Main work from the group:

  1. Esteves F, Xavier JM, Ford AM, Rocha C, Pharoah PDP, Caldas C, Chin SF, Maia AT. “Germline Allelic Expression of Genes at 17q22 Locus Associates with Risk of Breast Cancer#. European Journal of Cancer. 2022;172:146-157. DOI: 10.1016/j.ejca.2022.05.034
  2. Correia L#, Magno R#, Xavier JM, de Almeida BP, Duarte I, Esteves F, Ghezzo M, Eldrige M, Sun C, Bosma A, Mittempergher L, Marreiros A, Bernards R, Caldas C, Chin SF, and Maia AT. “Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant”. NPJ Breast Cancer. 2022;8(1):71. DOI: 10.1038/s41523-022-00435-9
  3. Magno R#, Duarte I#, Maia AT. “quincunx: an R package to query, download and wrangle PGS Catalog data”. Bioinformatics. 2021;38(1):294-6. DOI:10.1093/bioinformatics/btab522
  4. Jacinta-Fernandes AC, Xavier JM, Magno R, Lage J and Maia AT. “Breast cancer risk loci potentially alter miRNA regulation through cis-regulatory polymorphisms”. NPJ Genomic Medicine. 2020;5:4. DOI: 10.1038/s41525-019-0112-9
  5. Magno R \& Maia AT. “gwasrapidd: an R package to query, download and wrangle GWAS Catalog data”. Bioinformatics. 2020;36(2):649-650. DOI: 10.1093/bioinformatics/btz605
  6. Maia AT}, Sammut SJ, Jacinta-Fernandes A, Chin SF. “Big data in cancer genomics”. Current Opinion in Systems Biology 2017;4:78-84. DOI: 10.1016/j.coisb.2017.07.007

Previous work:

