Ioannis Ragoussis Ph.D.

Publications: 2007-15

  1. Colella S, Yau C, Taylor JM, Mirza G, Butler H, Clouston P, Bassett AS, Seller A, Holmes CC, Ragoussis J. 2007. QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data. Nucleic acids research 35(6): 2013-2025.
  2. Copley RR, Totrov M, Linnell J, Field S, Ragoussis J, Udalova IA. 2007. Functional conservation of Rel binding sites in drosophilid genomes. Genome research 17(9): 1327-1335.
  3. Field S, Udalova I, Ragoussis J. 2007. Accuracy and reproducibility of protein-DNA microarray technology. Advances in biochemical engineering/biotechnology 104: 87-110.
  4. Francks C, Maegawa S, Lauren J, Abrahams BS, Velayos-Baeza A, Medland SE, Colella S, Groszer M, McAuley EZ, Caffrey TM, Timmusk T, Pruunsild P, Koppel I, Lind PA, Matsumoto-Itaba N, Nicod J, Xiong L, Joober R, Enard W, Krinsky B, Nanba E, Richardson AJ, Riley BP, Martin NG, Strittmatter SM, Moller HJ, Rujescu D, St Clair D, Muglia P, Roos JL, Fisher SE, Wade-Martins R, Rouleau GA, Stein JF, Karayiorgou M, Geschwind DH, Ragoussis J, Kendler KS, Airaksinen MS, Oshimura M, DeLisi LE, Monaco AP. 2007. LRRTM1 on chromosome 2p12 is a maternally suppressed gene that is associated paternally with handedness and schizophrenia. Molecular psychiatry 12(12): 1129-1139, 1057.
  5. Anderson CA, Pettersson FH, Barrett JC, Zhuang JJ, Ragoussis J, Cardon LR, Morris AP. 2008. Evaluating the effects of imputation on the power, coverage, and cost efficiency of genome-wide SNP platforms. American journal of human genetics 83(1): 112-119.
  6. Butler H, Ragoussis J. 2008. BeadArray-based genotyping. Methods in molecular biology 439: 53-74.
  7. Camps C, Buffa FM, Colella S, Moore J, Sotiriou C, Sheldon H, Harris AL, Gleadle JM, Ragoussis J. 2008. hsa-miR-210 Is induced by hypoxia and is an independent prognostic factor in breast cancer. Clinical cancer research : an official journal of the American Association for Cancer Research 14(5): 1340-1348.
  8. Figtree GA, Grieve SM, Speller B, Geiger MJ, Robinson BG, Channon KM, Ragoussis J, Collins P, Watkins H. 2008. A commonly occurring polymorphism upstream of the estrogen receptor alpha alters transcription and is associated with increased HDL. Atherosclerosis 199(2): 354-361.
  9. Gee HE, Camps C, Buffa FM, Colella S, Sheldon H, Gleadle JM, Ragoussis J, Harris AL. 2008. MicroRNA-10b and breast cancer metastasis. Nature 455(7216): E8-9; author reply E9.
  10. Giannoulatou E, Yau C, Colella S, Ragoussis J, Holmes CC. 2008. GenoSNP: a variational Bayes within-sample SNP genotyping algorithm that does not require a reference population. Bioinformatics 24(19): 2209-2214.
  11. Paracchini S, Steer CD, Buckingham LL, Morris AP, Ring S, Scerri T, Stein J, Pembrey ME, Ragoussis J, Golding J, Monaco AP. 2008. Association of the KIAA0319 dyslexia susceptibility gene with reading skills in the general population. The American journal of psychiatry 165(12): 1576-1584.
  12. Szumska D, Pieles G, Essalmani R, Bilski M, Mesnard D, Kaur K, Franklyn A, El Omari K, Jefferis J, Bentham J, Taylor JM, Schneider JE, Arnold SJ, Johnson P, Tymowska-Lalanne Z, Stammers D, Clarke K, Neubauer S, Morris A, Brown SD, Shaw-Smith C, Cama A, Capra V, Ragoussis J, Constam D, Seidah NG, Prat A, Bhattacharya S. 2008. VACTERL/caudal regression/Currarino syndrome-like malformations in mice with mutation in the proprotein convertase Pcsk5. Genes & development 22(11): 1465-1477.
  13. Winchester L, Newbury DF, Monaco AP, Ragoussis J. 2008. Detection, breakpoint identification and detailed characterisation of a CNV at the FRA16D site using SNP assays. Cytogenetic and genome research 123(1-4): 322-332.
  14. Brooks JT, Elvidge GP, Glenny L, Gleadle JM, Liu C, Ragoussis J, Smith TG, Talbot NP, Winchester L, Maxwell PH, Robbins PA. 2009. Variations within oxygen-regulated gene expression in humans. Journal of applied physiology 106(1): 212-220.
  15. Herrera BM, Lockstone HE, Taylor JM, Wills QF, Kaisaki PJ, Barrett A, Camps C, Fernandez C, Ragoussis J, Gauguier D, McCarthy MI, Lindgren CM. 2009. MicroRNA-125a is over-expressed in insulin target tissues in a spontaneous rat model of Type 2 Diabetes. BMC medical genomics 2: 54.
  16. Iseri SU, Osborne RJ, Farrall M, Wyatt AW, Mirza G, Nurnberg G, Kluck C, Herbert H, Martin A, Hussain MS, Collin JR, Lathrop M, Nurnberg P, Ragoussis J, Ragge NK. 2009. Seeing clearly: the dominant and recessive nature of FOXE3 in eye developmental anomalies. Human mutation 30(10): 1378-1386.
