Barbosa-Morais et al. (2012) Science 338:1587 Barbosa-Morais et al. (2010) NAR 38:e17 Wilson, Barbosa-Morais et al. (2008) Science 322:434 Palmer et al. (2008) Cancer Research 68:4239 Barbosa-Morais et al. (2006) Genome Res 16:66

Publications

[Google Scholar] [PubMed search]

[Selected Articles] [All Journal Articles] [Book Chapters] [PhD Thesis]


Selected Articles

Gallego-Paez LM, Bordone MC, Leote AC, Saraiva-Agostinho N, Ascensao-Ferreira M, Barbosa-Morais NL+. "Alternative splicing: the pledge, the turn, and the prestige - The key role of alternative splicing in human biological systems." Hum Gen, 2017 Apr 3. doi: 10.1007/s00439-017-1790-y. [PUBMED]
(+ corresponding author)

Braunschweig U, Barbosa-Morais NL, Pan Q, Nachman EN, Alipahani B, Gonatopoulos-Pournatzis T, Frey B, Irimia M, Blencowe BJ. "Widespread intron retention in mammals functionally tunes transcriptomes". Genome Res, 2014 Nov;24(11):1774-86. [PUBMED]

Barbosa-Morais NL, Irimia M, Pan Q, Xiong HY, Gueroussov S, Lee LJ, Slobodeniuc V, Kutter C, Watt S, Colak R, Kim T, Misquitta-Ali CM, Wilson MD, Kim PM, Odom DT, Frey BJ, Blencowe BJ. "The evolutionary landscape of alternative splicing in vertebrate species". Science, 2012 Dec 21;338(6114):1587-93. [PUBMED]
. Perspectives - Evolution: "Splicing in 4D" [PUBMED]
. Recommended by Faculty of 1000
. Media coverage: [The Scientist] [Science Daily] [University of Toronto - Faculty of Medicine]

Barbosa-Morais NL+, Dunning MJ, Samarajiwa SA, Darot JFJ, Ritchie ME, Lynch AG, Tavaré S. "A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data". Nucleic Acids Research, 2010 Jan 1;38(3):e17. [PUBMED]
(+ corresponding author)

Wilson MD*, Barbosa-Morais NL*, Schmidt D, Conboy CM, Vanes L, Tybulewicz VLJ, Fisher EMC, Tavaré S, Odom DT. "Species-specific transcription in mice carrying human chromosome 21". Science, 2008 Oct 17;322(5900):434-8. [PUBMED]
(* equal contributions)
. Perspectives - Genetics: "It's the sequence, stupid!" [PUBMED]
. Review in Genome Biology [PUBMED]
. Review on Faculty of 1000 - Biology (top article of its month)

Palmer RD, Barbosa-Morais NL, Gooding EL, Muralidhar B, Thornton CM, Pett MR, Roberts I, Schneider DT, Thorne N, Tavaré S, Nicholson JC, Coleman N; On behalf of The Childrens Cancer and Leukaemia Group (CCLG). "Pediatric malignant germ cell tumours show characteristic transcriptome profiles". Cancer Research, 2008 Jun 1;68(11):4239-47. [PUBMED]

Barbosa-Morais NL, Carmo-Fonseca M, Aparicio S. "Systematic genome-wide annotation of spliceosomal proteins reveals differential gene family expansion", Genome Res, 2006 Jan, 16(1):66-77. [PUBMED]


All Journal Articles

denotes key papers

2017

[39] Cardoso V, Chesné J, Ribeiro H, García-Cassani B, Carvalho T, Bouchery T, Shah K, Barbosa-Morais NL, Harris N, Veiga-Fernandes H. "Neuronal regulation of type 2 innate lymphoid cells via neuromedin U". Nature, 2017 Sep 14;549(7671):277–281. [PUBMED]
. "O sistema imunitário também tem uma “adrenalina”"

[38] Gallego-Paez LM, Bordone MC, Leote AC, Saraiva-Agostinho N, Ascensao-Ferreira M, Barbosa-Morais NL+. "Alternative splicing: the pledge, the turn, and the prestige - The key role of alternative splicing in human biological systems." Hum Gen, 2017 Apr 3. doi: 10.1007/s00439-017-1790-y. [PUBMED]
(+ corresponding author)

[37] Rijo-Ferreira F, Pinto-Neves D, Barbosa-Morais NL, Takahashi JS, Figueiredo LM. "Trypanosoma brucei metabolism is under circadian control". Nat Microbiol, 2017 Mar 13;2:17032. [PUBMED]
. Behind the paper: "Do parasites know what time it is?"

