Elli Papaemmanuil, PhD

Assistant Attending
Elli Papaemmanuil

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Dr. Papaemmanuil is an Assistant Attending Computational Oncologist. She is affiliated with the Marie-Josée and Henry R. Kravis Center for Molecular Oncology and is the Associate Director for the Center of Hematological Malignancies. Dr. Papaemmanuil was trained in Human Molecular Genetics at the University of Glasgow, completed PhD studies in Population Genetics and Epidemiology, and conducted her postdoctoral research at the Cancer Genome Project at the Wellcome Trust Sanger Institute in Cambridge UK. Dr. Papaemmanuil is a certified computer systems and operations development analyst by the British Society of Computing. Dr. Papaemmanuil’s research is focused on developing comprehensive laboratory and novel analytical methodologies to study the role of acquired mutations in cancer, and how these define clinical phenotype and determine therapeutic response. Dr. Papaemmanuil works with large and well-annotated clinical trial cohorts to study the diagnostic, prognostic and predictive value of genomic variation and how this knowledge can guide development of future clinical protocols. To this effect she is leading a number of international multi-center consortia including the prospective molecular characterization for the International Working Group in myelo-displastic syndromes, the pan-myeloid meta-analysis, and genome profiling of the UK acute lymphocytic leukemia clinical trials. At MSK, Dr. Papaemmanuil leads integrative whole genome, transcriptome and methylation studies of spatially and temporally separated samples in pediatric tumours. These studies are focused on understanding the genomic and clonal structure of pediatric genomes at diagnosis and how these change during therapy, and importantly, at disease progression. Informed by genomic findings, Dr. Papaemmanuil uses primary patient tissues to study the biological consequences of disease defining mutations in cancer using single cell and iPSC cell lies. Dr. Papaemmanuil is a European Society of Hematology Fellow, an American Society for Hematology Scholar, and a Josie Robertson Investigator.


Selected peer-reviewed publications:

  1. Gerstung M, Papaemmanuil E, Martincorena I, Bullinger L, Gaidzik VI, Paschka P, Heuser M, Thol F, Bolli N, Ganly P, Ganser A, McDermott U, Döhner K, Schlenk RF, Döhner H, Campbell PJ. Precision oncology for acute myeloid leukemia using a knowledge bank approach. Nat Genet. 2017 Mar;49(3):332-340. doi: 10.1038/ng.3756.Epub 2017 Jan 16. PubMed PMID: 28092685; PubMed Central PMCID: PMC5764082.
  2. Papaemmanuil E, Gerstung M, Bullinger L, Gaidzik VI, Paschka P, Roberts ND, Potter NE, Heuser M, Thol F, Bolli N, Gundem G, Van Loo P, Martincorena I, Ganly  P, Mudie L, McLaren S, O’Meara S, Raine K, Jones DR, Teague JW, Butler AP, Greaves MF, Ganser A, Döhner K, Schlenk RF, Döhner H, Campbell PJ. Genomic Classification and Prognosis in Acute Myeloid Leukemia. N Engl J Med. 2016 Jun 9;374(23):2209-2221. doi: 10.1056/NEJMoa1516192. PubMed PMID: 27276561; PubMed Central PMCID: PMC4979995.
  3. Papaemmanuil E, Rapado I, Li Y, Potter NE, Wedge DC, Tubio J, Alexandrov LB, Van Loo P, Cooke SL, Marshall J, Martincorena I, Hinton J, Gundem G, van Delft FW, Nik-Zainal S, Jones DR, Ramakrishna M, Titley I, Stebbings L, Leroy C, Menzies A, Gamble J, Robinson B, Mudie L, Raine K, O’Meara S, Teague JW, Butler AP, Cazzaniga G, Biondi A, Zuna J, Kempski H, Muschen M, Ford AM, Stratton MR, Greaves M, Campbell PJ. RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia. Nat Genet. 2014 Feb;46(2):116-25. doi: 10.1038/ng.2874. Epub 2014 Jan 12. PubMed PMID: 24413735; PubMed Central PMCID: PMC3960636.
  4. Papaemmanuil E, Cazzola M, Boultwood J, Malcovati L, Vyas P, Bowen D, Pellagatti A, Wainscoat JS, Hellstrom-Lindberg E, Gambacorti-Passerini C, Godfrey AL, Rapado I, Cvejic A, Rance R, McGee C, Ellis P, Mudie LJ, Stephens PJ, McLaren S, Massie CE, Tarpey PS, Varela I, Nik-Zainal S, Davies HR, Shlien A, Jones D, Raine K, Hinton J, Butler AP, Teague JW, Baxter EJ, Score J, Galli A, Della Porta MG, Travaglino E, Groves M, Tauro S, Munshi NC, Anderson KC, El-Naggar A, Fischer A, Mustonen V, Warren AJ, Cross NC, Green AR, Futreal PA, Stratton MR, Campbell PJ; Chronic Myeloid Disorders Working Group of the International Cancer Genome Consortium. Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts. N Engl J Med. 2011 Oct 13;365(15):1384-95. doi: 10.1056/NEJMoa1103283. Epub 2011 Sep 26. PubMed PMID: 21995386; PubMed Central PMCID: PMC3322589.
  5. Gerstung M, Papaemmanuil E, Campbell PJ. Subclonal variant calling with multiple samples and prior knowledge. Bioinformatics. 2014 May 1;30(9):1198-204.  doi: 10.1093/bioinformatics/btt750. Epub 2014 Jan 16. PubMed PMID: 24443148; PubMed Central PMCID: PMC3998123.

View a full listing of Elli Papaemmanuil’s journal articles.


Doctors and faculty members often work with pharmaceutical, device, biotechnology, and life sciences companies, and other organizations outside of MSK, to find safe and effective cancer treatments, to improve patient care, and to educate the health care community.

MSK requires doctors and faculty members to report (“disclose”) the relationships and financial interests they have with external entities. As a commitment to transparency with our community, we make that information available to the public.

Elli Papaemmanuil discloses the following relationships and financial interests:

  • Isabl Inc.
    Fiduciary Role/Position; Intellectual Property Rights; Ownership / Equity Interests
  • TenSixteen Bio, Inc.
    Ownership / Equity Interests; Provision of Services

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This page and data include information for a specific MSK annual disclosure period (January 1, 2021 through disclosure submission in spring 2022). This data reflects interests that may or may not still exist. This data is updated annually.

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