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Researchers at UCD

researcher

John Browne

Senior Technical Officer

School Of Agriculture & Food Science
Veterinary Science Centre
Belfield
Dublin 4

Tel: +353 1 7166243
Email: john.a.browne@ucd.ie

Biography

Dr. John Browne is a senior technical officer in the School of Agriculture and Food Science in UCD. He successfully completed his PhD studies in NUI Maynooth where he gained a thorough understanding of the challenges of working with RNA and developed expertise in a number of methods to identify differentially expressed genes.  After completing a postdoctoral fellowship in clinical research he returned to animal science in UCD where he is responsible for managing both the Transcriptomics and the Containment Level 3 Laboratories.  He contributes directly to a number of funded research projects and has extensive expertise in the use of qPCR and next generation sequencing to study gene expression. He is actively involved in promoting best practice for qPCR experiments through the MIQE guidelines, and has received certified training in the management of Containment Level 3 facilities.

Publications

     

Peer Reviewed Journals

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]
Morine MJ, Toomey S, McGillicuddy FC, Reynolds CM, Power KA, Browne JA, Loscher C, Mills KH, Roche HM. (2013) 'Network analysis of adipose tissue gene expression highlights altered metabolic and regulatory transcriptomic activity in high-fat-diet-fed IL-1RI knockout mice'. Journal of Nutritional Biochemistry, 24 :788-799. [Details]
Vegh, P., Foroushani, A. B., Magee, D. A., McCabe, M. S., Browne, J. A., Nalpas, N. C., Conlon, K. M., Gordon, S. V., Bradley, D. G., Machugh, D. E., Lynn, D. J. (2013) 'Profiling microRNA expression in bovine alveolar macrophages using RNA-seq'. Vet Immunol Immunopathol, 155 (4):238-44. [Details]
Vegh P, Foroushani AB, Magee DA, McCabe MS, Browne JA, Nalpas NC, Conlon KM, Gordon SV, Bradley DG, Machugh DE, Lynn DJ (2013) 'Profiling microRNA expression in bovine alveolar macrophages using RNA-seq'. VET IMMUNOL IMMUNOP, 155 (4):238-244. [DOI] [Details]
MacHugh, D. E., Gormley, E., Park, S. D. E., Browne, J. A., Taraktsoglou, M., O'Farrelly, C., Meade, K. G. (2009) 'Gene Expression Profiling of the Host Response to Mycobacterium bovis Infection in Cattle'. Transboundary and Emerging Diseases, 56 (6-7):204-214. Available Online [Details]
Hill, E. W., Eivers, S. S., McGivney, B. A., Fonseca, R. G., Gu, J., Smith, N. A., Browne, J. A., MacHugh, D. E., Katz, L. M. (2010) 'Moderate and high intensity sprint exercise induce differential responses in COX4I2 and PDK4 gene expression in Thoroughbred horse skeletal muscle'. Equine Veterinary Journal, 42 :576-581. Available Online [Details]
Killick, K. E., Browne, J. A., Park, S. D., Magee, D. A., Martin, I., Meade, K. G., Gordon, S. V., Gormley, E., O'Farrelly, C., Hokamp, K., MacHugh, D. E. (2011) 'Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genes'. BMC Genomics, 12 . Available Online [Details]
Killick, KE,Browne, JA,Park, SDE,Magee, DA,Martin, I,Meade, KG,Gordon, SV,Gormley, E,O'Farrelly, C,Hokamp, K,MacHugh, DE (2011) 'Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genes'. BMC Genomics, 12 . [DOI] [Details]
McGivney, BA,Browne, JA,Fonseca, RG,Katz, LM,MacHugh, DE,Whiston, R,Hill, EW (2012) 'MSTN genotypes in Thoroughbred horses influence skeletal muscle gene expression and racetrack performance'. Animal Genetics, 43 :810-812. [DOI] [Details]
Pluta, K,McGettigan, PA,Reid, CJ,Browne, JA,Irwin, JA,Tharmalingam, T,Corfield, A,Baird, A,Loftus, BJ,Evans, ACO,Carrington, SD (2012) 'Molecular aspects of mucin biosynthesis and mucus formation in the bovine cervix during the periestrous period'. Physiological genomics, 44 :1165-1178. [DOI] [Details]
Walsh, SW,Fair, T,Browne, JA,Evans, ACO,McGettigan, PA (2012) 'Physiological status alters immunological regulation of bovine follicle differentiation in dairy cattle'. JOURNAL OF REPRODUCTIVE IMMUNOLOGY, 96 :34-44. [DOI] [Details]
Mansouri-Attia, N,Oliveira, LJ,Forde, N,Fahey, AG,Browne, JA,Roche, JF,Sandra, O,Reinaud, P,Lonergan, P,Fair, T (2012) 'Pivotal Role for Monocytes/Macrophages and Dendritic Cells in Maternal Immune Response to the Developing Embryo in Cattle'. Biology of Reproduction, 87 . [DOI] [Details]
