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Detection of rare and novel EGFR mutations in NSCLC patients: Implications for treatment-decision.

Sousa AC, Silveira C, Janeiro A, Malveiro S, Oliveira AR, Felizardo M, Nogueira F, Teixeira E, Martins J, Carmo-Fonseca M.

Lung Cancer. 2019 Nov 4;139:35-40. doi: 10.1016/j.lungcan.2019.10.030. [Epub ahead of print]


Targeting mRNA processing as an anticancer strategy.

Desterro J, Bak-Gordon P, Carmo-Fonseca M.

Nat Rev Drug Discov. 2019 Sep 25. doi: 10.1038/s41573-019-0042-3. [Epub ahead of print] Review.


Analysis of Mammalian Native Elongating Transcript sequencing (mNET-seq) high-throughput data.

Prudêncio P, Rebelo K, Grosso AR, Martinho RG, Carmo-Fonseca M.

Methods. 2019 Sep 5. pii: S1046-2023(18)30484-5. doi: 10.1016/j.ymeth.2019.09.003. [Epub ahead of print]


Negative MR4·0 chronic myeloid leukaemia and its possible implications for treatment-free remission.

Cerveira N, Diamond J, Matos S, Amorim ML, Coucelo M, Bizarro S, Simões AT, Pierdomenico F, Lopes M, Ribeiro L, do Carmo-Fonseca M, Guimarães JE, Almeida A, Teixeira MR.

Br J Haematol. 2019 Sep;186(6):e181-e184. doi: 10.1111/bjh.16058. Epub 2019 Jun 19. No abstract available.


Design Principles for Pluripotent Stem Cell-Derived Organoid Engineering.

Silva TP, Cotovio JP, Bekman E, Carmo-Fonseca M, Cabral JMS, Fernandes TG.

Stem Cells Int. 2019 Apr 18;2019:4508470. doi: 10.1155/2019/4508470. eCollection 2019. Review.


Catalyzing Transcriptomics Research in Cardiovascular Disease: The CardioRNA COST Action CA17129.

Gomes CPC, Ágg B, Andova A, Arslan S, Baker A, Barteková M, Beis D, Betsou F, Wettinger SB, Bugarski B, Condorelli G, Silva GJJD, Danilin S, de Gonzalo-Calvo D, Buil A, Carmo-Fonseca M, Enguita FJ, Felekkis K, Ferdinandy P, Gyöngyösi M, Hackl M, Karaduzovic-Hadziabdic K, Hellemans J, Heymans S, Hlavackova M, Hoydal MA, Jankovic A, Jusic A, Kardassis D, Kerkelä R, Kuster GM, Lakkisto P, Leszek P, Lustrek M, Maegdefessel L, Martelli F, Novella S, O'Brien T, Papaneophytou C, Pedrazzini T, Pinet F, Popescu O, Potočnjak I, Robinson E, Sasson S, Scholz M, Simionescu M, Stoll M, Varga ZV, Vinciguerra M, Xuereb A, Yilmaz MB, Emanueli C, Devaux Y, on behalf of the EU-CardioRNA COST Action (CA17129).

Noncoding RNA. 2019 Mar 29;5(2). pii: E31. doi: 10.3390/ncrna5020031.


RNA Polymerase II Phosphorylated on CTD Serine 5 Interacts with the Spliceosome during Co-transcriptional Splicing.

Nojima T, Rebelo K, Gomes T, Grosso AR, Proudfoot NJ, Carmo-Fonseca M.

Mol Cell. 2018 Oct 18;72(2):369-379.e4. doi: 10.1016/j.molcel.2018.09.004.


Silencing of the lncRNA Zeb2-NAT facilitates reprogramming of aged fibroblasts and safeguards stem cell pluripotency.

Bernardes de Jesus B, Marinho SP, Barros S, Sousa-Franco A, Alves-Vale C, Carvalho T, Carmo-Fonseca M.

Nat Commun. 2018 Jan 8;9(1):94. doi: 10.1038/s41467-017-01921-6.


Whole gene sequencing identifies deep-intronic variants with potential functional impact in patients with hypertrophic cardiomyopathy.

Mendes de Almeida R, Tavares J, Martins S, Carvalho T, Enguita FJ, Brito D, Carmo-Fonseca M, Lopes LR.

PLoS One. 2017 Aug 10;12(8):e0182946. doi: 10.1371/journal.pone.0182946. eCollection 2017.


Short (16-mer) locked nucleic acid splice-switching oligonucleotides restore dystrophin production in Duchenne Muscular Dystrophy myotubes.

Pires VB, Simões R, Mamchaoui K, Carvalho C, Carmo-Fonseca M.

PLoS One. 2017 Jul 24;12(7):e0181065. doi: 10.1371/journal.pone.0181065. eCollection 2017.


Deep intronic mutations and human disease.

Vaz-Drago R, Custódio N, Carmo-Fonseca M.