2014

[36] Liu Y, Noon AP, Cabeza EA, Shen J, Kuk C, Ilczynski C, Ni R, Sukhu B, Chan K, Barbosa-Morais NL, Hermanns T, Blencowe BJ, Azad A, van der Kwast TH, Catto JWF, Zlotta AR, Wrana JL. "Next generation RNA sequencing of archival formalin fixed paraffin embedded urothelial bladder cancer". European Urology, 2014 Dec;66(6):982-6. [PUBMED]
. Press release: "New advances in next generation RNA sequencing of bladder cancer is personalizing patient care"

[35] Braunschweig U, Barbosa-Morais NL, Pan Q, Nachman EN, Alipahani B, Gonatopoulos-Pournatzis T, Frey B, Irimia M, Blencowe BJ. "Widespread intron retention in mammals functionally tunes transcriptomes". Genome Res, 2014 Nov;24(11):1774-86. [PUBMED]

[34] Pena AC, Pimentel MR, Manso H, Vaz-Drago R, Neves D, Aresta-Branco F, Ferreira FR, Guegan F, Coelho LP, Carmo-Fonseca M, Barbosa-Morais NL, Figueiredo LM. "Trypanosoma brucei histone H1 inhibits RNA polymerase I transcription and is important for parasite fitness in vivo". Mol Microbiol, 2014 Aug;93(4):645-63. [PUBMED]

2013

[33] Han H, Irimia M, Ross PJ, Sung HK, Alipanahi B, David L, Golipour A, Gabut M, Michael IP, Nachman EN, Wang E, Trcka D, Thompson T, O'Hanlon D, Slobodeniuc V, Barbosa-Morais NL, Burge CB, Moffat J, Frey BJ, Nagy A, Ellis J, Wrana JL, Blencowe BJ. "MBNL proteins repress ES-cell-specific alternative splicing and reprogramming". Nature, 2013 Jun 13;498(7453):241-5. [PUBMED]
. News and Views - Stem Cells: "Regulation by alternative splicing" [PUBMED]
. Research Highlight in Nature Reviews Molecular Cell Biology: "Stem Cells: Tailored splicing patterns" [PUBMED]

[32] Ward MC, Wilson MD, Barbosa-Morais NL, Schmidt D, Stark R, Pan Q, Schwalie PC, Menon S, Lukk M, Watt S, Thybert D, Kutter C, Kirschner K, Flicek P, Blencowe BJ, Odom DT. "Latent Regulatory Potential of Human-Specific Repetitive Elements". Mol Cell, 2013 Jan 24;49(2):262-72. [PUBMED]

2012

[31] Barbosa-Morais NL, Irimia M, Pan Q, Xiong HY, Gueroussov S, Lee LJ, Slobodeniuc V, Kutter C, Watt S, Colak R, Kim T, Misquitta-Ali CM, Wilson MD, Kim PM, Odom DT, Frey BJ, Blencowe BJ. "The evolutionary landscape of alternative splicing in vertebrate species". Science, 2012 Dec 21;338(6114):1587-93. [PUBMED]
. Perspectives - Evolution: "Splicing in 4D" [PUBMED]
. Recommended by Faculty of 1000
. Media coverage: [The Scientist] [Science Daily] [University of Toronto - Faculty of Medicine]

2011

[30] Muralidhar B, Winder D, Murray M, Palmer R, Barbosa-Morais N, Saini H, Roberts I, Pett M, Coleman N. "Functional evidence that Drosha overexpression in cervical squamous cell carcinoma affects cell phenotype and microRNA profiles". J Pathol, 2011 Aug;224(4):496-507. [PUBMED]

2010

[29] Ahmed AA, Lu Z, Jennings NB, Etemadmoghadam D, Capalbo L, Jacamo RO, Barbosa-Morais N, Le XF; Australian Ovarian Cancer Study Group, Vivas-Mejia P, Lopez-Berestein G, Grandjean G, Bartholomeusz G, Liao W, Andreeff M, Bowtell D, Glover DM, Sood AK, Bast RC Jr. "SIK2 is a centrosome kinase required for bipolar mitotic spindle formation that provides a potential target for therapy in ovarian cancer". Cancer Cell, 2010 Aug 9;18(2):109-21. [PUBMED]

[28] Dunning MJ, Curtis C, Barbosa-Morais NL, Caldas C, Tavaré S, Lynch AG. "The importance of platform annotation in interpreting microarray data". Lancet Oncol, 2010 Aug;11(8):717. [PUBMED]

[27] Barbosa-Morais NL+, Dunning MJ, Samarajiwa SA, Darot JFJ, Ritchie ME, Lynch AG, Tavaré S. "A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data". Nucleic Acids Research, 2010 Jan 1;38(3):e17. [PUBMED]
(+ corresponding author)

