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Dan Levy

Dan Levy

Associate Professor

Ph.D., University of California, Berkeley 2005

levy@cshl.edu | (516) 367-5039

We have recently come to appreciate that many unrelated diseases, such as autism, congenital heart disease and cancer, are derived from rare and unique mutations, many of which are not inherited but instead occur spontaneously. I am generating algorithms to analyze massive datasets comprising thousands of affected families to identify disease-causing mutations.

There is increasing evidence that rare and unique mutations have a significant role in the etiology of many diseases such as autism, congenital heart disease, and cancer. Dan Levy’s group develops algorithms to identify these mutations from large, high-throughput data sets comprising thousands of nuclear families. After earlier working with high-resolution CGH arrays, Levy’s group now uses targeted sequence data. Levy has developed methods for identifying de novo mutations (i.e., those seen in a child but not in his or her parents) by simultaneously genotyping the entire family; the team is currently focused on building algorithms to detect copy-number variants and multiscale genomic rearrangements. Although their copy-number methods are based on “read” density, there are classes of mutations that require analysis at the level of the read. Thus, they are developing algorithms to identify insertions, deletions, inversions, transpositions, and other complex events. Other projects in the Levy lab include analysis of single-cell RNA, phylogenetic reconstruction from sparse data sets, and disentangling haplotypes from sperm and subgenomic sequence data.

    Portrait of a Neuroscience Powerhouse

    Portrait of a Neuroscience Powerhouse

    April 27, 2018

    At noon every Tuesday from September through June, scenes from a revolution in neuroscience are playing out at Cold Spring Harbor Laboratory. Week after week, over 100 scientists cram themselves into a ground-floor meeting room in the Beckman Laboratory. It’s standing-room only as everyone in the Neuroscience Program settles in to hear details of the...


    New study casts sharpest light yet on genetic mysteries of autism

    New study casts sharpest light yet on genetic mysteries of autism

    October 29, 2014

    Our picture of how genetic errors contribute to autism has just gotten sharper. Cold Spring Harbor, NY — Our picture of how genetic errors contribute to autism has just gotten sharper. The latest series of clarifications in what, in its totality, is a very complex puzzle, emerges from new research published in Nature today by...


Iossifov, I. and Ronemus, M. and Levy, D. and Wang, Z. H. and Hakker, I. and Rosenbaum, J. and Yamrom, B. and Lee, Y. H. and Narzisi, G. and Leotta, A. and Kendall, J. and Grabowska, E. and Ma, B. C. and Marks, S. and Rodgers, L. and Stepansky, A. and Troge, J. and Andrews, P. and Bekritsky, M. and Pradhan, K. and Ghiban, E. and Kramer, M. and Parla, J. and Demeter, R. and Fulton, L. L. and Fulton, R. S. and Magrini, V. J. and Ye, K. and Darnell, J. C. and Darnell, R. B. and Mardis, E. R. and Wilson, R. K. and Schatz, M. C. and McCombie, W. R. and Wigler, M. (2012) De Novo Gene Disruptions in Children on the Autistic Spectrum. Neuron, 74(2) pp. 285-299.

Gilman, S. R and Iossifov, I. and Levy, D. and Ronemus, M. and Wigler, M. H. and Vitkup, D. (2011) Rare De Novo Variants Associated with Autism Implicate a Large Functional Network of Genes Involved in Formation and Function of Synapses. Neuron, 70(5) pp. 898-907.

Levy, D. and Ronemus, M. and Yamrom, B. and Lee, Y. H. and Leotta, A. and Kendall, J. T. and Marks, S. and Lakshmi, B. and Pai, D. and Ye, Kenny and Buja, Andreas and Krieger, Abba and Yoon, S. and Troge, J. E. and Rodgers,  L. and Iossifov, I. and Wigler, M. H. (2011) Rare De Novo and Transmitted Copy-Number Variation in Autistic Spectrum Disorders. Neuron, 70(5) pp. 886-897.

Navin, N. E. and Kendall, J. T. and Troge, J. E. and Andrews, P. and Rodgers,  L. and McIndoo, J. and Cook, K. and Stepansky,  A. and Levy, D. and Esposito, D. and Muthuswamy, L. and Krasnitz, A. and McCombie, W. R. and Hicks, J. B. and Wigler, M. H. (2011) Tumour evolution inferred by single-cell sequencing. Nature, 472(7341) pp. 90-94.

Additional materials of the author at
CSHL Institutional Repository