Selected publications

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”"

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]

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?"

Sridhara SC, Carvalho S, Grosso AR, Gallego-Paez LM, Carmo-Fonseca M, de Almeida SF. "Transcription Dynamics Prevent RNA-Mediated Genomic Instability through SRPK2-Dependent DDX23 Phosphorylation." Cell Rep., 2017 Jan 10;18(2):334-343. [PUBMED]

Deng M, Brägelmann J, Kryukov I, Saraiva-Agostinho N, Perner S. "FirebrowseR: an R client to the Broad Institute's Firehose Pipeline." Database (Oxford), 2017 Jan 6;2017. pii: baw160. doi: 10.1093/database/baw160. [PUBMED]

Munoz-Ruiz M, Ribot JC, Grosso AR, Goncalves-Sousa N, Pamplona A, Pennington DJ, Regueiro JR, Fernandez-Malave E, Silva-Santos B. "TCR signal strength controls thymic differentiation of discrete proinflammatory γδ T cell subsets". Nat Immunol, 2016 Jun;17(6):721-7. [PUBMED]

Grosso AR, Leite AP, Carvalho S, Matos MR, Martins FB, Vitor AC, Desterro JM, Carmo-Fonseca M, de Almeida SF. "Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma". Elife, 2015 Nov 17;4. pii: e09214. [PUBMED]

Nojima T, Gomes T, Grosso AR, Kimura H, Dye MJ, Dhir S, Carmo-Fonseca M, Proudfoot NJ. "Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing". Cell, 2015 Apr 23;161(3):526-40. [PUBMED]

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]

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]

Schmolka N, Serre K, Grosso AR, Rei M, Pennington DJ, Gomes AQ, Silva-Santos B. "Epigenetic and transcriptional signatures of stable versus plastic differentiation of proinflammatory γδ T cell subsets". Nat Immunol, 2013 Oct;14(10):1093-100. [PUBMED]

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]

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]

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]

Grosso AR, de Almeida SF, Braga J, Carmo-Fonseca M. "Dynamic transitions in RNA polymerase II density profiles during transcription termination". Genome Res, 2012 Aug;22(8):1447-56. [PUBMED]

de Almeida SF, Grosso AR, Koch F, Fenouil R, Carvalho S, Andrade J, Levezinho H, Gut M, Eick D, Gut I, Andrau JC, Ferrier P, Carmo-Fonseca M. "Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36". Nat Struct Mol Biol, 2011 Jul 26;18(9):977-83. [PUBMED]

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)

Grosso AR, Martins S, Carmo-Fonseca M. "The emerging role of splicing factors in cancer". EMBO Rep, 2008 Nov;9(11):1087-93. [PUBMED]

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)

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]

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]