Dr Niall Haslam
Contact Details
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Biography:
| I completed my BSc in Human Genetics at the University of Nottingham. Upon graduation I worked at Galen Pharmaceuticals in Northern Ireland for one year before returning to formal education and taking an MSc in Bioinformatics at the University of Exeter. This enabled me to find a research position as a PhD student at the University of Southampton working on Next-Gen DNA sequencing. After completion of my PhD I went to work in Germany for a few years before returning to work at University College Dublin. I now work in protein bioinformatics and the analysis of short linear motifs and protein protein interaction networks. |
Research Interests
| I am interested in Protein Bioinformatics, specifically how short linear motifs mediate protein interactions. I am developing new methods for the discovery of novel motifs using a variety of approaches. Data integration and visualisation are increasingly important in computational biology and I have some experience in creating ontologies, exchange formats and data integration in particular with the Distributed Annotation System and webservices. I have created a number of bioinformatics related websites to visualise protein data - e.g. http://epic.embl.de and http://bioware.ucd.ie |
Peer Reviewed Journals
| Mooney, C. Haslam, NJ. Pollastri1, G. Shields, DC (2012) 'Towards the Improved Discovery and Design of Functional Peptides: Common Features of Diverse Classes Permit Generalized Prediction of Bioactivity'. PLoS ONE, 7 (10). [DOI] Link to full text [Details] |
| Niall J Haslam and Denis C Shields (2012) 'Profile-based short linear protein motif discovery'. BMC Bioinformatics, . Link to full text [Details] |
| Dinkel H, Michael S, Weatheritt RJ, Davey NE, Van Roey K, Altenberg B, Toedt G, Uyar B, Seiler M, Budd A, Jödicke L, Dammert MA, Schroeter C, Hammer M, Schmidt T, Jehl P, McGuigan C, Dymecka M, Chica C, Luck K, Via A, Chatr-Aryamontri A, Haslam N, Grebnev G, Edwards RJ, Steinmetz MO, Meiselbach H, Diella F, Gibson TJ (2012) 'ELM--the database of eukaryotic linear motifs'. Nucleic Acids Research, 40 (Database issue):1-51. [DOI] Link to full text [Details] |
Mooney C, Pollastri G, Shields DC, Haslam NJ; (2011) 'Prediction of short linear protein binding regions'. Journal of molecular biology, .  [DOI] Link to full text [Details] |
| Davey, NE,Haslam, NJ,Shields, DC,Edwards, RJ; (2011) 'SLiMSearch 2.0: biological context for short linear motifs in proteins'. Nucleic Acids Research, 39 :56-60. [DOI] Link to full text [Details] |
| Niall J. Haslam and Toby J. Gibson; (2010) 'EpiC: an open resource for exploring epitopes to aid antibody-based experiments'. Journal of Proteome Research, . [DOI] [Details] | |||||||||
| Davey, NE,Haslam, NJ,Shields, DC,Edwards, RJ; (2010) 'SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs'. Nucleic Acids Research, 38 :534-539. [DOI] Link to full text [Details] | |||||||||
| Julie Bourbeillon, Sandra Orchard, Itai Benhar, Carl Borrebaeck, Antoine de Daruvar, Stefan Dubel, Ronald Frank, Frank Gibson, David Gloriam, Niall Haslam, Tara Hiltker, Ian Humphrey-Smith, Michael Hust, David Juncker, Manfred Koegl, Zoltan Konthur, Bernhard Korn, Sylvia Krobitsch, Serge Muyldermans, Per-Ake Nygren, Sandrine Palcy, Bojan Polic, Henry Rodriguez, Alan Sawyer, Martin Schlapshy, Michael Snyder, Oda Stoevesandt, Michael J. Taussig, Markus Templin, Matthias Uhlen, Silvere van der Maarel, Christer Wingren, Henning Hermjakob, David Sherman; (2010) 'Minimum information about a protein affinity reagent (MIAPAR)'. Nature biotechnology, 28 (7):650-653. [DOI] [Details] | |||||||||
