Publications by authors named "Karen H Miga"

24Publications

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads.

Genome Res 2020 Sep 14;30(9):1291-1305. Epub 2020 Aug 14.

Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20894, USA.

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http://dx.doi.org/10.1101/gr.263566.120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7545148PMC
September 2020

TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats.

Bioinformatics 2020 Jul;36(Supplement_1):i75-i83

Department of Computer Science and Engineering, University of California, San Diego, CA 92093, USA.

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http://dx.doi.org/10.1093/bioinformatics/btaa440DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7355294PMC
July 2020

Centromere studies in the era of 'telomere-to-telomere' genomics.

Authors:
Karen H Miga

Exp Cell Res 2020 Sep 3;394(2):112127. Epub 2020 Jun 3.

UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, CA, 95064, USA. Electronic address:

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http://dx.doi.org/10.1016/j.yexcr.2020.112127DOI Listing
September 2020

Human Artificial Chromosomes that Bypass Centromeric DNA.

Cell 2019 07;178(3):624-639.e19

Department of Biochemistry and Biophysics, Graduate Program in Biochemistry and Molecular Biophysics, and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.06.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6657561PMC
July 2019

Haplotypes spanning centromeric regions reveal persistence of large blocks of archaic DNA.

Elife 2019 06 25;8. Epub 2019 Jun 25.

Department of Evolution and Ecology, University of California, Davis, Davis, United States.

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http://dx.doi.org/10.7554/eLife.42989DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6592686PMC
June 2019

DNA replication acts as an error correction mechanism to maintain centromere identity by restricting CENP-A to centromeres.

Nat Cell Biol 2019 06 3;21(6):743-754. Epub 2019 Jun 3.

Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/s41556-019-0331-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7015266PMC
June 2019

Centromeric Satellite DNAs: Hidden Sequence Variation in the Human Population.

Authors:
Karen H Miga

Genes (Basel) 2019 05 8;10(5). Epub 2019 May 8.

UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California, CA 95064, USA.

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http://dx.doi.org/10.3390/genes10050352DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6562703PMC
May 2019

Heterochromatin-Encoded Satellite RNAs Induce Breast Cancer.

Mol Cell 2018 06 31;70(5):842-853.e7. Epub 2018 May 31.

Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2018.04.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6545586PMC
June 2018

Linear assembly of a human centromere on the Y chromosome.

Nat Biotechnol 2018 04 19;36(4):321-323. Epub 2018 Mar 19.

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

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http://dx.doi.org/10.1038/nbt.4109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5886786PMC
April 2018

The Promises and Challenges of Genomic Studies of Human Centromeres.

Authors:
Karen H Miga

Prog Mol Subcell Biol 2017;56:285-304

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

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http://dx.doi.org/10.1007/978-3-319-58592-5_12DOI Listing
May 2019

Human centromeric CENP-A chromatin is a homotypic, octameric nucleosome at all cell cycle points.

J Cell Biol 2017 03 24;216(3):607-621. Epub 2017 Feb 24.

Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093

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http://dx.doi.org/10.1083/jcb.201608083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5350519PMC
March 2017

Chromosome-Specific Centromere Sequences Provide an Estimate of the Ancestral Chromosome 2 Fusion Event in Hominin Genomes.

Authors:
Karen H Miga

J Hered 2017 01 16;108(1):45-52. Epub 2016 Jul 16.

From the Center for Biomolecular Science and Engineering, University of California, 501 Engineering 2 Building, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064.

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http://dx.doi.org/10.1093/jhered/esw039DOI Listing
January 2017

Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing.

Bioinformatics 2016 07 24;32(13):1921-1924. Epub 2016 Feb 24.

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

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http://dx.doi.org/10.1093/bioinformatics/btw101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4920115PMC
July 2016

Completing the human genome: the progress and challenge of satellite DNA assembly.

Authors:
Karen H Miga

Chromosome Res 2015 Sep;23(3):421-6

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

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http://dx.doi.org/10.1007/s10577-015-9488-2DOI Listing
September 2015

Utilizing mapping targets of sequences underrepresented in the reference assembly to reduce false positive alignments.

Nucleic Acids Res 2015 Nov 10;43(20):e133. Epub 2015 Jul 10.

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

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkv671DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4787761PMC
November 2015

Improved data analysis for the MinION nanopore sequencer.

Nat Methods 2015 Apr 16;12(4):351-6. Epub 2015 Feb 16.

1] UC Santa Cruz Genomics Institute, Santa Cruz, California, USA. [2] Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA.

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http://dx.doi.org/10.1038/nmeth.3290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907500PMC
April 2015

Replication of alpha-satellite DNA arrays in endogenous human centromeric regions and in human artificial chromosome.

Nucleic Acids Res 2014 Oct 16;42(18):11502-16. Epub 2014 Sep 16.

Developmental Therapeutics Branch, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA.

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http://dx.doi.org/10.1093/nar/gku835DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4191410PMC
October 2014

Genomic characterization of large heterochromatic gaps in the human genome assembly.

PLoS Comput Biol 2014 May 15;10(5):e1003628. Epub 2014 May 15.

Genome Biology Group, Duke Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003628DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4022460PMC
May 2014

Centromere reference models for human chromosomes X and Y satellite arrays.

Genome Res 2014 Apr 5;24(4):697-707. Epub 2014 Feb 5.

Duke Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27708, USA;

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http://dx.doi.org/10.1101/gr.159624.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3975068PMC
April 2014