A flexible R package for nonnegative matrix factorization von Gaujoux, Renaud, Seoighe, Cathal

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Controlling for background genetic effects using polygenic scores improves the power of genome-wide association studies von Bennett, Declan, O’Shea, Donal, Ferguson, John, Morris, Derek, Seoighe, Cathal

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Inference of Candidate Germline Mutator Loci in Humans from Genome-Wide Haplotype Data von Seoighe, Cathal, Scally, Aylwyn

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Bias and inconsistency in the estimation of tumour mutation burden von Makrooni, Mohammad A, O'Sullivan, Brian, Seoighe, Cathal

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Random-effects meta-analysis of effect sizes as a unified framework for gene set analysis von Makrooni, Mohammad A, O'Shea, Dónal, Geeleher, Paul, Seoighe, Cathal

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No evidence that HLA genotype influences the driver mutations that occur in cancer patients von Kherreh, Noor, Cleary, Siobhán, Seoighe, Cathal

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A Database of Human Immune Receptor Alleles Recovered from Population Sequencing Data von Yu, Yaxuan, Ceredig, Rhodri, Seoighe, Cathal

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Impact of the Choice of Normalization Method on Molecular Cancer Class Discovery Using Nonnegative Matrix Factorization von Yang, Haixuan, Seoighe, Cathal

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High throughput gene expression measurement with real time PCR in a microfluidic dynamic array von Spurgeon, Sandra L, Jones, Robert C, Ramakrishnan, Ramesh

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Gene-set analysis is severely biased when applied to genome-wide methylation data von Geeleher, Paul, Hartnett, Lori, Egan, Laurance J, Golden, Aaron, Raja Ali, Raja Affendi, Seoighe, Cathal

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Insights from deconvolution of cell subtype proportions enhance the interpretation of functional genomic data von Kong, Yu, Rastogi, Deepa, Seoighe, Cathal, Greally, John M, Suzuki, Masako

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Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome von Seoighe, Cathal, Gehring, Chris

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Distinctive patterns of microRNA expression associated with karyotype in acute myeloid leukaemia von Dixon-McIver, Amanda, East, Phil, Mein, Charles A, Cazier, Jean-Baptiste, Molloy, Gael, Chaplin, Tracy, Andrew Lister, T, Young, Bryan D, Debernardi, Silvana

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vcfView: An Extensible Data Visualization and Quality Assurance Platform for Integrated Somatic Variant Analysis von O’Sullivan, Brian, Seoighe, Cathal

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The shared genomic architecture of human nucleolar organizer regions von Floutsakou, Ioanna, Agrawal, Saumya, Nguyen, Thong T, Seoighe, Cathal, Ganley, Austen R D, McStay, Brian

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Regulatory landscape enrichment analysis (RLEA): a computational toolkit for non-coding variant enrichment and cell type prioritization von Rosean, Samuel, Sosa, Eric A, O'Shea, Dónal, Raj, Srilakshmi M, Seoighe, Cathal, Greally, John M

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Differences in the tumor microenvironment between African-American and European-American breast cancer patients von Martin, Damali N, Boersma, Brenda J, Yi, Ming, Reimers, Mark, Howe, Tiffany M, Yfantis, Harry G, Tsai, Yien Che, Williams, Erica H, Lee, Dong H, Stephens, Robert M, Weissman, Allan M, Ambs, Stefan

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Selection Shapes Synonymous Stop Codon Use in Mammals von Seoighe, Cathal, Kiniry, Stephen J., Peters, Andrew, Baranov, Pavel V., Yang, Haixuan

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Classification and analysis of regulatory pathways using graph property, biochemical and physicochemical property, and functional property von Huang, Tao, Chen, Lei, Cai, Yu-Dong, Chou, Kuo-Chen

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Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection von Keele, Brandon F, Giorgi, Elena E, Salazar-Gonzalez, Jesus F, Decker, Julie M, Pham, Kimmy T, Salazar, Maria G, Sun, Chuanxi, Grayson, Truman, Wang, Shuyi, Li, Hui, Wei, Xiping, Jiang, Chunlai, Kirchherr, Jennifer L, Gao, Feng, Anderson, Jeffery A, Ping, Li-Hua, Swanstrom, Ronald, Tomaras, Georgia D, Blattner, William A, Goepfert, Paul A, Kilby, J. Michael, Saag, Michael S, Delwart, Eric L, Busch, Michael P, Cohen, Myron S, Montefiori, David C, Haynes, Barton F, Gaschen, Brian, Athreya, Gayathri S, Lee, Ha Y, Wood, Natasha, Seoighe, Cathal, Perelson, Alan S, Bhattacharya, Tanmoy, Korber, Bette T, Hahn, Beatrice H, Shaw, George M

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