  17. Jallow M, Teo YY, Small KS, Rockett KA, Deloukas P, Clark TG, Kivinen K, Bojang KA, Conway DJ, Pinder M, Sirugo G, Sisay-Joof F, Usen S, Auburn S, Bumpstead SJ, Campino S, Coffey A, Dunham A, Fry AE, Green A, Gwilliam R, Hunt SE, Inouye M, Jeffreys AE, Mendy A, Palotie A, Potter S, Ragoussis J, Rogers J, Rowlands K, Somaskantharajah E, Whittaker P, Widden C, Donnelly P, Howie B, Marchini J, Morris A, SanJoaquin M, Achidi EA, Agbenyega T, Allen A, Amodu O, Corran P, Djimde A, Dolo A, Doumbo OK, Drakeley C, Dunstan S, Evans J, Farrar J, Fernando D, Hien TT, Horstmann RD, Ibrahim M, Karunaweera N, Kokwaro G, Koram KA, Lemnge M, Makani J, Marsh K, Michon P, Modiano D, Molyneux ME, Mueller I, Parker M, Peshu N, Plowe CV, Puijalon O, Reeder J, Reyburn H, Riley EM, Sakuntabhai A, Singhasivanon P, Sirima S, Tall A, Taylor TE, Thera M, Troye-Blomberg M, Williams TN, Wilson M, Kwiatkowski DP, Wellcome Trust Case Control C, Malaria Genomic Epidemiology N. 2009. Genome-wide and fine-resolution association analysis of malaria in West Africa. Nature genetics 41(6): 657-665.
  18. Kaur K, Ragge NK, Ragoussis J. 2009. Molecular analysis of FOXC1 in subjects presenting with severe developmental eye anomalies. Molecular vision 15: 1366-1373.
  19. Koukourakis MI, Giatromanolaki A, Sheldon H, Buffa FM, Kouklakis G, Ragoussis I, Sivridis E, Harris AL, Tumour, Angiogenesis Research G. 2009. Phase I/II trial of bevacizumab and radiotherapy for locally advanced inoperable colorectal cancer: vasculature-independent radiosensitizing effect of bevacizumab. Clinical cancer research : an official journal of the American Association for Cancer Research 15(22): 7069-7076.
  20. McRonald FE, Morris MR, Gentle D, Winchester L, Baban D, Ragoussis J, Clarke NW, Brown MD, Kishida T, Yao M, Latif F, Maher ER. 2009. CpG methylation profiling in VHL related and VHL unrelated renal cell carcinoma. Molecular cancer 8: 31.
  21. Mole DR, Blancher C, Copley RR, Pollard PJ, Gleadle JM, Ragoussis J, Ratcliffe PJ. 2009. Genome-wide association of hypoxia-inducible factor (HIF)-1alpha and HIF-2alpha DNA binding with expression profiling of hypoxia-inducible transcripts. The Journal of biological chemistry 284(25): 16767-16775.
  22. Newbury DF, Winchester L, Addis L, Paracchini S, Buckingham LL, Clark A, Cohen W, Cowie H, Dworzynski K, Everitt A, Goodyer IM, Hennessy E, Kindley AD, Miller LL, Nasir J, O'Hare A, Shaw D, Simkin Z, Simonoff E, Slonims V, Watson J, Ragoussis J, Fisher SE, Seckl JR, Helms PJ, Bolton PF, Pickles A, Conti-Ramsden G, Baird G, Bishop DV, Monaco AP. 2009. CMIP and ATP2C2 modulate phonological short-term memory in language impairment. American journal of human genetics 85(2): 264-272.
  23. Pagnamenta AT, Wing K, Sadighi Akha E, Knight SJ, Bolte S, Schmotzer G, Duketis E, Poustka F, Klauck SM, Poustka A, Ragoussis J, Bailey AJ, Monaco AP, International Molecular Genetic Study of Autism C. 2009. A 15q13.3 microdeletion segregating with autism. European journal of human genetics : EJHG 17(5): 687-692.
  24. Pilgaard L, Lund P, Duroux M, Lockstone H, Taylor J, Emmersen J, Fink T, Ragoussis J, Zachar V. 2009. Transcriptional signature of human adipose tissue-derived stem cells (hASCs) preconditioned for chondrogenesis in hypoxic conditions. Experimental cell research 315(11): 1937-1952.
  25. Ragoussis J. 2009. Genotyping technologies for genetic research. Annual review of genomics and human genetics 10: 117-133.
  26. Tinline-Purvis H, Savory AP, Cullen JK, Dave A, Moss J, Bridge WL, Marguerat S, Bahler J, Ragoussis J, Mott R, Walker CA, Humphrey TC. 2009. Failed gene conversion leads to extensive end processing and chromosomal rearrangements in fission yeast. The EMBO journal 28(21): 3400-3412.
  27. Van Es MA, Van Vught PW, Veldink JH, Andersen PM, Birve A, Lemmens R, Cronin S, Van Der Kooi AJ, De Visser M, Schelhaas HJ, Hardiman O, Ragoussis I, Lambrechts D, Robberecht W, Wokke JH, Ophoff RA, Van Den Berg LH. 2009. Analysis of FGGY as a risk factor for sporadic amyotrophic lateral sclerosis. Amyotrophic lateral sclerosis : official publication of the World Federation of Neurology Research Group on Motor Neuron Diseases 10(5-6): 441-447.
  28. Wilder SP, Kaisaki PJ, Argoud K, Salhan A, Ragoussis J, Bihoreau MT, Gauguier D. 2009. Comparative analysis of methods for gene transcription profiling data derived from different microarray technologies in rat and mouse models of diabetes. BMC genomics 10: 63.
  29. Winchester L, Yau C, Ragoussis J. 2009. Comparing CNV detection methods for SNP arrays. Briefings in functional genomics & proteomics 8(5): 353-366.
