Publications

Peer-Reviewed Publications

1. Hibar D*, Stein J*, Renteria M*, Arias-Vasquez A*, Desrivieres S*, …, Ramasamy A, …, Martin NG#, Wright MJ#, Schumann G#, Franke B#, Thompson PM#, Medland SE# (2014). Common genetic variants influence human subcortical brain structures. Nature (accepted).
2. Ramasamy A*, Trabzuni D*, Guelfi S*, Varghese V, Smith C, Walker R, De T, UK Brain Expression Consortium, North American Brain Consortium, Coin L, de Silva R, Cookson M, Singleton A, Hardy J, Ryten M^#, Weale ME^# (2014). Genetic variability in the regulation of gene expression in multiple regions of the human brain. Nature Neuroscience 17(10):1418 – 28. http://dx.doi.org/10.1038/nn.3801 
3. Ferrari R, Hernandez DG, Nalls MA, Rohrer JD, Ramasamy A, 150 authors, Hardy J, Momeni P, Singleton AB (2014). Frontotemporal dementia and its subtypes: a genome wide association study. Lancet Neurology 13(7):686-99. http://dx.doi.org/10.1016/S1474-4422(14)70065-1
4. Loth D*, Artigas MS*, Gharib SA*, Wain LV*, Franceschini N*, Koch B*, Pottinger TD*, Smith AV*, Duan Q*, 6 authors,Ramasamy A, …, Sood A^#, Hayward^#, Dupuis J^#, Hall IP^#, Brusselle GG^#, Tobin MD^#, London SJ^# (2014). Genome-wide association analysis identifies six new loci associated with forced vital capacity. Nature Genetics 46(7): 669 – 77. http://dx.doi.org/10.1038/ng.3011
5. Ferrari R, Ryten M, Simone R, Trabzuni D, Nicolaou N, Hondhamuni G, Ramasamy A, UK Brain Expression Consortium, Weale ME, Lees AJ, Momeni P, Hardy J, de Silva R (2014). Assessment of common variability and expression quantitative trait loci for GWAS associations for progressive supranuclear palsy. Neurobiol Aging 35(6):1514.e1-1514.e12. http://dx.doi.org/10.1016/j.neurobiolaging.2014.01.010
6. Amaral AF, Ramasamy A, 15 authors, Jarvis DL (2014). Interaction between gas cooking and GSTM1 null genotype in bronchial responsiveness: results from the European Community Respiratory Health Survey. Thorax 69:558 – 564 http://dx.doi.org/10.1136/thoraxjnl-2013-204574
7. Scholtens S, 9 authors, Ramasamy A, 39 authors, Strachan DP, Koppelman GH, Boezen HM. Novel genes for childhood asthma that interact with in utero and childhood smoke exposure. Journal of Allergy and Clinical Immunology 133(3):885-8. http://dx.doi.org/10.1016/j.jaci.2013.08.049
8. Thompson PM, 210 authors, Ramasamy A, 81 authors (2014). The ENIGMA Consortium: large-scale collaborative analyses of neuroimaging and genetic data. Brain Imaging Behav. 8(2):153-182. http://dx.doi.org/10.1007/s11682-013-9269-5
9. Cruchaga C, 22 authors, Ramasamy A, 61 authors, Goate AM (2014). Rare coding variants in the phospholipase D3 gene confer risk for Alzheimer’s disease. Nature 23;505(7484):550-4. http://dx.doi.org/10.1038/nature12825
10. Trabzuni D*, Ramasamy A*, Imran S, Walker R, Smith C, North American Brain Expression Consortium, Weale M, Hardy H, Ryten M. Sex-biased gene expression, splicing and regulation in the adult human brain (accepted in Nature Communications).
11. Alves AC, Bruhn S, Ramasamy A, Wang H, Holloway JW, Hartikainen A-L, Jarvelin M-R, Benson M, Balding DJ, Coin L (2013). Dysregulation of complement system and CD4+ T cell activation pathways implicated in allergic response. PLOS ONE 8(10):e74821. http://dx.doi.org/10.1371/journal.pone.0074821
    
