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  1. Article

    Open Access

    BreakTrans: uncovering the genomic architecture of gene fusions

    Producing gene fusions through genomic structural rearrangements is a major mechanism for tumor evolution. Therefore, accurately detecting gene fusions and the originating rearrangements is of great importance...

    Ken Chen, Nicholas E Navin, Yong Wang, Heather K Schmidt, John W Wallis… in Genome Biology (2013)

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  2. Article

    Open Access

    Whole-genome analysis informs breast cancer response to aromatase inhibition

    To correlate the variable clinical features of oestrogen-receptor-positive breast cancer with somatic alterations, we studied pretreatment tumour biopsies accrued from patients in two studies of neoadjuvant ar...

    Matthew J. Ellis, Li Ding, Dong Shen, **gqin Luo, Vera J. Suman, John W. Wallis… in Nature (2012)

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  3. Article

    Open Access

    Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing

    The sequencing of AML genomes of eight patients before and after relapse reveals two major patterns of clonal evolution, with chemotherapy appearing to have a role in both patterns.

    Li Ding, Timothy J. Ley, David E. Larson, Christopher A. Miller… in Nature (2012)

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  4. No Access

    Article

    Genome remodelling in a basal-like breast cancer metastasis and xenograft

    Massively parallel DNA sequencing technologies provide an unprecedented ability to screen entire genomes for genetic changes associated with tumour progression. Here we describe the genomic analyses of four DN...

    Li Ding, Matthew J. Ellis, Shunqiang Li, David E. Larson, Ken Chen… in Nature (2010)

  5. No Access

    Article

    BreakDancer: an algorithm for high-resolution map** of genomic structural variation

    This software package provides genome-wide detection of structural variants (insertions, deletions, inversions and inter- and intrachromosomal translocations) from 50-base-pair paired-end reads. The sizes of t...

    Ken Chen, John W Wallis, Michael D McLellan, David E Larson… in Nature Methods (2009)

  6. No Access

    Article

    Generation and annotation of the DNA sequences of human chromosomes 2 and 4

    Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes. Chromosome 4 has received attention primarily related to the sea...

    LaDeana W. Hillier, Tina A. Graves, Robert S. Fulton, Lucinda A. Fulton… in Nature (2005)

  7. No Access

    Article

    A physical map of the chicken genome

    Strategies for assembling large, complex genomes have evolved to include a combination of whole-genome shotgun sequencing and hierarchal map-assisted sequencing1,2. Whole-genome maps of all types can aid genome a...

    John W. Wallis, Jan Aerts, Martien A. M. Groenen, Richard P. M. A. Crooijmans… in Nature (2004)

  8. No Access

    Article

    The DNA sequence of human chromosome 7

    Human chromosome 7 has historically received prominent attention in the human genetics community, primarily related to the search for the cystic fibrosis gene and the frequent cytogenetic changes associated wi...

    LaDeana W. Hillier, Robert S. Fulton, Lucinda A. Fulton, Tina A. Graves… in Nature (2003)

  9. No Access

    Article

    Evidence for a nucleotide-dependent topoisomerase activity from yeast mitochondria

    Yeast mitochondria were found to contain a novel topoisomerase-like activity which required nucleoside di- or tri-phosphates as a cofactor. ADP supported activity as effectively as ATP and the optimal concentr...

    Uthayashanker R. Ezekiel, Eric M. Towler, John W. Wallis… in Current Genetics (1994)