  30. Anney R Klei L Pinto D Regan R Conroy J Magalhaes TR Correia C Abrahams BS Sykes N Pagnamenta AT Almeida J Bacchelli E Bailey AJ Baird G Battaglia A Berney T Bolshakova N Bolte S Bolton PF Bourgeron T Brennan S Brian J Carson AR Casallo G Casey J Chu SH Cochrane L Corsello C Crawford EL Crossett A Dawson G de Jonge M Delorme R Drmic I Duketis E Duque F Estes A Farrar P Fernandez BA Folstein SE Fombonne E Freitag CM Gilbert J Gillberg C Glessner JT Goldberg J Green J Guter SJ Hakonarson H Heron EA Hill M Holt R Howe JL Hughes G Hus V Igliozzi R Kim C Klauck SM Kolevzon A Korvatska O Kustanovich V Lajonchere CM Lamb JA Laskawiec M Leboyer M Le Couteur A Leventhal BL Lionel AC Liu XQ Lord C Lotspeich L Lund SC Maestrini E Mahoney W Mantoulan C Marshall CR McConachie H McDougle CJ McGrath J McMahon WM Melhem NM Merikangas A Migita O Minshew NJ Mirza GK Munson J Nelson SF Noakes C Noor A Nygren G Oliveira G Papanikolaou K Parr JR Parrini B Paton T Pickles A Piven J Posey DJ Poustka A Poustka F Prasad A Ragoussis J Renshaw K Rickaby J Roberts W Roeder K Roge B Rutter ML Bierut LJ Rice JP Salt J Sansom K Sato D Segurado R Senman L Shah N Sheffield VC Soorya L Sousa I Stoppioni V Strawbridge C Tancredi R Tansey K Thiruvahindrapduram B Thompson AP Thomson S Tryfon A Tsiantis J Van Engeland H Vincent JB Volkmar F Wallace S Wang K Wang Z Wassink TH Wing K Wittemeyer K Wood S Yaspan BL Zurawiecki D Zwaigenbaum L Betancur C Buxbaum JD Cantor RM Cook EH Coon H Cuccaro ML Gallagher L Geschwind DH Gill M Haines JL Miller J Monaco AP Nurnberger JI, Jr. Paterson AD Pericak-Vance MA Schellenberg GD Scherer SW Sutcliffe JS Szatmari P Vicente AM Vieland VJ Wijsman EM Devlin B Ennis S, Hallmayer J. 2010. A genome-wide scan for common alleles affecting risk for autism. Human molecular genetics 19(20): 4072-4082.
  31. Butler HT, Warden DR, Hogervorst E, Ragoussis J, Smith AD, Lehmann DJ. 2010. Association of the aromatase gene with Alzheimer's disease in women. Neuroscience letters 468(3): 202-206.
  32. De Santa F, Barozzi I, Mietton F, Ghisletti S, Polletti S, Tusi BK, Muller H, Ragoussis J, Wei CL, Natoli G. 2010. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS biology 8(5): e1000384.
  33. Favaro E, Ramachandran A, McCormick R, Gee H, Blancher C, Crosby M, Devlin C, Blick C, Buffa F, Li JL, Vojnovic B, Pires das Neves R, Glazer P, Iborra F, Ivan M, Ragoussis J, Harris AL. 2010. MicroRNA-210 regulates mitochondrial free radical response to hypoxia and krebs cycle in cancer cells by targeting iron sulfur cluster protein ISCU. PloS one 5(4): e10345.
  34. Gee HE, Camps C, Buffa FM, Patiar S, Winter SC, Betts G, Homer J, Corbridge R, Cox G, West CM, Ragoussis J, Harris AL. 2010. hsa-mir-210 is a marker of tumor hypoxia and a prognostic factor in head and neck cancer. Cancer 116(9): 2148-2158.
  35. Ghisletti S, Barozzi I, Mietton F, Polletti S, De Santa F, Venturini E, Gregory L, Lonie L, Chew A, Wei CL, Ragoussis J, Natoli G. 2010. Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. Immunity 32(3): 317-328.
  36. Grzmil M, Rzymski T, Milani M, Harris AL, Capper RG, Saunders NJ, Salhan A, Ragoussis J, Norbury CJ. 2010. An oncogenic role of eIF3e/INT6 in human breast cancer. Oncogene 29(28): 4080-4089.
  37. Jefferson A, Colella S, Moralli D, Wilson N, Yusuf M, Gimelli G, Ragoussis J, Volpi EV. 2010. Altered intra-nuclear organisation of heterochromatin and genes in ICF syndrome. PloS one 5(6): e11364.
  38. Law MJ, Lower KM, Voon HP, Hughes JR, Garrick D, Viprakasit V, Mitson M, De Gobbi M, Marra M, Morris A, Abbott A, Wilder SP, Taylor S, Santos GM, Cross J, Ayyub H, Jones S, Ragoussis J, Rhodes D, Dunham I, Higgs DR, Gibbons RJ. 2010. ATR-X syndrome protein targets tandem repeats and influences allele-specific expression in a size-dependent manner. Cell 143(3): 367-378.
  39. Lee LN, Baban D, Ronan EO, Ragoussis J, Beverley PC, Tchilian EZ. 2010. Chemokine gene expression in lung CD8 T cells correlates with protective immunity in mice immunized intra-nasally with Adenovirus-85A. BMC medical genomics 3: 46.
  40. McCormick R, Buffa FM, Ragoussis J, Harris AL. 2010. The role of hypoxia regulated microRNAs in cancer. Current topics in microbiology and immunology 345: 47-70.
