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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
...://doi.org/10.5281/zenodo.5776772).Phylogenetic gene treesInitial gene trees were built using the Ensembl Compara pipeline (Vilella et al. 2009). Briefly, starting from the sets of proteins derived from the longest transcripts in each , we performed an all-against-all BLASTP+ (Altschul et al. 1990...
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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
...) and 6903 (total reads: 390 Gbp) against the size were produced to assemble the fosmids, respectively. In addition, whole- shotgun reads were separately produced, and these data were also used in those projects. Therefore, if highly heterozygous s could be assembled from whole- shotgun data alone, the cost...
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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
...annotation pipelines (Mudge and Harrow 2016), and this problem is confounded by the fact that 28 of these 50 loci are single-exon genes. It is also probable that protein size thwarted our proteogenomics pipeline (see below), as small proteins may be harder to identify in “shotgun” mass spectrometry...
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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
...-quality reads from the instrument, or insufficient data to allow alignment against the human reference standard. Because of low coverage limitations, we applied strict filtering criteria to ensure high-quality data for downstream processing. The human origin of the specimen was further confirmed by aligning...
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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
...of the C9orf72 repeat expansion with repeat-primed PCR (RP-PCR). Compared against this truth data, ExpansionHunter correctly classified all (212/212, 95%CI [0.98, 1.00]) of the expanded samples as either expansions (208) or potential expansions (4). Additionally, 99.9% (2786/2789, 95% CI [0.997, 1...
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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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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
...Differential retention and divergent resolution of duplicate genes following whole-genome duplication Casey L. McGrath 1 , 3 , Jean-Francois Gout 1 , 3 , Parul Johri 1 , Thomas G. Doak 1 , 2 and Michael Lynch 1...
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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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METHODS: ARACHNE: A Whole-Genome Shotgun Assembler
- Serafim Batzoglou,
- David B. Jaffe,
- Ken Stanley,
- Jonathan Butler,
- Sante Gnerre,
- Evan Mauceli,
- Bonnie Berger,
- Jill P. Mesirov,
- and Eric S. Lander
Genome Res. January 1, 2002 12: 177-189; doi:10.1101/gr.208902
...ARACHNE: A Whole-Genome Shotgun Assembler Serafim Batzoglou 1 , 2 , 3 , David B. Jaffe 2 , 3 , 4 , Ken Stanley 2 , Jonathan Butler 2 , Sante Gnerre 2 , Evan Mauceli 2 , Bonnie Berger 1 , 5 , Jill P. Mesirov...
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Method: Sequence-based physical mapping of complex genomes by whole genome profiling
- Jan van Oeveren,
- Marjo de Ruiter,
- Taco Jesse,
- Hein van der Poel,
- Jifeng Tang,
- Feyruz Yalcin,
- Antoine Janssen,
- Hanne Volpin,
- Keith E. Stormo,
- Robert Bogden,
- Michiel J.T. van Eijk,
- and Marcel Prins
Genome Res. April 2011 21: 618-625; Published in Advance February 1, 2011, doi:10.1101/gr.112094.110
...Sequence-based physical mapping of complex genomes by whole genome profiling Jan van Oeveren 1 , Marjo de Ruiter 1 , Taco Jesse 1 , Hein van der Poel 1 , Jifeng Tang 1 , Feyruz Yalcin 1 , Antoine Janssen 1 , Hanne...

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