Uncovering influence links in molecular knowledge networks to streamline personalized medicine

[1]  Henning Hermjakob,et al.  The Reactome pathway Knowledgebase , 2015, Nucleic acids research.

[2]  J. van Soest,et al.  An umbrella protocol for standardized data collection (SDC) in rectal cancer: a prospective uniform naming and procedure convention to support personalized medicine. , 2014, Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology.

[3]  Jos De Roo,et al.  Diagnosis Support System based on clinical guidelines: comparison between Case-Based Fuzzy Cognitive Maps and Bayesian Networks , 2014, Comput. Methods Programs Biomed..

[4]  Marie-Christine Jaulent,et al.  Formalization of Clinical Practice Guidelines: Nonalcoholic Steatohepatitis Diagnosis Model-Related Personalized Medicine , 2014 .

[5]  Kenji Araki,et al.  Creating personalised clinical pathways by semantic interoperability with electronic health records , 2013, Artif. Intell. Medicine.

[6]  Christopher G. Chute,et al.  A Framework of Knowledge Integration and Discovery for Supporting Pharmacogenomics Target Predication of Adverse Drug Events: A Case Study of Drug-Induced Long QT Syndrome , 2013, AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science.

[7]  Zhihui Wang,et al.  Accelerating cancer systems biology research through Semantic Web technology , 2013, Wiley interdisciplinary reviews. Systems biology and medicine.

[8]  M. Loh,et al.  Targeting JAK1/2 and mTOR in murine xenograft models of Ph-like acute lymphoblastic leukemia. , 2012, Blood.

[9]  Christopher J. Ott,et al.  BET bromodomain inhibition targets both c-Myc and IL7R in high-risk acute lymphoblastic leukemia. , 2012, Blood.

[10]  W. Hsu,et al.  Overexpression of P-glycoprotein, STAT3, phospho-STAT3 and KIT in spontaneous canine cutaneous mast cell tumours before and after prednisolone treatment. , 2012, Veterinary journal.

[11]  T. Zimmers,et al.  JAK/STAT3 pathway inhibition blocks skeletal muscle wasting downstream of IL-6 and in experimental cancer cachexia. , 2012, American journal of physiology. Endocrinology and metabolism.

[12]  Stefan Heinrichs,et al.  Tyrosine kinase pathways modulate tumor susceptibility to natural killer cells. , 2012, The Journal of clinical investigation.

[13]  D. Ichikawa,et al.  PSK induces apoptosis through the inhibition of activated STAT3 in human esophageal carcinoma cells. , 2012, International journal of oncology.

[14]  Bozena Kaminska,et al.  Novel small molecular inhibitors disrupt the JAK/STAT3 and FAK signaling pathways and exhibit a potent antitumor activity in glioma cells , 2012, Cancer biology & therapy.

[15]  J. Lv,et al.  [Expression of STAT3 and PIAS3 in renal tissues of MRL/lpr mice]. , 2012, Nan fang yi ke da xue xue bao = Journal of Southern Medical University.

[16]  R. Meehan,et al.  Targeting of Rac GTPases blocks the spread of intact human breast cancer , 2012, Oncotarget.

[17]  P. Yue,et al.  Orally bioavailable small-molecule inhibitor of transcription factor Stat3 regresses human breast and lung cancer xenografts , 2012, Proceedings of the National Academy of Sciences.

[18]  S. Mustjoki,et al.  Somatic STAT3 mutations in large granular lymphocytic leukemia. , 2012, The New England journal of medicine.

[19]  Michael S Lajiness,et al.  Systems chemical biology and the Semantic Web: what they mean for the future of drug discovery research. , 2012, Drug discovery today.

[20]  I. Shin,et al.  Apigenin induces apoptosis via extrinsic pathway, inducing p53 and inhibiting STAT3 and NFκB signaling in HER2-overexpressing breast cancer cells , 2012, Molecular and Cellular Biochemistry.

[21]  H. Qiu,et al.  Celecoxib induces apoptosis and cell-cycle arrest in nasopharyngeal carcinoma cell lines via inhibition of STAT3 phosphorylation , 2012, Acta Pharmacologica Sinica.

