Researchers at UCD


Brendan Loftus

Conway Institute of Biomolecular & Biomedical Research
RM G043
Conway Institute
University College Dublin
Belfield, Dublin 4



My research publications can be viewed at Google Scholar

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.

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. 




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)
Year: 2002.
Title: Comparative genomics of Anopheline mosquitoes (NIH) (Subcontract to R21-AI063252)
Year: 2002.
Title: Genome sequencing of Aedes aegypti as part of Microbial sequencing contract for biodefense related organisms N01-AI-30071 (NIAID)

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 .


Committee : UCD research board 2008-2009
Committee : Conway Insittue Strategy board
Committee : Conway Institute executive committee
Committee : Chairman Conway core technology (genomics) steering committee


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

Journals Edited

Briefings In Bioinformatics: Reviewer.
Plos Genetics: Reviewer.
Genome Research: Reviewer.
Plos One: Reviewer.
Molecular And Biochemical Parasitology: Reviewer.



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. , pp.65-81 [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

Dinan AM, Tong P, Lohan AJ, Conlon KM, Miranda-CasoLuengo AA, Malone KM, Gordon SV, Loftus BJ (2014) 'Relaxed Selection Drives a Noisy Noncoding Transcriptome in Members of the Mycobacterium tuberculosis Complex'. mBio, . Available Online [Details]
Martin-Navarro, CM,Lorenzo-Morales, J,Machin, RP,Lopez-Arencibia, A,Garcia-Castellano, JM,de Fuentes, I,Loftus, B,Maciver, SK,Valladares, B,Pineroa, JE (2013) 'Inhibition of 3-Hydroxy-3-Methylglutaryl-Coenzyme A Reductase and Application of Statins as a Novel Effective Therapeutic Approach against Acanthamoeba Infections'. Antimicrobial Agents and Chemotherapy, 57 :375-381. [DOI] [Details]
Adam M. Dinan and Brendan J. Loftus (2013) '(Non)translational medicine: RNA-based therapeutics in bacteria'. Frontiers in Bioscience, . Available Online [Details]
Nalpas, NC,Park, SDE,Magee, DA,Taraktsoglou, M,Browne, JA,Conlon, KM,Rue-Albrecht, K,Killick, KE,Hokamp, K,Lohan, AJ,Loftus, BJ,Gormley, E,Gordon, SV,MacHugh, DE (2013) 'Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro'. BMC Genomics, 14 . [DOI] [Details]
Firdessa R, Berg S, Hailu E, Schelling E, Gumi B, Erenso G, Gadisa E, Kiros T, Habtamu M, Hussein J, Zinsstag J, Robertson BD, Ameni G, Lohan AJ, Loftus B, Comas I, Gagneux S, Tschopp R, Yamuah L, Hewinson G, Gordon SV, Young DB, Aseffa A. (2013) 'Mycobacterial lineages causing pulmonary and extrapulmonary tuberculosis, Ethiopia'. Emerging Infectious Diseases, . [Details]
Pawlik A, Garnier G, Orgeur M, Tong P, Lohan A, Le Chevalier F, Sapriel G, Roux AL, Conlon K, Honoré N, Dillies MA, Ma L, Bouchier C, Coppée JY, Gaillard JL, Gordon SV, Loftus B, Brosch R, Herrmann JL. (2013) 'Identification and characterization of the genetic changes responsible for the characteristic smooth-to-rough morphotype alterations of clinically persistent Mycobacterium abscessus'. Molecular Microbiology, . [Details]
ÓMaoiléidigh DS, Wuest SE, Rae L, Raganelli A, Ryan PT, Kwasniewska K, Das P, Lohan AJ, Loftus B, Graciet E, Wellmer F (2013) 'Control of reproductive floral organ identity specification in Arabidopsis by the C function regulator AGAMOUS'. Plant Cell, . [Details]
Nalpas, N. C., Park, S. D., Magee, D. A., Taraktsoglou, M., Browne, J. A., Conlon, K. M., Rue-Albrecht, K., Killick, K. E., Hokamp, K., Lohan, A. J., Loftus, B. J., Gormley, E., Gordon, S. V., Machugh, D. E. (2013) 'Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro'. BMC Genomics, 14 (1). [Details]
Clarke M, Lohan AJ, Liu B, Lagkouvardos I, Roy S, Zafar N, Bertelli C, Schilde C, Kianianmomeni A, Burglin TR, Frech C, Turcotte B, Kopec KO, Synnott JM, Choo C, Paponov I, Finkler A, Soon Heng Tan C, Hutchins AP, Weinmeier T, Rattei T, Chu JS, Gimenez G, Irimia M, Rigden DJ, Fitzpatrick DA, Lorenzo-Morales J, Bateman A, Chiu CH, Tang P, Hegemann P, Fromm H, Raoult D, Greub G, Miranda-Saavedra D, Chen N, Nash P, Ginger ML, Horn M, Schaap P, Caler L, Loftus B (2013) 'Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling'. Genome Biology, . Available Online [Details]
Brien GL, Gambero G, O'Connell DJ, Jerman E, Turner SA, Egan CM, Dunne EJ, Jurgens MC, Wynne K, Piao L, Lohan AJ, Ferguson N, Shi X, Sinha KM, Loftus BJ, Cagney G, Bracken AP (2012) 'Polycomb PHF19 binds H3K36me3 and recruits PRC2 and demethylase NO66 to embryonic stem cell genes during differentiation'. Nature structural & molecular biology, . [DOI] [Details]
Kröger C, Dillon SC, Cameron AD, Papenfort K, Sivasankaran SK, Hokamp K, Chao Y, Sittka A, Hébrard M, Händler K, Colgan A, Leekitcharoenphon P, Langridge GC, Lohan AJ, Loftus B, Lucchini S, Ussery DW, Dorman CJ, Thomson NR, Vogel J, Hinton JC (2012) 'The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium'. Proceedings of the National Academy of Sciences of the United States of America, 109 (20):1-86. [DOI] [Details]
Wuest SE, O'Maoileidigh DS, Rae L, Kwasniewska K, Raganelli A, Hanczaryk K, Lohan AJ, Loftus B, Graciet E, Wellmer F (2012) 'Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA'. Proceedings of the National Academy of Sciences of the United States of America, 109 (33):13452-13457. [DOI] [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, . Available Online [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, . Available Online [Details]
Pozzi C, Waters EM, Rudkin JK, Schaeffer CR, Lohan AJ, Tong P, Loftus BJ, Pier GB, Fey PD, Massey RC and O'Gara JP (2012) 'Methicillin Resistance Alters the Biofilm Phenotype and Attenuates Virulence in Staphylococcus aureus Device-Associated Infections'. PLoS Pathogens, 8 (4):e-1002626. [Details]
McGivney, BA,McGettigan, PA,Browne, JA,Evans, ACO,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 . [DOI] [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). Available Online [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]
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]
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]
Loftus, B. et al; (2005) 'The genome of the protist parasite Entamoeba histolytica'. Nature, 433 (7028):865-868. [Details]
Loftus, B.J., Hall, N.; (2005) 'Entamoeba: still more to be learned from the genome'. Trends in Parasitology, 21 (10). [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]
Anderson, I.J., Loftus, B.J. ; (2005) 'Entamoeba histolytica: Observations on metabolism based on the genome sequence'. Experimental Parasitology, 110 (3):173-177. [Details]
Loftus, B.J et al ; (2005) 'The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans'. Science, 307 (5713):1321-1324. [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]
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]
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]
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]
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]
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]
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]
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]
Klenk, H.P., et al ; (1997) 'The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus'. Nature, 390 (6658):364-370. [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]
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]

