Publications by authors named "Glenn Hickey"

20Publications

Pangenome Graphs.

Annu Rev Genomics Hum Genet 2020 Aug 26;21:139-162. Epub 2020 May 26.

Genomics Institute, University of California, Santa Cruz, California 95064, USA; email:

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http://dx.doi.org/10.1146/annurev-genom-120219-080406DOI Listing
August 2020

Genotyping structural variants in pangenome graphs using the vg toolkit.

Genome Biol 2020 02 12;21(1):35. Epub 2020 Feb 12.

UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California, USA.

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http://dx.doi.org/10.1186/s13059-020-1941-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7017486PMC
February 2020

Sequence tube maps: making graph genomes intuitive to commuters.

Bioinformatics 2019 12;35(24):5318-5320

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1093/bioinformatics/btz597DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6954646PMC
December 2019

Superbubbles, Ultrabubbles, and Cacti.

J Comput Biol 2018 07 20;25(7):649-663. Epub 2018 Feb 20.

1 UC Santa Cruz Genomics Institute, University of California Santa Cruz , Santa Cruz, California.

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http://www.liebertpub.com/doi/10.1089/cmb.2017.0251
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http://dx.doi.org/10.1089/cmb.2017.0251DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6067107PMC
July 2018

Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs.

BMC Bioinformatics 2016 Sep 29;17(1):400. Epub 2016 Sep 29.

Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, 95064, CA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5043639PMC
http://dx.doi.org/10.1186/s12859-016-1258-4DOI Listing
September 2016

A call for benchmarking transposable element annotation methods.

Mob DNA 2015 4;6:13. Epub 2015 Aug 4.

School of Computer Science, McGill University, McConnell Engineering Bldg., Rm. 318, 3480 Rue University, Montréal, Québec H3A 0E9 Canada ; McGill Centre for Bioinformatics, McGill University, Montréal, Québec Canada.

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http://dx.doi.org/10.1186/s13100-015-0044-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4524446PMC
August 2015

Building a pan-genome reference for a population.

J Comput Biol 2015 May 7;22(5):387-401. Epub 2015 Jan 7.

1 Center for Biomolecular Science and Engineering, University of California , Santa Cruz, California.

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http://dx.doi.org/10.1089/cmb.2014.0146DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4424974PMC
May 2015

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

Science 2014 Dec 11;346(6215):1254449. Epub 2014 Dec 11.

Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA.

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http://jarvislab.net/wp-content/uploads/2012/02/Green-et-al-
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http://www.sciencemag.org/cgi/doi/10.1126/science.1254449
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http://dx.doi.org/10.1126/science.1254449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386873PMC
December 2014

Alignathon: a competitive assessment of whole-genome alignment methods.

Genome Res 2014 Dec 1;24(12):2077-89. Epub 2014 Oct 1.

Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA; Biomolecular Engineering Department, University of California Santa Cruz, Santa Cruz, California 95064, USA;

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http://dx.doi.org/10.1101/gr.174920.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248324PMC
December 2014

Comparative assembly hubs: web-accessible browsers for comparative genomics.

Bioinformatics 2014 Dec 18;30(23):3293-301. Epub 2014 Aug 18.

Center for Biomolecular Sciences and Engineering, CBSE/ITI, UC Santa Cruz, 1156 High St, Santa Cruz, CA 95064, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu534DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296145PMC
December 2014

A unifying model of genome evolution under parsimony.

BMC Bioinformatics 2014 Jun 19;15:206. Epub 2014 Jun 19.

University of California, Santa Cruz, 1156 High St, 95064 Santa Cruz, USA.

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http://dx.doi.org/10.1186/1471-2105-15-206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4082375PMC
June 2014

HAL: a hierarchical format for storing and analyzing multiple genome alignments.

Bioinformatics 2013 May 16;29(10):1341-2. Epub 2013 Mar 16.

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

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http://dx.doi.org/10.1093/bioinformatics/btt128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654707PMC
May 2013

A probabilistic model for sequence alignment with context-sensitive indels.

J Comput Biol 2011 Nov 27;18(11):1449-64. Epub 2011 Sep 27.

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

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http://dx.doi.org/10.1089/cmb.2011.0157DOI Listing
November 2011

An approximation algorithm for the Noah's Ark problem with random feature loss.

IEEE/ACM Trans Comput Biol Bioinform 2011 Mar-Apr;8(2):551-6

School of Computer Science,McGill University, 3480 University Street, McConnell Engineering Building, Room 318, Montreal, QC H3A 2A7, Canada.

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https://www.computer.org/csdl/trans/tb/2011/02/ttb2011020551
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http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumbe
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http://dx.doi.org/10.1109/TCBB.2010.37DOI Listing
June 2011

A practical algorithm for estimation of the maximum likelihood ancestral reconstruction error.

Pac Symp Biocomput 2010 :31-42

McGill Centre for Bioinformatics and School of Computer Science, McGill University, 3480 University St., Montréal, Québec, H3A 2B4, Canada.

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http://dx.doi.org/10.1142/9789814295291_0005DOI Listing
November 2013

SPR distance computation for unrooted trees.

Evol Bioinform Online 2008 Feb 9;4:17-27. Epub 2008 Feb 9.

School of Computer Science, Carleton University, Ottawa, Canada K1S 5B6.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614206PMC
http://dx.doi.org/10.4137/ebo.s419DOI Listing
February 2008