Research Menu
Michael Schatz

Michael Schatz

Adjunct Associate Professor

mschatz@cshl.edu | (516) 367-5218

Schatz Lab

Michael Schatz is a computational biologist and an expert at large-scale computational examination of DNA sequencing data, including the alignment, assembly, and analysis of next-generation sequencing reads. These methods have been used to reconstruct the genomes of previously unsequenced organisms, probe sequence variations, and explore a host of biological features across the tree of life. Recent improvements in sequencing technologies are challenging our capacity to store and analyze the huge volume of DNA sequence data being generated. Consequently, Schatz is particularly interested in capitalizing on the latest advances in distributed and parallel computing, especially cloud computing technologies, to advance the state of the art in bioinformatics and genomics. In a recent breakthrough, Schatz was able to create a hybrid software-based solution to eliminate errors in so-called third-generation sequencing. This makes it remarkably easier to compile, align, and analyze full-genome sequences.

2015:  Sloan Foundation Research Fellowship

2014 NSF Early CAREER Award

2012 CSHL Winship Herr Award for Excellence in Teaching

2011 CSHL Winship Herr Award for Excellence in Teaching

2010 Young Investigator of the Year, Genome Technology

    Massive genome havoc in breast cancer is revealed

    Massive genome havoc in breast cancer is revealed

    July 12, 2018

    Cold Spring Harbor, NY — In cancer cells, genetic errors wreak havoc. Misspelled genes, as well as structural variations—larger-scale rearrangements of DNA that can encompass large chunks of chromosomes—disturb carefully balanced mechanisms that have evolved to regulate cell growth. Genes that are normally silent are massively activated and mutant proteins are formed. These and other...


    New method can more precisely determine when a cell has ‘cashed’ RNA ‘checks’ written by active genes

    New method can more precisely determine when a cell has ‘cashed’ RNA ‘checks’ written by active genes

    January 26, 2018

    Cold Spring Harbor, NY — DNA has often been called “the book of life,” but this popular phrase makes some biologists squirm a bit. True, DNA bears our genes, which spell out the instructions our cells use to make proteins—those workhorse molecules that make just about everything in life possible. But the precise relationship between...


    Scientists sequence genome of worm that can regrow body parts, seek stem cell insights

    Scientists sequence genome of worm that can regrow body parts, seek stem cell insights

    September 21, 2015

    Worm’s genome could lead to better understanding of its regenerative prowess and advance stem cell biology Cold Spring Harbor, NY — Tourists spending a recuperative holiday on the Italian coast may be envious of the regenerative abilities of locally found flatworm Macrostomum lignano. Named for its discovery near the Italian beach town of Lignano Sabbiadoro,...


    Mathematical ‘Gingko trees’ reveal mutations in single cells that characterize diseases

    Mathematical ‘Gingko trees’ reveal mutations in single cells that characterize diseases

    September 4, 2015

    The Schatz lab, in collaboration with the Wigler and Atwal labs, has developed a new interactive, open-source analysis program called Gingko that can be used to reduce the uncertainty of single-cell analysis and visualize patterns in copy number mutations across populations of cells.


    The biggest beast in the Big Data forest? One field’s astonishing growth is, well, ‘genomical’!

    The biggest beast in the Big Data forest? One field’s astonishing growth is, well, ‘genomical’!

    July 6, 2015

    Cold Spring Harbor, NY — Who’s about to become the biggest beast in the Big Data forest? A group of math and computing experts have arrived at what they say is a clear answer. It’s not YouTube or Twitter, social media sites that gobble up awesome quantities of bandwidth and generate hard-to-grasp numbers of electronic...


    A unique partnership

    A unique partnership

    March 24, 2015

    LabDish blog Written by Skyler Palatnick This post was written by Skyler Palatnick, a junior at Cold Spring Harbor High School with a penchant for writing about scientists. His first contribution to LabDish was about CSHL Director of Research David L. Spector. In this post, he introduces us to someone closer to home. A 14-year-old...