  1. Peterlongo P, Chang-Claude J, Moysich KB, Rudolph A, Schmutzler RK, Simard J, Soucy P, Eeles RA, Easton DF, Hamann U, Wilkening S, Chen B, Rookus MA, Schmidt MK, van der Baan FH, Spurdle AB, Walker LC, Lose F, \textbf{Maia AT}, et al., \textit{Candidate genetic modifiers for breast and ovarian cancer risk in BRCA1 and BRCA2 mutation carriers.} Cancer Epidemiology, Biomarkers and Prevention. 2015 Jan;24(1):308-16. DOI: 10.1158/1055-9965.EPI-14-0532
  2. Vollan HK, Rueda OM, Chin SF, Curtis C, Turashvili G, et al. “A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer”. Molecular Oncology. 2015;9(1):115-27. DOI:10.1016/j.molonc.2014.07.019
  3. Jones JO, Chin SF, Wong-Taylor LA, Leaford D, Ponder BA, Caldas C, Maia AT. “TOX3 mutations in breast cancer”. PLoS One. 2013;8(9):e74102. DOI: 10.1371/journal.pone.0074102
  4. French JD, Ghoussaini M, Edwards SL, et al. “Functional variants at the 11q13 risk locus for breast cancer regulate cyclin D1 expression through long-range enhancers”. American Journal of Human Genetics. 2013;92(4):489-503. DOI:10.1016/j.ajhg.2013.01.002
  5. Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, Speed D, Lynch AG, Samarajiwa S, Yuan Y, Gräf S, Ha G, Haffari G, Bashashati A, Russell R, McKinney S; \textbf{METABRIC Group}, et al. \textit{The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.} Nature. 2012;486(7403):346-52. DOI: 10.1038/nature10983
  6. Maia AT, Antoniou AC, O’Reilly M, Samarajiwa S, Dunning M, Kartsonaki C, Chin SF, Curtis CN, McGuffog L, Domchek SM; EMBRACE, et al. “Effects of BRCA2 cis-regulation in normal breast and cancer risk amongst BRCA2 mutation carriers”. Breast Cancer Research. 2012;14(2):R63. DOI: 10.1186/bcr3169
  7. Liu R, Maia AT, Russell R, Caldas C, Ponder BA, Ritchie ME. “Allele-specific expression analysis methods for high-density SNP microarray data”. Bioinformatics. 2012;28(8):1102-8. DOI: 10.1093/bioinformatics/bts089
  8. Meyer KB, Maia AT, O’Reilly M, Ghoussaini M, Prathalingam R, Porter-Gill P, Ambs S, Prokunina-Olsson L, Carroll J, Ponder BA. “A functional variant at a prostate cancer predisposition locus at 8q24 is associated with PVT1 expression”. PLoS Genet. 2011;7(7):e1002165. DOI: 10.1371/journal.pgen.1002165
  9. Azzato EM, Lee AJ, Teschendorff A, Ponder BA, Pharoah P, Caldas C, Maia AT. “Common germ-line polymorphism of C1QA and breast cancer survival”. British Journal of Cancer. 2010;102(8):1294-9. DOI:10.1038/sj.bjc.6605625
  10. Udler MS, Ahmed S, Healey CS, Meyer K, Struewing J, Maranian M, Kwon EM, Zhang J, Tyrer J, Karlins E, Platte R, Kalmyrzaev B, Dicks E, Field H, Maia AT, et al. “Fine scale mapping of the breast cancer 16q12 locus”. Human Molecular Genetics. 2010;19(12):2507-15. DOI: 10.1093/hmg/ddq122
  11. Alves M, Carreira I, Liberato P, Ramos S, Mafra M, Inverno AS, Maia AT, et al. “Identification of a 0.4 Kb deletion region in 10q26 associated with endometrial carcinoma”. Oncology Reports. 2010;23(2):519-22. DOI: 10.3892/or_00000664
  12. Maia AT, Spiteri I, Lee AJ, O’Reilly M, Jones L, Caldas C, Ponder BA. “Extent of differential allelic expression of candidate breast cancer genes is similar in blood and breast”. Breast Cancer Research. 2009;11(6):R88. DOI: 10.1186/bcr2458
  13. Dunning AM, Healey CS, Baynes C, Maia AT, Scollen S, Vega A, Rodríguez R, Barbosa-Morais NL, Ponder BA; SEARCH, et al. “Association of ESR1 gene tagging SNPs with breast cancer risk”. Human Molecular Genetics. 2009;18(6):1131-9. DOI: 10.1093/hmg/ddn429
  14. Barber M, Murrell A, Ito Y, Maia AT, Hyland S, Oliveira C, et al. “Mechanisms and sequelae of E-cadherin silencing in hereditary diffuse gastric cancer”. Journal of Pathology. 2008;216(3):295-306. DOI: 10.1002/path.2426
  15. Ito Y, Koessler T, Ibrahim AE, Rai S, Vowler SL, Abu-Amero S, Silva AL, Maia AT, et al. “Somatically acquired hypomethylation of IGF2 in breast and colorectal cancer”. Human Molecular Genetics. 2008;17(17):2633-43. DOI: 10.1093/hmg/ddn163
  16. Meyer KB#, Maia AT#, O’Reilly M, Teschendorff AE, Chin SF, Caldas C, Ponder BA. “Allele-specific up-regulation of FGFR2 increases susceptibility to breast cancer”. PLoS Biol. 2008;6(5):e108. DOI:10.1371/journal.pbio.0060108
  17. Udler M#, Maia AT#, Cebrian A, Brown C, Greenberg D, Shah M, Caldas C, Dunning A, Easton D, Ponder B, Pharoah P. “Common germline genetic variation in antioxidant defense genes and survival after diagnosis of breast cancer”. Journal of Clinical Oncology. 2007;25(21):3015-23. DOI: 10.1200/JCO.2006.10.0099
  18. Bundy JG, Iyer NG, Gentile MS, Hu DE, Kettunen M, Maia AT, Thorne NP, Brenton JD, Caldas C, Brindle KM. “Metabolic consequences of p300 gene deletion in human colon cancer cells”. Cancer Research. 2006;66(15):7606-14. DOI: 10.1200/JCO.2006.10.0099
  19. Maia AT, Tussiwand R, Cazzaniga G, Rebulla P, Colman S, Biondi A, Greaves M. “Identification of preleukemic precursors of hyperdiploid acute lymphoblastic leukemia in cord blood”. Genes Chromosomes Cancer. 2004;40(1):38-43. DOI: 10.1002/gcc.20010
  20. Maia AT, Koechling J, Corbett R, Metzler M, Wiemels JL, Greaves M. “Protracted postnatal natural histories in childhood leukemia”. Genes Chromosomes Cancer. 2004;39(4):335-40. DOI: 10.1002/gcc.20003
  21. Zuna J, Muzikova K, Ford AM, Maia AT, Krejci O, Tousovska K, Oravkinova I, Greaves M, Trka J. “Pre-natal, clonal origin of acute lymphoblastic leukaemia in triplets”. Leukemia and Lymphoma. 2003;44(12):2099-102. DOI: 10.1080/1042819031000123393
  22. Maia AT, van der Velden VH, Harrison CJ, Szczepanski T, Williams MD, Griffiths MJ, van Dongen JJ, Greaves MF. “Prenatal origin of hyperdiploid acute lymphoblastic leukemia in identical twins”. Leukemia. 2003;17(11):2202-6. DOI: 10.1038/sj.leu.2403101
  23. Greaves MF, Maia AT, Wiemels JL, Ford AM. “Leukemia in twins: lessons in natural history”. Blood. 2003;102(7):2321-33. DOI: 10.1182/blood-2002-12-3817
  24. Wiemels JL, Xiao Z, Buffler PA, Maia AT, Ma X, Dicks BM, Smith MT, Zhang L, Feusner J, Wiencke J, Pritchard-Jones K, Kempski H, Greaves M. “In utero origin of t(8;21) AML1-ETO translocations in childhood acute myeloid leukemia”. Blood. 2002;99(10):3801-5. DOI: 10.1182/blood.v99.10.3801
  25. Maia AT, Ford AM, Jalali GR, Harrison CJ, Taylor GM, Eden OB, Greaves MF. “Molecular tracking of leukemogenesis in a triplet pregnancy”. Blood. 2001;98(2):478-82. DOI: 10.1182/blood.v98.2.478

