Dr. Papaemmanouil has employed genome profiling methodologies to study role of acquired mutations in cancer development and how these determine clinical phenotype and response to therapy. During her PhD using a combination of linkage and GWAS approaches, Dr. Papaemmanouil mapped novel genetic predisposition loci in colorectal cancer and childhood leukemia. During her postdoctoral research studies Dr. Papaemmanouil employed next generation sequencing approaches to characterize new gene mutations in myeloid neoplasms, and her work led to the first characterization of splicing factor mutations, CALR, CUX1 amongst other genes mutated I cancer. She used wholegenome sequencing and single cell sequencing approaches to characterize mechanisms that cause genomic rearrangements in childhood leukemia and identified aberrant RAG targeting as the dominant driver of childhood B-ALL. More recently she has established high-throughput laboratory profiling approaches and developed statistical modelling methodologies that integrate clinical and molecular parameters to inform patient tailored disease classification and clinical decision support (prognosis and treatment decisions).

Her main research motivation is to develop research that helps translate recent cancer genome discoveries into clinical practice. Her current research spans, bioinformatic and algorithmic platform development, biomarker discovery and validation and experimental models of disease biology.

For biomarker development Dr. Papaemmanouil employs large cohort analyses to study the genetic and clinical inter-relationships of well annotated clinical cohorts and develop patient tailored prognostic models. This includes:
• International Working Group for Prognostication in MDS (IWG-PM)
• European, and US based analyses to define disease classification and prognostication in AML
• UK MRC trials in Adult Lymphoblastic Leukemia
• Pan-myeloid consortium
• International working group in Ovarian Clear Cell Carcinoma

Additionally, Dr. Papaemmanouil has a strong interest to understand the effects of treatment in disease progression and genetic drivers of treatment response. This includes three major initiatives to include:
• Population genomic approaches to study the impact of oncologic therapy in clonal hematopoiesis and risk of tMN.
• Wholegenome sequencing studies of temporally and spatially separated samples at diagnosis, disease progression and metastasis
• Single-cell sequencing studies in myeloid neoplasms using paired pre and post treatment samples from patients receiving targeted therapies

Experimentally, Dr. Papaemmanouil is using integrative single cell approaches (DNA and RNA) and iPSC modelling of mutations in myeloid disease to study disease progression and treatment response.

Last, Dr. Papaemmanouil leads the Pediatrics Precision medicine initiative for MSK Kids, which sets out to evaluate, validate and deliver a clinical prototype for integrative wholegenome and whole transcriptome sequencing analyses to understand mechanisms of disease biology and guide treatment strategies in pediatric cancers.