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- Core Technologies
Professor Brendan Loftus BSc PhD
Contact Details
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Biography:
| My research publications can be viewed at Google Scholar (http://scholar.google.com/citations?user=kaBKAPgAAAAJ&hl=en) I am an SFI professor in Host-pathogen interactions at the Conway Institute and the Director of Genomics at the Conway Institute. Prof Loftus is interested in Genomics, Bioinformatics, transcriptomics and high throughput mechanisms for identifying host-pathogen interactions. I set up an Illumina based high throughput sequencing facility at the Conway Institute and am the head of genomics at the Conway Institute. I am also a PI on an Science foundation Ireland (SFI) funded research cluster in reproductive biology which has been funded for 5 years. History Prof Loftus completed a PhD in the molecular biology of Prion disease in UCD in 1996. He then went on to work as a post-doc in what is now the J. Craig Venter Institute on the human genome project. He then went on to work in the Bioinformatics department as an analyst on a variety of bacterial genome projects and HMM based protein classification projects. He subsequently joined the faculty leading the publication of both the amoebal pathogen Entamoeba histolytica and the fungal pathogen Cryptococcus neoformans in Nature and Science respectively. He has also worked on genome projects for both the malaria and dengue virus vectors Anopheles gambiae and Aedes aegypti published in both Science and Nature. Overall, publications involving Prof Loftus have been cited over 8900 times and have received widespread media attention. In 2007 Prof Loftus returned to Ireland after receiving an SFI research professorship in host response to intracellular pathogens. |
Research Interests
| I have recently changed my primary research focus into microbial pathogenesis and the use of functional genomics to uncover the complex interplay between host and pathogen during the invasion and persistence processes. In particular we are focusing on a subset of intracellular pathogens who display broad host range and perhaps have derived their virulence and pathogenic potential through interaction with non human invertebrate hosts. Both the simplicity of using surrogate host systems and the recent advances in genomic and proteomic technologies means it is possible to look at whole host response in tandem with pathogen behaviour during key time points in the infection process. The availability of genetic tools for a number of these hosts also allows for the study of outcomes following the perturbation of pathways or processes found to be of significance. It is hoped that by targeting evolutionarily conserved pathways at the level of pathogen and host broad spectrum targets can be identified. In addition to the host-pathogen work, as we run a sequencing core I have collaborations with many groups both inside and outside UCD- working from microbial to human, ancient to modern and genome to transcriptiome Finally as the Bioinformatics PI of the SFI funded research cluster in Reproductive Biology we are involved in the analysis of large scale transcriptomics datasets using RNA.seq
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Research Projects
| Sponsor : Science Foundation Ireland (SFI) University College Dublin (UCD) Title : Next Generation sequencing platform Start Date / End Date : 01-DEC-07 / 30-MAY-08 |
| Sponsor : Science Foundation Ireland (SFI) Title : Modelling the whole host response to pathogens Start Date / End Date : 01-NOV-06 / 31-DEC-12 |
