Publications

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. Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API. bioRxiv, 2018.

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. Circulating miRNAs, isomiRs and small RNA clusters in human plasma and breast milk. PLoS ONE, 2018.

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. bcbioRNASeq: R package for bcbio RNA-seq analysis. F1000Research, 2017.

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. Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives. Scientific Data, 2017.

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. Maintenance of macrophage transcriptional programs and intestinal homeostasis by epigenetic reader SP140. Science Immunology, 2017.

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. Viewing RNA-seq data on the entire human genome. F1000Research, 2017.

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. Empirical comparison of reduced representation bisulfite sequencing and Infinium BeadChip reproducibility and coverage of DNA methylation in humans. npj Genomic Medicine, 2017.

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. Comparative analysis of LIN28-RNA binding sites identified at single nucleotide resolution. RNA Biology, 2017.

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. Genomic analyses identify molecular subtypes of pancreatic cancer. Nature, 2016.

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. Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis.. Bioinformatics (Oxford, England), 2015.

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. The small RNA content of human sperm reveals pseudogene-derived piRNAs complementary to protein-coding genes.. RNA (New York, N.Y.), 2015.

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. Functional Impact and Evolution of a Novel Human Polymorphic Inversion That Disrupts a Gene and Creates a Fusion Transcript. PLoS Genetics, 2015.

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. Paternal Diet Defines Offspring Chromatin State and Intergenerational Obesity. Cell, 2014.

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. Regulation of miRNA strand selection: follow the leader?. Biochemical Society transactions, 2014.

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. InvFEST, a database integrating information of polymorphic inversions in the human genome. Nucleic Acids Research, 2014.

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. Microarray and deep sequencing cross-platform analysis of the mirRNome and isomiR variation in response to epidermal growth factor.. BMC genomics, 2013.

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. A highly expressed miR-101 isomiR is a functional silencing small RNA.. BMC genomics, 2013.

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. A Pathogenic Mechanism in Huntington's Disease Involves Small CAG-Repeated RNAs with Neurotoxic Activity.. PLoS genetics, 2012.

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. A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome.. Bioinformatics (Oxford, England), 2011.

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. A myriad of miRNA variants in control and Huntington's disease brain regions detected by massively parallel sequencing. Nucleic Acids Research, 2010.

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. Fibroblast-derived induced pluripotent stem cells show no common retroviral vector insertions.. Stem cells (Dayton, Ohio), 2009.

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. Identification of Copy Number Variants Defining Genomic Differences among Major Human Groups. PLoS ONE, 2009.

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. ProSeeK: A web server for MLPA probe design. BMC Genomics, 2008.

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. Genome assembly comparison identifies structural variants in the human genome.. Nature Genetics, 2006.

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