  41. Pagnamenta AT, Bacchelli E, de Jonge MV, Mirza G, Scerri TS, Minopoli F, Chiocchetti A, Ludwig KU, Hoffmann P, Paracchini S, Lowy E, Harold DH, Chapman JA, Klauck SM, Poustka F, Houben RH, Staal WG, Ophoff RA, O'Donovan MC, Williams J, Nothen MM, Schulte-Korne G, Deloukas P, Ragoussis J, Bailey AJ, Maestrini E, Monaco AP, International Molecular Genetic Study Of Autism C. 2010. Characterization of a family with rare deletions in CNTNAP5 and DOCK4 suggests novel risk loci for autism and dyslexia. Biological psychiatry 68(4): 320-328.
  42. Pinto D Pagnamenta AT Klei L Anney R Merico D Regan R Conroy J Magalhaes TR Correia C Abrahams BS Almeida J Bacchelli E Bader GD Bailey AJ Baird G Battaglia A Berney T Bolshakova N Bolte S Bolton PF Bourgeron T Brennan S Brian J Bryson SE Carson AR Casallo G Casey J Chung BH Cochrane L Corsello C Crawford EL Crossett A Cytrynbaum C Dawson G de Jonge M Delorme R Drmic I Duketis E Duque F Estes A Farrar P Fernandez BA Folstein SE Fombonne E Freitag CM Gilbert J Gillberg C Glessner JT Goldberg J Green A Green J Guter SJ Hakonarson H Heron EA Hill M Holt R Howe JL Hughes G Hus V Igliozzi R Kim C Klauck SM Kolevzon A Korvatska O Kustanovich V Lajonchere CM Lamb JA Laskawiec M Leboyer M Le Couteur A Leventhal BL Lionel AC Liu XQ Lord C Lotspeich L Lund SC Maestrini E Mahoney W Mantoulan C Marshall CR McConachie H McDougle CJ McGrath J McMahon WM Merikangas A Migita O Minshew NJ Mirza GK Munson J Nelson SF Noakes C Noor A Nygren G Oliveira G Papanikolaou K Parr JR Parrini B Paton T Pickles A Pilorge M Piven J Ponting CP Posey DJ Poustka A Poustka F Prasad A Ragoussis J Renshaw K Rickaby J Roberts W Roeder K Roge B Rutter ML Bierut LJ Rice JP Salt J Sansom K Sato D Segurado R Sequeira AF Senman L Shah N Sheffield VC Soorya L Sousa I Stein O Sykes N Stoppioni V Strawbridge C Tancredi R Tansey K Thiruvahindrapduram B Thompson AP Thomson S Tryfon A Tsiantis J Van Engeland H Vincent JB Volkmar F Wallace S Wang K Wang Z Wassink TH Webber C Weksberg R Wing K Wittemeyer K Wood S Wu J Yaspan BL Zurawiecki D Zwaigenbaum L Buxbaum JD Cantor RM Cook EH Coon H Cuccaro ML Devlin B Ennis S Gallagher L Geschwind DH Gill M Haines JL Hallmayer J Miller J Monaco AP Nurnberger JI, Jr. Paterson AD Pericak-Vance MA Schellenberg GD Szatmari P Vicente AM Vieland VJ Wijsman EM Scherer SW Sutcliffe JS, Betancur C. 2010. Functional impact of global rare copy number variation in autism spectrum disorders. Nature 466(7304): 368-372.
  43. Rzymski T, Milani M, Pike L, Buffa F, Mellor HR, Winchester L, Pires I, Hammond E, Ragoussis I, Harris AL. 2010. Regulation of autophagy by ATF4 in response to severe hypoxia. Oncogene 29(31): 4424-4435.
  44. Yang J, Jubb AM, Pike L, Buffa FM, Turley H, Baban D, Leek R, Gatter KC, Ragoussis J, Harris AL. 2010. The histone demethylase JMJD2B is regulated by estrogen receptor alpha and hypoxia, and is a key mediator of estrogen induced growth. Cancer research 70(16): 6456-6466.
  45. Yau C, Mouradov D, Jorissen RN, Colella S, Mirza G, Steers G, Harris A, Ragoussis J, Sieber O, Holmes CC. 2010. A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data. Genome biology 11(9): R92.
  46. Buffa FM, Camps C, Winchester L, Snell CE, Gee HE, Sheldon H, Taylor M, Harris AL, Ragoussis J. 2011. microRNA-associated progression pathways and potential therapeutic targets identified by integrated mRNA and microRNA expression profiling in breast cancer. Cancer research 71(17): 5635-5645.
  47. Celona B, Weiner A, Di Felice F, Mancuso FM, Cesarini E, Rossi RL, Gregory L, Baban D, Rossetti G, Grianti P, Pagani M, Bonaldi T, Ragoussis J, Friedman N, Camilloni G, Bianchi ME, Agresti A. 2011. Substantial histone reduction modulates genomewide nucleosomal occupancy and global transcriptional output. PLoS biology 9(6): e1001086.
  48. Gee HE, Buffa FM, Camps C, Ramachandran A, Leek R, Taylor M, Patil M, Sheldon H, Betts G, Homer J, West C, Ragoussis J, Harris AL. 2011. The small-nucleolar RNAs commonly used for microRNA normalisation correlate with tumour pathology and prognosis. British journal of cancer 104(7): 1168-1177.
  49. Jiang C, Mithani A, Gan X, Belfield EJ, Klingler JP, Zhu JK, Ragoussis J, Mott R, Harberd NP. 2011. Regenerant Arabidopsis lineages display a distinct genome-wide spectrum of mutations conferring variant phenotypes. Current biology : CB 21(16): 1385-1390.
  50. Kollias G, Papadaki P, Apparailly F, Vervoordeldonk MJ, Holmdahl R, Baumans V, Desaintes C, Di Santo J, Distler J, Garside P, Hegen M, Huizinga TW, Jungel A, Klareskog L, McInnes I, Ragoussis I, Schett G, Hart B, Tak PP, Toes R, van den Berg W, Wurst W, Gay S. 2011. Animal models for arthritis: innovative tools for prevention and treatment. Annals of the rheumatic diseases 70(8): 1357-1362.
