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LETTER: Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis
- Mulu Ayele,
- Brian J. Haas,
- Nikhil Kumar,
- Hank Wu,
- Yongli Xiao,
- Susan Van Aken,
- Teresa R. Utterback,
- Jennifer R. Wortman,
- Owen R. White,
- and Christopher D. Town
Genome Res. April 2005 15: 487-495; doi:10.1101/gr.3176505
...Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis Mulu Ayele 1 , Brian J. Haas , Nikhil Kumar , Hank Wu , Yongli Xiao , Susan Van Aken , Teresa R. Utterback...
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Research: An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication
- Elise Parey,
- Alexandra Louis,
- Jérôme Montfort,
- Yann Guiguen,
- Hugues Roest Crollius,
- and Camille Berthelot
Genome Res. September 2022 32: 1685-1697; Published in Advance August 12, 2022, doi:10.1101/gr.276953.122
...several duplicated chromosomes, contradicting current paradigms that asymmetrical evolution is specific to allopolyploids. Altogether, our results offer novel insights into evolutionary dynamics following ancient polyploidizations in vertebrates.Since the first teleost fish sequence was published in 2002...
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Research: Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia
- Sanchita Bhattacharya,
- Jian Li,
- Alexandra Sockell,
- Matthew J. Kan,
- Felice A. Bava,
- Shann-Ching Chen,
- María C. Ávila-Arcos,
- Xuhuai Ji,
- Emery Smith,
- Narges B. Asadi,
- Ralph S. Lachman,
- Hugo Y.K. Lam,
- Carlos D. Bustamante,
- Atul J. Butte,
- and Garry P. Nolan
Genome Res. April 2018 28: 423-431; Published in Advance March 22, 2018, doi:10.1101/gr.223693.117
..., Kumar P, Hu J, Henikoff S, Schneider G, Ng PC. 2012. SIFT web server: predicting effects of amino acid substitutions on proteins. Nucleic Acids Res 40: W452–W457. ↵Skoglund P, Stora J, Gotherstrom A, Jakobsson M. 2013. Accurate sex identification of ancient human remains using DNA shotgun sequencing. J...
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Resource: Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
- Rei Kajitani,
- Kouta Toshimoto,
- Hideki Noguchi,
- Atsushi Toyoda,
- Yoshitoshi Ogura,
- Miki Okuno,
- Mitsuru Yabana,
- Masayuki Harada,
- Eiji Nagayasu,
- Haruhiko Maruyama,
- Yuji Kohara,
- Asao Fujiyama,
- Tetsuya Hayashi,
- and Takehiko Itoh
Genome Res. August 2014 24: 1384-1395; Published in Advance April 22, 2014, doi:10.1101/gr.170720.113
...been successful in meeting the functional goals of each sequencing project, all are costly compared with a simple whole- shotgun sequencing strategy. Model organisms whose lineages have been maintained in laboratories have long been the main targets of sequencing. However, various wild-type organisms...
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Resource: Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci
- Jonathan M. Mudge,
- Irwin Jungreis,
- Toby Hunt,
- Jose Manuel Gonzalez,
- James C. Wright,
- Mike Kay,
- Claire Davidson,
- Stephen Fitzgerald,
- Ruth Seal,
- Susan Tweedie,
- Liang He,
- Robert M. Waterhouse,
- Yue Li,
- Elspeth Bruford,
- Jyoti S. Choudhary,
- Adam Frankish,
- and Manolis Kellis
Genome Res. December 2019 29: 2073-2087; Published in Advance September 19, 2019, doi:10.1101/gr.246462.118
...experimental characterization.It has been almost two decades since the first high-quality sequences from the human became available (International Human Genome Sequencing Consortium 2001; Venter et al. 2001). Nonetheless, efforts to decipher the information contained in our remain ongoing, and a key challenge...