12. Forabosco P, Ramasamy A, Trabzuni D, Walker R, Smith C, Bras J, Levine AP, Hardy J, Pocock JM, Guerreiro R, Weale ME, Ryten M (2013). Insights into TREM2 biology using whole genome network analysis of gene expression data from post-mortem human brain tissue. Neurobiology of Aging pii: S0197-4580(13)00199-1. http://dx.doi.org/10.1016/j.neurobiolaging.2013.05.001
    • We reached broadly similar conclusion to this Cell paper published a couple of months earlier.
13. Ramasamy A*, Trabzuni D*, Forabosco P, Smith C, Walker R, Dillman A, North American Brain Expression Consortium (NABEC), UK Brain Expression Consortium (UKBEC), Hardy J, Weale ME, Ryten M (2013). Genetic evidence for a causal role for vitamin D3 in the pathogenesis of multiple sclerosis. Multiple Sclerosis and Related Disorders PII: 3(2) 211-219. http://dx.doi.org/10.1016/j.msard.2013.08.009
14. Glass D*, Vinuela A*, Davies MN, Ramasamy A, 10 authors, McCarthy MI, Deloukos P, Dermitzakis ET, Bataille V, Spector TD (2013). Altered gene expression with adult ageing: a cross tissue comparison in skin, adipose, blood and brain tissues. Genome Biology 14:R75. http://dx.doi.org/10.1186/gb-2013-14-7-r75
15. Kasperaviciute D*, Catarino CB*, Matarin M*, 8 authors, Ramasamy A, 55 authors, Sisodiya SM (2013). Genome-wide association study implicates SCN1A in mesial temporal lobe epilepsy with hippocampal sclerosis (accepted in Brain).
16. Trabzuni D*, Ryten M*, Emmett W, Ramasamy A, 23 authors, Michael E. Weale, John Hardy, Vincent Plagnol. Fine-Mapping, Gene Expression and Splicing Analysis of the Disease Associated LRRK2 Locus PLoS ONE 8(8): e70724. http://dx.doi.org/10.1371/journal.pone.0070724
17. Ramasamy A, Trabzuni T, Gibbs JR, Dillman A, Hernandez DG, Arepalli S, Walker R, Smith C, Shabalin AA, Li Y, Singleton AB, Cookson MR, Hardy J, Ryten M#, Weale ME# (2013). Resolving the polymorphism-in-probe problem is critical for correct interpretation of expression QTL studies. Nucleic Acids Research 41 (7):e88. http://dx.doi.org/10.1093/nar/gkt069
    • Selected as a featured article (top 5% most interesting in the journal)
18. Hancock DB*, Artigas MS*, Gharib SA*, Henry A*, Manichaikul‎ A*, Ramasamy A*, Loth D*, 72 authors, Cassano PA#, Strachan DP#, Fornage M#, Hall‎ IP#, Dupuis J#, Tobin MD#, London‎ SJ# (2012). Genome-wide joint meta-analysis of SNP and SNP by smoking interaction identifies novel loci for pulmonary function. PLoS Genetics 8(12): e1003098. http://dx.doi.org/10.1371/journal.pgen.1003098.
19. Ramasamy A*, Kuokkanen M*, Vedantam S*, Gajdos ZKZ*, 40 authors, Salomaa V#, Jarvelin M-R#, Hirschhorn JN# for the Analysis in Population-based Cohorts of Asthma Traits (APCAT) consortium (2012). Genome-wide association studies of asthma in population-based cohorts confirm known and suggested loci and identify an additional association in the HLA region. PLoS ONE 7(9):e44008. http://dx.doi.org/10.1371/journal.pone.0044008.
20. Trabzuni D, Wray S, Vandrovcova J, Ramasamy A, Walker R, Smith C, Luk C, Gibbs JR, Dillman A, Hernandez DG, Arepalli S, Singleton AB, Cookson MR, Pittman A, de Silva R, Weale ME, Hardy J and Ryten M (2012). MAPT expression and splicing is differentially regulated by brain region: relation to genotype and implication for tauopathies. Human Molecular Genetics 21(18):4094-103. http://dx.doi.org/10.1093/hmg/dds238