  51. Korpal M, Ell BJ, Buffa FM, Ibrahim T, Blanco MA, Celia-Terrassa T, Mercatali L, Khan Z, Goodarzi H, Hua Y, Wei Y, Hu G, Garcia BA, Ragoussis J, Amadori D, Harris AL, Kang Y. 2011. Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization. Nature medicine 17(9): 1101-1108.
  52. Min JL, Taylor JM, Richards JB, Watts T, Pettersson FH, Broxholme J, Ahmadi KR, Surdulescu GL, Lowy E, Gieger C, Newton-Cheh C, Perola M, Soranzo N, Surakka I, Lindgren CM, Ragoussis J, Morris AP, Cardon LR, Spector TD, Zondervan KT. 2011. The use of genome-wide eQTL associations in lymphoblastoid cell lines to identify novel genetic pathways involved in complex traits. PloS one 6(7): e22070.
  53. Schodel J, Oikonomopoulos S, Ragoussis J, Pugh CW, Ratcliffe PJ, Mole DR. 2011. High-resolution genome-wide mapping of HIF-binding sites by ChIP-seq. Blood 117(23): e207-217.
  54. Vernes SC, Oliver PL, Spiteri E, Lockstone HE, Puliyadi R, Taylor JM, Ho J, Mombereau C, Brewer A, Lowy E, Nicod J, Groszer M, Baban D, Sahgal N, Cazier JB, Ragoussis J, Davies KE, Geschwind DH, Fisher SE. 2011. Foxp2 regulates gene networks implicated in neurite outgrowth in the developing brain. PLoS genetics 7(7): e1002145.
  55. Wong D, Teixeira A, Oikonomopoulos S, Humburg P, Lone IN, Saliba D, Siggers T, Bulyk M, Angelov D, Dimitrov S, Udalova IA, Ragoussis J. 2011. Extensive characterization of NF-kappaB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits. Genome biology 12(7): R70.
  56. Anney R Klei L Pinto D Almeida J Bacchelli E Baird G Bolshakova N Bolte S Bolton PF Bourgeron T Brennan S Brian J Casey J Conroy J Correia C Corsello C Crawford EL de Jonge M Delorme R Duketis E Duque F Estes A Farrar P Fernandez BA Folstein SE Fombonne E Gilbert J Gillberg C Glessner JT Green A Green J Guter SJ Heron EA Holt R Howe JL Hughes G Hus V Igliozzi R Jacob S Kenny GP Kim C Kolevzon A Kustanovich V Lajonchere CM Lamb JA Law-Smith M Leboyer M Le Couteur A Leventhal BL Liu XQ Lombard F Lord C Lotspeich L Lund SC Magalhaes TR Mantoulan C McDougle CJ Melhem NM Merikangas A Minshew NJ Mirza GK Munson J Noakes C Nygren G Papanikolaou K Pagnamenta AT Parrini B Paton T Pickles A Posey DJ Poustka F Ragoussis J Regan R Roberts W Roeder K Roge B Rutter ML Schlitt S Shah N Sheffield VC Soorya L Sousa I Stoppioni V Sykes N Tancredi R Thompson AP Thomson S Tryfon A Tsiantis J Van Engeland H Vincent JB Volkmar F Vorstman JA Wallace S Wing K Wittemeyer K Wood S Zurawiecki D Zwaigenbaum L Bailey AJ Battaglia A Cantor RM Coon H Cuccaro ML Dawson G Ennis S Freitag CM Geschwind DH Haines JL Klauck SM McMahon WM Maestrini E Miller J Monaco AP Nelson SF Nurnberger JI, Jr. Oliveira G Parr JR Pericak-Vance MA Piven J Schellenberg GD Scherer SW Vicente AM Wassink TH Wijsman EM Betancur C Buxbaum JD Cook EH Gallagher L Gill M Hallmayer J Paterson AD Sutcliffe JS Szatmari P Vieland VJ Hakonarson H, Devlin B. 2012. Individual common variants exert weak effects on the risk for autism spectrum disorderspi. Human molecular genetics 21(21): 4781-4792.
  57. Belfield EJ, Gan X, Mithani A, Brown C, Jiang C, Franklin K, Alvey E, Wibowo A, Jung M, Bailey K, Kalwani S, Ragoussis J, Mott R, Harberd NP. 2012. Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana. Genome research 22(7): 1306-1315.
  58. Brookes E, de Santiago I, Hebenstreit D, Morris KJ, Carroll T, Xie SQ, Stock JK, Heidemann M, Eick D, Nozaki N, Kimura H, Ragoussis J, Teichmann SA, Pombo A. 2012. Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs. Cell stem cell 10(2): 157-170.
  59. Casey JP Magalhaes T Conroy JM Regan R Shah N Anney R Shields DC Abrahams BS Almeida J Bacchelli E Bailey AJ Baird G Battaglia A Berney T Bolshakova N Bolton PF Bourgeron T Brennan S Cali P Correia C Corsello C Coutanche M Dawson G de Jonge M Delorme R Duketis E Duque F Estes A Farrar P Fernandez BA Folstein SE Foley S Fombonne E Freitag CM Gilbert J Gillberg C Glessner JT Green J Guter SJ Hakonarson H Holt R Hughes G Hus V Igliozzi R Kim C Klauck SM Kolevzon A Lamb JA Leboyer M Le Couteur A Leventhal BL Lord C Lund SC Maestrini E Mantoulan C Marshall CR McConachie H McDougle CJ McGrath J McMahon WM Merikangas A Miller J Minopoli F Mirza GK Munson J Nelson SF Nygren G Oliveira G Pagnamenta AT Papanikolaou K Parr JR Parrini B Pickles A Pinto D Piven J Posey DJ Poustka A Poustka F Ragoussis J Roge B Rutter ML Sequeira AF Soorya L Sousa I Sykes N Stoppioni V Tancredi R Tauber M Thompson AP Thomson S Tsiantis J Van Engeland H Vincent JB Volkmar F Vorstman JA Wallace S Wang K Wassink TH White K Wing K Wittemeyer K Yaspan BL Zwaigenbaum L Betancur C Buxbaum JD Cantor RM Cook EH Coon H Cuccaro ML Geschwind DH Haines JL Hallmayer J Monaco AP Nurnberger JI, Jr. Pericak-Vance MA Schellenberg GD Scherer SW Sutcliffe JS Szatmari P Vieland VJ Wijsman EM Green A Gill M Gallagher L Vicente A, Ennis S. 2012. A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder. Human genetics 131(4): 565-579.
