Lab's publications

Schneider AL*, Martins-Silva R*, Kaizeler A*, Saraiva-Agostinho N, Barbosa-Morais NL+. "voyAGEr: free web interface for the analysis of age-related gene expression alterations in human tissues." eLife, 2024;12:RP88623.
(* co-first authors, + corresponding author)

Ascensao-Ferreira M*, Martins-Silva R*, Saraiva-Agostinho N, Barbosa-Morais NL+. "betAS: intuitive analysis and visualisation of differential alternative splicing using beta distributions." RNA, 2024;rna.079764.123. [PUBMED]
(* co-first authors, + corresponding author)

Sousa NS, Bica M, Bras MF, Antunes IB, Encarnacao IA, Costa T, Martins IB, Barbosa-Morais NL, Sousa-Victor P, Neves J. "The immune landscape of murine skeletal muscle regeneration and aging." bioRxiv, 2023.11.07.565995.

Martins I, Neves-Silva D, Ascensao-Ferreira M, Dias AF, Ribeiro D, Isidro AF, Quiteria R, Paramos-de-Carvalho D, Barbosa-Morais NL, Saude L. "Mouse Spinal Cord Vascular Transcriptome Analysis Identifies CD9 and MYLIP as Injury-Induced Players." Int J Mol Sci, 2023;24(7):6433. [PUBMED]

Moreno-Marin N, Marteil G, Fresmann NC, de Almeida BP, Dores K, Fragoso R, Cardoso J, Pereira-Leal JB, Barata JT, Godinho S, Barbosa-Morais NL, Bettencourt-Dias M. "High prevalence and dependence of centrosome clustering in mesenchymal tumors and leukemia." bioRxiv, 2023.03.13.532472.

Goulielmaki E, Tsekrekou M, Batsiotos N, Ascensao-Ferreira M, Ledaki E, Stratigi K, Chatzinikolaou G, Topalis P, Kosteas T, Altmüller J, Demmers JA, Barbosa-Morais NL, Garinis GA. "The splicing factor XAB2 interacts with ERCC1-XPF and XPG for R-loop processing." Nature Communications, 2021 May 26;12(1):3153. [PUBMED]

Conde J, Pumroy RA, Baker C, Rodrigues T, Guerreiro A, Sousa BB, Marques MC, de Almeida BP, Lee S, Leites EP, Picard D, Samanta A, Vaz SH, Sieglitz F, Langini M, Remke M, Roque R, Weiss T, Weller M, Liu Y, Han S, Corzana F, Morais VA, Faria CC, Carvalho T, Filippakopoulos P, Snijder B, Barbosa-Morais NL, Moiseenkova-Bell VY, Bernardes GJL. "Allosteric Antagonist Modulation of TRPV2 by Piperlongumine Impairs Glioblastoma Progression." ACS Central Science, 2021 April 14;7(5):868-881. [PUBMED]
. Media coverage in Portugal: "Identificado potencial fármaco para tratamento do glioblastoma multiforme " (Público)

Bordone MC, Barbosa-Morais NL+. "Unraveling Targetable Systemic and Cell-Type-Specific Molecular Phenotypes of Alzheimer's and Parkinson's Brains With Digital Cytometry." Frontiers in Neuroscience, 2020 Dec 9;14:607215. [PUBMED]
(+ corresponding author)

Rathore OS, Silva RD, Ascensao-Ferreira M, Matos R, Carvalho C, Marques B, Tiago MN, Prudencio P, Andrade RP, Roignant JY, Barbosa-Morais NL+, Martinho RG +. "NineTeen Complex-subunit Salsa is required for efficient splicing of a subset of introns and dorsal-ventral patterning." RNA, 2020 Dec;26(12):1935-1956. [PUBMED]
(+ corresponding author)

Gomes I, de Almeida BP, Dâmaso S, Mansinho A, Correia I, Henriques S, Cruz-Duarte R, Vilhais G, Félix P, Alves P, Corredeira P, Barbosa-Morais NL, Costa L, Casimiro S. "Expression of receptor activator of NFkB (RANK) drives stemness and resistance to therapy in ER+HER2- breast cancer." Oncotarget, 2020 May 12;11(19):1714-1728. [PUBMED]

Santos AF, Barbosa-Morais NL, Hurlburt BK, Ramaswamy S, Hemmings O, Kwok M, O'Rourke C, Bahnson HT, Cheng H, James L, Gould HJ, Sutton BJ, Maleki SJ, Lack G. "IgE to epitopes of Ara h 2 enhance the diagnostic accuracy of Ara h 2-specific IgE." Allergy, 2020 Sep;75(9):2309-2318. [PUBMED]

