Michael C Schatz
Affiliation: Cold Spring Harbor Laboratory
- The rise of a digital immune systemMichael C Schatz
Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
Gigascience 1:4. 2012....
- Hawkeye and AMOS: visualizing and assessing the quality of genome assembliesMichael 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...
- Current challenges in de novo plant genome sequencing and assemblyMichael 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...
- Quake: quality-aware detection and correction of sequencing errorsDavid 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...
- The missing graphical user interface for genomicsMichael 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...
- Indel variant analysis of short-read sequencing data with ScalpelHan Fang
Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
Nat Protoc 11:2529-2548. 2016..Using a standard server, indel discovery and characterization in the exonic regions of the example sequencing data can be completed in ∼5 h after read mapping...
- Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability scoreHayan 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...
- Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genomeSara Goodwin
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
Genome Res 25:1750-6. 2015....
- Genotyping in the cloud with CrossbowJames Gurtowski
Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
Curr Protoc Bioinformatics . 2012....
- TGF-β reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24- cancer cellsDebjani Pal
Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
elife 6:. 2017..Together, these data suggest that the transition into a CD44+/CD24- cell state can promote intra-tumor genetic heterogeneity, spur tumor evolution and increase tumor fitness...
- Dual functions of Macpiwi1 in transposon silencing and stem cell maintenance in the flatworm Macrostomum lignanoXin 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. ..
- Interactive analysis and assessment of single-cell copy-number variationsTyler 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. ..
- Accurate de novo and transmitted indel detection in exome-capture data using microassemblyGiuseppe 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. ..
- SplitMEM: a graphical algorithm for pan-genome analysis with suffix skipsShoshana 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...