Book Chapters
| Loftus, B. ; (2003) 'Genome sequencing, assembly and gene prediction in fungi' In: D. K. Arora and Khachatourians, G. G (eds). Fungal Genomics. *: Elsevier Science. [Details] |
| Mann, BJ, Loftus, BJ. ; (2002) 'The Molecular Biology and Pathogenicity of Entamoeba histolytica' In: Karen Joy Shaw (eds). Pathogen Genomics: Impact on Human Health. Totowa, NJ: Humana Press, Inc. [Details] |
Peer Reviewed Journals
| Pozzi, C., Waters, E.M. Rudkin, J.K., Schaeffer, C.R., Lohan, A.J., Tong, P., Loftus, B.J., Pier, G.B., Fey, P.D., Massey, R.C. and O'Gara, J.P. (2012) 'Methicillin Resistance Alters the Biofilm Phenotype and Attenuates Virulence in Staphylococcus aureus Device-Associated Infections'. PLoS Pathogens, 8 (4):e-1002626. [Details] |
Weissenmayer BA, Prendergast JG, Lohan AJ, Loftus BJ; (2011) 'Sequencing Illustrates the Transcriptional Response of Legionella pneumophila during Infection and Identifies Seventy Novel Small Non-Coding RNAs'. PLoS ONE, .  [Details] |
| Tong P, Prendergast JG, Lohan AJ, Farrington SM, Cronin S, Friel N, Bradley DG, Hardiman O, Evans A, Wilson JF, Loftus B.; (2010) 'Sequencing and analysis of an Irish human genome'. Genome Biology, . [Details] |
| Edwards, C. J.Edwards, C. J.,Magee, D. A.Magee, D. A.,Park, S. D.Park, S. D.,McGettigan, P. A.McGettigan, P. A.,Lohan, A. J.Lohan, A. J.,Murphy, A.Murphy, A.,Finlay, E. K.Finlay, E. K.,Shapiro, B.Shapiro, B.,Chamberlain, A. T.Chamberlain, A. T.,Richards, M. B.Richards, M. B.,Bradley, D. G.Bradley, D. G.,Loftus, B. J.Loftus, B. J.,Machugh, D. E.Machugh, D. E.; (2010) 'A complete mitochondrial genome sequence from a mesolithic wild aurochs (Bos primigenius)'. PLoS ONE, 5 (22). [Details] |
| McGivney BA, McGettigan PA, Browne JA, Evans AC, Fonseca RG, Loftus BJ, Lohan A, MacHugh DE, Murphy BA, Katz LM, Hill EW.; (2010) 'Characterization of the equine skeletal muscle transcriptome identifies novel functional responses to exercise training'. BMC Genomics, 11 . [Details] |
| Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B et al; (2007) 'Genome Sequence of Aedes aegypti, a Major Arbovirus Vector'. Science, 316 :1718-1723. [Details] | |||||||||
| Lobo NF, Campbell KS, Thaner D, Debruyn B, Koo H, Gelbart WM, Loftus BJ, Severson DW, Collins FH.; (2007) 'Analysis of 14 BAC sequences from the Aedes aegypti genome: a benchmark for genome annotation and assembly'. Genome Biology, 8 (5). [Details] | |||||||||
| Loftus, B. et al; (2005) 'The genome of the protist parasite Entamoeba histolytica'. Nature, 433 (7028):865-868. [Details] | |||||||||
| Loftus, B.J et al ; (2005) 'The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans'. Science, 307 (5713):1321-1324. [Details] | |||||||||
| Graham Clark, Ibne Karim M. Ali, Mehreen Zaki, Brendan J. Loftus and Neil Hall. ; (2006) 'Unique organization of tRNA genes in the protistan parasite Entamoeba histolytica'. Molecular and Biochemical Parasitology, 146 (1):24-29. [Details] | |||||||||
| Yumiko Saito-Nakano, Brendan J. Loftus, Neil Hall and Tomoyoshi Nozaki. ; (2005) 'The diversity of Rab GTPases in Entamoeba histolytica'. Experimental Parasitology, 10 (3):244-252. [Details] | |||||||||
| Loftus, B.J., Hall, N.; (2005) 'Entamoeba: still more to be learned from the genome'. Trends in Parasitology, 21 (10). [Details] | |||||||||
| Anderson, I.J., Loftus, B.J. ; (2005) 'Entamoeba histolytica: Observations on metabolism based on the genome sequence'. Experimental Parasitology, 110 (3):173-177. [Details] | |||||||||