[22]  L. Hazlehurst,et al.  Role of STAT3 in Transformation and Drug Resistance in CML , 2012, Front. Oncol..

[23]  J. Zhu,et al.  The usefulness of phosphorylated-signal transduction and activators of transcription 3 in detecting prostate cancer from negative biopsies. , 2012, European journal of surgical oncology : the journal of the European Society of Surgical Oncology and the British Association of Surgical Oncology.

[24]  J. Silberg,et al.  A transposase strategy for creating libraries of circularly permuted proteins , 2012, Nucleic acids research.

[25]  Chi-Ren Shyu,et al.  A pathologist-in-the-loop IHC antibody test selection using the entropy-based probabilistic method , 2012, Journal of pathology informatics.

[26]  The UniProt Consortium,et al.  Reorganizing the protein space at the Universal Protein Resource (UniProt) , 2011, Nucleic Acids Res..

[27]  X. Sun,et al.  The expression and clinical significance of pSTAT3, VEGF and VEGF-C in pancreatic adenocarcinoma. , 2012, Neoplasma.

[28]  Jos De Roo,et al.  Clinical Diagnosis Support System Based on Case Based Fuzzy Cognitive Maps and Semantic Web , 2012, MIE.

[29]  Lei-na Sun,et al.  Correlation of Activated STAT3 Expression with Clinicopathologic Features in Lung Adenocarcinoma and Squamous Cell Carcinoma , 2011, Molecular Diagnosis & Therapy.

[30]  Robert E. Brown,et al.  Morphoproteomics demonstrates activation of mammalian target of rapamycin pathway in papillary thyroid carcinomas with nuclear translocation of MTOR in aggressive histological variants , 2011, Modern Pathology.

[31]  Vipul Kashyap,et al.  The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside , 2011, J. Biomed. Semant..

[32]  Laurence Doyle,et al.  Targeted Morphoproteomic Profiling of Ewing's Sarcoma Treated with Insulin-Like Growth Factor 1 Receptor (IGF1R) Inhibitors: Response/Resistance Signatures , 2011, PloS one.

[33]  Shuji Ogino,et al.  STAT3 Expression, Molecular Features, Inflammation Patterns, and Prognosis in a Database of 724 Colorectal Cancers , 2011, Clinical Cancer Research.

[34]  Lincoln Stein,et al.  Reactome: a database of reactions, pathways and biological processes , 2010, Nucleic Acids Res..

[35]  E. Prud hommeaux,et al.  SPARQL query language for RDF , 2011 .

[36]  Robert E. Brown,et al.  Morphoproteomic analysis reveals an overexpressed and constitutively activated phospholipase D1-mTORC2 pathway in endometrial carcinoma. , 2011, International journal of clinical and experimental pathology.

[37]  Gary D Bader,et al.  BioPAX – A community standard for pathway data sharing , 2010, Nature Biotechnology.

[38]  Jing Liu,et al.  Morphoproteomics demonstrates activation of mTOR pathway in anaplastic thyroid carcinoma: a preliminary observation. , 2010, Annals of clinical and laboratory science.

[39]  P. Yue,et al.  A novel small-molecule disrupts Stat3 SH2 domain-phosphotyrosine interactions and Stat3-dependent tumor processes. , 2010, Biochemical pharmacology.

[40]  Baris E. Suzek,et al.  The Universal Protein Resource (UniProt) in 2010 , 2009, Nucleic Acids Res..

[41]  María Martín,et al.  The Universal Protein Resource (UniProt) in 2010 , 2010 .

[42]  H Tanaka,et al.  Omics-based Medicine and Systems Pathology , 2010, Methods of Information in Medicine.

[43]  Vipul Kashyap,et al.  The Translational Medicine Ontology: Driving personalized medicine by bridging the gap from bedside to bench , 2010 .

[44]  J. Fridman,et al.  INCB16562, a JAK1/2 selective inhibitor, is efficacious against multiple myeloma cells and reverses the protective effects of cytokine and stromal cell support. , 2010, Neoplasia.

