Publications by authors named "Kyle Ellrott"

44Publications

Exploring Integrative Analysis Using the BioMedical Evidence Graph.

JCO Clin Cancer Inform 2020 02;4:147-159

Biomedical Engineering, Oregon Health and Science University, Portland OR.

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http://dx.doi.org/10.1200/CCI.19.00110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7049249PMC
February 2020

neoepiscope improves neoepitope prediction with multivariant phasing.

Bioinformatics 2020 02;36(3):713-720

Computational Biology Program, Oregon Health & Science University, Portland, OR 97201, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz653DOI Listing
February 2020

Germline contamination and leakage in whole genome somatic single nucleotide variant detection.

BMC Bioinformatics 2018 01 31;19(1):28. Epub 2018 Jan 31.

Informatics & Biocomputing Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, M5G 0A3, Canada.

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https://bmcbioinformatics.biomedcentral.com/articles/10.1186
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http://dx.doi.org/10.1186/s12859-018-2046-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5793408PMC
January 2018

Prophetic Granger Causality to infer gene regulatory networks.

PLoS One 2017 6;12(12):e0170340. Epub 2017 Dec 6.

University of California Santa Cruz, Department of Biomolecular Engineering, Santa Cruz, CA, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170340PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5718405PMC
January 2018

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.

Nat Methods 2015 Jul 18;12(7):623-30. Epub 2015 May 18.

1] Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada. [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. [3] Department of Pharmacology &Toxicology, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/nmeth.3407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4856034PMC
July 2015

The Cancer Genome Atlas Pan-Cancer analysis project.

Nat Genet 2013 Oct;45(10):1113-20

Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.

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http://dx.doi.org/10.1038/ng.2764DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3919969PMC
October 2013

The UCSC Cancer Genomics Browser: update 2013.

Nucleic Acids Res 2013 Jan 29;41(Database issue):D949-54. Epub 2012 Oct 29.

Center for Biomolecular Science and Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/nar/gks1008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531186PMC
January 2013

TOPSAN: a dynamic web database for structural genomics.

Nucleic Acids Res 2011 Jan 20;39(Database issue):D494-6. Epub 2010 Oct 20.

Joint Center for Structural Genomics, Bioinformatics Core, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1093/nar/gkq902DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013775PMC
January 2011

Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families.

PLoS Comput Biol 2010 Jun 3;6(6):e1000798. Epub 2010 Jun 3.

Joint Center for Structural Genomics, Bioinformatics Core, University of California San Diego, La Jolla, California, USA.

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https://dx.plos.org/10.1371/journal.pcbi.1000798
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http://dx.doi.org/10.1371/journal.pcbi.1000798DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880560PMC
June 2010

Improving the performance of protein threading using insertion/deletion frequency arrays.

J Bioinform Comput Biol 2008 Jun;6(3):585-602

Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.1142/s0219720008003552DOI Listing
June 2008

A historical perspective of template-based protein structure prediction.

Methods Mol Biol 2008 ;413:3-42

Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.

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http://dx.doi.org/10.1007/978-1-59745-574-9_1DOI Listing
June 2008

Improvement in protein sequence-structure alignment using insertion/deletion frequency arrays.

Comput Syst Bioinformatics Conf 2007 ;6:335-42

Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, The University of Georgia, Athens, Georgia 30602, USA.

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December 2007

A generalized threading model using integer programming that allows for secondary structure element deletion.

Genome Inform 2006 ;17(2):248-58

Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30622, USA.

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June 2007

PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W522-5

Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30606, USA.

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http://dx.doi.org/10.1093/nar/gkh414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441552PMC
July 2004

PROSPECT II: protein structure prediction program for genome-scale applications.

Protein Eng 2003 Sep;16(9):641-50

Protein Informatics Group, Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6480, USA.

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http://dx.doi.org/10.1093/protein/gzg081DOI Listing
September 2003

Restriction enzyme recognition sequence search program.

Biotechniques 2002 Dec;33(6):1322-6

University of California, Riverside, Riverside, CA, USA.

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https://www.future-science.com/doi/10.2144/02336bc02
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http://dx.doi.org/10.2144/02336bc02DOI Listing
December 2002

Identifying transcription factor binding sites through Markov chain optimization.

Bioinformatics 2002 ;18 Suppl 2:S100-9

Department of Computer Science, University of California, Riverside, 92521, USA.

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http://dx.doi.org/10.1093/bioinformatics/18.suppl_2.s100DOI Listing
September 2005