2009

[26] Lynch AG, Dunning MJ, Iddawela M, Barbosa-Morais NL, Ritchie ME. "Considerations for the processing and analysis of GoldenGate-based two-colour Illumina platforms". Statistical Methods in Medical Research, 2009 Oct;18(5):437-52. [PUBMED]

[25] White V, Scarpini C, Barbosa-Morais NL, Ikele E, Carter S, Laskey RA, Miller R, Coleman N. "Isolation of stool-derived mucus provides a high yield of coloncytes suitable for early detection of colorectal carcinoma". Cancer Epidemiology, Biomarkers & Prevention, 2009 Jul;18(7):2006-13. [PUBMED]

[24] Dunning AM, Healey CS, BaynesC, Maia AT, Scollen S, Vega A, Rodríguez R, Barbosa-Morais NL, Ponder BAJ, et al. "Association of ESR1 gene tagging SNPs with breast cancer risk". Human Molecular Genetics, 2009 Mar 15;18(6):1131-9. [PUBMED]

2008

[23] Wilson MD*, Barbosa-Morais NL*, Schmidt D, Conboy CM, Vanes L, Tybulewicz VLJ, Fisher EMC, Tavaré S, Odom DT. "Species-specific transcription in mice carrying human chromosome 21". Science, 2008 Oct 17;322(5900):434-8. [PUBMED]
(* equal contributions)
. Perspectives - Genetics: "It's the sequence, stupid!" [PUBMED]
. Review in Genome Biology [PUBMED]
. Review on Faculty of 1000 - Biology (top article of its month)

[22] Grosso AR, Gomes AQ, Barbosa-Morais NL, Caldeira S, Thorne NP, Grech G, von Lindern M, Carmo-Fonseca M. "Tissue-specific splicing factor gene expression signatures". Nucleic Acids Research, 2008 Sep;36(15):4823-32. [PUBMED]

[21] Dunning MJ, Ritchie ME, Barbosa-Morais NL, Tavaré S, Lynch AG. "A first spike-in validation of the Illumina specific Variance-Stabilizing Transformation". BMC Research Notes, 2008;1:18. [PUBMED]

[20] Palmer RD, Barbosa-Morais NL, Gooding EL, Muralidhar B, Thornton CM, Pett MR, Roberts I, Schneider DT, Thorne N, Tavaré S, Nicholson JC, Coleman N; On behalf of The Childrens Cancer and Leukaemia Group (CCLG). "Pediatric malignant germ cell tumours show characteristic transcriptome profiles". Cancer Research, 2008 Jun 1;68(11):4239-47. [PUBMED]

[19] Dunning MJ, Barbosa-Morais NL, Lynch AG, Tavaré S, Ritchie ME. "Statistical issues in the analysis of Illumina data". BMC Bioinformatics, 2008 Feb 6;9(1):85. [PUBMED]

[18] Driver K, Song S, Lesueur F, Ahmed S, Barbosa-Morais NL, Tyrer J, Ponder BAJ, Easton DF, Pharoah PDP, Dunning AM, for the SEARCH Team. "Association of single-nucleotide polymorphisms in the Cell Cycle genes with breast cancer in the British population". Carcinogenesis, 2008 Feb;29(2):333-41. [PUBMED]

2007

[17] Conboy CM, Spyrou C, Thorne NP, Wade EJ, Barbosa-Morais NL, Bhattacharjee A, Young RA, Tavaré S, Lees JA, Odom DT. "Cell cycle genes are the evolutionarily conserved targets of mammalian DREAM member E2F4". PLoS ONE. 2007 Oct 24;2(10):e1061. [PUBMED]

[16] Chin SF, Teschendorff AE, Marioni JC, Wang Y, Barbosa-Morais NL, Thorne NP, Costa J, Pinder SE, van de Wiel MA, Green AR, Ellis IO, Porter PL, Tavaré S, Brenton JD, Ylstra B, Caldas C. "High-resolution array-CGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer". Genome Biol. 2007 Oct 9;8(10):R215. [PUBMED]

[15] Blenkiron C, Goldstein LD, Thorne NP, Spiteri MI, Chin SF, Dunning M, Barbosa-Morais NL, Tavaré S, Caldas C, Miska EA. "MicroRNA expression profiling of human breast cancer identifies new markers of tumour subtype". Genome Biol. 2007 Oct 8;8(10):R214. [PUBMED]

[14] Massie CE, Adryan B, Barbosa-Morais NL, Lynch AG, Tran M, Neal DE, Mills IG. "New Androgen Receptor genomic targets reveal an interaction with the ETS1 transcription factor", EMBO Rep. 2007 Sep;8(9):871-8. Epub 2007 Aug 17. [PUBMED]

