Faculty

Michael Schatz

BLOOMBERG DISTINGUISHED associate professor

Research Interests

  • Computational Biology
  • Genomics
  • DNA Sequencing & Analysis
  • Scalable Computing

Michael Schatz, Bloomberg Distinguished Associate Professor of Computer Science and Biology at Johns Hopkins University, is among the world’s foremost experts in solving computational problems in genomics research. His innovative biotechnologies and computational tools to study the sequence and function of genomes are advancing the understanding of the structure, evolution, and function of genomes for medicine – particularly autism spectrum disorders, cancer, and other human disease – and agriculture.

Schatz, who founded and directs the Schatz Lab, has created many of the most widely used methods and software to assemble the full genetic material for a single person or a species, including:

  • NGMLR and Sniffles are long-read sequencing analysis methods to study the longer fragments of DNA, a breakthrough that may yield critical information about how cancer genomes evolve. Genomes in malignant tumors often house sections of chromosomes that are deleted, duplicated or fused together. By examining an unstable genome, Schatz identified almost 20,000 structural alterations – changes previously missed by other researchers when examining shorter DNA fragments.
  • Scalpel, the leading genetic variants discovery tool, to identify and analyze mutations in autism spectrum disorders and somatic mutations (or post-conception DNA alterations) in cancer genomes, including pancreatic cancers.
  • GECCO (Genomic Enrichment Computational Clustering Operation), a novel algorithm to study complex non-coding and structural variations in genomes, through which his lab identified recurrent non-coding somatic mutations (DNA alterations that occur post-conception) in pancreatic cancer, including some that substantially changed survival outcomes.
  • Ginkgo, a computational tool for single cell copy number profiling in heterogeneous tumors to study the progression of primary and metastatic breast tumors and adult acute myeloid leukemia.
  • New computational methods including FALCON and Assemblytics for assembling and analyzing the genomes of different species using single molecule sequencing, especially plant and animal species, to study their evolution and adaption.
  • CloudBurst and Crossbow, the first published algorithms to use cloud computing technologies in genomics for mapping and variant discovery.

Schatz holds appointments in the Department of Computer Science at the Whiting School of Engineering and in the Department of Biology at JHU Krieger School of Arts and Sciences. He also serves as a cancer prevention and control program member for the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins. Prior to joining JHU in 2016, he spent six years at the Cold Spring Harbor Laboratory (CSHL) where he co-led the Cancer Genetics & Genomics Program in the CSHL Cancer Center. Schatz remains a CSHL adjunct associate professor of Quantitative Biology.

Recent awards include the Alfred P. Sloan Foundation Fellowship, Computational and Evolutionary Molecular Biology, in 2015, and the NSF CAREER Award in 2014. Schatz’s earlier honors are Young Investigator of the Year, Genome Technology (2010) and the twice-awarded Winship Herr Award for Excellence in Teaching, Watson School for Biological Science. His leadership of the computational biology field includes founding in 2012 a new, interdisciplinary CSHL conference on Biological Data Science, as well as a regular member of the program committees to Genome Informatics, RECOMB, ISMB, WABI, and several other top conferences.. Schatz serves on the editorial boards of Genome Biology, GigaScience, and Cell Systems, and he has served as a reviewer for Nature, Cell, Science, Nature Biotechnology, Nature Methods, Genome Research, Genome Medicine, and Bioinformatics. His innovative discoveries have been featured in The New York Times, The Washington Post, and Wired.

He holds a BS in Computer Science from Carnegie Mellon University (2000) and an MS (2008) and PhD (2010), both in Computer Science, from the University of Maryland, College Park.

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