Elli Papaemmanouil, PhD

Associate Attending, Computational Oncologist

Elli Papaemmanouil, PhD

Associate Attending, Computational Oncologist
Elli Papaemmanouil

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Dr. Papaemmanuil 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. Papaemmanuil mapped novel genetic predisposition loci in colorectal cancer and childhood leukemia. During her postdoctoral research studies Dr. Papaemmanuil 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. Papaemmanuil 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. Papaemmanuil 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. Papaemmanuil 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. Papaemmanuil 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.


Selected peer-reviewed publications:

  1. Hultcrantz M, Rustad EH, Yellapantula V, Jacob A, Akhlaghi T, Korde N, Mailankody S, Lesokhin AM, Hassoun H, Smith EL, Lahoud OB, Landau HJ, Shah GL, Scordo M, Chung DJ, Giralt S, Papaemmanuil E, Landgren O. Capture Rate of V(D)J Sequencing for Minimal Residual Disease Detection in Multiple Myeloma. Clin Cancer Res. 2022 May 13;28(10):2160-2166. doi: 10.1158/1078-0432.CCR-20-2995. PMID: 35553646; PMCID: PMC9179004.28, 2160–2166. 
  2. Spitzer B, Rutherford KD, Gundem G, McGovern EM, Millard NE, Arango Ossa JE, Cheung IY, Gao T, Levine MF, Zhang Y, Medina-Martínez JS, Feng Y, Ptashkin RN, Bolton KL, Farnoud N, Zhou Y, Patel MA, Asimomitis G, Cobbs CC, Mohibullah N, Huberman KH, Arcilla ME, Kushner BH, Modak S, Kung AL, Zehir A, Levine RL, Armstrong SA, Cheung NKV, Papaemmanuil E. Bone Marrow Surveillance of Pediatric Cancer Survivors Identifies Clones that Predict Therapy-Related Leukemia. Clin Cancer Res. 2022 Apr 14;28(8):1614-1627. doi: 10.1158/1078-0432.CCR-21-2451. PMID: 35078859.
  3. Tazi Y, Arango-Ossa JE, Zhou Y, Bernard E, Thomas I, Gilkes A, Freeman S, Pradat Y, Johnson SJ, Hills R, Dillon R, Levine MF, Leongamornlert D, Butler A, Ganser A, Bullinger L, Döhner K, Ottmann O, Adams R, Döhner H, Campbell PJ, Burnett AK, Dennis M, Russell NH, Devlin SM, Huntly BJP, Papaemmanuil E. Unified classification and risk-stratification in Acute Myeloid Leukemia. Nat Commun. 2022 Aug 8;13(1):4622. PMCID: PMC9360033
  4. Gao T, Ptashkin R, Bolton KL, Sirenko M, Fong C, Spitzer B, Menghrajani K, Ossa JEA, Zhou Y, Bernard E, Levine M, Martinez JSM, Zhang Y, Franch-Expósito S, Patel M, Braunstein LZ, Kelly D, Yabe M, Benayed R, Caltabellotta NM, Philip J, Paraiso E, Mantha S, Solit DB, Diaz LA Jr, Berger MF, Klimek V, Levine RL, Zehir A, Devlin SM, Papaemmanuil E. Interplay between chromosomal alterations and gene mutations shapes the evolutionary trajectory of clonal hematopoiesis. Nat Commun. 2021 Jan 12;12(1):338. doi: 10.1038/s41467-020-20565-7. PMID: 33436578; PMCID: PMC7804935.
  5. Shahid S, Kushner BH, Modak S, Basu EM, Rubin EM, Gundem G, Papaemmanuil E, Roberts SS. Association of BRAF V600E mutations with vasoactive intestinal peptide syndrome in MYCN-amplified neuroblastoma. Pediatr Blood Cancer. Wiley; 2021 Oct;68(10):e29265. PMCID: PMC9527949.
  6. Bolton KL, Koh Y, Foote MB, Im H, Jee J, Sun CH, Safonov A, Ptashkin R, Moon JH, Lee JY, Jung J, Kang CK, Song KH, Choe PG, Park WB, Kim HB, Oh MD, Song H, Kim S, Patel M, Derkach A, Gedvilaite E, Tkachuk KA, Wiley BJ, Chan IC, Braunstein LZ, Gao T, Papaemmanuil E, Esther Babady N, Pessin MS, Kamboj M, Diaz LA, Jr., Ladanyi M, Rauh MJ, Natarajan P, Machiela MJ, Awadalla P, Joseph V, Offit K, Norton L, Berger MF, Levine RL, Kim ES, Kim NJ, Zehir A. Clonal hematopoiesis is associated with risk of severe Covid-19. Nat Commun. 2021;12(1):5975.
  7. Gao T, Ptashkin R, Bolton KL, Sirenko M, Fong C, et al. Papaemmanuil E. Interplay between chromosomal alterations and gene mutations shapes the evolutionary trajectory of clonal hematopoiesis. Nat Commun. 2021;12(1):338.
  8. Maura F, Diamond B, Maclachlan KH, Derkach A, Yellapantula VD, Rustad EH, Hultcrantz M, Shah UA, Hong J, Landau HJ, Iacobuzio-Donahue CA, Papaemmanuil E, Irby S, Crowley L, Crane M, Webber MP, Goldfarb DG, Zeig-Owens R, Giricz O, Verma A, Prezant DJ, Dogan A, Shah SP, Zhang Y, Landgren O. Initial Whole-Genome Sequencing of Plasma Cell Neoplasms in First Responders and Recovery Workers Exposed to the World Trade Center Attack of September 11, 2001. Clin Cancer Res. 2021;27(7):2111-8.
  9. Shahid S, Kushner BH, Modak S, Basu EM, Rubin EM, Gundem G, Papaemmanuil E, Roberts SS. Association of BRAF V600E mutations with vasoactive intestinal peptide syndrome in MYCN-amplified neuroblastoma. Pediatr Blood Cancer. 2021;68(10):e29265.
  10. Landau HJ, Yellapantula V, Diamond BT, Rustad EH, Maclachlan KH, Gundem G, et al., Papaemmanuil E, Iacobuzio-Donahue C, Maura F. Accelerated single cell seeding in relapsed multiple myeloma. Nat Commun. 2020 Jul 17;11(1):3617. doi: 10.1038/s41467-020-17459-z. PMID: 32680998.
  11. Gerstung M, …, Papaemmanuil E, et al. Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes. Nat Commun. 2015 Jan 9;6:5901. doi: 10.1038/ncomms6901. PubMed PMID: 25574665; PubMed Central PMCID: PMC4338540.
  12. Papaemmanuil E, et al. 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.

View a full listing of Elli Papaemmanouil’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 Papaemmanouil discloses the following relationships and financial interests:

  • Isabl Inc.
    Equity; Fiduciary Role / Position; Intellectual Property Rights
  • TenSixteen Bio, Inc.
    Equity; Professional Services and Activities

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This page and data include information for a specific MSK annual disclosure period (January 1, 2022 through disclosure submission in spring 2023). This data reflects interests that may or may not still exist. This data is updated annually.

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