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Imielinski Lab

The Imielinski lab applies cancer genome assembly to study long range DNA structure in tumors. A key goal of the lab is to understand how complex somatic DNA rearrangements shape the tumor epigenome and drive cancer progression. More fundamentally, the lab is interested in using structural variation as a lens to study genomic plasticity and somatic evolution. The lab is committed to translating clinically relevant basic research findings into genomic diagnostics and incorporating these into precision cancer care.

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    Marcin Imielinski, MD, PhD

    Marcin Imielinski, MD, PhD, is a Core Faculty Member at the New York Genome Center. He holds a joint appointment as Assistant Professor of Computational Genomics and Assistant Professor of Pathology and Laboratory Medicine at Weill Cornell Medicine, working directly with its Meyer Cancer Center and Englander Institute for Precision Medicine. Dr. Imielinski is also an Attending Molecular Pathologist at NewYork-Presbyterian Hospital.

    Dr. Imielinski is a board-certified molecular genetic pathologist. His research includes more than 40 peer-reviewed publications across several areas of genomics and computational biology. His lab uses cutting-edge sequencing technology and genomic data science to study patterns of complex and noncoding somatic DNA variation in cancer. Dr. Imielinski’s research interests are to apply high-throughput sequencing and computation to study patterns of somatic genomic variation in cancer. He is specifically interested in probing long-range cancer genome structure through the use of cutting-edge sequencing protocols and the development of novel machine learning and data visualization approaches. Dr. Imielinski is committed to expanding the role of computation and data science in laboratory medicine, and envisions a future in which “quantitative pathologists” help direct treatment choices through the application of statistical intuition and sophisticated multivariate analyses.

    He is a recipient of a Burroughs Wellcome Career Award for Medical Scientists, a Clinical Scientist Development Award from the Doris Duke Charitable Foundation, and The Black Family-MRA Team Science Award

    Dr. Imielinski received a BS in Computer Science from Rutgers College. He obtained a PhD in genomics and computational biology and his MD from the University of Pennsylvania School of Medicine. He completed his residency in pathology at the Massachusetts General Hospital, and a fellowship in molecular genetic pathology at Harvard Medical School.

    Prior to joining the New York Genome Center, he was a postdoctoral fellow in computational cancer genomics at the Broad Institute of Harvard and MIT, under the mentorship of Drs. Matthew Meyerson and Gad Getz.

  • Recent Publications

    • The evolutionary history of 2,658 cancers.

      PCAWG Evolution and Heterogeneity Working GroupPCAWG network (includes Imielinski M)

      Nature. 2020 Feb. 6.

    • Next-generation characterization of the Cancer Cell Line Encyclopedia.

      Mahmoud Ghandi, Franklin W. Huang, Judit Jané-Valbuena, Gregory V. Kryukov , Christopher C. Lo, E. Robert McDonald III, Jordi Barretina, Ellen T. Gelfand, Craig M. Bielski, Haoxin Li, Kevin Hu , Alexander Y. Andreev-Drakhlin , Jaegil Kim, Julian M. Hess, Brian J. Haas, François Aguet, Barbara A. Weir, Michael V. Rothberg, Brenton R. Paolella, Michael S. Lawrence, Rehan Akbani, Yiling Lu, Hong L. Tiv, Prafulla C. Gokhale, Antoine de Weck, Ali Amin Mansour, Coyin Oh, Juliann Shih, Kevin Hadi, Yanay Rosen, Jonathan Bistline, Kavitha Venkatesan, Anupama Reddy, Dmitriy Sonkin, Manway Liu, Joseph Lehar, Joshua M. Korn, Dale A. Porter, Michael D. Jones, Javad Golji, Giordano Caponigro, Jordan E. Taylor , Caitlin M. Dunning, Amanda L. Creech, Allison C. Warren, James M. McFarland, Mahdi Zamanighomi, Audrey Kauffmann, Nicolas Stransky, Marcin Imielinski, Yosef E. Maruvka, Andrew D. Cherniack, Aviad Tsherniak, Francisca Vazquez , Jacob D. Jaffe, Andrew A. Lane, David M. Weinstock, Cory M. Johannessen, Michael P. Morrissey, Frank Stegmeier, Robert Schlegel, William C. Hahn, Gad Getz, Gordon B. Mills , Jesse S. Boehm, Todd R. Golub, Levi A. Garraway & William R. Sellers.

      Nature. 2019 May 8.

    • Fusion oncogenes-genetic musical chairs.

      Imielinski M, Ladanyi M.

      Science. 2018 Aug. 31.

    • SvABA: genome-wide detection of structural variants and indels by local assembly.

      Wala JA, Bandopadhayay P, Greenwald N, O’Rourke R, Sharpe T, Stewart C, Schumacher S, Li Y, Weischenfeldt J, Yao X, Nusbaum C, Campbell P, Getz G, Meyerson M, Zhang CZ, Imielinski M, Beroukhim R.

      Genome Research. 2018 Mar. 13.

    • Prostate cancer: Clinical hallmarks in whole cancer genomes.

      Imielinski M, Rubin MA.

      Nature Reviews Clinical Oncology. 2017 Apr 4.

    • Insertions and Deletions Target Lineage-Defining Genes in Human Cancers.

      Imielinski M, Guo G, Meyerson M.

      Cell. 2017 Jan 11.

  • Preprints

    • Novel patterns of complex structural variation revealed across thousands of cancer genome graphs.

      Kevin Hadi, Xiaotong Yao, Julie M. Behr, Aditya Deshpande, Charalampos Xanthopoulakis, Joel Rosiene, Madison Darmofal, Huasong Tian, Joseph DeRose, Rick Mortensen, Emily Adney, Zoran Gajic, Kenneth Eng, Jeremiah Anthony Wala, Kazimierz O. Wrzeszczyński, Kanika Arora, Minita Shah, Anne-Katrin Emde, Vanessa Felice, Mayu O. Frank, Robert Darnell, Mahmoud Ghandi, Franklin Huang, John Maciejowski, Titia De Lange, Jeremy Setton, Nadeem Riaz, Jorge S. Reis-Filho, Simon Powell, David Knowles, Ed Reznik, Bhubaneswar Mishra, Rameen Beroukhim, Michael Zody, Nicolas Robine, Kenji Oman, Carissa A. Sanchez, Mary K. Kuhner, Lucian P. Smith, Patricia C. Galipeau, Thomas G. Paulson, Brian J. Reid, Xiaohong Li, David Wilkes, Andrea Sboner, Juan Miguel Mosquera, Olivier Elemento, Marcin Imielinski

      bioRxiv. 2019 November 9.

This work was partially supported by a gift from the Simons Foundation.