Saraiva-Agostinho N+, Barbosa-Morais NL+. "Interactive Alternative Splicing Analysis of Human Stem Cells Using psichomics." Methods in Molecular Biology, 2020;2117:179-205. [PUBMED]
(+ corresponding author)

Godinho-Silva C, Domingues RG, Rendas M, Raposo B, Ribeiro H, da Silva JA, Vieira A, Costa RM, Barbosa-Morais NL, Carvalho T, Veiga-Fernandes H. "Light-entrained and brain-tuned circadian circuits regulate ILC3s and gut homeostasis." Nature, 2019 Oct;574(7777):254-258. [PUBMED]

Munkley J, Li L, Krishnan SRG, Hysenaj G, Scott E, Dalgliesh C, Oo HZ, Maia TM, Cheung K, Ehrmann I, Livermore KE, Zielinska H, Thompson O, Knight B, McCullagh P, McGrath J, Crundwell M, Harries LW, Daugaard M, Cockell S, Barbosa-Morais NL+, Oltean S +, Elliott DJ +. "Androgen-regulated transcription of ESRP2 drives alternative splicing patterns in prostate cancer." eLife, 2019 Sep 3;8:e47678. [PUBMED]
(+ corresponding author)

Rodrigues T, de Almeida BP, Barbosa-Morais NL, Bernardes GJL. "Dissecting celastrol with machine learning to unveil dark pharmacology." Chem Commun (Camb), 2019 May 30;55(45):6369-6372. [PUBMED]

Baker C, Rodrigues T, de Almeida BP, Barbosa-Morais NL, Bernardes GJL. "Natural product-drug conjugates for modulation of TRPV1-expressing tumors." Bioorg Med Chem, 2019 Jun 15;27(12):2531-2536. [PUBMED]

de Almeida BP, Vieira AF, Paredes J, Bettencourt-Dias M, Barbosa-Morais NL. "Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome." PLoS Computational Biology, 2019 Mar 11;15(3):e1006832. [PUBMED]
. Media coverage in Portugal: "Investigadores portugueses criam novo método para definir agressividade de cancros" (DN) [RTP] [TSF] [Visão] [RTP video]
. International media coverage: "When a cell's 'fingerprint' can be a weapon against cancer" (Science Daily) [InfoSalus (ES)] [ANSA (IT)] [il Fatto Quotidiano (IT)] [TuniseSoir - Tunisia] [Vaaju - Singapore]

Saraiva-Agostinho N, Barbosa-Morais NL. "psichomics: graphical application for alternative splicing quantification and analysis." Nucleic Acids Research, 2019 Jan 25;47(2):e7. [PUBMED]
. Press release: "New approach on the use of big data in clinical decision support"

Braun S, Enculescu M, Setty S, Cortés-López M, de Almeida B, Sutandy FXR, Schulz L, Busch A, Seiler M, Ebersberger S, Barbosa-Morais NL, Legewie S, Konig J, Zarnack K. "Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis". Nat Commun, 2018 Aug 17;9(1):3315. [PUBMED]

Georgilis A, Klotz S, Hanley CJ, Herranz N, Weirich B, Morancho B, Leote AC, D'Artista L, Gallage S, Seehawer M, Carroll T, Dharmalingam G, Wee KB, Mellone M, Pombo J, Heide D, Guccione E, Arribas J, Barbosa-Morais NL, Heikenwalder M, Thomas GJ, Zender L, Gil J. "PTBP1-Mediated Alternative Splicing Regulates the Inflammatory Secretome and the Pro-tumorigenic Effects of Senescent Cells." Cancer Cell, 2018 Jul 9;34(1):85-102.e9. [PUBMED]

Marteil G, Guerrero A, Vieira AF, de Almeida BP, Machado P, Mendonça S, Mesquita M, Villarreal B, Fonseca I, Francia ME, Dores K, Martins NP, Jana SC, Tranfield EM, Barbosa-Morais NL, Paredes J, Pellman D, Godinho SA, Bettencourt-Dias M. "Over-elongation of centrioles in cancer promotes centriole amplification and chromosome missegregation". Nat Commun, 2018 Mar 28;9(1):1258. [PUBMED]
. "Finding the Achilles heel of cancer"
. "Cancers of Many Kinds Give Centriole Amplification Starring Role"
. "Identificadas características das células cancerosas que podem ser o seu calcanhar de Aquiles"
. "Identificadas características das células cancerígenas que podem ajudar médicos"
. "Equipa liderada por portuguesa dá mais um passo no combate ao cancro"
. "Cientistas portugueses descobrem “calcanhar de Aquiles“ das células cancerígenas"
. "Portuguesa lidera equipa que descobriu novos traços das células do cancro"

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 Sep;136(9):1015-1042. [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]


Selected pre-lab publications

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]

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]

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)

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]