| Iain J. Anderson, Russell F. Watkins, John Samuelson, David F. Spencer, Michael W. Gray, and Brendan J. Loftus. ; (2005) 'Gene discovery in the Acanthamoeba castellanii genome'. Protist, 156 (2):203-214. [Details] | |||||||||
| Holt, R.A., et al ; (2002) 'The genome sequence of the malaria mosquito Anopheles gambiae'. Science, 298 (5591):129-49. [Details] | |||||||||
| Nixon, J.E., Wang, A., Morrison, H.G., McArthur, A.G., Sogin, M.L., Loftus, B.J. and Samuelson, J.; (2002) 'A spliceosomal intron in Giardia lamblia'. Proceedings of the National Academy of Sciences, 99 (6):3701-3705. [Details] | |||||||||
| Loftus, B., Monks, E., Hanlon, J., Weavers, E., and Rogers, M.; (1999) 'Prion protein genotypes of Suffolk-type sheep representative of natural scrapie in Ireland'. IRISH VETERINARY JOURNAL, 52 :81-85. [Details] | |||||||||
| Haft, D.H., Loftus, B.J., Richardson, D.L., Yang, F., Eisen, J.A., Paulsen, I.T. and White, O. ; (2001) 'TIGRFAMs: a protein family resource for the functional identification of proteins'. Nucleic Acids Research, 29 (1):41-43. [Details] | |||||||||
| Tettelin, H et al ; (2001) 'Complete genome sequence of a virulent isolate of Streptococcus pneumoniae'. Science, 293 (5529):498-506. [Details] | |||||||||
| Horvath, J.E., Viggiano, L., Loftus, B.J., Adams, M.D., Archidiacono, N., Rocchi, M. and Eichler, E.E.; (2000) 'Molecular structure and evolution of an alpha satellite/nonalpha satellite junction at 16p11'. Human Molecular Genetics, 9 (1):113-123. [Details] | |||||||||
| Loftus, B.J., Kim, U.J., Sneddon, V.P., Kalush, F., Brandon, R., Fuhrmann, J., Mason, T., Crosby, M.L., Barnstead, M., Cronin, L., Deslattes Mays, A., Cao, Y., Xu, R.X., Kang, H.L., Mitchell, S., Eichler, E.E., Harris, P.C., Venter, J.C. and Adams, M.D. ; (1999) 'Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q'. Genomics, 60 (3):295-308. [Details] | |||||||||
| Klenk, H.P., et al ; (1997) 'The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus'. Nature, 390 (6658):364-370. [Details] | |||||||||
| Tomb, J.F., et al ; (1997) 'The complete genome sequence of the gastric pathogen Helicobacter pylori'. Nature, 388 (6642):539-547. [Details] | |||||||||
| Loftus B, Rogers M ; (1997) 'Characterization of a prion protein (PrP) gene from rabbit; a species with apparent resistance to infection by prions'. Gene, 184 (2):215-219. [Details] | |||||||||
| Severson, D.W., Knudson, D.L., Soares, M.B., Loftus, B.J. ; (2004) 'Aedes aegypti genomics'. Insect Biochem Mol Biol, 34 (7):715-721. [Details] | |||||||||
| Wang Z, Samuelson J, Clark CG, Eichinger D, Paul J, Van Dellen K, Hall N, Anderson I, Loftus B.; (2003) 'Gene discovery in the Entamoeba invadens genome'. Molecular and Biochemical Parasitology, 129 (1):23-31. [Details] | |||||||||
| Bruchhaus, I., Loftus, B.J., Hall, N. and Tannich, E. ; (2003) 'The Intestinal Protozoan Parasite Entamoeba histolytica Contains 20 Cysteine Protease Genes, of which only a small subset Is expressed during in vitro cultivation'. Eukaryotic Cell, 2 (3):501-509. [Details] | |||||||||
| Nixon, J.E., Field, J., McArthur, A.G., Sogin, M.L., Yarlett, N., Loftus, B.J. and Samuelson, J. ; (2003) 'Iron-Dependent Hydrogenases of Entamoeba histolytica and Giardia lamblia: Activity of the Recombinant Entamoebic Enzyme and Evidence for Lateral Gene Transfer'. Biological Bulletin, 204 (1):1-9. [Details] | |||||||||
| Van Dellen, K., Ghosh, S.K., Robbins, P.W., Loftus, B. and Samuelson, J.; (2002) 'Entamoeba histolytica lectins contain unique 6-Cys or 8-Cys chitin-binding domains'. Infection and Immunity, 70 (6):3259-3263. [Details] | |||||||||
| Loftus, B,Rogers, M; (1997) 'Characterization of a prion protein (PrP) gene from rabbit; A species with apparent resistance to infection by prions'. Gene, 184 :215-219. [Details] | |||||||||