21. Barrenas F, Chavali S, Coin L, Alves A.C., Jarvelin M.R., Langston M.A., Ramasamy A, Rogers G, Wang H, Benson M (2012). Identification of susceptibility regions of highly interconnected genes to prioritize complex diseases genes. Genome Biology 13(6):R46. http://dx.doi.org/10.1186/gb-2012-13-6-r46
22. Stein JL*, Medland SE*, Arias-Vasquez A*, Hibar DP*, 35 authors, Ramasamy A, 156 authors, Wright MJ#, Franke B#, Martin NG#, Thompson PM# for the Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA) Consortium (2012). Identification of common variants associated with human hippocampal and intracranial volumes. Nature Genetics 44, 552 – 561. http://dx.doi.org/10.1038/ng.2250
23. Imboden M*, Bouzigon E*, Curjuric I, Ramasamy A, 21 authors, Kauffmann F, Jarvis DL, Demenais F, Probst-Hensch N (2012). Genome wide association study of lung function decline in adults with and without asthma. Journal of Allergy and Clinical Immunology 129 (5) 1218 – 1228. http://dx.doi.org/10.1016/j.jaci.2012.01.074
24. Jensen AM, Ramasamy A, Hotek J, Roel B, Riffe D (2012). The benefits of giving a massage on the mental state of massage therapists: A randomised, controlled trial. Journal of Alternative and Complementary Medicine. http://dx.doi.org/10.1089/acm.2011.0643
    • Also featured in the Massage Magazine here.
25. Paternoster L*, Standl M*, Chen C-M, Ramasamy A, 98 authors, Heinrich J#, Evans DM#, Weidinger S# (2011). Meta-analysis of genome-wide association studies on atopic dermatitis identifies three novel risk loci. Nature Genetics 44 187 – 192. http://dx.doi.org/10.1038/ng.1017.
26. Ramasamy A, Curjuric I, Coin LJ, Kumar A, McArdle WL, Imboden M, Leynaert B, Kogevinas M, Schmid-Grendelmeier P, Pekkanen J, Wjst M, Bircher AJ, Sovio U, Rochat T, Hartikainen A-L, Balding D, Jarvelin M-R, Probst-Hensch N, Strachan DP#, Jarvis DL# (2011). A genome-wide meta-analysis of genetic variants associated with allergic rhinitis and grass sensitization, and their interaction with birth order. Journal of Allergy and Clinical Immunology 128 (5) 996 – 1005. http://dx.doi.org/10.1016/j.jaci.2011.08.030
27. Jensen AM, Ramasamy A, Marten K, Hall MW (2011). Improving General Muscular Flexibility with a Mindbody Approach: A Randomized, Controlled Trial using Neuro Emotional Technique®. Journal of Strength and Conditioning Research. http://dx.doi.org/10.1097/JSM.0b013e31823a46ce
28. Liu M, Rogers L, Cheng Q, Shao Y, Fernandez-Beros ME, Hirschhorn JN, Lyon HN, Gajdos ZK, Vedantam S, Gregersen P, Seldin MF, Bleck B, Ramasamy A, Hartikainen AL, Jarvelin MR, Kuokkanen M, Laitinen T, Eriksson J, Lehtimäki T, Raitakari OT, Reibman J (2011). Genetic Variants of TSLP and Asthma in an Admixed Urban Population. PLoS ONE 6(9): e25099. http://dx.doi.org/10.1371/journal.pone.0025099
29. Artigas MS*, Loth DW*, Wain LV*, Gharib SA*, Obeidat M*, Tang W*, 27 authors, Ramasamy A, 129 authors, Stricker BHC#, Elliott P#, O’Connor GT#, Strachan DP#, London SJ#, Hall IP#, Gudnason V#, Tobin MD# (2011). Genome-wide association and large scale follow-up identifies 16 new loci influencing lung function. Nature Genetics 43, 1082 – 1090.  http://dx.doi.org/10.1038/ng.941
