Geo Pertea

Geo Pertea

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Geo Pertea

Geo Pertea

Publications by authors named "Geo Pertea"

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23Publications

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Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing.

PLoS Genet 2020 Jan 27;16(1):e1008571. Epub 2020 Jan 27.

Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1008571DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7004385PMC
January 2020

Transcriptome assembly from long-read RNA-seq alignments with StringTie2.

Genome Biol 2019 12 16;20(1):278. Epub 2019 Dec 16.

Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA.

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http://dx.doi.org/10.1186/s13059-019-1910-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6912988PMC
December 2019

CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise.

Genome Biol 2018 11 28;19(1):208. Epub 2018 Nov 28.

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

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http://dx.doi.org/10.1186/s13059-018-1590-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6260756PMC
November 2018

First Draft Genome Sequence of the Pathogenic Fungus (Formerly ).

G3 (Bethesda) 2017 11 6;7(11):3831-3836. Epub 2017 Nov 6.

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205

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http://dx.doi.org/10.1534/g3.117.300107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5677167PMC
November 2017

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.

Nat Protoc 2016 09 11;11(9):1650-67. Epub 2016 Aug 11.

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA.

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http://www.ccb.jhu.edu/people/infphilo/data/nprot.2016.095.p
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http://dx.doi.org/10.1038/nprot.2016.095DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5032908PMC
September 2016

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.

Nat Biotechnol 2015 Mar 18;33(3):290-5. Epub 2015 Feb 18.

1] Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA. [2] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA. [3] Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA. [4] Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1038/nbt.3122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4643835PMC
March 2015

Ballgown bridges the gap between transcriptome assembly and expression analysis.

Nat Biotechnol 2015 Mar;33(3):243-6

1] Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA. [2] Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1038/nbt.3172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4792117PMC
March 2015

Detection of lineage-specific evolutionary changes among primate species.

BMC Bioinformatics 2011 Jul 4;12:274. Epub 2011 Jul 4.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.

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http://dx.doi.org/10.1186/1471-2105-12-274DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3143108PMC
July 2011

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.

PLoS Biol 2010 Sep 7;8(9). Epub 2010 Sep 7.

Avian Immunobiology Laboratory, Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1000475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935454PMC
September 2010

Global comparative analysis of ESTs from the southern cattle tick, Rhipicephalus (Boophilus) microplus.

BMC Genomics 2007 Oct 12;8:368. Epub 2007 Oct 12.

Lorus Therapeutics Inc; 2 Meridian Road, Toronto, ON M9W 4Z7, Canada.

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http://dx.doi.org/10.1186/1471-2164-8-368DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2100071PMC
October 2007

The TIGR Maize Database.

Nucleic Acids Res 2006 Jan;34(Database issue):D771-6

The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.

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http://dx.doi.org/10.1093/nar/gkj072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347435PMC
January 2006

Porcine gene discovery by normalized cDNA-library sequencing and EST cluster assembly.

Mamm Genome 2002 Aug;13(8):475-8

USDA, ARS, U.S. Meat Animal Research Center, P.O. Box 166, Clay Center, Nebraska 68933, USA.

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http://dx.doi.org/10.1007/s00335-001-2072-4DOI Listing
August 2002