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Method: Combining DNA and protein alignments to improve genome annotation with LiftOn

Kuan-Hao Chao,
Jakob M. Heinz,
Celine Hoh,
Alan Mao,
Alaina Shumate,
Mihaela Pertea,
and Steven L. Salzberg

Genome Res. February 2025 35: 311-325; Published in Advance December 27, 2024, doi:10.1101/gr.279620.124

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Method: Effects of transcriptional noise on estimates of gene and transcript expression in RNA sequencing experiments

Ales Varabyou,
Steven L. Salzberg,
and Mihaela Pertea

Genome Res. February 2021 31: 301-308; Published in Advance December 23, 2020, doi:10.1101/gr.266213.120

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Research: Human contamination in bacterial genomes has created thousands of spurious proteins

Florian P. Breitwieser,
Mihaela Pertea,
Aleksey V. Zimin,
and Steven L. Salzberg

Genome Res. June 2019 29: 954-960; Published in Advance May 7, 2019, doi:10.1101/gr.245373.118

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Method: Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm

Aleksey V. Zimin,
Daniela Puiu,
Ming-Cheng Luo,
Tingting Zhu,
Sergey Koren,
Guillaume Marçais,
James A. Yorke,
Jan Dvořák,
and Steven L. Salzberg

Genome Res. May 2017 27: 787-792; Published in Advance January 27, 2017, doi:10.1101/gr.213405.116

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Method: Centrifuge: rapid and sensitive classification of metagenomic sequences

Daehwan Kim,
Li Song,
Florian P. Breitwieser,
and Steven L. Salzberg

Genome Res. December 2016 26: 1721-1729; Published in Advance October 17, 2016, doi:10.1101/gr.210641.116

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Resource: Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms

Tsung-Cheng Chang,
Mihaela Pertea,
Sungyul Lee,
Steven L. Salzberg,
and Joshua T. Mendell

Genome Res. September 2015 25: 1401-1409; Published in Advance August 19, 2015, doi:10.1101/gr.193607.115

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Resource: GAGE: A critical evaluation of genome assemblies and assembly algorithms

Steven L. Salzberg,
Adam M. Phillippy,
Aleksey Zimin,
Daniela Puiu,
Tanja Magoc,
Sergey Koren,
Todd J. Treangen,
Michael C. Schatz,
Arthur L. Delcher,
Michael Roberts,
Guillaume Marçais,
Mihai Pop,
and James A. Yorke

Genome Res. March 2012 22: 557-567; Published in Advance December 6, 2011, doi:10.1101/gr.131383.111

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Perspective: Assembly of large genomes using second-generation sequencing

Michael C. Schatz,
Arthur L. Delcher,
and Steven L. Salzberg

Genome Res. September 2010 20: 1165-1173; Published in Advance May 27, 2010, doi:10.1101/gr.101360.109

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Methods: Computational Gene Prediction Using Multiple Sources of Evidence

Jonathan E. Allen,
Mihaela Pertea,
and Steven L. Salzberg

Genome Res. January 2004 14: 142-148; doi:10.1101/gr.1562804

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Methods: Hierarchical Scaffolding With Bambus

Mihai Pop,
Daniel S. Kosack,
and Steven L. Salzberg

Genome Res. January 2004 14: 149-159; doi:10.1101/gr.1536204

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