[13] Muralidhar B, Goldstein LD, Ng G, Winder DM, Palmer RD, Gooding EL, Barbosa-Morais NL, Mukherjee G, Thorne NP, Roberts I, Pett MR, Coleman N. "Global microRNA profiles in cervical squamous cell carcinoma depend on Drosha expression levels", J Pathol. 2007 Aug;212(4):368-77. [PUBMED]

[12] Chin SF, Wang Y, Thorne NP, Teschendorff AE, Pinder SE, Vias M, Naderi A, Roberts I, Barbosa-Morais NL, Garcia MJ, Iyer NG, Kranjac T, Robertson JF, Aparicio S, Tavaré S, Ellis I, Brenton JD, Caldas C. "Using array-comparative genomic hybridization to define molecular portraits of primary breast cancers", Oncogene. 2007 Mar 22;26(13):1959-70. Epub 2006 Sep 25. [PUBMED]

[11] Naderi A, Teschendorff AE, Barbosa-Morais NL, Pinder SE, Green AR, Powe DG, Robertson JF, Aparicio S, Ellis IO, Brenton JD, Caldas C. "A gene-expression signature to predict survival in breast cancer across independent data sets", Oncogene. 2007 Mar 1;26(10):1507-16. Epub 2006 Aug 28. [PUBMED]

2006

[10] Mollet I, Barbosa-Morais NL, Andrade J, Carmo-Fonseca M. "Diversity of human U2AF splicing factors", FEBS J. 2006 Nov;273(21):4807-16. Epub 2006 Oct 17. [PUBMED]

[9] Teschendorff AE, Naderi A, Barbosa-Morais NL, Caldas C. "PACK: Profile Analysis using Clustering and Kurtosis to find molecular classifiers in cancer", Bioinformatics. 2006 Sep 15;22(18):2269-75. Epub 2006 May 8. [PUBMED]

[8] Gama-Carvalho M, Barbosa-Morais NL, Brodsky AS, Silver PA, Carmo-Fonseca M. "Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors", Genome Biol. 2006;7(11):R113. [PUBMED]

[7] Teschendorff AE, Naderi A, Barbosa-Morais NL, Pinder SE, Ellis IO, Aparicio S, Brenton JD, Caldas C. "A consensus prognostic gene expression classifier for ER positive breast cancer", Genome Biol. 2006;7(10):R101. Epub 2006 Oct 31. [PUBMED]

[6] Barbosa-Morais NL, Carmo-Fonseca M, Aparicio S. "Systematic genome-wide annotation of spliceosomal proteins reveals differential gene family expansion", Genome Res, 2006 Jan, 16(1):66-77. [PUBMED]

[5] Ibrahim AEK, Thorne NP, Baird K, Barbosa-Morais NL, Tavaré S, Collins VP, Wyllie AH, Arends MJ, Brenton JD. "MMASS: an optimized array-based method for assessing CpG island methylation", Nucleic Acids Res. 2006;34(20):e136. Epub 2006 Oct 13. [PUBMED]

[4] Stamm S, Riethoven JJ, Le Texier V, Gopalakrishnan C, Kumanduri V, Tang Y, Barbosa-Morais NL, Thanaraj TA. "ASD: a bioinformatics resource on alternative splicing", Nucleic Acids Res, 2006 Jan 1, 34(Database issue):D46-55. [PUBMED]

2005

[3] Teschendorff AE, Wang Y, Barbosa-Morais NL, Brenton JD, Caldas C. "A variational Bayesian mixture modelling framework for cluster analysis of gene-expression data", Bioinformatics, 2005 Jul 1, 21(13):3025-33. [PUBMED]

2004

[2] Pacheco TR, Gomes AQ, Barbosa-Morais NL, Benes V, Ansorge W, Wollerton M, Smith CW, Valcarcel J, Carmo-Fonseca M. "Diversity of vertebrate splicing factor U2AF35: identification of alternatively spliced U2AF1 mRNAS", J Biol Chem, 2004 Jun 25, 279(26):27039-49. [PUBMED]

[1] Naderi A, Ahmed AA, Barbosa-Morais NL, Aparicio S, Brenton JD, Caldas C. "Expression microarray reproducibility is improved by optimising purification steps in RNA amplification and labelling", BMC Genomics, 2004 Jan 30, 5(1):9. [PUBMED]


Book chapters

Lynch AG, Smith ML, Dunning MJ, Cairns JM, Barbosa-Morais NL, Tavaré S. "beadarray, BASH and HULK - tools to increase the value of Illumina BeadArray experiments". In A. Gusnato, K.V. Mardia, & C.J. Fallaize (eds), Statistical Tools for Challenges in Bioinformatics, 2009 pp33-37. Leeds, Leeds University Press


PhD thesis

Barbosa-Morais NL (2007). "Bioinformatics Studies on the Complexity of Splicing and Gene Expression". Faculdade de Medicina, Universidade de Lisboa