks , 2003, Molecular & Cellular Proteomics.

[8]  U. Landegren,et al.  Direct observation of individual endogenous protein complexes in situ by proximity ligation , 2006, Nature Methods.

[9]  Roland Eils,et al.  Computational Systems Biology , 2006 .

[10]  M. Ingelman-Sundberg,et al.  Polymorphic human cytochrome P450 enzymes: an opportunity for individualized drug treatment. , 1999, Trends in pharmacological sciences.

[11]  U. Landegren,et al.  Protein detection using proximity-dependent DNA ligation assays , 2002, Nature Biotechnology.

[12]  D. Lauffenburger,et al.  Physicochemical modelling of cell signalling pathways , 2006, Nature Cell Biology.

[13]  Michael B. Yaffe,et al.  Data-driven modelling of signal-transduction networks , 2006, Nature Reviews Molecular Cell Biology.

[14]  Mehmet Toner,et al.  Multifunctional Encoded Particles for High-Throughput Biomolecule Analysis , 2007, Science.

[15]  S. Gygi,et al.  Quantitative analysis of complex protein mixtures using isotope-coded affinity tags , 1999, Nature Biotechnology.

[16]  P. Bastiaens,et al.  Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate , 2007, Nature Cell Biology.

[17]  T. Ideker,et al.  Integrating phenotypic and expression profiles to map arsenic-response networks , 2004, Genome Biology.

[18]  F. X. Bosch,et al.  Epidemiology of Primary Liver Cancer , 1999, Seminars in liver disease.

[19]  D. Flockhart,et al.  Clinical Significance of the Cytochrome P450 2C19 Genetic Polymorphism , 2002, Clinical pharmacokinetics.

[20]  Sorin Draghici,et al.  Machine Learning and Its Applications to Biology , 2007, PLoS Comput. Biol..

[21]  Kamel Jabbari,et al.  Cytosine methylation and CpG, TpG (CpA) and TpA frequencies. , 2004, Gene.

[22]  Roland Eils,et al.  Computational Systems Biology Platforms (Computergestützte Systembiologieplattformen) , 2006, it Inf. Technol..

[23]  Rui Alves,et al.  Tools for kinetic modeling of biochemical networks , 2006, Nature Biotechnology.

[24]  D. Lauffenburger,et al.  A Systems Model of Signaling Identifies a Molecular Basis Set for Cytokine-Induced Apoptosis , 2005, Science.

[25]  S. Thorgeirsson,et al.  Molecular pathogenesis of human hepatocellular carcinoma , 2002, Nature Genetics.

[26]  N. Anderson,et al.  The Human Plasma Proteome , 2002, Molecular & Cellular Proteomics.

[27]  Julio Saez-Rodriguez,et al.  Flexible informatics for linking experimental data to mathematical models via DataRail , 2008, Bioinform..

[28]  M. Mann,et al.  Proteomics to study genes and genomes , 2000, Nature.

[29]  S. Gabriel,et al.  EGFR Mutations in Lung Cancer: Correlation with Clinical Response to Gefitinib Therapy , 2004, Science.

[30]  R. Aebersold,et al.  Mass spectrometry-based proteomics , 2003, Nature.

[31]  G. Abou-Alfa Hepatocellular carcinoma: molecular biology and therapy. , 2006, Seminars in oncology.

[32]  D. Kell,et al.  Metabolomics by numbers: acquiring and understanding global metabolite data. , 2004, Trends in biotechnology.

[33]  Mudita Singhal,et al.  Enabling high-throughput data management for systems biology: The Bioinformatics Resource Manager , 2007, Bioinform..

[34]  A. Syvänen Toward genome-wide SNP genotyping , 2005, Nature Genetics.

[35]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[36]  Gaudenz Danuser,et al.  Linking data to models: data regression , 2006, Nature Reviews Molecular Cell Biology.

[37]  L. Liotta,et al.  Proteomic profiling of the cancer microenvironment by antibody arrays , 2001, Proteomics.

[38]  D. Lauffenburger,et al.  A Compendium of Signals and Responses Triggered by Prodeath and Prosurvival Cytokines*S , 2005, Molecular & Cellular Proteomics.

[39]  C. Wadelius,et al.  In vitro analysis of DNA–protein interactions by proximity ligation , 2007, Proceedings of the National Academy of Sciences.

[40]  D. Kell,et al.  A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations , 2001, Nature Biotechnology.

[41]  K. Sachs,et al.  Causal Protein-Signaling Networks Derived from Multiparameter Single-Cell Data , 2005, Science.

[42]  E. Petricoin,et al.  Proteins, drug targets and the mechanisms they control: the simple truth about complex networks , 2007, Nature Reviews Drug Discovery.

[43]  Benno Schwikowski,et al.  Graph-based methods for analysing networks in cell biology , 2006, Briefings Bioinform..

[44]  Howard L McLeod,et al.  Pharmacogenomics--drug disposition, drug targets, and side effects. , 2003, The New England journal of medicine.

[45]  Hyung-Seok Choi,et al.  Reverse engineering of gene regulatory networks. , 2007, IET systems biology.

[46]  Steffen Klamt,et al.  Structural and functional analysis of cellular networks with CellNetAnalyzer , 2007, BMC Systems Biology.

[47]  M. Relling,et al.  Pharmacogenomics: translating functional genomics into rational therapeutics. , 1999, Science.

[48]  Ulf Landegren,et al.  Sensitive protein detection via triple-binder proximity ligation assays , 2007, Nature Methods.

[49]  Frank Staib,et al.  Genetics of hepatocellular carcinoma. , 2007, World journal of gastroenterology.

[50]  A. Barabasi,et al.  Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.

[51]  Hidde de Jong,et al.  Genetic Network Analyzer: qualitative simulation of genetic regulatory networks , 2003, Bioinform..

[52]  Steffen Klamt,et al.  A methodology for the structural and functional analysis of signaling and regulatory networks , 2006, BMC Bioinformatics.

[53]  N. Anderson,et al.  HISTORY, CHARACTER, AND DIAGNOSTIC PROSPECTS* , 2002 .

[54]  T. Bumol,et al.  Genetic information, genomic technologies, and the future of drug discovery. , 2001, JAMA.

[55]  D Thieffry,et al.  GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks. , 2006, Bio Systems.

[56]  Hyung-Lae Kim,et al.  Comparison of oligonucleotide-microarray and serial analysis of gene expression (SAGE) in transcript profiling analysis of megakaryocytes derived from CD34+ cells , 2003, Experimental & Molecular Medicine.

[57]  D. Hanahan,et al.  The Hallmarks of Cancer , 2000, Cell.

[58]  M. Mann,et al.  Proteomic analysis of post-translational modifications , 2003, Nature Biotechnology.

[59]  Wei Jiang,et al.  High-throughput DNA methylation profiling using universal bead arrays. , 2006, Genome research.

[60]  J. Klempnauer,et al.  Differentiation of multicentric origin from intra‐organ metastatic spread of hepatocellular carcinomas by comparative genomic hybridization , 2000, The Journal of pathology.

[61]  A Kremling,et al.  Systems biology--an engineering perspective. , 2007, Journal of biotechnology.