30. Ferreira MA, 16 authors, Ramasamy A, 54 authors, Montgomery GW#, Thompson PJ# (2011). Identification of IL6R and chromosome 1 1 1q13.5 as risk loci for asthma. Lancet vol 378 (9795) p1006 – 1014 http://dx.doi.org/10.1016/S0140-6736(11)60874-X
31. Bakolis I,  Doekes G, Heinrich J, Zock JP, Heederick D, Kogevinas M, Guerra S, Norback D,  Ramasamy A, Nevalainen A, Svanes C, Chem CM, Verlato G, Olivieri M, Castro-Giner F, Jarvis D (2011). Respiratory health and endotoxin – associations and modification by CD14/-260 genotype. European Respiratory Journal 39(3) 573 – 581. http://dx.doi.org/10.1183/09031936.00164410
32. Trabzuni D, Ryten M, Walker R, Smith C, Imran S, Ramasamy A, Weale ME, Hardy J (2011). Quality control parameters on a large dataset of regionally-dissected human control brains for whole genome expression studies. Journal of Neurochemistry Vol 119 (2) p275-282. http://dx.doi.org/10.1111/j.1471-4159.2011.07432.x
33. Obeidat M, Wain LV, Shrine N, Kalsheker N, Artigas MS, Repapi E, Burton PR, Johnson T, Ramasamy A, 49 authors, Elliot P, Strachan DP, Tobin MD, Sayers I and Hall IP for the SpiroMeta consortium (2011). A Comprehensive evaluation of potential lung function associated genes in the SpiroMeta general population sample. PLoS One. 6:e19382.  http://dx.doi.org/10.1371/journal.pone.0019382
34. Freathy RM, Mook-Kanamori DO, Sovio U, Prokopenko I, Timpson NJ, Berry DJ, Warrington, 43 authors, Ramasamy A, 29 authors, Boomsma DI, Smith GD, Power C, Jaddoe VWV, Jarvelin M-R, McCarthy MI for the Early Growth Genetics (EGG) consortium (2010). Variants at two loci (in ADCY5 and near CCNL1) influence fetal growth and birth weight. Nature Genetics; 42:430-435. http://dx.doi.org/10.1038/ng.567
35. Repapi E*, Sayers I*, Wain LV*, Burton PR, Johnson T, Obeidat M, Zhao JH, Ramasamy A, 84 authors, Elliot P#, Strachan DP#, Hall IP#, Tobin MD# for the SpiroMeta Genetics Consortium (2010). Genome-wide association study identifies five new loci associated with lung function. Nature Genetics; 42(1):36 – 44. http://dx.doi.org/10.1038/ng.501
36. Jensen A and Ramasamy A (2009). Treating Spider Phobia Using Neuro Emotional Technique (NET): Findings from a Pilot Study. Journal of Alternative and Complementary Medicine; 15(12):1363 – 1374. http://dx.doi.org/10.1089/acm.2008.0595
37. Ramasamy A, Mondry A, Holmes CC, Altman DG (2008). Key Issues in Conducting a Meta-Analysis of Gene Expression Microarray Datasets. PLoS Medicine; 5(9):e184 http://dx.doi.org/10.1371/journal.pmed.0050184
38. Nam SW, Park JY, Ramasamy A, Shevade S, Islam A, Long PM, Park CK, Park SE, Kim SY, Lee SH, Park WS, Yoo NJ, Liu ET, Miller LD and Lee JY (2005). Molecular changes from dysplastic nodule to hepatocellular carcinoma through gene expression. Hepatology; 42(4):809-18. http://dx.doi.org/10.1002/hep.20878
39. Lin CY, Strom A, Vega VB, Kong SL, Yeo AL, Thomsen JS, Chan WC, Doray B, Bangarusamy DK, Ramasamy A, Vergara LA, Tang S, Chong A, Bajic VB, Miller LD, Gustafsson JA and Liu ET (2004). Discovery of estrogen receptor alpha target genes and response elements in breast tumor cells. Genome Biology; 5(9):R66. http://dx.doi.org/10.1186/gb-2004-5-9-r66

