1. BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence.

    Nature Genetics 47(1):22 (2015) PMID 25485837

    Prostate cancer is driven by a combination of genetic and/or epigenetic alterations. Epigenetic alterations are frequently observed in all human cancers, yet how aberrant epigenetic signatures are established is poorly understood. Here we show that the gene encoding BAZ2A (TIP5), a factor previo...
  2. ARH-seq: identification of differential splicing in RNA-seq data.

    Nucleic Acids Research 42(14):e110 (2014) PMID 24920826 PMCID PMC4132698

    The computational prediction of alternative splicing from high-throughput sequencing data is inherently difficult and necessitates robust statistical measures because the differential splicing signal is overlaid by influencing factors such as gene expression differences and simultaneous expressi...
  3. Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma.

    Nature 511(7510):428 (2014) PMID 25043047 PMCID PMC4201514

    Medulloblastoma is a highly malignant paediatric brain tumour currently treated with a combination of surgery, radiation and chemotherapy, posing a considerable burden of toxicity to the developing child. Genomics has illuminated the extensive intertumoral heterogeneity of medulloblastoma, ident...
  4. Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma.

    Nature 511(7510):428 (2014) PMID 25043047 PMCID PMC4201514

    Medulloblastoma is a highly malignant paediatric brain tumour currently treated with a combination of surgery, radiation and chemotherapy, posing a considerable burden of toxicity to the developing child. Genomics has illuminated the extensive intertumoral heterogeneity of medulloblastoma, ident...
  5. Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma.

    Nature 511(7510):428 (2014) PMID 25043047 PMCID PMC4201514

    Medulloblastoma is a highly malignant paediatric brain tumour currently treated with a combination of surgery, radiation and chemotherapy, posing a considerable burden of toxicity to the developing child. Genomics has illuminated the extensive intertumoral heterogeneity of medulloblastoma, ident...
  6. Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma.

    Nature 511(7510):428 (2014) PMID 25043047 PMCID PMC4201514

    Medulloblastoma is a highly malignant paediatric brain tumour currently treated with a combination of surgery, radiation and chemotherapy, posing a considerable burden of toxicity to the developing child. Genomics has illuminated the extensive intertumoral heterogeneity of medulloblastoma, ident...
  7. Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing.

    Nature 510(7506):537 (2014) PMID 24847876

    Epigenetic alterations, that is, disruption of DNA methylation and chromatin architecture, are now acknowledged as a universal feature of tumorigenesis. Medulloblastoma, a clinically challenging, malignant childhood brain tumour, is no exception. Despite much progress from recent genomics studie...
  8. Parallel profiling of the transcriptome, cistrome, and epigenome in the cellular response to ionizing radiation.

    Science Signaling 7(325):rs3 (2014) PMID 24825921

    The DNA damage response (DDR) is a vast signaling network that is robustly activated by DNA double-strand breaks, the critical lesion induced by ionizing radiation (IR). Although much of this response operates at the protein level, a critical component of the network sustains many DDR branches b...
  9. Parallel profiling of the transcriptome, cistrome, and epigenome in the cellular response to ionizing radiation.

    Science Signaling 7(325):rs3 (2014) PMID 24825921

    The DNA damage response (DDR) is a vast signaling network that is robustly activated by DNA double-strand breaks, the critical lesion induced by ionizing radiation (IR). Although much of this response operates at the protein level, a critical component of the network sustains many DDR branches b...
  10. The nerve growth factor receptor CD271 is crucial to maintain tumorigenicity and stem-like properties of melanoma cells.

    PLoS ONE 9(5):e92596 (2014) PMID 24799129 PMCID PMC4010406

    Large-scale genomic analyses of patient cohorts have revealed extensive heterogeneity between individual tumors, contributing to treatment failure and drug resistance. In malignant melanoma, heterogeneity is thought to arise as a consequence of the differentiation of melanoma-initiating cells th...
  11. Influence of RNA extraction methods and library selection schemes on RNA-seq data.

