Searching journal content for articles similar to Sandberg et al. 11 (8): 1404.

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  1. Research: Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution
    • Hoon Kim,
    • Siyuan Zheng,
    • Seyed S. Amini,
    • Selene M. Virk,
    • Tom Mikkelsen,
    • Daniel J. Brat,
    • Jonna Grimsby,
    • Carrie Sougnez,
    • Florian Muller,
    • Jian Hu,
    • Andrew E. Sloan,
    • Mark L. Cohen,
    • Erwin G. Van Meir,
    • Lisa Scarpace,
    • Peter W. Laird,
    • John N. Weinstein,
    • Eric S. Lander,
    • Stacey Gabriel,
    • Gad Getz,
    • Matthew Meyerson,
    • Lynda Chin,
    • Jill S. Barnholtz-Sloan,
    • and Roel G.W. Verhaak
    Genome Res. March 2015 25: 316-327; Published in Advance February 3, 2015, doi:10.1101/gr.180612.114
    ...mutations To investigate the clonal architecture of GBM, we classified somatic mutations into clonal and subclonal categories by integrating variant allele fraction, DNA copy number, genotype, and tumor purity (Methods). We used PyClone, a Bayesian clustering method that simultaneously estimates...
  2. Resource: SNP detection for massively parallel whole-genome resequencing
    • Ruiqiang Li,
    • Yingrui Li,
    • Xiaodong Fang,
    • Huanming Yang,
    • Jian Wang,
    • Karsten Kristiansen,
    • and Jun Wang
    Genome Res. June 2009 19: 1124-1132; Published in Advance May 6, 2009, doi:10.1101/gr.088013.108
    ...∼200 CPU hours with a RAM usage of <2 GB. The computing process can also be parallelized by splitting the input data into chromosomes or genomic fragments. Discussion Ultrahigh throughput and the characteristics of short read length make next-generation sequencing technologies particularly suitable...
  3. Method: HIT'nDRIVE: patient-specific multidriver gene prioritization for precision oncology
    • Raunak Shrestha,
    • Ermin Hodzic,
    • Thomas Sauerwald,
    • Phuong Dao,
    • Kendric Wang,
    • Jake Yeung,
    • Shawn Anderson,
    • Fabio Vandin,
    • Gholamreza Haffari,
    • Colin C. Collins,
    • and S. Cenk Sahinalp
    Genome Res. September 2017 27: 1573-1588; Published in Advance July 18, 2017, doi:10.1101/gr.221218.117
    ...and a central target node (i.e., a hub) is usually very short, implying a low hitting time and, thus, high influence of the source node on the target. We also observed negative correlation between a node’s total incoming influence and the median outgoing influence (R =−0.54) (Fig. 3C). Although the central hub...
  4. Methods: Resolving the structural features of genomic islands: A machine learning approach
    • Georgios S. Vernikos and
    • Julian Parkhill
    Genome Res. February 2008 18: 331-342; Published in Advance December 10, 2007, doi:10.1101/gr.7004508
    ...quantifying and modeling the contribution of each feature to the GI structure. Performing a whole-genome-based comparative analysis between 37 strains of three different genera and 12 outgroup genomes, 668 genomic regions were sampled and used to train structural GI models. The data show that, overall, GIs...
  5. Methods: Inferring genomic flux in bacteria
    • Xavier Didelot,
    • Aaron Darling,
    • and Daniel Falush
    Genome Res. February 2009 19: 306-317; Published in Advance November 17, 2008, doi:10.1101/gr.082263.108
    ...molecular processes underlying genomic flux operate without regard to gene boundaries. Short segments within genes, such as protein domains, are often gained or lost ( Spratt 1988 ; Riley and Labedan 1997 ), and intergenic regulatory regions may also be subject to such pressures. Clusters of neighboring...
  6. Research: Shifts in the intensity of purifying selection: An analysis of genome-wide polymorphism data from two closely related yeast species
    • Eyal Elyashiv,
    • Kevin Bullaughey,
    • Shmuel Sattath,
    • Yosef Rinott,
    • Molly Przeworski,
    • and Guy Sella
    Genome Res. November 2010 20: 1558-1573; Published in Advance September 4, 2010, doi:10.1101/gr.108993.110
    ...and species? How uniform are the shifts in selective pressures across the genome? To address these questions, we took advantage of a recent, whole-genome polymorphism data set from two closely related species of yeast, Saccharomyces cerevisiae and S. paradoxus , paying close attention to the population...
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