Author

James Gurtowski

Cold Spring Harbor Laboratory

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 5 Genomics· 2

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Research Focus:genome assembly· 5 Assay:whole-genome sequencing· 5 Approach:statistical model· 4 Research Focus:variant calling· 4 Approach:experimental assay· 3 Assay:long-read sequencing· 3 Organism:human· 2 Organism:multiple species· 2

Frequent Co-Authors

Hayan Lee· 3 shared Michael C. SchatziD· 3 shared Doreen WareiD· 2 shared Fritz Joachim SedlazeckiD· 2 shared Han FangiD· 2 shared Jer-Ming Chia· 2 shared Maria NattestadiD· 2 shared Melissa KrameriD· 2 shared

Activity by Year

2014-2018 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 25 mutual co-author links

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3 shared papersBioinformatics

Hayan Lee

Mutual co-authors in cluster

Author profile →

7 papers

Recent·Most cited

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line

Maria Nattestad, Sara Goodwin, Karen Ng, Timour Baslan, Fritz Joachim Sedlazeck, Philipp Rescheneder, Tyler H. Garvin, Han Fang, James Gurtowski, Elizabeth Hutton, Elizabeth Tseng, Chen-Shan Chin, Tim Beck, Yogi Sundaravadanam, Melissa Kramer, , Michael C. Schatz

The paper uses long-read sequencing to analyze structural variations in the SK-BR-3 breast cancer cell line, revealing complex rearrangements and novel gene fusions.

Genome Research · Aug 1, 2018Peer-reviewedGenomics

The DOE Systems Biology Knowledgebase (KBase)

Adam P. Arkin, Robert W. Cottingham, Christopher S. Henry, Nomi L. Harris, Rick L. Stevens, Sergei Maslov, Paramvir Dehal, Doreen Ware, Fernando Pérez, Richard Shane Canon, Michael W. Sneddon, Matthew L Henderson, William J. Riehl, Dan Murphy-Olson, Stephen Y. Chan, , Dantong Yu

Open-source KBase platform unites reference genomes and biochemistry, over 70 apps, Jupyter-based Narratives with provenance, and a Docker SDK for reproducible plant and microbial systems biology.

Nature Biotechnology · Jul 1, 2018Peer-reviewedBioinformatics✦ In-depth digest

GenomeScope: Fast reference-free genome profiling from short reads

Gregory W. Vurture, Fritz Joachim Sedlazeck, Maria Nattestad, Charles J. Underwood, Han Fang, James Gurtowski, Michael C. Schatz

GenomeScope estimates genome size, heterozygosity, and repeat content from short reads to aid in genome analysis parameter selection.

Bioinformatics · Mar 17, 2017Peer-reviewedBioinformatics

Third-generation sequencing and the future of genomics

Hayan Lee, James Gurtowski, Shinjae Yoo, Maria Nattestad, Shoshana Marcus, Sara Goodwin, W. Richard McCombie, Michael C. Schatz

This paper discusses third-generation sequencing technologies and their potential to improve genome assembly, structural variation analysis, and haplotype phasing.

bioRxiv · Apr 13, 2016 · PreprintBioinformatics

Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome

Sara Goodwin, James Gurtowski, Scott Ethe-Sayers, Panchajanya Deshpande, Michael Schatz, W Richard McCombie

The paper develops a hybrid error correction method for Oxford Nanopore reads and produces a highly contiguous and accurate de novo assembly of the S. cerevisiae genome.

Genome Research · Oct 7, 2015Peer-reviewedBioinformatics

Error correction and assembly complexity of single molecule sequencing reads.

Hayan Lee, James Gurtowski, Shinjae Yoo, Shoshana Marcus, W. Richard McCombie, Michael Schatz

This paper evaluates the impact of long-read sequencing on genome assembly across multiple species and introduces a new error correction algorithm and predictive model.

bioRxiv · Jun 18, 2014 · PreprintBioinformatics

New whole genome de novo assemblies of three divergent strains of rice (O. sativa) documents novel gene space of aus and indica

Michael C Schatz, Lyza G Maron, Joshua C Stein, Alejandro Hernandez Wences, James Gurtowski, Eric Biggers, Hayan Lee, Melissa Kramer, Eric Antonio, Elena Ghiban, Mark H Wright, Jer-ming Chia, Doreen Ware, Susan R McCouch, William Richard McCombie

The paper presents de novo genome assemblies of three rice strains, revealing novel gene spaces and structural variations not captured by reference-based resequencing.

bioRxiv · Apr 2, 2014Genomics