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Method: Gene discovery by chemical mutagenesis and whole-genome sequencing in Dictyostelium
- Cheng-Lin Frank Li,
- Balaji Santhanam,
- Amanda Nicole Webb,
- Blaž Zupan,
- and Gad Shaulsky
Genome Res. September 2016 26: 1268-1276; Published in Advance June 15, 2016, doi:10.1101/gr.205682.116
...Gene discovery by chemical mutagenesis and whole-genome sequencing in Dictyostelium Cheng-Lin Frank Li 1 , Balaji Santhanam 2 , Amanda Nicole Webb 1 , Blaž Zupan 1 , 3 and Gad Shaulsky 1 1Department of Molecular and Human...
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Method: Detection of long repeat expansions from PCR-free whole-genome sequence data
- Egor Dolzhenko,
- Joke J.F.A. van Vugt,
- Richard J. Shaw,
- Mitchell A. Bekritsky,
- Marka van Blitterswijk,
- Giuseppe Narzisi,
- Subramanian S. Ajay,
- Vani Rajan,
- Bryan R. Lajoie,
- Nathan H. Johnson,
- Zoya Kingsbury,
- Sean J. Humphray,
- Raymond D. Schellevis,
- William J. Brands,
- Matt Baker,
- Rosa Rademakers,
- Maarten Kooyman,
- Gijs H.P. Tazelaar,
- Michael A. van Es,
- Russell McLaughlin,
- William Sproviero,
- Aleksey Shatunov,
- Ashley Jones,
- Ahmad Al Khleifat,
- Alan Pittman,
- Sarah Morgan,
- Orla Hardiman,
- Ammar Al-Chalabi,
- Chris Shaw,
- Bradley Smith,
- Edmund J. Neo,
- Karen Morrison,
- Pamela J. Shaw,
- Catherine Reeves,
- Lara Winterkorn,
- Nancy S. Wexler,
- The US–Venezuela Collaborative Research Group,
- David E. Housman,
- Christopher W. Ng,
- Alina L. Li,
- Ryan J. Taft,
- Leonard H. van den Berg,
- David R. Bentley,
- Jan H. Veldink,
- and Michael A. Eberle
Genome Res. November 2017 27: 1895-1903; Published in Advance September 8, 2017, doi:10.1101/gr.225672.117
...by genotyping them across the population with ExpansionHunter. Methods Whole- sequencing Whole- shotgun sequencing was performed for all of the samples analyzed in this study. For 1231 of the ALS samples, we used TruSeq DNA PCR-free sample preparation with 100 bp paired-end reads sequenced on Illumina Hi...
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Research: C. elegans whole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency
- Bettina Meier,
- Susanna L. Cooke,
- Joerg Weiss,
- Aymeric P. Bailly,
- Ludmil B. Alexandrov,
- John Marshall,
- Keiran Raine,
- Mark Maddison,
- Elizabeth Anderson,
- Michael R. Stratton,
- Anton Gartner,
- and Peter J. Campbell
Genome Res. October 2014 24: 1624-1636; Published in Advance July 16, 2014, doi:10.1101/gr.175547.114
...C. elegans whole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency Bettina Meier 1 , 6 , Susanna L. Cooke 2 , 6 , Joerg Weiss 1 , Aymeric P. Bailly 1 , 3 , Ludmil B. Alexandrov...
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Method: Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing
- Andrew Adey and
- Jay Shendure
Genome Res. June 2012 22: 1139-1143; Published in Advance March 30, 2012, doi:10.1101/gr.136242.111
...shotgun library construction (“tagmentation”) for whole-genome bisulfite sequencing. This method, Tn5mC-seq, enables a &gt;100-fold reduction in starting material relative to conventional protocols, such that we generate highly complex bisulfite sequencing libraries from as little as 10 ng of input DNA...
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Research: Differential retention and divergent resolution of duplicate genes following whole-genome duplication
- Casey L. McGrath,
- Jean-Francois Gout,
- Parul Johri,
- Thomas G. Doak,
- and Michael Lynch
Genome Res. October 2014 24: 1665-1675; Published in Advance August 1, 2014, doi:10.1101/gr.173740.114
...equally to this work. Abstract The Paramecium aurelia complex is a group of 15 species that share at least three past whole-genome duplications (WGDs). The macronuclear genome sequences of P. biaurelia and P. sexaurelia are presented and compared to the published sequence of P...

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