  60. Jiang C, Belfield EJ, Mithani A, Visscher A, Ragoussis J, Mott R, Smith JA, Harberd NP. 2012. ROS-mediated vascular homeostatic control of root-to-shoot soil Na delivery in Arabidopsis. The EMBO journal 31(22): 4359-4370.
  61. Kivlehan F, Paolucci M, Brennan D, Ragoussis I, Galvin P. 2012. Three-dimensional hydrogel structures as optical sensor arrays, for the detection of specific DNA sequences. Analytical biochemistry 421(1): 1-8.
  62. Lise S, Clarkson Y, Perkins E, Kwasniewska A, Sadighi Akha E, Schnekenberg RP, Suminaite D, Hope J, Baker I, Gregory L, Green A, Allan C, Lamble S, Jayawant S, Quaghebeur G, Cader MZ, Hughes S, Armstrong RJ, Kanapin A, Rimmer A, Lunter G, Mathieson I, Cazier JB, Buck D, Taylor JC, Bentley D, McVean G, Donnelly P, Knight SJ, Jackson M, Ragoussis J, Nemeth AH. 2012. Recessive mutations in SPTBN2 implicate beta-III spectrin in both cognitive and motor development. PLoS genetics 8(12): e1003074.
  63. Margariti A, Winkler B, Karamariti E, Zampetaki A, Tsai TN, Baban D, Ragoussis J, Huang Y, Han JD, Zeng L, Hu Y, Xu Q. 2012. Direct reprogramming of fibroblasts into endothelial cells capable of angiogenesis and reendothelialization in tissue-engineered vessels. Proceedings of the National Academy of Sciences of the United States of America 109(34): 13793-13798.
  64. Ohman H, Bailey R, Natividad A, Ragoussis J, Johnson LL, Tiitinen A, Halttunen M, Paavonen J, Surcel HM. 2012. Effect of IL12A and IL12B polymorphisms on the risk of Chlamydia trachomatis-induced tubal factor infertility and disease severity. Human reproduction 27(7): 2217-2223.
  65. Pandis I, Ospelt C, Karagianni N, Denis MC, Reczko M, Camps C, Hatzigeorgiou AG, Ragoussis J, Gay S, Kollias G. 2012. Identification of microRNA-221/222 and microRNA-323-3p association with rheumatoid arthritis via predictions using the human tumour necrosis factor transgenic mouse model. Annals of the rheumatic diseases 71(10): 1716-1723.
  66. Parkinson NJ, Maslau S, Ferneyhough B, Zhang G, Gregory L, Buck D, Ragoussis J, Ponting CP, Fischer MD. 2012. Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA. Genome research 22(1): 125-133.
  67. Siggers T, Chang AB, Teixeira A, Wong D, Williams KJ, Ahmed B, Ragoussis J, Udalova IA, Smale ST, Bulyk ML. 2012. Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-kappaB family DNA binding. Nature immunology 13(1): 95-102.
  68. Winchester L, Ragoussis J. 2012. Algorithm implementation for CNV discovery using Affymetrix and Illumina SNP array data. Methods in molecular biology 838: 291-310.
  69. Goggolidou P, Soneji S, Powles-Glover N, Williams D, Sethi S, Baban D, Simon MM, Ragoussis I, Norris DP. 2013. A chronological expression profile of gene activity during embryonic mouse brain development. Mammalian genome : official journal of the International Mammalian Genome Society 24(11-12): 459-472.
  70. Hughes JR, Lower KM, Dunham I, Taylor S, De Gobbi M, Sloane-Stanley JA, McGowan S, Ragoussis J, Vernimmen D, Gibbons RJ, Higgs DR. 2013. High-resolution analysis of cis-acting regulatory networks at the alpha-globin locus. Philosophical transactions of the Royal Society of London Series B, Biological sciences 368(1620): 20120361.
  71. Karamariti E, Margariti A, Winkler B, Wang X, Hong X, Baban D, Ragoussis J, Huang Y, Han JD, Wong MM, Sag CM, Shah AM, Hu Y, Xu Q. 2013. Smooth muscle cells differentiated from reprogrammed embryonic lung fibroblasts through DKK3 signaling are potent for tissue engineering of vascular grafts. Circulation research 112(11): 1433-1443.
  72. McCormick RI, Blick C, Ragoussis J, Schoedel J, Mole DR, Young AC, Selby PJ, Banks RE, Harris AL. 2013. miR-210 is a target of hypoxia-inducible factors 1 and 2 in renal cancer, regulates ISCU and correlates with good prognosis. British journal of cancer 108(5): 1133-1142.
  73. Nemeth AH, Kwasniewska AC, Lise S, Parolin Schnekenberg R, Becker EB, Bera KD, Shanks ME, Gregory L, Buck D, Zameel Cader M, Talbot K, de Silva R, Fletcher N, Hastings R, Jayawant S, Morrison PJ, Worth P, Taylor M, Tolmie J, O'Regan M, Consortium UKA, Valentine R, Packham E, Evans J, Seller A, Ragoussis J. 2013. Next generation sequencing for molecular diagnosis of neurological disorders using ataxias as a model. Brain : a journal of neurology 136(Pt 10): 3106-3118.
