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Open AccessTransposon insertion profiling by sequencing (TIPseq) for map** LINE-1 insertions in the human genome
Transposable elements make up a significant portion of the human genome. Accurately locating these mobile DNAs is vital to understand their role as a source of structural variation and somatic mutation. To thi...
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Open AccessSomatic retrotransposition is infrequent in glioblastomas
Gliomas are the most common primary brain tumors in adults. We sought to understand the roles of endogenous transposable elements in these malignancies by identifying evidence of somatic retrotransposition in ...
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FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells
Screening of cells transduced with a lentivirus library harboring nucleosome-free regions of mammalian genomes identifies cis elements that regulate transcription.
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Open AccessCo-expression network analysis identifies Spleen Tyrosine Kinase (SYK) as a candidate oncogenic driver in a subset of small-cell lung cancer
Oncogenic mechanisms in small-cell lung cancer remain poorly understood leaving this tumor with the worst prognosis among all lung cancers. Unlike other cancer types, sequencing genomic approaches have been of...
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Article
Relapse-specific mutations in NT5C2 in childhood acute lymphoblastic leukemia
William Carroll and colleagues report the identification of mutations in NT5C2, encoding cytosolic 5′-nucleotidase II, which are specific for relapsed childhood acute lymphoblastic leukemia. The mutations confer ...
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Open AccessCombining multiple ChIP-seq peak detection systems using combinatorial fusion
Due to the recent rapid development in ChIP-seq technologies, which uses high-throughput next-generation DNA sequencing to identify the targets of Chromatin Immunoprecipitation, there is an increasing amount o...
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Article
Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia
T cell acute lymphoblastic leukemia (T-ALL) is an immature hematopoietic malignancy driven mainly by oncogenic activation of NOTCH1 signaling1. In this study we report the presence of loss-of-function mutations a...
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Open AccessAssessing quality and completeness of human transcriptional regulatory pathways on a genome-wide scale
Pathway databases are becoming increasingly important and almost omnipresent in most types of biological and translational research. However, little is known about the quality and completeness of pathways stor...
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Article
Open AccessEST and microarray analysis of horn development in Onthophagus beetles
The origin of novel traits and their subsequent diversification represent central themes in evo-devo and evolutionary ecology. Here we explore the genetic and genomic basis of a class of traits that is both no...
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Open AccessESTPiper – a web-based analysis pipeline for expressed sequence tags
EST sequencing projects are increasing in scale and scope as the genome sequencing technologies migrate from core sequencing centers to individual research laboratories. Effectively, generating EST data is no ...
