1. Temporary loss of moral behavior in a patient undergoing chemotherapy with cisplatin - breaking bad.

    BMC Psychiatry 15(1):9 (2015) PMID 25651838 PMCID PMC4321323

    Behavioral disturbances following chemotherapy with cisplatin are rare. Here, we report a patient with temporary loss of moral behavior in the setting of cisplatin-based chemotherapy for treatment of tonsillar cancer. A 66-year-old Caucasian male with no psychiatric or violent history was starte...
  2. Personalized medicine approaches for colon cancer driven by genomics and systems biology: OncoTrack.

    Biotechnology Journal 9(9):1104 (2014) PMID 25074435 PMCID PMC4314672

    The post-genomic era promises to pave the way to a personalized understanding of disease processes, with technological and analytical advances helping to solve some of the world's health challenges. Despite extraordinary progress in our understanding of cancer pathogenesis, the disease remains o...
  3. Personalized medicine approaches for colon cancer driven by genomics and systems biology: OncoTrack.

    Biotechnology Journal 9(9):1104 (2014) PMID 25074435 PMCID PMC4314672

    The post-genomic era promises to pave the way to a personalized understanding of disease processes, with technological and analytical advances helping to solve some of the world's health challenges. Despite extraordinary progress in our understanding of cancer pathogenesis, the disease remains o...
  4. Personalized medicine approaches for colon cancer driven by genomics and systems biology: OncoTrack.

    Biotechnology Journal 9(9):1104 (2014) PMID 25074435

    The post-genomic era promises to pave the way to a personalized understanding of disease processes, with technological and analytical advances helping to solve some of the world's health challenges. Despite extraordinary progress in our understanding of cancer pathogenesis, the disease remains o...
  5. 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...
  6. 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...
  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. 5-Fluorouracil affects assembly of stress granules based on RNA incorporation.

    Nucleic Acids Research 42(10):6436 (2014) PMID 24728989 PMCID PMC4041438

    The antimetabolite 5-fluorouracil is a widely used chemotherapeutic for the treatment of several solid cancers. However, resistance to 5-fluorouracil remains a major drawback in its clinical use. In this study we report that treatment of HeLa cells with 5-fluorouracil resulted in de novo assembl...
  9. 5-Fluorouracil affects assembly of stress granules based on RNA incorporation.

    Nucleic Acids Research 42(10):6436 (2014) PMID 24728989 PMCID PMC4041438

    The antimetabolite 5-fluorouracil is a widely used chemotherapeutic for the treatment of several solid cancers. However, resistance to 5-fluorouracil remains a major drawback in its clinical use. In this study we report that treatment of HeLa cells with 5-fluorouracil resulted in de novo assembl...
  10. 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...
  11. 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...
  12. 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...
  13. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris).

    Nature 505(7484):546 (2014) PMID 24352233

    Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% of the world's annual sugar production and is a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n = 18 chromosomes, has an est...
  14. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris).

    Nature 505(7484):546 (2014) PMID 24352233

    Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% of the world's annual sugar production and is a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n = 18 chromosomes, has an est...
  15. 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...
  16. Exome sequencing from nanogram amounts of starting DNA: comparing three approaches.

    PLoS ONE 9(7):e101154 (2014) PMID 24992588 PMCID PMC4081514

    Hybridization-based target enrichment protocols require relatively large starting amounts of genomic DNA, which is not always available. Here, we tested three approaches to pre-capture library preparation starting from 10 ng of genomic DNA: (i and ii) whole-genome amplification of DNA samples wi...
  17. 5-Fluorouracil affects assembly of stress granules based on RNA incorporation.

    Nucleic Acids Research 42(10):6436 (2014) PMID 24728989 PMCID PMC4041438

    The antimetabolite 5-fluorouracil is a widely used chemotherapeutic for the treatment of several solid cancers. However, resistance to 5-fluorouracil remains a major drawback in its clinical use. In this study we report that treatment of HeLa cells with 5-fluorouracil resulted in de novo assembl...
  18. 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...
  19. 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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  20. Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes.

    Nature Communications 5:5569 (2014) PMID 25424553 PMCID PMC4263165

    To fully understand human biology and link genotype to phenotype, the phase of DNA variants must be known. Here we present a comprehensive analysis of haplotype-resolved genomes to assess the nature and variation of haplotypes and their pairs, diplotypes, in European population samples. We use a...