| Loftus, B,Monks, E,Hanlon, J,Weavers, E,Rogers, M; (1999) 'Prion protein genotypes of Suffolk-type sheep representative of natural scrapie in Ireland'. Irish Veterinary Journal, 52 :81-85. [Details] | |||||||||
| Beck, D.L., Tanyuksel, M., Mackey, A.J., Haque, R., Trapaidze, N., Pearson, W.R., Loftus, B. and Petri, W.A. ; (2002) 'Entamoeba histolytica: sequence conservation of the Gal/GalNAc lectin from clinical isolates'. Experimental Parasitology, 101 (2-3):157-163. [Details] | |||||||||
| Cheng, X.J., Hughes, M.A., Huston, C.D., Loftus, B., Gilchrist, C.A., Lockhart, L.A., Ghosh, S., Miller-Sims, V., Mann, B.J., Petri, W.A., Jr. and Tachibana, H.; (2001) 'Intermediate subunit of the Gal/GalNAc lectin of Entamoeba histolytica is a member of a gene family containing multiple CXXC sequence motifs'. Infection and Immunity, 69 (9):5892-5898. [Details] | |||||||||
| Loftus B, Monks E, Hanlon J, et al.; (1999) 'Prion protein genotypes of Suffolk-type sheep representative of natural scrapie in Ireland'. Irish Veterinary Journal, 52 (2):81-85. [Details] | |||||||||
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Conference Publications
| O¿Sullivan NC, McGettigan PA, Loftus B and Murphy KJ (2009) Identification of functional gene regulatory elements in the hippocampus of a rat model of schizophrenia using FAIRE-seq Neuroscience Ireland [Details] |
| Forde N, McGettigan PA, Browne JA, Carter F, Loftus BJ, Roche JF, Lonergan P, Crowe MA, and Evans ACO; (2009) Pregnancy specific endometrial gene expression at the initiation of conceptus elongation in cattle 42nd Annual meeting of the Society for the Study of Reproduction, Biology of Reproduction 81, Abstract 303 Pittsburgh, , 18-JUL-09 - 22-JUL-09 [Details] |
Honours and Awards
| Year: 2007. Title: Next Generation sequencing platform |
| Year: 2006. Title: SFI Research Professorship |
| Year: 2000. Title: Entamoeba genomics R01-AI46516-01A1 |
| Year: 2000. Title: Cryptococcus U01-AI48594-01 |
| Year: 2001. Title: Aedes Aegypti genomics U01-48846-01 |
| Year: 2002. Title: Comparative mosquito genomics (NIH) (Subcontract to R01-AI42121) |
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| Year: 2002. Title: Comparative genomics of Anopheline mosquitoes (NIH) (Subcontract to R21-AI063252) |
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| Year: 2002. Title: Genome sequencing of Aedes aegypti as part of Microbial sequencing contract for biodefense related organisms N01-AI-30071 (NIAID) |
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Conference Contributions
| Loftus B, J. Harmey, T. Barry, M. Rogers; Cloning and sequencing of the rabbit prion protein gene. [Non Refereed Paper/Abstract Presented at Conference], Irish Genetical society meeting, Belfast.1993, Belfast . |
Committees
| Committee : UCD research board 2008-2009 |
| Committee : Conway Insittue Strategy board |
| Committee : Conway Institute executive committee |
| Committee : Chairman Conway core technology (genomics) steering committee |
Education
| Year 1992 Institution: Dublin City University (DCU), IRL Qualification: BSc Subject: |
| Year 1996 Institution: University College Dublin Qualification: PhD Subject: |
Outreach Activities
| Expert evaluator for FP7 Marie Curie Fellowship grant |
Reviews
| Briefings In Bioinformatics: Reviewer. |
| Plos Genetics: Reviewer. |
| Genome Research: Reviewer. |
| Plos One: Reviewer. |
| Molecular And Biochemical Parasitology: Reviewer. |
Modules Coordinated
| 201200 CNWY40150 Conway Institute: Genomics -Principles&Practical |