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]


Research Interests

Our Lab now works primarily on the rapidly growing mycobacterium Mycobacterium abscessus. M. abscessus is an important human pathogen and one of the most important mycobacteria involved in broncho-pulmonary infection in patients with cystic fibrosis or chronic pulmonary disease. The intrinsic and acquired resistance of Mycobacterium abscessus to commonly used antibiotics limits the chemotherapeutic options for infections involving M. abscessus.
M. abscessus manifests as either a smooth (S) or a rough (R) colony morphotype, which is of clinical importance as R morphotypes are associated with more severe and persistent infections.

Our lab works on a number of aspects of the virulence of M. abscessus including the transition from smooth to rough (PMID:2399876) and the regulation of its transcriptome by small non coding RNAs and their use as potential therapeutic targets (PMID:24265632).

We are also looking at the differential host response to the differing morphotypes using dual RNA-seq of host and pathogen in a macrophage infection model and using quantiative proteomics approaches to determine the host-pathogen interface during infection..

Finally we are studying mechanisms of innate antibiotic resistance found in M. abscessus which are shared across all mycobacteria  

In addition to the host-pathogen work, we run a sequencing core involving collaborations with many groups both inside and outside UCD- working from microbial to human, ancient to modern and genome to transcriptiome to translatome.

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-JAN-15