Searching journal content for articles similar to Dubchak et al. 19 (4): 682.

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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
..., Faculty of Biosciences, Norwegian University of Life Sciences, 1432 Ås, Norway; 2Aquaculture Programme, Commonwealth Scientific and Industrial Research Organisation, St. Lucia, Queensland 4067, Australia; 3School of Biological Sciences–Organisms and the Environment, University of East Anglia, NR4 7TU...
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Method: Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples
- Shuangxi Ji,
- Tong Zhu,
- Ankit Sethia,
- and Wenyi Wang
Genome Res. April 2024 34: 633-641; Published in Advance April 8, 2024, doi:10.1101/gr.278456.123
...in multiple pipelines, including as a major contributing caller to reach final consensus calls by The Cancer Genome Atlas (TCGA) PanCanAtlas project ( Ellrott et al. 2018 ), across approximately 13,000 tumor samples, and the International Cancer Genome Consortium Pan-Cancer Analysis of Whole Genomes (ICGC...
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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
...), with the following parameters “-seg no -max_hsps 1 -use_sw_tback -evalue 1e-5”. We then performed clustering with hcluster_sg to define gene families, using parameters “-m 750 -w 0 -s 0.34 –O”. We built multiple alignments using M-Coffee (Wallace et al. 2006), with the command “t-coffee -type = PROTEIN -method...
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Method: Whole-genome bisulfite sequencing with improved accuracy and cost
- Masako Suzuki,
- Will Liao,
- Frank Wos,
- Andrew D. Johnston,
- Justin DeGrazia,
- Jennifer Ishii,
- Toby Bloom,
- Michael C. Zody,
- Soren Germer,
- and John M. Greally
Genome Res. September 2018 28: 1364-1371; Published in Advance August 9, 2018, doi:10.1101/gr.232587.117
...bisulfite conversion, short-read alignment to the Homo sapiens (GRCh37/hg19) reference was performed with bwa-meth with R2 reads mapped as a typical C>T converted R1 read and R1 reads mapped as a standard G>A converted read (Pedersen et al. 2014) (bwameth.py –prefix <OUTPUT PREFIX> --threads <N> --reference...
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Method: TraDIS-Xpress: a high-resolution whole-genome assay identifies novel mechanisms of triclosan action and resistance
- Muhammad Yasir,
- A. Keith Turner,
- Sarah Bastkowski,
- David Baker,
- Andrew J. Page,
- Andrea Telatin,
- Minh-Duy Phan,
- Leigh Monahan,
- George M. Savva,
- Aaron Darling,
- Mark A. Webber,
- and Ian G. Charles
Genome Res. February 2020 30: 239-249; Published in Advance February 12, 2020, doi:10.1101/gr.254391.119
...) toolkits. Bio-TraDIS was used to align sequence reads (using SMALT version 0.7.4) to the reference and to create insertion plots. To identify gene essentiality for the different conditions, genes that have very few or no insertions are identified. Within the Bio-TraDIS toolkit (tradis...
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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
...of the hg38/GRCh38 human reference assembly in each of the six reading frames using alignments of 29 mammalian s. Each codon gets a positive score if the alignment of that codon is more likely to have arisen under a model of protein-coding evolution than under a model of noncoding evolution. Because...
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Research: Whole-genome sequencing reveals high complexity of copy number variation at insecticide resistance loci in malaria mosquitoes
- Eric R. Lucas,
- Alistair Miles,
- Nicholas J. Harding,
- Chris S. Clarkson,
- Mara K.N. Lawniczak,
- Dominic P. Kwiatkowski,
- David Weetman,
- Martin J. Donnelly,
- and The Anopheles gambiae 1000 Genomes Consortium
Genome Res. August 2019 29: 1250-1261; Published in Advance July 25, 2019, doi:10.1101/gr.245795.118
...pairs (A–C) and breakpoint reads (D) were used to identify different CNV alleles. (A) In tandem duplications, read pairs derived from segments spanning the CNV breakpoint (red arrows) align facing away from each other around the breakpoint on the reference (dark blue arrows). (B) In tandem inversions...
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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
...-throughput WGS technologies are currently limited to ∼150 base pair (bp) read lengths, variantcallingmethods that rely on reads aligned to the reference are subsequently limited to repeat lengths less than 150 bases (Narzisi and Schatz 2015). Many pathogenic repeat expansions have repeats spanning hundreds...
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Method: Detection of structural mosaicism from targeted and whole-genome sequencing data
- Daniel A. King,
- Alejandro Sifrim,
- Tomas W. Fitzgerald,
- Raheleh Rahbari,
- Emma Hobson,
- Tessa Homfray,
- Sahar Mansour,
- Sarju G. Mehta,
- Mohammed Shehla,
- Susan E. Tomkins,
- Pradeep C. Vasudevan,
- Matthew E. Hurles,
- and The Deciphering Developmental Disorders Study
Genome Res. October 2017 27: 1704-1714; Published in Advance August 30, 2017, doi:10.1101/gr.212373.116
...material is available for this article.] Genetic mutations that arise post-zygotically lead to genetic heterogeneity in an organism, a phenomenon called mosaicism. The detection of mosaic mutations that are small (single-base or indel) is still a great technical challenge, but can be achieved in specific...
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Research: A comparative analysis of whole genome sequencing of esophageal adenocarcinoma pre- and post-chemotherapy
- Ayesha Noorani,
- Jan Bornschein,
- Andy G. Lynch,
- Maria Secrier,
- Achilleas Achilleos,
- Matthew Eldridge,
- Lawrence Bower,
- Jamie M.J. Weaver,
- Jason Crawte,
- Chin-Ann Ong,
- Nicholas Shannon,
- Shona MacRae,
- Nicola Grehan,
- Barbara Nutzinger,
- Maria O'Donovan,
- Richard Hardwick,
- Simon Tavaré,
- Rebecca C. Fitzgerald,
- and on behalf of the Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium
Genome Res. June 2017 27: 902-912; Published in Advance May 2, 2017, doi:10.1101/gr.214296.116
...and size of pretreatment endoscopic samples are limiting. This study compares whole- sequencing data obtained from chemo-naive and chemo-treated samples. The quality of whole-genomic sequencing data is comparable across all samples regardless of chemotherapy status. Inclusion of samples collected post...
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