The Papaemmanuil lab started in 2015/2016 and includes a collective of clinical fellows, postdoctoral research fellows in computational biology and machine learning, PhD research students and software engineers. We have formed a strong network of research and clinical collaborations, to pursue innovative studies in cancer research.We like to perform ambitious research but operate in a fun, collaborative and team oriented environment and we are strongly committed to mentoring young scientists through internal and international internship schemes.
We have developed isabl I plug and play platform for scalable bioinformatics operations. Isabl encapsulates more than 10 years engineering experience of NGS data asset management and represents a modern version of a digital biobank. The platform support project registration, NGS assets data management, a patient-centric meta-data model, fully automated bioinformatics applications and delivers and end to end audit trail of all bioinformatics operations and a user friendly front end to track project status and visualize results.
View available career opportunities in the lab here.
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.
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.
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
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.
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.
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.
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.
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.
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.
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.
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.
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.
International Working Group for Prognostication in MDS – a prospective sequencing study of well-annotated clinical samples collected by clinical and research collaborators around the world
Leukemia Genomics at MSK – brings together collaborators who are working together to deliver a computational infrastructure for molecular profiling, analysis, and databasing of clinical and research specimens
Pan Myeloid meta-analysis – cohorts of well-annotated clinical samples across myeloid neoplasms that have been molecularly profiled using extensive genome profiling platforms (exomes, 100 gene plus gene panels) to conduct an agnostic meta-analysis
isabl – a plug-and-play framework for scalable bioinformatics operations designed to support automated processing and management of NGS assets and their metadata
Please visit Dr. Papaemmanuil’s faculty page, PubMed or Google Scholar for more publications.