Walsh SW, Matthews D, Browne JA, Forde N, Crowe MA, Mihm M, Diskin M, Evans AC (2012) 'Acute dietary restriction in heifers alters expression of genes regulating exposure and response to gonadotrophins and IGF in dominant follicles'. Animal Reproduction Science, 133 (1-2):43-51. [DOI] [Details]
Mansouri-Attia N, Oliveira LJ, Forde N, Fahey AG, Browne JA, Roche JF, Sandra O, Reinaud P, Lonergan P, Fair T (2012) 'Pivotal Role for Monocytes/Macrophages and Dendritic Cells in Maternal Immune Response to the Developing Embryo in Cattle'. Biology of Reproduction, . [DOI] [Details]
Pluta K, McGettigan PA, Reid CJ, Browne JA, Irwin JA, Tharmalingam T, Corfield A, Baird A, Loftus BJ, Evans AC, Carrington SD. (2012) 'Molecular aspects of mucin biosynthesis and mucus formation in the bovine cervix during the periestrous period'. Physiological genomics, . [Details]
Sheridan, MP,Browne, JA,MacHugh, DE,Costello, E,Gormley, E (2012) 'Impact of delayed processing of bovine peripheral blood on differential gene expression'. VET IMMUNOL IMMUNOP, 145 :199-205. [DOI] [Details]
Magee, DA,Taraktsoglou, M,Killick, KE,Nalpas, NC,Browne, JA,Park, SDE,Conlon, KM,Lynn, DJ,Hokamp, K,Gordon, SV,Gormley, E,MacHugh, DE (2012) 'Global Gene Expression and Systems Biology Analysis of Bovine Monocyte-Derived Macrophages in Response to In Vitro Challenge with Mycobacterium bovis'. PLoS ONE, 7 . [DOI] [Details]
Walsh, SW,Mehta, JP,McGettigan, PA,Browne, JA,Forde, N,Alibrahim, RM,Mulligan, FJ,Loftus, B,Crowe, MA,Matthews, D,Diskin, M,Mihm, M,Evans, ACO (2012) 'Effect of the metabolic environment at key stages of follicle development in cattle: focus on steroid biosynthesis'. Physiological genomics, 44 :504-517. [DOI] [Details]
MacHugh, DE,Taraktsoglou, M,Killick, KE,Nalpas, NC,Browne, JA,Park, SDE,Hokamp, K,Gormley, E,Magee, DA (2012) 'Pan-genomic analysis of bovine monocyte-derived macrophage gene expression in response to in vitro infection with Mycobacterium avium subspecies paratuberculosis'. Veterinary Research, 43 . [DOI] [Details]
Walsh, SW,Matthews, D,Browne, JA,Forde, N,Crowe, MA,Mihm, M,Diskin, M,Evans, ACO (2012) 'Acute dietary restriction in heifers alters expression of genes regulating exposure and response to gonadotrophins and IGF in dominant follicles'. Animal Reproduction Science, 133 :43-51. [DOI] [Details]
Forde, N,Duffy, GB,McGettigan, PA,Browne, JA,Mehta, JP,Kelly, AK,Mansouri-Attia, N,Sandra, O,Loftus, BJ,Crowe, MA,Fair, T,Roche, JF,Lonergan, P,Evans, ACO (2012) 'Evidence for an early endometrial response to pregnancy in cattle: both dependent upon and independent of interferon tau'. Physiological genomics, 44 :799-810. [DOI] [Details]
Machugh, D. E., Taraktsoglou, M., Killick, K. E., Nalpas, N. C., Browne, J. A., D. E. Park S, Hokamp, K., Gormley, E., Magee, D. A. (2012) 'Pan-genomic analysis of bovine monocyte-derived macrophage gene expression in response to in vitro infection with Mycobacterium avium subspecies paratuberculosis'. Veterinary Research, 43 (1). Available Online [Details]
Magee, D. A., Taraktsoglou, M., Killick, K. E., Nalpas, N. C., Browne, J. A., Park, S. D., Conlon, K. M., Lynn, D. J., Hokamp, K., Gordon, S. V., Gormley, E., MacHugh, D. E. (2012) 'Global gene expression and systems biology analysis of bovine monocyte-derived macrophages in response to in vitro challenge with Mycobacterium bovis'. PLoS ONE, 7 (2). Available Online [Details]
MacHugh, D. E., Taraktsoglou, M., Killick, K. E., Nalpas, N. C., Browne, J. A., D. E. Park S, Hokamp, K., Gormley, E., Magee, D. A. (2012) 'Pan-genomic analysis of bovine monocyte-derived macrophage gene expression in response to in vitro infection with Mycobacterium avium subspecies paratuberculosis'. Veterinary Research, 43 (1). Available Online [Details]
B McGivney, J Browne, R Fonseca, D MacHugh, R Whiston, L Katz, E Hill ; (2012) 'MSTN genotypes in Thoroughbred horses influence skeletal muscle gene expression and racetrack performance'. Animal Genetics, 43 (6). [DOI] [Details]
Walsh SW, Fair T, Browne JA, Evans AC, McGettigan PA. (2012) 'Physiological status alters immunological regulation of bovine follicle differentiation in dairy cattle'. JOURNAL OF REPRODUCTIVE IMMUNOLOGY, . [Details]
Forde N, Duffy GB, McGettigan PA, Browne JA, Mehta JP, Kelly AK, Mansouri-Attia N, Sandra O, Loftus BJ, Crowe MA, Fair T, Roche JF, Lonergan P, Evans AC. (2012) 'Evidence for an early endometrial response to pregnancy in cattle: both dependent upon and independent of interferon tau'. Physiolgical Genomics, 44 (16):799-810. [Details]