Named collaborator in peer-reviewed articles

1. Bis JC*, DeCarli C*, Smith AV*, van der Lijn F*, Crivello F*, Fornage M*, Debette S*, …, Seshadri S (2012). Common variants at 12q14 and 12q24 are associated with hippocampal volume. Nature Genetics 44, 545-551. http://dx.doi.org/10.1038/ng.2237
2. Kilpeläinen TO, den Hoed M, Ong KK, Grøntved A, Brage S; Early Growth Genetics Consortium, Jameson K, Cooper C, Khaw KT, Ekelund U, Wareham NJ, Loos RJ (2011). Obesity-susceptibility loci have a limited influence on birth weight: a meta-analysis of up to 28,219 individuals. American Journal of Clinical Nutrition Apr;93(4):851-60. Epub 2011 Jan 19.

Dissertation thesis

1. Ramasamy A (2010). Increasing statistical power and generalizability in genomics microarray research. DPhil Thesis. University of Oxford. Download PDF copy of my DPhil thesis.
2. Ramasamy A (2002). Pattern recognition methods for cDNA microarray datasets. MSc Thesis. University of Oxford. Download PDF copy of my MSc thesis.

Peer-Reviewed Conference proceedings

1. Weale ME, Ramasamy A, Trabzuni D, Walker R, Smith C, Ryten M, Hardy J, UK Brain Expression Consortium (2012). Gene-level and exon-level expression QTL signals in the UK Brain Expression Consortium dataset. American Society of Human Genetics (accepted for oral presentation).
2. Ramasamy A, Trabzuni T, Gibbs JR, Dillman A, Hernandez DG, Arepalli S, Walker R, Smith C, Shabalin AA, Li Y, Singleton AB, Cookson MR, Hardy J, Ryten M#, Weale ME#; North American Brain Expression Consortium and UK Brain Expression Consortium (2012). The impact of polymorphisms within probe sequence on expression QTL studies. American Society of Human Genetics (accepted for poster presentation).
3. Hofer TPJ., Probst-Hensch NM., Bouzigon E, Imboden M, Jarvelin M-R, Ramasamy A, Da Silva Couto Alves A,  Curjuric I, Heinrich J, Standl M, Schneider A, Hampel R, Siroux V, Kauffmann F, Demenais F, Rochat T, Strachan D, Jarvis DL, Eickelberg O, Konigshoff M, Wjst M (2012). Meta-analysis of genome-wide association studies of single nucleotide polymorphisms in selected genes of the WNT signaling pathway. European Respiratory Society (ERS) Vienna Congress (accepted for oral presentation) https://www.ersnetsecure.org/public/prg_congres.abstract?ww_i_presentation=56921
4. Lampi J, Koskela H, Hartikainen A-L., da Silva Couto Alves A, Ramasamy A, Jarvelin M-R., Pekkanen J (2012). Farming environment during infancy and lung function at age 31 – Prospective birth cohort study in Finland.  European Respiratory Society (ERS) Vienna Congress. (accepted for poster presentation) https://www.ersnetsecure.org/public/prg_congres.abstract?ww_i_presentation=58427
5. Paternoster L*, Standl M*, Chen C-M, Ramasamy A, 20 authors, Heinrich J#, Evans DM#, Weidinger S# (2011). Meta-analysis of genome-wide association studies on atopic dermatitis identifies three novel risk loci. The 12th International Congress of Human Genetics/61st Annual Meeting of The American Society of Human Genetics (accepted for poster presentation). http://www.ichg2011.org/cgi-bin/showdetail.pl?absno=20332
6. Imboden M, Bouzignon E, Curjuric I, Ramasamy A, Kumar A, Hancock D, Wilks JB, Vonk J, Koppelman G, Strachan DP, Postma D, London S, Schindler C, Kogevinas M, Kauffmann F, Jarvis D, Demenais F, Probst-Hensch N. Genome wide association study identifies locus determining genetic heterogeneity of lung function decline in asthmatics and non-asthmatic adults. American Thoraic Society conference (accepted for poster presentation). http://myats2011.zerista.com/event/member?item_id=998496
