Michael Schatz

About

Michael Schatz is the Bloomberg Distinguished Professor of Computational Biology and Oncology at Johns Hopkins University. His research focuses on solving computational problems in genomics research, developing innovative biotechnologies and computational tools to study the sequence and function of genomes. Schatz's work advances understanding of genome structure, evolution, and function, particularly in the context of medicine—such as autism spectrum disorders, cancer, and other human diseases—as well as agriculture. He has created many widely used methods and software for genome assembly and analysis, including NGMLR and Sniffles for long-read sequencing analysis, Scalpel for genetic variant discovery, and GECCO for studying complex genomic variations. His lab has identified numerous structural alterations in cancer genomes and developed tools like Ginkgo for single-cell copy number profiling. Schatz's contributions extend to computational methods for genome assembly and analysis across species, utilizing single molecule-sequencing technologies. He serves as a faculty member in the Department of Computer Science and the Department of Biology at Johns Hopkins, and is involved with the Cancer Prevention and Control Program at the Sidney Kimmel Comprehensive Cancer Center. His work has earned him several awards, including the 2015 Sloan Foundation Fellowship and an NSF CAREER Award, and he has been recognized for his leadership in the field of computational biology.

Research topics

• Genetics
• Biology
• Computer Science
• Computational biology
• Evolutionary biology
• Data Mining
• Data science
• Machine Learning
• Artificial Intelligence
• Biotechnology

Selected publications

• The complete sequence of a human genome

  Science · 2022 · 3273 citations

  Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion-base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequenc…

  PublisherOA PDFDOI

• GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes

  Nature Communications · 2020 · 2527 citations

  Senior authorCorresponding

  An important assessment prior to genome assembly and related analyses is genome profiling, where the k-mer frequencies within raw sequencing reads are analyzed to estimate major genome characteristics such as size, heterozygosity, and repetitiveness. Here we introduce GenomeScope 2.0 (https://github.com/tbenavi1/genomescope2.0), which applies combinatorial theory to establish a detailed mathematical model of how k-mer frequencies are distributed in heterozygous and polyploid genomes. We describe…

  DOI

• The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

  Nucleic Acids Research · 2022 · 1353 citations

  Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute to the project, with support from multiple national infrastructure providers that enable freely accessible analysis and training services. The Galaxy Training Network supports free, self-directed, virtual training with >230 integrated tutorials. Pro…

  PublisherOA PDFDOI

• Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

  Cell · 2020 · 867 citations

  DOI

• Complete genomic and epigenetic maps of human centromeres

  Science · 2022 · 612 citations

  Existing human genome assemblies have almost entirely excluded repetitive sequences within and near centromeres, limiting our understanding of their organization, evolution, and functions, which include facilitating proper chromosome segregation. Now, a complete, telomere-to-telomere human genome assembly (T2T-CHM13) has enabled us to comprehensively characterize pericentromeric and centromeric repeats, which constitute 6.2% of the genome (189.9 megabases). Detailed maps of these regions reveale…

  PublisherOA PDFDOI

Recent grants

• A Federated Galaxy for user-friendly large-scale cancer genomics research

  NIH · $3.9M · 2018–2024

• Expanding the AnVIL (Analysis, Visualization, and Informatics Lab-space)

  NIH · $20.8M · 2018–2028

• Integrative genomic and epigenomic analysis of cancer using long read sequencing

  NIH · $1.1M · 2021–2025

Frequent coauthors

• Fritz J. Sedlazeck

  Rice University

  125 shared

• Steven L. Salzberg

  Johns Hopkins University

  119 shared

• Brian J. Haas

  Broad Institute

  81 shared

• Mihaela Pertea

  Johns Hopkins University

  76 shared

• Owen White

  University of Maryland, Baltimore

  76 shared

• Claire M. Fraser

  University of Maryland, Baltimore

  76 shared

• Adam M. Phillippy

  National Human Genome Research Institute

  76 shared

• Jennifer R. Wortman

  76 shared

Education

• Ph.D., Computer Science

  University of Maryland at College Park

  2010

• BS, Computer Science

  Carnegie Mellon University

  2000

Awards & honors

• 2015 Alfred P. Sloan Foundation Fellowship for Computational…
• NSF CAREER Award (2014)
• Genome Technology ’s Young Investigator of the Year (2010)
• Winship Herr Award for Excellence in Teaching from the Watso…

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