Morine, MJ; Toomey, S; McGillicuddy, FC; Reynolds, CM; Power, KA; Browne, JA; Loscher, C; Mills, KH; Roche, HM (2012) 'Network analysis of adipose tissue gene expression highlights altered metabolic and regulatory transcriptomic activity in high fat diet-fed IL-1RI knock-out mice'. Journal of Nutritional Biochemistry, . [Details]
Morine, M. J., Toomey, S., McGillicuddy, F. C., Reynolds, C. M., Power, K. A., Browne, J. A., Loscher, C., Mills, K. H., Roche, H. M. (2012) 'Network analysis of adipose tissue gene expression highlights altered metabolic and regulatory transcriptomic activity in high-fat-diet-fed IL-1RI knockout mice'. J Nutr Biochem, . Available Online [Details]
Walsh SW, Matthews D, Browne JA Forde N, Crowe MA, Mihm M, Diskin MG, Evans ACO (2012) 'Acute dietary restriction in heifers alters expression of genes regulating exposure and response to gonadotrophins and IGF in dominant follicles'. Animal Reproduction Science, 133 (1-2):43-51. Available Online [DOI] [Details]
Pluta K, McGettigan PA, Reid CJ, Browne JA, Irwin JA, Tharmalingam T, Corfield A, Baird AW, Loftus BJ, Evans AC, Carrington SD (2012) 'Molecular aspects of mucin biosynthesis and mucus formation in the bovine cervix during the periestrous period'. Physiological genomics, . [DOI] [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]
Kelly AK, Waters SM, McGee M, Browne JA, Magee DA, Kenny DA (2013) 'Expression of key genes of the somatotropic axis in longissimus dorsi muscle of beef heifers phenotypically divergent for residual feed intake'. Journal of Animal Science, 91 (1):159-167. [DOI] [Details]
Regeai, SO,Dolan, KM,Fitzpatrick, DA,Browne, JA,Jones, JT,Burnell, AM; (2009) 'Novel primers for the amplification of nuclear DNA introns in the entomopathogenic nematode Heterorhabditis bacteriophora and their cross-amplification in seven other Heterorhabditis species'. Ecology, 9 :421-424. [DOI] [Details]
McGivney BA, Browne JA, Fonseca RG, Katz LM, Machugh DE, Whiston R, Hill EW (2012) 'MSTN genotypes in Thoroughbred horses influence skeletal muscle gene expression and racetrack performance'. Gene, . [DOI] [Details]
Forde N, Duffy GB, McGettigan PA, Browne JA, Mehta JP, Kelly AK, Mansouri-Attia N, Sandra O, Loftus BJ, Crowe MA, Fair T, Roche JF, Lonergan P, Evans AC (2012) 'Evidence for an early endometrial response to pregnancy in cattle: both dependent upon and independent of interferon tau'. Genomics, 44 (16):799-810. [DOI] [Details]
Morine MJ, Toomey S, McGillicuddy FC, Reynolds CM, Power KA, Browne JA, Loscher C, Mills KH, Roche HM (2012) 'Network analysis of adipose tissue gene expression highlights altered metabolic and regulatory transcriptomic activity in high-fat-diet-fed IL-1RI knockout mice'. The Journal of nutrition, . [DOI] [Details]
Walsh SW, Mehta JP, McGettigan PA, Browne JA, Forde N, Alibrahim RM, Mulligan FJ, Loftus B, Crowe MA, Matthews D, Diskin M, Mihm M, Evans AC (2012) 'Effect of the metabolic environment at key stages of follicle development in cattle: focus on steroid biosynthesis'. Genomics, 44 (9):504-517. [DOI] [Details]
Machugh DE, Taraktsoglou M, Killick KE, Nalpas NC, Browne JA, Park SD, Hokamp K, Gormley E, Magee DA (2012) 'Pan-genomic analysis of bovine monocyte-derived macrophage gene expression in response to in vitro infection with Mycobacterium avium subspecies paratuberculosis'. Veterinary Research, 43 (1). [DOI] [Details]
Magee DA, Taraktsoglou M, Killick KE, Nalpas NC, Browne JA, Park SD, Conlon KM, Lynn DJ, Hokamp K, Gordon SV, Gormley E, MacHugh DE (2012) 'Global gene expression and systems biology analysis of bovine monocyte-derived macrophages in response to in vitro challenge with Mycobacterium bovis'. PLoS ONE, 7 (2). [DOI] [Details]
Sheridan MP, Browne JA, MacHugh DE, Costello E, Gormley E (2012) 'Impact of delayed processing of bovine peripheral blood on differential gene expression'. VET IMMUNOL IMMUNOP, 145 (1-2):199-205. [DOI] [Details]
Devitt, E. J., Power, K. A., Lawless, M. W., Browne, J. A., Gaora, P. O., Gallagher, W. M., and Crowe, J. ; (2011) 'Early proteomic analysis may allow noninvasive identification of hepatitis C response to treatment with pegylated interferon α-2b and ribavirin'. European Journal of Gastroenterology & Hepatology, 23 (2):177-183. [Details]
Killick KE, Browne JA, Park SD, Magee DA, Martin I, Meade KG, Gordon SV, Gormley E, O'Farrelly C, Hokamp K, MacHugh DE (2011) 'Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genes'. BMC Genomics, 12 . [DOI] [Details]
