Emek Demir
- Associate Professor of Molecular and Medical Genetics, School of Medicine
- Scientific Co-Director, CBDS, OHSU Knight Cancer Institute, School of Medicine
- CEDAR Member, OHSU Knight Cancer Institute, School of Medicine
- Program Director of Computational Biology, Brenden-Colson Center for Pancreatic Care, School of Medicine
Biography
Emek is an associate professor in OHSU’s Department of Molecular and Medical Genetics and the program director of OHSU’s Brenden-Colson Center for Pancreatic Care Computational Biology. He received his Ph.D. in computer engineering from Bilkent University in Turkey in 2005 under the direction of Ugur Dogrusoz, Ph.D., and completed his postdoctoral training with Chris Sander at the Computational Biology Center at the Memorial Sloan Kettering Cancer Center (MSKCC) in New York. Before coming to OHSU, he was a manager at Pathway Informatics at MSKCC.
Emek focuses on integrating rich, detailed pathway information and using the resulting "cell maps" to answer cancer biology problems in conjunction with omic data. His work runs the gamut on Pathway Informatics, from pathway curation, visualization, NLP, data standardization and integration to machine learning, mechanistic assembly and simulation. He led the development of the BioPAX standard for pathway information and built an extensive software stack for aggregating and using pathway information from all major public data sources. These efforts resulted in Pathway Commons, a resource with more than 2 million interactions and more than 400,000 highly-detailed reactions of human pathways. Pathway Commons is the largest process-level pathway database.
Emek also led the development of several pathway analysis algorithms for detecting highly-altered sub-networks in a cancer context, finding modulators of transcription factors, inferring differentially active networks from proteomic measurements and finding mutually exclusive altered pathway modules.
Publications
Publications
Targeting the CD74 signaling axis suppresses inflammation and rescues defective hematopoiesis in RUNX1–familial platelet disorder
Science translational medicineMultiplex imaging of localized prostate tumors reveals altered spatial organization of AR-positive cells in the microenvironment
iSciencePredicting transcription factor activity using prior biological information
iScienceAsxl1 deletion disrupts MYC and RNA polymerase II function in granulocyte progenitors
LeukemiaDisruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia
Molecular Cancer ResearchSelective enrichment of plasma cell-free messenger RNA in cancer-associated extracellular vesicles
Communications BiologyAn omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer
Cell Reports MedicineThe reactome pathway knowledgebase 2022
Nucleic acids research2D MXenes with antiviral and immunomodulatory properties
Nano TodayAnalyzing causal relationships in proteomic profiles using CausalPath
STAR ProtocolsAuthor-sourced capture of pathway knowledge in computable form using Biofactoid
eLifeCausal interactions from proteomic profiles
PatternsCOVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms
Molecular Systems BiologyNewt
BioinformaticsProteogenomic and metabolomic characterization of human glioblastoma
Cancer CellProteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma
Cancer CellRibavirin shows antiviral activity against sars-cov-2 and downregulates the activity of tmprss2 and the expression of ace2 in vitro
Canadian Journal of Physiology and PharmacologySystematic interrogation of mutation groupings reveals divergent downstream expression programs within key cancer genes
BMC bioinformaticsThe AML microenvironment catalyzes a stepwise evolution to gilteritinib resistance
Cancer CellPathway Commons 2019 Update
Nucleic acids researchPhosphoproteomic quantitation and causal analysis reveal pathways in GPVI/ITAM-mediated platelet activation programs
BloodProteogenomic Characterization of Endometrial Carcinoma
Cell