[45]  H. Khatib,et al.  Effects of signal transducer and activator of transcription (STAT) genes STAT1 and STAT3 genotypic combinations on fertilization and embryonic survival rates in Holstein cattle. , 2009, Journal of dairy science.

[46]  M. Hallek,et al.  High TCL1 levels are a marker of B-cell receptor pathway responsiveness and adverse outcome in chronic lymphocytic leukemia. , 2009, Blood.

[47]  Ian H. Witten,et al.  The WEKA data mining software: an update , 2009, SKDD.

[48]  Robert E. Brown,et al.  Morphogenomics and morphoproteomics: a role for anatomic pathology in personalized medicine. , 2009, Archives of pathology & laboratory medicine.

[49]  Clive R Taylor,et al.  IHC and the WHO Classification of Lymphomas: Cost Effective Immunohistochemistry Using a Deductive Reasoning “Decision Tree” Approach , 2009, Applied immunohistochemistry & molecular morphology : AIMM.

[50]  D. Hori,et al.  Expression of activated signal transducer and activator of transcription-3 predicts poor prognosis in cervical squamous-cell carcinoma , 2009, British Journal of Cancer.

[51]  Robin T Vollmer,et al.  Differential diagnosis in immunohistochemistry with Bayes theorem. , 2009, American journal of clinical pathology.

[52]  Robert E. Brown,et al.  Morphoproteomic confirmation of constitutively activated mTOR, ERK, and NF-kappaB pathways in Ewing family of tumors. , 2009, Annals of clinical and laboratory science.

[53]  Michel Dumontier,et al.  Towards pharmacogenomics knowledge discovery with the semantic web , 2009, Briefings Bioinform..

[54]  Kei-Hoi Cheung,et al.  Semantic Web-Based Integration of Cancer Pathways and Allele Frequency Data , 2009, Cancer informatics.

[55]  Kenneth H. Buetow,et al.  PID: the Pathway Interaction Database , 2008, Nucleic Acids Res..

[56]  Akhilesh Pandey,et al.  Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology. , 2009, Methods in molecular biology.

[57]  Wei Feng,et al.  Morphoproteomic evidence of constitutively activated and overexpressed mTOR pathway in cervical squamous carcinoma and high grade squamous intraepithelial lesions. , 2009, International journal of clinical and experimental pathology.

[58]  Eric K. Neumann,et al.  Identifying disease-causal genes using Semantic Web-based representation of integrated genomic and phenomic knowledge , 2008, J. Biomed. Informatics.

[59]  Amit P. Sheth,et al.  An ontology-driven semantic mashup of gene and biological pathway information: Application to the domain of nicotine dependence , 2008, J. Biomed. Informatics.

[60]  Dean Allemang,et al.  Semantic Web for the Working Ontologist , 2008 .

[61]  Robert E. Brown,et al.  Morphoproteomic profile of mTOR, Ras/Raf kinase/ERK, and NF-kappaB pathways in human gastric adenocarcinoma. , 2008, Annals of clinical and laboratory science.

[62]  Robert E. Brown,et al.  Morphoproteomic confirmation of a constitutively activated mTOR pathway in high grade prostatic intraepithelial neoplasia and prostate cancer. , 2008, International journal of clinical and experimental pathology.

[63]  Robert E. Brown,et al.  Morphoproteomic expression of H-ras (p21ras) correlates with serum monoclonal immunoglobulin reduction in multiple myeloma patients following pamidronate treatment. , 2007, Annals of clinical and laboratory science.

[64]  Diego Calvanese,et al.  The Description Logic Handbook , 2007 .

[65]  Kei-Hoi Cheung,et al.  Advancing translational research with the Semantic Web , 2007, BMC Bioinformatics.

[66]  Robert E. Brown,et al.  Morphoproteomic confirmation of constitutively activated mTOR, ERK, and NF-kappaB pathways in high risk neuro-blastoma, with cell cycle and protein analyte correlates. , 2007, Annals of clinical and laboratory science.

[67]  Tatiana A. Tatusova,et al.  Entrez Gene: gene-centered information at NCBI , 2004, Nucleic Acids Res..