Taraktsoglou, M., Szalabska, U., Magee, D.A., Browne, J.A., Sweeney, T., Gormley, E., MacHugh, D.E.; (2011) 'Transcriptional profiling of immune genes in bovine monocyte-derived macrophages exposed to bacterial antigens'. Veterinary Immunology and Immunopathology, 140 :130-139. Available Online [DOI] [Details]
Martin, A.M., Elliott, J.A., Duffy, P., Blake, C., Attia, S.B., Browne, J.A., Katz, L.M., Gath, V., McGivney, B.A., Hill, E.W., Murphy, B.A. ; (2010) 'Circadian regulation of locomotor activity and skeletal muscle gene expression in the horse'. Journal of Applied Physiology, 109 (5):1328-1336. Available Online [DOI] [Details]
McGlynn, OF,Browne, JA,Blake, CM,Murphy, BA; (2010) 'Time of day influences cytokine and clock gene response to immune stimulation in equine whole blood'. Animal Genetics, 41 :202-204. [DOI] [Details]
Devitt, E,Lawless, MW,Sadlier, D,Browne, JA,Walsh, C,Crowe, J; (2010) 'Early viral and peripheral blood mononuclear cell responses to pegylated interferon and ribavirin treatment: the first 24 h'. European Journal of Gastroenterology & Hepatology, 22 :1211-1220. [DOI] [Details]
Hill, E.W., Eivers, S.S., McGivney, B.A., Fonseca, R.G., Gu, J., Smith, N.A., Browne, J.A., MacHugh, D.E., Katz, L.M.; (2010) 'Moderate and high intensity sprint exercise induce differential responses in COX4I2 and PDK4 gene expression in Thoroughbred horse skeletal muscle'. Equine Veterinary Journal, 42 :576-581576. Available Online [DOI] [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]
de Ross, B,Rungapamestry, V,Ross, K,Rucklidge, G,Reid, M,Duncan, G,Horgan, G,Toomey, S,Browne, J,Loscher, CE,Mills, KHG,Roche, HM; (2009) 'Attenuation of inflammation and cellular stress-related pathways maintains insulin sensitivity in obese type I interleukin-1 receptor knockout mice on a high-fat diet'. Proteomics, 9 :3244-3256. [DOI] [Details]
Machugh DE, Gormley E, Park SD, Browne JA, Taraktsoglou M, O'Farrelly C, Meade KG; (2009) 'Gene Expression Profiling of the Host Response to Mycobacterium bovis Infection in Cattle'. Transboundary and emerging diseases, . Available Online [DOI] [Details]
Tyson, T, Reardon, W, Browne, JA, Burnell, AM, ; (2007) 'Gene induction by desiccation stress in the entomopathogenic nematode Steinernema carpocapsae reveals parallels with drought tolerance mechanisms in plants'. International Journal for Parasitology, 37 :763-776. [Details]
Burnell AM, Shannon AJ, Browne JA, Boyd J, Fitzpatrick DA, ; (2005) 'The anhydrobiotic potential and molecular phylogenetics of species and strains of Panagrolaimus (Nematoda, Panagrolaimidae)'. Experimental Biology, 208 (Pt 12):2433-2445. [DOI] [Details]
Tunnacliffe A, Goyal K, Browne JA, Burnell AM, ; (2005) 'Dehydration-induced tps gene transcripts from an anhydrobiotic nematode contain novel spliced leaders and encode atypical GT-20 family proteins'. Biochimie, 87 (6):565-574. [DOI] [Details]
De Roos B, Rucklidge G, Reid M, Pickard K, Navarro MA, Arbones-Mainar JM, Guzman-Garcia MA, Osada J, Browne J, Loscher CE & Roche HM.; (2005) 'Divergent mechanisms of cis9, trans11-and trans10, cis12-conjugated linoleic acid affecting insulin resistance and inflammation in apolipoprotein E knockout mice: a proteomics approach'. Faseb Journal, 19 :1746-1748. [Details]
Roche HM, de Roos B, Rucklidge G, Reid M, Ross K, Duncan G, Navarro MA, Arbones-Mainar JM, Guzman-Garcia MA, Osada J, Browne J, Loscher CE, ; (2005) 'Divergent mechanisms of cis9, trans11-and trans10, cis12-conjugated linoleic acid affecting insulin resistance and inflammation in apolipoprotein E knockout mice: a proteomics approach'. FASEB Journal, 19 (12):1746-1748. [DOI] [Details]
Goyal K, Walton LJ, Browne JA, Burnell AM, Tunnacliffe A; (2005) 'Molecular anhydrobiology: Identifying molecules implicated in invertebrate anhydrobiosis'. INTEGRATIVE AND COMPARATIVE BIOLOGY, 45 :702-709. [Details]
Browne JA, Dolan KM, Tyson T, Goyal K, Tunnacliffe A,Burnell AM, ; (2004) 'Dehydration-specific induction of hydrophilic protein genes in the anhydrobiotic nematode Aphelenchus avenae'. Eukaryotic Cell, 3 (4):966-975. [DOI] [Details]
Tunnacliffe A, Goyal K, Tisi L, Basran A, Browne J, Burnell A, Zurdo J, ; (2003) 'Transition from natively unfolded to folded state induced by desiccation in an anhydrobiotic nematode protein'. Journal of Biological Chemistry, 278 (15):12977-12984. [DOI] [Details]
Browne J, Tunnacliffe A,Burnell A, ; (2002) 'Anhydrobiosis: plant desiccation gene found in a nematode'. Nature, 416 (6876). [DOI] [Details]
 

