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Clustal W and Clustal X version 2.0.
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. Larkin MA, et al. Bioinformatics. 2007 Nov 1;23(21):2947-8. doi: 10.1093/bioinformatics/btm404. Epub 2007 Sep 10. Bioinformatics. 2007. PMID: 17846036
Sequence embedding for fast construction of guide trees for multiple sequence alignment.
Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG. Blackshields G, et al. Algorithms Mol Biol. 2010 May 14;5:21. doi: 10.1186/1748-7188-5-21. Algorithms Mol Biol. 2010. PMID: 20470396 Free PMC article.
Fast embedding methods for clustering tens of thousands of sequences.
Blackshields G, Larkin M, Wallace IM, Wilm A, Higgins DG. Blackshields G, et al. Comput Biol Chem. 2008 Aug;32(4):282-6. doi: 10.1016/j.compbiolchem.2008.03.005. Epub 2008 Mar 26. Comput Biol Chem. 2008. PMID: 18450519
Multiple sequence alignments.
Wallace IM, Blackshields G, Higgins DG. Wallace IM, et al. Curr Opin Struct Biol. 2005 Jun;15(3):261-6. doi: 10.1016/j.sbi.2005.04.002. Curr Opin Struct Biol. 2005. PMID: 15963889 Review.
Analysis and comparison of benchmarks for multiple sequence alignment.
Blackshields G, Wallace IM, Larkin M, Higgins DG. Blackshields G, et al. In Silico Biol. 2006;6(4):321-39. In Silico Biol. 2006. PMID: 16922695
Mind the gaps: progress in progressive alignment.
Higgins DG, Blackshields G, Wallace IM. Higgins DG, et al. Proc Natl Acad Sci U S A. 2005 Jul 26;102(30):10411-2. doi: 10.1073/pnas.0504801102. Epub 2005 Jul 18. Proc Natl Acad Sci U S A. 2005. PMID: 16027352 Free PMC article. No abstract available.
Ligation of TLR7 on CD19(+) CD1d(hi) B cells suppresses allergic lung inflammation via regulatory T cells.
Khan AR, Amu S, Saunders SP, Hams E, Blackshields G, Leonard MO, Weaver CT, Sparwasser T, Sheils O, Fallon PG. Khan AR, et al. Eur J Immunol. 2015 Jun;45(6):1842-54. doi: 10.1002/eji.201445211. Epub 2015 Apr 14. Eur J Immunol. 2015. PMID: 25763771
Interleukin-15 is associated with disease severity in viral bronchiolitis.
Leahy TR, McManus R, Doherty DG, Grealy R, Coulter T, Smyth P, Blackshields G, Sheils O, Carr MJ, Purandare N, Geary M, Hodemaekers HM, Janssen R, Bont L, Slattery D, Ryan T. Leahy TR, et al. Eur Respir J. 2016 Jan;47(1):212-22. doi: 10.1183/13993003.00642-2015. Epub 2015 Nov 5. Eur Respir J. 2016. PMID: 26541527 Clinical Trial.
An integrated analysis of the SOX2 microRNA response program in human pluripotent and nullipotent stem cell lines.
Vencken SF, Sethupathy P, Blackshields G, Spillane C, Elbaruni S, Sheils O, Gallagher MF, O'Leary JJ. Vencken SF, et al. BMC Genomics. 2014 Aug 25;15:711. doi: 10.1186/1471-2164-15-711. BMC Genomics. 2014. PMID: 25156079 Free PMC article.
MyD88 is an essential component of retinoic acid-induced differentiation in human pluripotent embryonal carcinoma cells.
Sulaiman G, Cooke A, Ffrench B, Gasch C, Abdullai OA, O'Connor K, Elbaruni S, Blackshields G, Spillane C, Keegan H, McEneaney V, Knittel R, Rogers A, Jeffery IB, Doyle B, Bates M, d'Adhemar C, Lee MY, Campbell EL, Moynagh PN, Higgins DG, O'Toole S, O'Neill L, O'Leary JJ, Gallagher MF. Sulaiman G, et al. Among authors: blackshields g. Cell Death Differ. 2017 Nov;24(11):1975-1986. doi: 10.1038/cdd.2017.124. Epub 2017 Sep 8. Cell Death Differ. 2017. PMID: 28885616 Free PMC article.
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