| David E. Gloriam, Sandra Orchard, Daniela Bertinetti, Erik Björling, Erik Bongcam-Rudloff, Carl A. Borrebaeck, Julie Bourbeillon, Andrew R. Bradbury, Antoine de Daruvar, Stefan Dübel, Ronald Frank, Toby J. Gibson, Larry Gold, Niall Haslam, Friedrich W. Herberg, Tara Hiltke, Jörg D. Hoheisel, Samuel Kerrien, Manfred Koegl, Zoltán Konthur, Bernhard Korn, Ulf Landegren, Luisa Montecchi-Palazzi, Sandrine Palcy, Henry Rodriguez, Sonja Schweinsberg, Volker Sievert, Oda Stoevesandt, Michael J. Taussig, Marius Ueffing, Mathias Uhlén, Silvère van der Maarel, Christer Wingren, Peter Woollard, David J. Sherman, Henning Hermjakob; (2009) 'A community standard format for the representation of protein affinity reagents'. Molecular & Cellular Proteomics, . [DOI] [Details] | |||||||||
| Gerald Weber, Niall Haslam, Jonathan W. Essex, Cameron Neylon; (2009) 'Thermal equivalence of DNA duplexes for probe design'. Journal of Physics-Condensed Matter, . [DOI] [Details] | |||||||||
| F. Diella, N. Haslam, C. Chica, A. Budd, S. Michael, N. P. Brown, G. Trave, T. J. Gibson; (2008) 'Understanding eukaryotic linear motifs and their role in cell signaling and regulation'. Frontiers in Bioscience, 13 :6580-6703. [Details] | |||||||||
| N. E. Whiteford, N. Haslam, G. Weber, A. Prügel-Bennett, J. W. Essex and C. Neylon; (2008) 'A Novel Method for Whole Genome Repeat Visualisation'. Journal of Complex Systems, 17 (4):381-398. [Details] | |||||||||
| Niall J. Haslam, Nava E. Whiteford, Gerald Weber, Adam Prügel-Bennett, Jonathan W. Essex, Cameron Neylon; (2008) 'Optimal Probe Length Varies for Targets with High Sequence Variation: Implications for Probe Library Design for Resequencing Highly Variable Genes'. PLoS ONE, e . [DOI] Link to full text [Details] |
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| G. Weber, N. Haslam, N. Whiteford, A. Prügel- Bennett, J. W. Essex and C. Neylon; (2006) 'Thermal Equivalence of DNA Duplexes Without Melting Temperature Calculation'. Nature Physics, 2 :55-59. [Details] | |||||||||
| N. E. Whiteford, N. Haslam, G. Weber, A. Prügel-Bennett, J. W. Essex, P. L. Roach, M. Bradley and C. Neylon, ; (2005) 'An Analysis of the Feasibility of Short Read Sequencing'. Nucleic Acids Research, 33 (19). [Details] | |||||||||
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Conference Publications
| Norman E. Davey, Niall J. Haslam, Denis C. Shields, and Richard J. Edwards ; (2010) SLiMSearch: A Webserver for Finding Novel Occurrences of Short Linear Motifs in Proteins, Incorporating Sequence Context . In: Dijkstra, T.M.H.; Tsivtsivadze, E.; Marchiori, E.; Heskes, T eds. Pattern Recognition in Bioinformatics [Details] |
| Nial Haslam and Toby Gibson; (2009) EpiC: A Resource for Integrating Information and Analyses to Enable Selection of Epitopes for Antibody Based Experiments . In: Norman W. Paton, Paolo Missier, Cornelia Hedeler eds. Data Integration in the Life Sciences Manchester, , pp.173-181 [DOI] [Details] |
Book Reviews
| Niall Haslam; (2010) What a time I am having ¿ Selected letters of Max Perutz. Book Reviews [DOI] [Details] |
Associations
| Association: Biochemical Society, Function/Role: Member |
Outreach Activities
| I have delivered information sessions to primary schools in the local area to promote biology. These involved interactive games to teach children about the fundamentals of biological systems. I am available to give these lectures again, if you are interested please get in touch. |
Reviews
| Plos One: Editor. |