Pre-Prints & Proceedings Abstracts

  1. Xavier JM, Magno R, Russell R, Almeida BP, Jacinta-Fernandes A, Duarte A, Dunning M, Samarajiwa S, O’Reilly M, Rocha CL, Rosli N, Ponder BAJ, Maia AT. “Mapping of cis-regulatory variants by differential allelic expression analysis identifies candidate risk variants and target genes of 27 breast cancer risk loci”. medRxiv 2022. DOI: 10.1101/2022.03.08.22271889
  2. Machado J, Magno R, Xavier JM, Maia AT. “Alternative splicing regulation by GWAS risk loci for breast cancer”. biorxiv. 2019; DOI: 10.1101/766394
  3. Duarte I, Magno R, Maia AT. “Monoallelic expression of breast cancer driver genes reveals functional passenger mutations”. Medicine 2022;101(30):p e29313. DOI:10.1097/MD.0000000000029313

Publlished Software

  1. Duarte A, Magno R, Martel P, Maia AT. “Alternative splicing in breast cancer risk (Version v1)”. Zenodo. 2020. DOI: 10.5281/zenodo.3776118

Other Publications

  1. Jacinta-Fernandes A, Maia AT. “Cis-regulatory variation mechanisms”. Figshare. 2021. Figure. DOI: 10.6084/m9.figshare.13643198.v1
  2. Jacinta-Fernandes A, Chin SF, Maia AT. “BigDataCancerGenomics_graphical_abstract”. Figshare. 2019. Figure. DOI:10.6084/m9.figshare.7795184.v1

Work from collaborations:

  1. Apolónio JD, Dias JS , Fernandes MT, Komosa M, et al. “THOR is a targetable epigenetic biomarker with clinical implications in breast cancer”. Under Review in Clinical Epigenetics.
  2. Liber M, Duarte I, Maia AT, Oliveira HR. “The history of lentil (Lens culinaris subsp. culinaris) domestication and spread revealed with Genotype-by-Sequencing of wild and landrace accessions”. Frontiers in Plant Science. 2021;12:628439. DOI:10.3389/fpls.2021.628439
  3. Faleiro I, Leão R, Binnie A, de Mello RA, Maia AT, Castelo-Branco P. “Epigenetic therapy in urologic cancers: an update on clinical trials”. Oncotarget. 2017;8(7):12484-12500 DOI:10.18632/oncotarget.14226