Conference Publications

Taraktsoglou, M., Magee, D. A., Browne, J. A., Park, S. D., Szalabaska, U., Gormley, E., MacHugh, D. E. (2009) Functional genomics studies of bovine macrophages stimulated in vitro with Mycobacterium bovis and M. bovis BCGFunctional genomics studies of bovine macrophages stimulated in vitro with Mycobacterium bovis and M. bovis BCG Proceedings of the Fifth International M. bovis Conference Wellington, New Zealand, [Details]
Taraktsoglou, M., Magee, D. A., Browne, J. A., Park, S. D., Szalabaska, U., Gormley, E., MacHugh, D. E. (2009) Functional genomics studies of bovine macrophages stimulated in vitro with Mycobacterium bovis and M. bovis BCG. Proceedings of the Fifth International M. bovis Conference Wellington, New Zealand, [Details]
McGivney, B. A., McGettigan, P., Browne, J. A., Fonseca, R. G., Eivers, S. S., Evans, A. C., Loftus, B. J., Lohan, A., MacHugh, D. E., Katz, L. M., Hill, E. W. (2009) Digital gene expression profiling in Thoroughbred horse skeletal muscle following exercise training. Proceedings of The Physiological Society Meeting University College Dublin, Dublin, Ireland, [Details]
McGivney, B. A., McGettigan, P., Browne, J. A., Fonseca, R. G., Eivers, S. S., Evans, A. C., Loftus, B. J., Lohan, A., MacHugh, D. E., Katz, L. M., Hill, E. W. (2009) Digital gene expression profiling in Thoroughbred horse skeletal muscle following exercise trainingDigital gene expression profiling in Thoroughbred horse skeletal muscle following exercise training Proceedings of The Physiological Society Meeting University College Dublin, Dublin, Ireland, [Details]
MacHugh, D. E., Taraktsoglou, M., Magee, D. A., Browne, J. A., Park, S. D. E., Szalabaska, U., Gormley, E. (2009) A functional genomics study of bovine monocyte-derived macrophages stimulated in vitro with Mycobacterium bovis and M. bovis BCG. Proceedings of Functional Genomics and Systems Biology Workshop Wellcome Trust Conference Centre, Hinxton, UK, [Details]
Taraktsoglou, M., Magee, D. A., Browne, J. A., Park, S. D., Szalabaska, U., Sweeney, T., Gormley, E., MacHugh, D. E. (2009) Identification of resistance genes via functional genomics expression studies of bovine macrophages exposed to the causative agents of tuberculosis (M. bovis) and Johneâ¿¿s Disease (M. avium subsp. paratuberculosis)Identification of resistance genes via functional genomics expression studies of bovine macrophages exposed to the causative agents of tuberculosis (M. bovis) and Johneâ¿¿s Disease (M. avium subsp. paratuberculosis) Proceedings of the Fifth International M. bovis Conference Wellington, New Zealand, [Details]
Taraktsoglou, M., Magee, D. A., Browne, J. A., Park, S. D., Szalabaska, U., Sweeney, T., Gormley, E., MacHugh, D. E. (2009) Identification of resistance genes via functional genomics expression studies of bovine macrophages exposed to the causative agents of tuberculosis (M. bovis) and Johneâ¿¿s Disease (M. avium subsp. paratuberculosis). Proceedings of the Fifth International M. bovis Conference Wellington, New Zealand, [Details]
McGivney, B. A., McGettigan, P., Browne, J. A., Fonseca, R. G., Eivers, S. S., Evans, A. C., Loftus, B., Lohan, A., MacHugh, D. E., Katz, L. M., MacHugh, D. E. (2009) Digital gene expression profiling in Thoroughbred horse skeletal muscle following exercise training Digital gene expression profiling in Thoroughbred horse skeletal muscle following exercise training The Physiological Society - Physiology 2009 University College Dublin, Ireland, [Details]
Browne, J. A., Park, S. D. E., McGettigan, P., Meade, K. G., O'Farrelly, C., Gormley, E., MacHugh, D. E. (2009) Identification of a gene signature associated with Mycobacterium bovis infection in cattleIdentification of a gene signature associated with Mycobacterium bovis infection in cattle Proceedings of the Fifth International M. bovis Conference Wellington, New Zealand, [Details]
Browne, J. A., Park, S. D. E., McGettigan, P., Meade, K. G., O'Farrelly, C., Gormley, E., MacHugh, D. E. (2009) Identification of a gene signature associated with Mycobacterium bovis infection in cattle. Proceedings of the Fifth International M. bovis Conference Wellington, New Zealand, [Details]
MacHugh, D. E., Taraktsoglou, M., Magee, D. A., Browne, J. A., Park, S. D. E., Szalabaska, U., Gormley, E. (2009) A functional genomics study of bovine monocyte-derived macrophages stimulated in vitro with Mycobacterium bovis and M. bovis BCGA functional genomics study of bovine monocyte-derived macrophages stimulated in vitro with Mycobacterium bovis and M. bovis BCG Proceedings of Functional Genomics and Systems Biology Workshop Wellcome Trust Conference Centre, Hinxton, UK, [Details]
Taraktsoglou, M., Magee, D. A., Killick, K. E., Browne, J. A., Park, S. D. E., Nalpas, N. C., Hokamp, K., Gormley, E., MacHugh, D. E. (2010) Functional genomics studies of bovine monocyte-derived macrophages (MDM) stimulated in vitro with Mycobacterium bovis, M. bovis-BCG and M. avium subsp. paratuberculosis (MAP). Proceedings of Gene Expression and Signaling in the Immune System Cold Spring Harbor Laboratory, New York, USA, [Details]
