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Fabian Sievers

Research Fellow

School Of Medicine
Conway Institute
Belfield
Dublin 4

Tel: +353 1 7166834
Email: fabian.sievers@ucd.ie

Biography

Hitachi Dublin Laboratory, Researcher (1997-2007).

 

Algorithm Design, Queueuing Theory, Reliability Engineering, Bioinformatics, High Performance Computing, Probabilistic Modelling

Professional

   

Patents

Patent WO2003019451A1 : A method for defining gene hunting studies
Patent EP1884878 A1 : Computer system for simulating a physical system
Patent EP1791064 A1 : Computer system for simulating a physical system
   

Conference Contributions

Sievers, F (2015) Benchmarking multiple protein sequence alignments and the effect of guide-tree topography. [Poster Presentation], RECOMB Comparative Genomics, Frankfurt , 04-OCT-15 - 07-OCT-15.
Sievers, F (2015) Systematic exploration of guide-tree topology effects for small protein alignments. [Poster Presentation], 23rd International Conference on Intelligent Systems for Molecular Biology & 14th European Conference on Computational Biology, Dublin , 10-JUL-15 - 14-JUL-15.
Sievers, F (2015) Clustal Omega. [Other], 23rd International Conference on Intelligent Systems for Molecular Biology & 14th European Conference on Computational Biology, Dublin , 10-JUL-15 - 14-JUL-15.
               

Publications

 

Book Chapters

Sievers, F; Higgins, DG (2014) 'Clustal Omega, Accurate alignment of very large numbers of sequences' In: Russell, DJ (eds). Multiple Sequence Alignment Methods. New York: Humana Press Springer. , pp.105-116 [Details]
Sievers, F; Higgins, DG (2014) 'Clustal Omega' In: Bateman, A; Draghici, S; Khurana, E; Orchard, S; Pearson, WR (eds). Current Protocols in Bioinformatics. New York: John Wiley. [Details]
 

Peer Reviewed Journals

Fox G, Sievers F;Higgins DG (2016) 'Using de novo protein structure predictions to measure the quality of very large multiple sequence alignments'. Bioinformatics, 32 (6):814-820. [DOI] [Details]
Jehl P, Sievers F;Higgins DG (2015) 'OD-seq: outlier detection in multiple sequence alignments'. BMC Bioinformatics, 16 . [DOI] Link to full text [Details]
Boyce K, Sievers F;Higgins DG (2015) 'Instability in progressive multiple sequence alignment algorithms'. Algorithms for Molecular Biology, 10 . [DOI] Link to full text [Details]
Sievers F, Higgins DG (2014) 'Clustal omega'. Current Protocols in Bioinformatics, 48 :1-1. [DOI] [Details]
Sievers F, Hughes GM;Higgins DG (2014) 'Systematic exploration of guide-tree topology effects for small protein alignments'. BMC Bioinformatics, 15 . [DOI] Link to full text [Details]
Boyce K, Sievers F, Higgins DG (2014) 'Simple chained guide trees give high-quality protein multiple sequence alignments'. Proceedings of the National Academy of Sciences of the United States of America, 111 (29):10556-10561. [DOI] [Details]
Sievers F, Higgins DG (2014) 'Clustal Omega, accurate alignment of very large numbers of sequences'. Methods, 1079 :105-116. [DOI] [Details]
Sievers F, Dineen D;Wilm A;Higgins DG (2013) 'Making automated multiple alignments of very large numbers of protein sequences'. Bioinformatics, 29 (8):989-995. [DOI] Link to full text [Details]
Sievers F, Wilm A;Dineen D;Gibson TJ;Karplus K;Li W;Lopez R;McWilliam H;Remmert M;S¿¿ding J;Thompson JD;Higgins DG (2011) 'Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega'. Molecular Systems Biology, 7 . [DOI] Link to full text [Details]
Shi W, Lei F, Zhu C, Sievers F, Higgins DG; (2010) 'A complete analysis of HA and NA genes of influenza A viruses'. PLoS ONE, 5 (12). [DOI] Link to full text [Details]
Blackshields G, Sievers F;Shi W;Wilm A;Higgins DG (2010) 'Sequence embedding for fast construction of guide trees for multiple sequence alignment'. Algorithms for Molecular Biology, 5 . [DOI] Link to full text [Details]
                                                                                             

Research

Research Interests

UCD Medicine Research Centre - Bioinformatics

Multiple sequence alignment (MSA): development and maintenance of Clustal Omega MSA software. Benchmarking of MSAs. Phylogenetic study of optimum guide-tree topologies for MSA creation 
 

Recent Postgraduates

Kieran Boyce
Gearoid Fox
Peter Jehl