  74. Papadopoulos GL, Karkoulia E, Tsamardinos I, Porcher C, Ragoussis J, Bungert J, Strouboulis J. 2013. GATA-1 genome-wide occupancy associates with distinct epigenetic profiles in mouse fetal liver erythropoiesis. Nucleic acids research 41(9): 4938-4948.
  75. Redshaw N, Camps C, Sharma V, Motallebipour M, Guzman-Ayala M, Oikonomopoulos S, Thymiakou E, Ragoussis J, Episkopou V. 2013. TGF-beta/Smad2/3 signaling directly regulates several miRNAs in mouse ES cells and early embryos. PloS one 8(1): e55186.
  76. Ryzhakov G, Teixeira A, Saliba D, Blazek K, Muta T, Ragoussis J, Udalova IA. 2013. Cross-species analysis reveals evolving and conserved features of the nuclear factor kappaB (NF-kappaB) proteins. The Journal of biological chemistry 288(16): 11546-11554.
  77. Severino P, Bruggemann H, Andreghetto FM, Camps C, Klingbeil Mde F, de Pereira WO, Soares RM, Moyses R, Wunsch-Filho V, Mathor MB, Nunes FD, Ragoussis J, Tajara EH. 2013. MicroRNA expression profile in head and neck cancer: HOX-cluster embedded microRNA-196a and microRNA-10b dysregulation implicated in cell proliferation. BMC cancer 13: 533.
  78. Shanks ME, Downes SM, Copley RR, Lise S, Broxholme J, Hudspith KA, Kwasniewska A, Davies WI, Hankins MW, Packham ER, Clouston P, Seller A, Wilkie AO, Taylor JC, Ragoussis J, Nemeth AH. 2013. Next-generation sequencing (NGS) as a diagnostic tool for retinal degeneration reveals a much higher detection rate in early-onset disease. European journal of human genetics : EJHG 21(3): 274-280.
  79. Twigg SR, Babbs C, van den Elzen ME, Goriely A, Taylor S, McGowan SJ, Giannoulatou E, Lonie L, Ragoussis J, Sadighi Akha E, Knight SJ, Zechi-Ceide RM, Hoogeboom JA, Pober BR, Toriello HV, Wall SA, Rita Passos-Bueno M, Brunner HG, Mathijssen IM, Wilkie AO. 2013. Cellular interference in craniofrontonasal syndrome: males mosaic for mutations in the X-linked EFNB1 gene are more severely affected than true hemizygotes. Human molecular genetics 22(8): 1654-1662.
  80. Belfield EJ, Brown C, Gan X, Jiang C, Baban D, Mithani A, Mott R, Ragoussis J, Harberd NP. 2014. Microarray-based ultra-high resolution discovery of genomic deletion mutations. BMC genomics 15: 224.
  81. Camps C, Saini HK, Mole DR, Choudhry H, Reczko M, Guerra-Assuncao JA, Tian YM, Buffa FM, Harris AL, Hatzigeorgiou AG, Enright AJ, Ragoussis J. 2014. Integrated analysis of microRNA and mRNA expression and association with HIF binding reveals the complexity of microRNA expression regulation under hypoxia. Molecular cancer 13: 28.
  82. Choudhry H, Schodel J, Oikonomopoulos S, Camps C, Grampp S, Harris AL, Ratcliffe PJ, Ragoussis J, Mole DR. 2014. Extensive regulation of the non-coding transcriptome by hypoxia: role of HIF in releasing paused RNApol2. EMBO reports 15(1): 70-76.
  83. Radovich M, Ragoussis J. 2014. Methods of Quantifying MicroRNAs for Hypoxia Research: Classic and Next Generation. Antioxidants & redox signaling 21(8): 1239-1248.
  84. Sagri E, Reczko M, Gregoriou ME, Tsoumani KT, Zygouridis NE, Salpea KD, Zalom FG, Ragoussis J, Mathiopoulos KD. 2014. Olive fly transcriptomics analysis implicates energy metabolism genes in spinosad resistance. BMC genomics 15(1): 714.
  85. Saliba DG, Heger A, Eames HL, Oikonomopoulos S, Teixeira A, Blazek K, Androulidaki A, Wong D, Goh FG, Weiss M, Byrne A, Pasparakis M, Ragoussis J, Udalova IA. 2014. IRF5:RelA Interaction Targets Inflammatory Genes in Macrophages. Cell reports 8(5): 1308-1317.
  86. Roulis M, Nikolaou C, Kotsaki E, Kaffe E, Karagianni N, Koliaraki V, Salpea K, Ragoussis J, Aidinis V, Martini E, Becker C, Herschman HR, Vetrano S, Danese S, Kollias G. 2014. Intestinal myofibroblast-specific Tpl2-Cox-2-PGE2 pathway links innate sensing to epithelial homeostasis. Proceedings of the National Academy of Sciences of the United States of America 111(43): E4658-4667.
  87. Sagri E, Reczko M, Tsoumani KT, Gregoriou ME, Harokopos V, Mavridou AM, Tastsoglou S, Athanasiadis K, Ragoussis J, Mathiopoulos KD. 2014b. The molecular biology of the olive fly comes of age. BMC genetics 15 Suppl 2: S8.