Taraktsoglou, M., Magee, D. A., Killick, K. E., Browne, J. A., Park, S. D. E., Nalpas, N. C., Hokamp, K., Gormley, E., MacHugh, D. E. (2010) Functional genomics studies of bovine monocyte-derived macrophages (MDM) stimulated in vitro with Mycobacterium bovis, M. bovis-BCG and M. avium subsp. paratuberculosis (MAP). Proceedings of the 32nd Conference of the International Society of Animal Genetics Edinburgh, UK, [Details]
Taraktsoglou, M., Magee, D. A., Killick, K. E., Browne, J. A., Park, S. D. E., Nalpas, N. C., Hokamp, K., Gormley, E., MacHugh, D. E. (2010) Functional genomics studies of bovine monocyte-derived macrophages (MDM) stimulated in vitro with Mycobacterium bovis, M. bovis-BCG and M. avium subsp. paratuberculosis (MAP)Functional genomics studies of bovine monocyte-derived macrophages (MDM) stimulated in vitro with Mycobacterium bovis, M. bovis-BCG and M. avium subsp. paratuberculosis (MAP) Proceedings of Gene Expression and Signaling in the Immune System Cold Spring Harbor Laboratory, New York, USA, [Details]
Taraktsoglou, M., Magee, D. A., Killick, K. E., Browne, J. A., Park, S. D. E., Nalpas, N. C., Hokamp, K., Gormley, E., MacHugh, D. E. (2010) Functional genomics studies of bovine monocyte-derived macrophages (MDM) stimulated in vitro with Mycobacterium bovis, M. bovis-BCG and M. avium subsp. paratuberculosis (MAP)Functional genomics studies of bovine monocyte-derived macrophages (MDM) stimulated in vitro with Mycobacterium bovis, M. bovis-BCG and M. avium subsp. paratuberculosis (MAP) Proceedings of the 32nd Conference of the International Society of Animal Genetics Edinburgh, UK, [Details]
Casey, M. E., Earley, B., McGee, M., Kennedy, E., Browne, J. A., MacHugh, D. E., Meade, K. G. (2011) Investigating the cellular and molecular mechanisms contributing to the development of bovine neonatal immunity. Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
Casey, M. E., Earley, B., McGee, M., Kennedy, E., Browne, J. A., MacHugh, D. E., Meade, K. G. (2011) Investigating the cellular and molecular mechanisms contributing to the development of bovine neonatal immunityInvestigating the cellular and molecular mechanisms contributing to the development of bovine neonatal immunity Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
Killick, K. E., Browne, J. A., Park, S. D. E., Magee, D. A., Martin, I., Meade, K. G., Gordon, S. V., Gormley, E., O'Farrelly, C., Hokamp, K., MacHugh, D. E. (2011) Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genesGenome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genes Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
Killick, K. E., Browne, J. A., Park, S. D. E., Magee, D. A., Martin, I., Meade, K. G., Gordon, S. V., Gormley, E., O'Farrelly, C., Hokamp, K., MacHugh, D. E. (2011) Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genes. Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
Killick, K. E., Magee, D. A., Taraktsoglou, M., Park, S. D. E., Browne, J. A., Nalpas, N. C., Conlon, K., McLoughlin K. E., Lynn, D. J., Gordon, S. V., Gormley, E., Hokamp, K., MacHugh, D. E. (2011) Systems biology analyses of the bovine macrophage response to Mycobacterium bovis infection identifies the NF-Systems biology analyses of the bovine macrophage response to Mycobacterium bovis infection identifies the NF-κB complex as a key regulatory network hub Proceedings of Functional Genomics and Systems Biology Workshop Wellcome Trust Conference Centre, Hinxton, UK, [Details]
Killick, K. E., Magee, D. A., Taraktsoglou, M., Park, S. D. E., Browne, J. A., Nalpas, N. C., Conlon, K., McLoughlin K. E., Lynn, D. J., Gordon, S. V., Gormley, E., Hokamp, K., MacHugh, D. E. (2011) Systems biology analyses of the bovine macrophage response to Mycobacterium bovis infection identifies the NF-κB complex as a key regulatory network hub. Proceedings of Functional Genomics and Systems Biology Workshop Wellcome Trust Conference Centre, Hinxton, UK, [Details]
Killick, K. E., Magee, D. A., Taraktsoglou, M., Park, S. D. E., Browne, J. A., Nalpas, N. C., Conlon, K., McLoughlin, K. E., Gordon, S. V., Gormley, E., Hokamp, K., MacHugh, D. E. (2011) Systems biology analyses of the bovine macrophage response to Mycobacterium bovis infection identifies the NF-Systems biology analyses of the bovine macrophage response to Mycobacterium bovis infection identifies the NF-κB complex as a key regulatory network hub Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
Killick, K. E., Magee, D. A., Taraktsoglou, M., Park, S. D. E., Browne, J. A., Nalpas, N. C., Conlon, K., McLoughlin, K. E., Gordon, S. V., Gormley, E., Hokamp, K., MacHugh, D. E. (2011) Systems biology analyses of the bovine macrophage response to Mycobacterium bovis infection identifies the NF-κB complex as a key regulatory network hub. Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
