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Cathal Seoighe
Researcher at National University of Ireland, Galway
Publications - 114
Citations - 8223
Cathal Seoighe is an academic researcher from National University of Ireland, Galway. The author has contributed to research in topics: Gene & Genome. The author has an hindex of 37, co-authored 108 publications receiving 7381 citations. Previous affiliations of Cathal Seoighe include University College Dublin & South African National Bioinformatics Institute.
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Journal ArticleDOI
Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection
Brandon F. Keele,Elena E. Giorgi,Elena E. Giorgi,Jesus F. Salazar-Gonzalez,Julie M. Decker,Kimmy T. Pham,Maria G. Salazar,Chuanxi Sun,Truman Grayson,Shuyi Wang,Hui Li,Xiping Wei,Chunlai Jiang,Jennifer L. Kirchherr,Feng Gao,Jeffery A. Anderson,Li Hua Ping,Ronald Swanstrom,Georgia D. Tomaras,William A. Blattner,Paul A. Goepfert,J. Michael Kilby,Michael S. Saag,Eric Delwart,Michael P. Busch,Myron S. Cohen,David C. Montefiori,Barton F. Haynes,Brian Gaschen,Gayathri Athreya,Ha Y. Lee,Natasha T. Wood,Cathal Seoighe,Alan S. Perelson,Tanmoy Bhattacharya,Tanmoy Bhattacharya,Bette T. Korber,Bette T. Korber,Beatrice H. Hahn,George M. Shaw +39 more
TL;DR: A mathematical model of random viral evolution and phylogenetic tree construction is developed and used to analyze 3,449 complete env sequences derived by single genome amplification from 102 subjects with acute HIV-1 (clade B) infection, suggesting a finite window of potential vulnerability of HIV- 1 to vaccine-elicited immune responses, although phenotypic properties of transmitted Envs pose a formidable defense.
Journal ArticleDOI
A flexible R package for nonnegative matrix factorization
Renaud Gaujoux,Cathal Seoighe +1 more
TL;DR: The NMF package helps realize the potential of Nonnegative Matrix Factorization, especially in bioinformatics, providing easy access to methods that have already yielded new insights in many applications and facilitating the combination of these to produce new NMF strategies.
Journal ArticleDOI
Quantitating the Multiplicity of Infection with Human Immunodeficiency Virus Type 1 Subtype C Reveals a Non-Poisson Distribution of Transmitted Variants
Melissa-Rose Abrahams,Jeffrey A. Anderson,Elena E. Giorgi,Elena E. Giorgi,Cathal Seoighe,Koleka Mlisana,Li-Hua Ping,Gayathri Athreya,Florette K. Treurnicht,Brandon F. Keele,Natasha T. Wood,Jesus F. Salazar-Gonzalez,Tanmoy Bhattacharya,Tanmoy Bhattacharya,Haitao Chu,Irving F. Hoffman,Shannon Galvin,Clement Mapanje,Peter N. Kazembe,Ruwayhida Thebus,Susan A. Fiscus,Winston Hide,Myron S. Cohen,S. S. Abdool Karim,Barton F. Haynes,George M. Shaw,Beatrice H. Hahn,Bette T. Korber,Bette T. Korber,Ronald Swanstrom,Carolyn Williamson +30 more
TL;DR: In a combined analysis of 171 subtype B and C transmission events, it is found that infection with more than one variant does not follow a Poisson distribution, indicating that transmission of individual virions cannot be seen as independent events, each occurring with low probability.
Journal ArticleDOI
Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome.
TL;DR: Genes retained in duplicate form a functionally biased set and include a significant over-representation of genes involved in the regulation of transcription in Arabidopsis thaliana.
Journal ArticleDOI
Genome-wide analysis of the structure of the South African Coloured Population in the Western Cape
Erika de Wit,Wayne Delport,Wayne Delport,Chimusa E. Rugamika,Ayton Meintjes,Marlo Möller,Paul D. van Helden,Cathal Seoighe,Eileen G. Hoal +8 more
TL;DR: Analysis by means of both the admixture and linkage models in STRUCTURE revealed that the major ancestral components of this population are predominantly Khoesan, Bantu-speaking Africans, European and a smaller Asian contribution, depending on the model used, which is consistent with historical data.