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Michael Schatz

Associate Professor
Ph.D., University of Maryland, 2010


Contact
mschatz@cshl.edu
(516) 367-5218 (p)
  Schatz Lab Website
DNA sequencing efforts produce trillions and trillions of As, Cs, Gs, and Ts each minute - but what do the letters mean?  My group develops novel computational methods to extract the information contained in biological sequences.  We are applying these tools to discover mutations associated with cancer and autism and to reconstruct the genomes of important plants, animals, and microbes.

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.

Schatz, M. C. and Delcher, A. L. and Salzberg, S. L. (2010) Assembly of large genomes using second-generation sequencing. Genome Research 20(9) pp. 1165-1173.

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

Langmead, B. and Schatz, M. C. and Lin, J. and Pop, M. and Salzberg, S. L. (2009) Searching for SNPs with cloud computing. Genome Biology 10(11)

Phillippy, A. M. and Schatz, M. C. and Pop, M. (2008) Genome assembly forensics: Finding the elusive mis-assembly. Genome Biology 9(3)

Carlton, J. M. and Hirt, R. P. and Silva, J. C. and Delcher, A. L. and Schatz, M. and Zhao, Q. and Wortman, J. R. and Bidwell, S. L. and Alsmark, U. C. M. and Besteiro, S. and Sicheritz-Ponten, T. and Noel, C. J. and Dacks, J. B. and Foster, P. G. and Simillion, C. and Van De Peer, Y. and Miranda-Saavedra, D. and Barton, G. J. and Westrop, G. D. and Müller, S. and Dessi, D. and Fiori, P. L. and Ren, Q. and Paulsen, I. and Zhang, H. and Bastida-Corcuera, F. D. and Simoes-Barbosa, A. and Brown, M. T. and Hayes, R. D. and Mukherjee, M. and Okumura, C. Y. and Schneider, R. and Smith, A. J. and Vanacova, S. and Villalvazo, M. and Haas, B. J. and Pertea, M. and Feldblyum, T. V. and Utterback, T. R. and Shu, C. L. and Osoegawa, K. and De Jong, P. J. and Hrdy, I. and Horvathova, L. and Zubacova, Z. and Dolezal, P. and Malik, S. B. and Logsdon Jr, J. M. and Henze, K. and Gupta, A. and Wang, C. C. and Dunne, R. L. and Upcroft, J. A. and Upcroft, P. and White, O. and Salzberg, S. L. and Tang, P. and Chiu, C. H. and Lee, Y. S. and Embley, T. M. and Coombs, G. H. and Mottram, J. C. and Tachezy, J. and Fraser-Liggett, C. M. and Johnson, P. J. (2007) Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science 315(5809) pp. 207-212.

Additional materials of the author at
CSHL Institutional Repository
2015:  Sloan Foundation Research Fellowship

NSF Early CAREER Award

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