  88. Choudhry H, Albukhari A, Morotti M, Hider S, Moralli D, Smythies J, Schodel J, Green CM, Camps C, Buffa F, Ratcliffe P, Ragoussis J*, Harris AL*, Mole DR*. 2014a. Tumor hypoxia induces nuclear paraspeckle formation through HIF-2alpha dependent transcriptional activation of NEAT1 leading to cancer cell survival. Oncogene. [Epub ahead of print] *senior co-author
  89. Lopez JP, Diallo A, Cruceanu C, Fiori LM, Laboissiere S, Guillet I, Fontaine J, Ragoussis J, Benes V, Turecki G, Ernst C. 2015. Biomarker discovery: quantification of microRNAs and other small non-coding RNAs using next generation sequencing. BMC Med Genomics 8: 35.
  90. Ohman H, Natividad A, Bailey R, Ragoussis J, Johnson LL, Tiitinen A, Halttunen M, Paavonen J, Surcel HM. 2015. Contribution of IL-12A and IL-12B polymorphisms to Chlamydia trachomatis-specific cell-mediated immune responses. Scand J Immunol 81(3): 209-213.
  91. Parolin Schnekenberg R, Perkins EM, Miller JW, Davies WI, D'Adamo MC, Pessia M, Fawcett KA, Sims D, Gillard E, Hudspith K, Skehel P, Williams J, O'Regan M, Jayawant S, Jefferson R, Hughes S, Lustenberger A, Ragoussis J, Jackson M, Tucker SJ, Nemeth AH. 2015. De novo point mutations in patients diagnosed with ataxic cerebral palsy. Brain : a journal of neurology 138(Pt 7): 1817-1832.
  92. Viollet C, Davis DA, Reczko M, Ziegelbauer JM, Pezzella F, Ragoussis J, Yarchoan R. 2015. Next-Generation Sequencing Analysis Reveals Differential Expression Profiles of MiRNA-mRNA Target Pairs in KSHV-Infected Cells. PloS one 10(5): e0126439.
  93. Lopez JP, Diallo A, Cruceanu C, Fiori LM, Laboissiere S, Guillet I, Fontaine J, Ragoussis J, Benes V, Turecki G, Ernst C. 2015. Biomarker discovery: quantification of microRNAs and other small non-coding RNAs using next generation sequencing. BMC Med Genomics 8: 35.
  94. Yang J, AlTahan A, Jones DT, Buffa FM, Bridges E, Interiano RB, Qu C, Vogt N, Li JL, Baban D, Ragoussis J, Nicholson R, Davidoff AM, Harris AL. 2015. Estrogen receptor-alpha directly regulates the hypoxia-inducible factor 1 pathway associated with antiestrogen response in breast cancer. Proc Natl Acad Sci U S A 112(49): 15172-15177.
  95. de Kock L, Wang YC, Revil T, Badescu D, Rivera B, Sabbaghian N, Wu M, Weber E, Sandoval C, Hopman SM, Merks JH, van Hagen JM, Bouts AH, Plager DA, Ramasubramanian A, Forsmark L, Doyle KL, Toler T, Callahan J, Engelenberg C, Bouron-Dal Soglio D, Priest JR, Ragoussis J, Foulkes WD. 2016. High-sensitivity sequencing reveals multi-organ somatic mosaicism causing DICER1 syndrome. J Med Genet 53(1): 43-52.
  96. Pichulik T, Khatamzas E, Liu X, Brain O, Delmiro Garcia M, Leslie A, Danis B, Mayer A, Baban D, Ragoussis J, Weber AN, Simmons A. 2016. Pattern recognition receptor mediated downregulation of microRNA-650 fine-tunes MxA expression in dendritic cells infected with influenza A virus. Eur J Immunol 46(1): 167-177.
  97. Binan L, Mazzaferri J, Choquet K, Lorenzo LE, Wang YC, Affar el B, De Koninck Y, Ragoussis J, Kleinman CL, Costantino S. 2016. Live single-cell laser tag. Nat Commun 7: 11636.
  98. de Kock L, Bah I, Revil T, Berube P, Wu MK, Sabbaghian N, Priest JR, Ragoussis J, Foulkes WD. 2016a. Deep Sequencing Reveals Spatially Distributed Distinct Hot Spot Mutations in DICER1-Related Multinodular Goiter. J Clin Endocrinol Metab 101(10): 3637-3645.
  99. de Kock L, Wang YC, Revil T, Badescu D, Rivera B, Sabbaghian N, Wu M, Weber E, Sandoval C, Hopman SM, Merks JH, van Hagen JM, Bouts AH, Plager DA, Ramasubramanian A, Forsmark L, Doyle KL, Toler T, Callahan J, Engelenberg C, Bouron-Dal Soglio D, Priest JR, Ragoussis J, Foulkes WD. 2016b. High-sensitivity sequencing reveals multi-organ somatic mosaicism causing DICER1 syndrome. J Med Genet 53(1): 43-52.
  100. Gao B, Shao Q, Choudhry H, Marcus V, Dong K, Ragoussis J, Gao ZH. 2016. Weighted gene co-expression network analysis of colorectal cancer liver metastasis genome sequencing data and screening of anti-metastasis drugs. Int J Oncol 49(3): 1108-1118.
  101. Oikonomopoulos S, Wang YC, Djambazian H, Badescu D, Ragoussis J. 2016. Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations. Sci Rep 6: 31602.
  102. Pichulik T, Khatamzas E, Liu X, Brain O, Delmiro Garcia M, Leslie A, Danis B, Mayer A, Baban D, Ragoussis J, Weber AN, Simmons A. 2016. Pattern recognition receptor mediated downregulation of microRNA-650 fine-tunes MxA expression in dendritic cells infected with influenza A virus. Eur J Immunol 46(1): 167-177.
  103. Viollet C, Davis DA, Tekeste SS, Reczko M, Ziegelbauer JM, Pezzella F, Ragoussis J, Yarchoan R. 2017. RNA Sequencing Reveals that Kaposi Sarcoma-Associated Herpesvirus Infection Mimics Hypoxia Gene Expression Signature. PLoS Pathog 13(1): e1006143.