Magee, D. A., Nalpas, N. C., Conlon, K., Browne, J. A., McLoughlin, K. E., Healy, C., Gormley, E., Gordon, S. V., MacHugh, D. E. (2011) Transcriptional profiling of key host genes using RNA from bovine alveolar macrophages co-cultured with Mycobacterium bovis and Mycobacterium tuberculosisTranscriptional profiling of key host genes using RNA from bovine alveolar macrophages co-cultured with Mycobacterium bovis and Mycobacterium tuberculosis Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
Magee, D. A., Nalpas, N. C., Conlon, K., Browne, J. A., McLoughlin, K. E., Healy, C., Gormley, E., Gordon, S. V., MacHugh, D. E. (2011) Transcriptional profiling of key host genes using RNA from bovine alveolar macrophages co-cultured with Mycobacterium bovis and Mycobacterium tuberculosis. Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
McGivney, B. A., Whiston, R., Browne, J. A., Fonseca, R. G., Gu, J., Katz, L. M., MacHugh, D. E., Hill, E. W. (2011) Investigation of myostatin pathway gene expression in untrained and trained Thoroughbred horse skeletal muscleInvestigation of myostatin pathway gene expression in untrained and trained Thoroughbred horse skeletal muscle Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
McLoughlin, K. E., Magee, D. A., Nalpas, N. C., Browne, J. A., Killick, K. E., Park, S. D. E., Whelan, A. O., Vordermeier, H. M., Hewinson, R. G., Gormley, E., Gordon, S. V., MacHugh, D. E. (2011) Technical assessment of bovine cytokine gene expression using compromised RNA samples from cattle experimentally infected with Mycobacterium bovisTechnical assessment of bovine cytokine gene expression using compromised RNA samples from cattle experimentally infected with Mycobacterium bovis Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
McLoughlin, K. E., Magee, D. A., Nalpas, N. C., Browne, J. A., Killick, K. E., Park, S. D. E., Whelan, A. O., Vordermeier, H. M., Hewinson, R. G., Gormley, E., Gordon, S. V., MacHugh, D. E. (2011) Technical assessment of bovine cytokine gene expression using compromised RNA samples from cattle experimentally infected with Mycobacterium bovis. Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
Nalpas, N. C., Park, S. D. E., Magee, D. A., Taraktsoglou, M., Browne, J. A., Lohan, A. J., Conlon, K., Gordon, S. V., Gormley, E., MacHugh, D. E. (2011) Whole-transcriptome high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis challenge in vitroWhole-transcriptome high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis challenge in vitro Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
Nalpas, N. C., Park, S. D. E., Magee, D. A., Taraktsoglou, M., Browne, J. A., Lohan, A. J., Conlon, K., Gordon, S. V., Gormley, E., MacHugh, D. E. (2011) Whole-transcriptome high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis challenge in vitro. Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
Vegh, P., McCabe, M., Magee, D. A., Conlon, K. M., Browne, J. A., Nalpas, N. C., Bradley, D. G., Gordon, S. V., MacHugh, D. E., Lynn, D. J. (2011) Profiling miRNA expression in bovine alveolar macrophagesProfiling miRNA expression in bovine alveolar macrophages Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
Vegh, P., McCabe, M., Magee, D. A., Conlon, K. M., Browne, J. A., Nalpas, N. C., Bradley, D. G., Gordon, S. V., MacHugh, D. E., Lynn, D. J. (2011) Profiling miRNA expression in bovine alveolar macrophages. Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
McGivney, B. A., Whiston, R., Browne, J. A., Fonseca, R. G., Gu, J., Katz, L. M., MacHugh, D. E., Hill, E. W. (2011) Investigation of myostatin pathway gene expression in untrained and trained Thoroughbred horse skeletal muscle. Proceedings of the 4th International Symposium on Animal Functional Genomics (ISAFG) Dublin, Ireland, [Details]
Killick, K. E., Park, S. D. E., Magee, D. A., Taraktsoglou, M., Browne, J. A., Conlon, K. M., Nalpas, N. C., Gormley, E., Gordon, S. V., MacHugh, D. E., Hokamp, K. (2012) Key hub and bottleneck genes differentiate the bovine macrophage response to virulent and avirulent strains of Mycobacterium bovisKey hub and bottleneck genes differentiate the bovine macrophage response to virulent and avirulent strains of Mycobacterium bovis Proceedings of Virtual Institute of Bioinformatics and Evolution Meeting Dublin, Ireland, [Details]
Killick, K. E., Park, S. D. E., Magee, D. A., Taraktsoglou, M., Browne, J. A., Conlon, K. M., Nalpas, N. C., Gormley, E., Gordon, S. V., MacHugh, D. E., Hokamp, K. (2012) Key hub and bottleneck genes differentiate the bovine macrophage response to virulent and avirulent strains of Mycobacterium bovis. Proceedings of Virtual Institute of Bioinformatics and Evolution Meeting Dublin, 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]
Murphy, BA; McGlynn, OF; Kharazian, F; Browne, JA.; (2011) The influence of exercise on entrainment of skeletal muscle transcription in the horse Equine Science Society Meeting [Details]
Hill EW, Eivers SS, McGivney BA, Fonseca RG, Gu J, Smith N, Browne J, MacHugh DE, Katz LM; (2010) Moderate and high intensity sprint exercise induce differential responses in COX4I2 and PDK4 gene expression in Thoroughbred horse skeletal muscle 8th International Conference on Equine Exercise Physiology [Details]
                       