[68]  Amit P. Sheth,et al.  From "Glycosyltransferase" to "Congenital Muscular Dystrophy": Integrating Knowledge from NCBI Entrez Gene and the Gene Ontology , 2007, MedInfo.

[69]  Robert E. Brown,et al.  Morphoproteomic demonstration of constitutive nuclear factor-kappaB activation in glioblastoma multiforme with genomic correlates and therapeutic implications. , 2006, Annals of clinical and laboratory science.

[70]  Shaobo Zhu,et al.  Morphoproteomic and pharmacoproteomic rationale for mTOR effectors as therapeutic targets in head and neck squamous cell carcinoma. , 2006, Annals of clinical and laboratory science.

[71]  Robert E. Brown,et al.  Morphoproteomic and molecular concomitants of an overexpressed and activated mTOR pathway in renal cell carcinomas. , 2006, Annals of clinical and laboratory science.

[72]  C. Ouzounis,et al.  Expansion of the BioCyc collection of pathway/genome databases to 160 genomes , 2005, Nucleic acids research.

[73]  Robert E. Brown,et al.  Morphoproteomics: exposing protein circuitries in tumors to identify potential therapeutic targets in cancer patients , 2005, Expert review of proteomics.

[74]  Cathy H. Wu,et al.  The Universal Protein Resource (UniProt) , 2004, Nucleic Acids Res..

[75]  Robert E. Brown,et al.  Morphoproteomic portrait of the mTOR pathway in mesenchymal chondrosarcoma. , 2004, Annals of clinical and laboratory science.

[76]  S. Warner.  Diagnostics + therapy = theranostics: strategy requires teamwork, partnering, and tricky regulatory maneuvering , 2004 .

[77]  Robert E. Brown,et al.  Morphoproteomic and pharmacoproteomic correlates in hormone-receptor-negative breast carcinoma cell lines. , 2004, Annals of clinical and laboratory science.

[78]  Robert E. Brown,et al.  Morphoproteomics and bortezomib/dexamethasone-induced response in relapsed acute lymphoblastic leukemia. , 2004, Annals of clinical and laboratory science.

[79]  H. Lan,et al.  SWRL : A semantic Web rule language combining OWL and ruleML , 2004 .

[80]  Deborah L. McGuinness,et al.  OWL Web ontology language overview , 2004 .

[81]  Dave Reynolds,et al.  Efficient RDF Storage and Retrieval in Jena2 , 2003, SWDB.

[82]  Tom Burr,et al.  Causation, Prediction, and Search , 2003, Technometrics.

[83]  Stephen B. Johnson,et al.  Central challenges facing the national clinical research enterprise. , 2003, JAMA.

[84]  Diego Calvanese,et al.  The Description Logic Handbook: Theory, Implementation, and Applications , 2003, Description Logic Handbook.

[85]  A. Gingras,et al.  Regulation of translation initiation by FRAP/mTOR. , 2001, Genes & development.

[86]  J. Pearl.  Causality: Models, Reasoning and Inference , 2000 .

[87]  R Scheines,et al.  The TETRAD Project: Constraint Based Aids to Causal Model Specification. , 1998, Multivariate behavioral research.

[88]  M. Vignais,et al.  Platelet-derived growth factor induces phosphorylation of multiple JAK family kinases and STAT proteins , 1996, Molecular and cellular biology.

[89]  J. Polak,et al.  Immunohistochemistry of nitric oxide synthase demonstrates immunoreactive neurons in spinal cord and dorsal root ganglia of man and rat , 1993, Journal of the Neurological Sciences.

[90]  Judea Pearl,et al.  An Algorithm for Deciding if a Set of Observed Independencies Has a Causal Explanation , 1992, UAI.

[91]  N. Ibrahim,et al.  Immunohistochemistry in sweat gland tumours , 1991, Histopathology.

[92]  N. Ibrahim,et al.  Lymph node schwannoma , 1988 .

[93]  J. Crocker,et al.  Immunohistochemistry of gastrointestinal lymphomas , 1988, Histopathology.