Michael C Schatz

Summary

Affiliation: Cold Spring Harbor Laboratory
Country: USA

Publications

  1. pmc The rise of a digital immune system
    Michael C Schatz
    Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
    Gigascience 1:4. 2012
  2. pmc Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies
    Michael C Schatz
    Cold Spring Harbor, New York, NY 11724, USA
    Brief Bioinform 14:213-24. 2013
  3. pmc Current challenges in de novo plant genome sequencing and assembly
    Michael C Schatz
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Genome Biol 13:243. 2012
  4. pmc Quake: quality-aware detection and correction of sequencing errors
    David R Kelley
    Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, and Department of Computer Science, University of Maryland, College Park, MD 20742, USA
    Genome Biol 11:R116. 2010
  5. pmc The missing graphical user interface for genomics
    Michael C Schatz
    Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Genome Biol 11:128. 2010
  6. pmc Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score
    Hayan Lee
    Department of Computer Science, Stony Brook University, Stony Brook, NY, USA
    Bioinformatics 28:2097-105. 2012
  7. pmc Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome
    Sara Goodwin
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 25:1750-6. 2015
  8. pmc Genotyping in the cloud with Crossbow
    James Gurtowski
    Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
    Curr Protoc Bioinformatics . 2012
  9. pmc Dual functions of Macpiwi1 in transposon silencing and stem cell maintenance in the flatworm Macrostomum lignano
    Xin Zhou
    Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA Molecular and Cellular Biology Graduate Program, Stony Brook University, Stony Brook, New York 11794, USA
    RNA 21:1885-97. 2015
  10. pmc Interactive analysis and assessment of single-cell copy-number variations
    Tyler Garvin
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
    Nat Methods 12:1058-60. 2015

Collaborators

Detail Information

Publications14

  1. pmc The rise of a digital immune system
    Michael C Schatz
    Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
    Gigascience 1:4. 2012
    ....
  2. pmc Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies
    Michael C Schatz
    Cold Spring Harbor, New York, NY 11724, USA
    Brief Bioinform 14:213-24. 2013
    ..Hawkeye and AMOS are available open source at http://amos.sourceforge.net...
  3. pmc Current challenges in de novo plant genome sequencing and assembly
    Michael C Schatz
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Genome Biol 13:243. 2012
    ..Genome sequencing is now affordable, but assembling plant genomes de novo remains challenging. We assess the state of the art of assembly and review the best practices for the community...
  4. pmc Quake: quality-aware detection and correction of sequencing errors
    David R Kelley
    Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, and Department of Computer Science, University of Maryland, College Park, MD 20742, USA
    Genome Biol 11:R116. 2010
    ..Quake can be used for any size project, including more than one billion human reads, and is freely available as open source software from http://www.cbcb.umd.edu/software/quake...
  5. pmc The missing graphical user interface for genomics
    Michael C Schatz
    Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Genome Biol 11:128. 2010
    ..The underlying data analysis tools can be almost any piece of software, written in any language, but all their complexity is neatly hidden inside of Galaxy, allowing users to focus on scientific rather than technical questions...
  6. pmc Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score
    Hayan Lee
    Department of Computer Science, Stony Brook University, Stony Brook, NY, USA
    Bioinformatics 28:2097-105. 2012
    ..The GMS is a weighted probability that any read could be unambiguously mapped to a given position and thus measures the overall composition of the genome itself...
  7. pmc Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome
    Sara Goodwin
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 25:1750-6. 2015
    ....
  8. pmc Genotyping in the cloud with Crossbow
    James Gurtowski
    Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
    Curr Protoc Bioinformatics . 2012
    ....
  9. pmc Dual functions of Macpiwi1 in transposon silencing and stem cell maintenance in the flatworm Macrostomum lignano
    Xin Zhou
    Cold Spring Harbor Laboratory and Watson School of Biological Sciences, Cold Spring Harbor, New York 11724, USA Molecular and Cellular Biology Graduate Program, Stony Brook University, Stony Brook, New York 11794, USA
    RNA 21:1885-97. 2015
    ..These results may suggest stem cell maintenance functions of PIWI proteins in flatworms that are distinguishable from their impact on transposons and that might function independently of what are considered canonical piRNA populations. ..
  10. pmc Interactive analysis and assessment of single-cell copy-number variations
    Tyler Garvin
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
    Nat Methods 12:1058-60. 2015
    ..After comparing three commonly used single-cell amplification techniques, we concluded that degenerate oligonucleotide-primed PCR is the most consistent for CNV analysis. ..
  11. pmc Accurate de novo and transmitted indel detection in exome-capture data using microassembly
    Giuseppe Narzisi
    1 Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA 2 New York Genome Center, New York, USA
    Nat Methods 11:1033-6. 2014
    ..We analyzed 593 families from the Simons Simplex Collection and demonstrated Scalpel's power to detect long (≥30 bp) transmitted events and enrichment for de novo likely gene-disrupting indels in autistic children. ..
  12. pmc SplitMEM: a graphical algorithm for pan-genome analysis with suffix skips
    Shoshana Marcus
    Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA and Department of Computer Science, Stony Brook University, Stony Brook, NY 11794, USA
    Bioinformatics 30:3476-83. 2014
    ..It robustly encodes shared segments, simple single-nucleotide polymorphisms and complex structural variations far beyond what can be represented in a collection of linear sequences alone...