Abstract

Devitt, EJ,Power, KA,Browne, JA,Gallagher, WM,Crowe, JP (2008) PROTEOMIC PROFILING OF SERUM USING SELDI-TOF MS IN HEPATITIS C (HCV) INFECTED INDIVIDUALS ON TREATMENT WITH PEGYLATED INTERFERON-alpha AND RIBAVIRIN. Abstract [Details]
Devitt, EJ,Power, KA,Browne, JA,Gallagher, WM,Crowe, JP (2008) PROTEOMIC PROFILING OF SERUM USING SELDI-TOF MS IN HEPATITIS C (HCV) INFECTED INDIVIDUALS ON TREATMENT WITH PEGYLATED INTERFERON-a AND RIBAVIRIN. Abstract [Details]
Walsh, SW,Browne, JA,Crowe, M,Mihm, M,Evans, ACO (2009) Comparison of Follicular Fluid Steroid Concentrations and mRNA Levels in Pre-Ovulatory Follicles Between Heifers and Lactating Cows. Abstract [Details]
Lorde, N,McGettigan, PA,Browne, JA,Carter, F,Loftus, BJ,Roche, JF,Lonergan, P,Crowe, MA,Evans, ACO (2009) Pregnancy-Specific Endometrial Gene Expression at the Initiation of Conceptus Elongation in Cattle. Abstract [Details]
Walsh, SW,Mehta, JP,Browne, JA,Forde, N,McGettigan, PA,Mihm, M,Loftus, B,Crowe, MA,Evans, ACO (2011) Differences in Gene Expression in Preovulatory Follicles after the LH Surge in Dairy Heifers Versus Lactating Cows. Abstract [Details]
Duffy, GB,McGettigan, P,Browne, JA,Mansouri-Attia, N,Charpigny, G,Sandra, O,Loftus, BJ,Roche, J,Crowe, M,Lonergan, P,Evans, ACO,Forde, N (2011) Next Generation Sequencing Identifies Novel Interferon Stimulated Genes in the Uterine Endometrium of Cattle During Early Pregnancy. Abstract [Details]
                                                               

Research

Research Interests

Dr. John Browne is a senior technical officer in the School of Agriculture and Food Science in UCD. He successfully completed his PhD studies in NUI Maynooth where he gained a thorough understanding of the challenges of working with RNA and developed expertise in a number of methods to identify differentially expressed genes.  After completing a postdoctoral fellowship in clinical research he returned to animal science in UCD where he is responsible for managing both the Transcriptomics and the Category Level 3 Laboratories.  He contributes directly to a number of funded research projects and has extensive expertise in the use of qPCR and next generation sequencing to study gene expression. He is actively involved in promoting best practice for qPCR experiments through the MIQE guidelines, and has received certified training in the management of Containment Level 3 facilities (Health Protection Agency, UK).