    BMC Genomics 15:675 (2014) PMID 25113896 PMCID PMC4148917

    Gene expression analysis by RNA sequencing is now widely used in a number of applications surveying the whole transcriptomes of cells and tissues. The recent introduction of ribosomal RNA depletion protocols, such as RiboZero, has extended the view of the polyadenylated transcriptome to the poly...
  12. ARH-seq: identification of differential splicing in RNA-seq data.

    Nucleic Acids Research 42(14):e110 (2014) PMID 24920826

    The computational prediction of alternative splicing from high-throughput sequencing data is inherently difficult and necessitates robust statistical measures because the differential splicing signal is overlaid by influencing factors such as gene expression differences and simultaneous expressi...
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  13. Comparative analysis and modeling of the severity of steatohepatitis in DDC-treated mouse strains.

    PLoS ONE 9(10):e111006 (2014) PMID 25347188 PMCID PMC4210132

    Non-alcoholic fatty liver disease (NAFLD) has a broad spectrum of disease states ranging from mild steatosis characterized by an abnormal retention of lipids within liver cells to steatohepatitis (NASH) showing fat accumulation, inflammation, ballooning and degradation of hepatocytes, and fibros...
  14. ARH-seq: identification of differential splicing in RNA-seq data.

    Nucleic Acids Research 42(14):e110 (2014) PMID 24920826 PMCID PMC4132698

    The computational prediction of alternative splicing from high-throughput sequencing data is inherently difficult and necessitates robust statistical measures because the differential splicing signal is overlaid by influencing factors such as gene expression differences and simultaneous expressi...
  15. Comparative Analysis and Modeling of the Severity of Steatohepatitis in DDC-Treated Mouse Strains.

    PLoS ONE 9(10):e111006 (2014) PMID 25347188 PMCID PMC4210132

    Non-alcoholic fatty liver disease (NAFLD) has a broad spectrum of disease states ranging from mild steatosis characterized by an abnormal retention of lipids within liver cells to steatohepatitis (NASH) showing fat accumulation, inflammation, ballooning and degradation of hepatocytes, and fibros...
  16. Hypermutation of the Inactive X Chromosome Is a Frequent Event in Cancer

    Cell 155(3):567 (2013)

    Mutation is a fundamental process in tumorigenesis. However, the degree to which the rate of somatic mutation varies across the human genome and the mechanistic basis underlying this variation remain to be fully elucidated. Here, we performed a cross-cancer comparison of 402 whole geno...
  17. Hypermutation of the inactive X chromosome is a frequent event in cancer.

    Cell 155(3):567 (2013) PMID 24139898 PMCID PMC3898475

    Mutation is a fundamental process in tumorigenesis. However, the degree to which the rate of somatic mutation varies across the human genome and the mechanistic basis underlying this variation remain to be fully elucidated. Here, we performed a cross-cancer comparison of 402 whole genomes compri...
  18. Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma.

    Nature Genetics 45(8):927 (2013) PMID 23817572 PMCID PMC3951336

    Pilocytic astrocytoma, the most common childhood brain tumor, is typically associated with mitogen-activated protein kinase (MAPK) pathway alterations. Surgically inaccessible midline tumors are therapeutically challenging, showing sustained tendency for progression and often becoming a chronic ...
  19. Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer.

    Cancer Cell 23(2):159 (2013) PMID 23410972

    Early-onset prostate cancer (EO-PCA) represents the earliest clinical manifestation of prostate cancer. To compare the genomic alteration landscapes of EO-PCA with "classical" (elderly-onset) PCA, we performed deep sequencing-based genomics analyses in 11 tumors diagnosed at young age, and pursu...
  20. Integrative Genomic Analyses Reveal an Androgen-Driven Somatic Alteration Landscape in Early-Onset Prostate Cancer

    Cancer Cell 23(2):159 (2013)

    Early-onset prostate cancer (EO-PCA) represents the earliest clinical manifestation of prostate cancer. To compare the genomic alteration landscapes of EO-PCA with “classical” (elderly-onset) PCA, we performed deep sequencing-based genomics analyses in 11 tumors diagnosed at young age,...