7. Gajdos ZKZ, Ramasamy A, Kuokkanen M, Vedantam S, Lyon H, Palmer C, Widen E, Eriksson J, Jousilahti P, Laitenen T, Salomaa V, Hirschhorn JN, Jarvelin MR for the APCAT consortium (2010). Analysis of known asthma-associated variants in population-based cohorts. American Society for Human Genetics. (accepted for poster presentation) http://tinyurl.com/36heaa9
8. Ramasamy A, Lampi J, Balding D, Jarvis D, Pekkanen J, Jarvelin M. Genome-wide scan for gene-environment interactions in NFBC66 for childhood contact with cows and pets identifies more genomic regions for asthma than allergic symptoms. Conference of Epidemiological Longitudinal Studies in Europe 2010 (CELSE2010), 13 Oct 2010 – 15 Oct 2010. (accepted for oral presentation).
9. Ramasamy A, Lampi J, Balding D, Hartikainen AL, Jarvis DJ, Jarvelin M, Pekkanen J (2010). A genome-wide scan for gene-environment interaction for childhood contact with cows and household pets identifies more regions for asthma than allergic symptoms. European Respiratory Society (ERS) Barcelona Congress. https://www.ersnetsecure.org/public/prg_congres.abstract?ww_i_presentation=45664
10. Freathy RM, Sovio U, Mook-Kanamori DO, Prokopenko, Timpson NJ, Berry DJ, Warrington NM et al (EGG Consortium). Identification of two novel loci associated with birth weight. Diabetes UK 2010 (accepted for oral presentation).
11. Ramasamy A, Kunzli N, Castro-Giner F,  Kogevinas M, Minelli,C. Heinrich J Jarvis D (2008). The association of bronchial reactivity with use of gas for cooking is modified by GSTM1 homozygous deletion. European Respiratory Society (ERS) Berlin Congress (accepted for oral presentation).  http://www.ersnet.org/learning_resources_player/abstract_print_08/search/2312.htm
12. Pellagatti A, Cazzola M, Giagounidis A, Malcovati L, Killick S, Ramasamy A, Oscier D, Aul C, Wainscoat JS, Boultwood J (2005) Expression profiling of CD34+cells in patients with myelodysplastic syndromes with and without a del(5q).34th Annual Meeting of the International-Society-for-Experimental-Hematology. 33:60-60. http://tinyurl.com/37t85hx 

Software

1. Ramasamy A. metaGEM: an R package for meta-analysis of gene expression microarray studies. Version: 0.4.2 available at http://hdl.handle.net/10044/1/4217 

Publications in Review/Submission

1. Lampi J, Koskela H, Hartikainen A-L, Ramasamy A, Couto-Alves A, Jarvelin M-R, Pekkanen. Farming environment during infancy and lung function at age 31 – Prospective birth cohort study in Finland (submitted to Thorax).
2. Hofer TPJ, Probst-Hensch NM, Bouzigon E, Imboden M, Jarvelin M-R, Ramasamy A, Couto-Alves A, Curjuric I, Heinrich J, Stand M, Schneider A, Hampel R, Siroux V, Kauffmann F, Demenais F, Rochat T, Strachan DP, Jarvis DL, Eickelberg O, Königshoff M, Wjst M. Meta-analysis of genome-wide association studies of SNPs in selected genes of the WNT signaling pathway (in review).

Publications in Preparation

1. Ramasamy A, Balding D, Jarvis D et al. Deletion of GSTM-1 modifies association of bronchial reactivity with use of gas for cooking.
2. Ramasamy A, …, Jarvis DL. A genome-wide meta-analysis of genetic variants associated with bronchial hyper reactivity.
3. Roth D, FVC GWAs.

* = Equal first authors
# = Equal senior authors