    CSHL quantitative biologist Michael Schatz awarded 2015 Sloan Foundation Research Fellowship

    CSHL quantitative biologist Michael Schatz awarded 2015 Sloan Foundation Research Fellowship

    February 20, 2015

    Cold Spring Harbor, NY — Associate Professor Michael Schatz of Cold Spring Harbor Laboratory (CSHL) will receive a 2015 Alfred P. Sloan Foundation Research Fellowship. This prestigious research award has been issued since 1955. Schatz is one of 126 outstanding early-career scientists from the U.S. and Canada recognized by the Foundation this year. Past honorees...


    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...


    A shift in the code: new method reveals hidden genetic landscape

    A shift in the code: new method reveals hidden genetic landscape

    August 18, 2014

    Scientists develop algorithm to uncover genomic insertions and deletions involved in autism, OCD Cold Spring Harbor, NY — With three billion letters in the human genome, it seems hard to believe that adding a DNA base here or removing a DNA base there could have much of an effect on our health. In fact, such...


    CSHL quantitative biologist Michael Schatz wins prestigious NSF Early CAREER Award

    CSHL quantitative biologist Michael Schatz wins prestigious NSF Early CAREER Award

    July 29, 2014

    The National Science Foundation (NSF) has selected Assistant Professor Michael Schatz, Ph.D., of Cold Spring Harbor Laboratory (CSHL) to receive its prestigious CAREER Award. Cold Spring Harbor, NY — The National Science Foundation (NSF) has selected Assistant Professor Michael Schatz, Ph.D., of Cold Spring Harbor Laboratory (CSHL) to receive its prestigious CAREER Award. The Faculty...


Stephens, Z. D. and Lee, S. Y. and Faghri, F. and Campbell, R. H. and Zhai, C. and Efron, M. J. and Iyer, R. and Schatz, M. C. and Sinha, S. and Robinson, G. E. (2015) Big Data: Astronomical or Genomical?. PLoS Biol, 13(7) pp. e1002195.

Iossifov, I. and O'Roak, B. J. and Sanders, S. J. and Ronemus, M. and Krumm, N. and Levy, D. and Stessman, H. A. and Witherspoon, K. T. and Vives, L. and Patterson, K. E. and Smith, J. D. and Paeper, B. and Nickerson, D. A. and Dea, J. and Dong, S. and Gonzalez, L. E. and Mandell, J. D. and Mane, S. M. and Murtha, M. T. and Sullivan, C. A. and Walker, M. F. and Waqar, Z. and Wei, L. and Willsey, A. J. and Yamrom, B. and Lee, Y. H. and Grabowska, E. and Dalkic, E. and Wang, Z. and Marks, S. and Andrews, P. and Leotta, A. and Kendall, J. and Hakker, I. and Rosenbaum, J. and Ma, B. and Rodgers, L. and Troge, J. and Narzisi, G. and Yoon, S. and Schatz, M. C. and Ye, K. and McCombie, W. R. and Shendure, J. and Eichler, E. E. and State, M. W. and Wigler, M. (2014) The contribution of de novo coding mutations to autism spectrum disorder. Nature, 515(7526) pp. 216-221.

Narzisi, G. and O'Rawe, Jason and Iossifov, I. and Fang, Han and Lee, Y. H. and Wang, Zihua and Wu, Yiyang and Lyon, Gholson J. and Wigler, M. H. and Schatz, M. C. (2014) Accurate de novo and transmitted indel detection in exome-capture data using microassembly. Nature Methods, 11(10) pp. 1033-1036.

Koren, S. and Schatz, M. C. and Walenz, B. P. and Martin, J. and Howard, J. T. and Ganapathy, G. and Wang, Z. and Rasko, D. A. and McCombie, W. R. and Jarvis, E. D. and Phillippy, A. M. (2012) Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology, 30(7) pp. 693-700.

Schatz, M. C. (2009) CloudBurst: Highly sensitive read mapping with MapReduce. Bioinformatics, 25(11) pp. 1363-1369.

Additional materials of the author at
CSHL Institutional Repository