Hum Genet. 2017 Sep;136(9):1093-1111. doi: 10.1007/s00439-017-1809-4. Epub 2017 May 12. Review.


Quantitative Image Analysis of Single-Molecule mRNA Dynamics in Living Cells.

Rino J, de Jesus AC, Carmo-Fonseca M.

Methods Mol Biol. 2017;1563:229-242. doi: 10.1007/978-1-4939-6810-7_15.


Pharmacological inhibition of the spliceosome subunit SF3b triggers exon junction complex-independent nonsense-mediated decay.

Carvalho T, Martins S, Rino J, Marinho S, Carmo-Fonseca M.

J Cell Sci. 2017 May 1;130(9):1519-1531. doi: 10.1242/jcs.202200. Epub 2017 Mar 16.


Transcription Dynamics Prevent RNA-Mediated Genomic Instability through SRPK2-Dependent DDX23 Phosphorylation.

Sridhara SC, Carvalho S, Grosso AR, Gallego-Paez LM, Carmo-Fonseca M, de Almeida SF.

Cell Rep. 2017 Jan 10;18(2):334-343. doi: 10.1016/j.celrep.2016.12.050.


Distinctive Patterns of Transcription and RNA Processing for Human lincRNAs.

Schlackow M, Nojima T, Gomes T, Dhir A, Carmo-Fonseca M, Proudfoot NJ.

Mol Cell. 2017 Jan 5;65(1):25-38. doi: 10.1016/j.molcel.2016.11.029. Epub 2016 Dec 22.


A rare missense variant in RET exon 8 in a Portuguese family with atypical multiple endocrine neoplasia type 2A.

Martins AF, Martins JM, do Vale S, Dias T, Silveira C, da Silva IR, Carmo-Fonseca M.

Hormones (Athens). 2016 Jul;15(3):435-440. doi: 10.14310/horm.2002.1691.


Co-transcriptional splicing and the CTD code.

Custódio N, Carmo-Fonseca M.

Crit Rev Biochem Mol Biol. 2016 Sep;51(5):395-411. Epub 2016 Sep 13. Review.


STaQTool: Spot tracking and quantification tool for monitoring splicing of single pre-mRNA molecules in living cells.

Rino J, de Jesus AC, Carmo-Fonseca M.

Methods. 2016 Apr 1;98:143-149. doi: 10.1016/j.ymeth.2016.02.005. Epub 2016 Feb 6.


Mammalian NET-seq analysis defines nascent RNA profiles and associated RNA processing genome-wide.

Nojima T, Gomes T, Carmo-Fonseca M, Proudfoot NJ.

Nat Protoc. 2016 Mar;11(3):413-28. doi: 10.1038/nprot.2016.012. Epub 2016 Feb 4.


Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma.

Grosso AR, Leite AP, Carvalho S, Matos MR, Martins FB, Vítor AC, Desterro JM, Carmo-Fonseca M, de Almeida SF.

Elife. 2015 Nov 17;4. pii: e09214. doi: 10.7554/eLife.09214.


Assembly of the nucleolus: in need of revision.

Carmo-Fonseca M.

EMBO J. 2015 Nov 12;34(22):2731-2. doi: 10.15252/embj.201593185. Epub 2015 Oct 15. Review. No abstract available.


Single-Molecule Live-Cell Visualization of Pre-mRNA Splicing.

Martin RM, Rino J, de Jesus AC, Carmo-Fonseca M.

Methods Mol Biol. 2016;1358:335-50. doi: 10.1007/978-1-4939-3067-8_22.


Single-Molecule Imaging of RNA Splicing in Live Cells.

Rino J, Martin RM, Carvalho C, de Jesus AC, Carmo-Fonseca M.

Methods Enzymol. 2015;558:571-585. doi: 10.1016/bs.mie.2015.01.013. Epub 2015 Feb 27.


Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing.

Nojima T, Gomes T, Grosso ARF, Kimura H, Dye MJ, Dhir S, Carmo-Fonseca M, Proudfoot NJ.

Cell. 2015 Apr 23;161(3):526-540. doi: 10.1016/j.cell.2015.03.027.


RNA imaging: seeing is believing.

Carmo-Fonseca M.

RNA. 2015 Apr;21(4):580-1. doi: 10.1261/rna.050393.115. No abstract available.


Transcription-coupled RNA surveillance in human genetic diseases caused by splice site mutations.

Vaz-Drago R, Pinheiro MT, Martins S, Enguita FJ, Carmo-Fonseca M, Custódio N.

Hum Mol Genet. 2015 May 15;24(10):2784-95. doi: 10.1093/hmg/ddv039. Epub 2015 Feb 4.


Trypanosoma brucei histone H1 inhibits RNA polymerase I transcription and is important for parasite fitness in vivo.

Pena AC, Pimentel MR, Manso H, Vaz-Drago R, Pinto-Neves D, Aresta-Branco F, Rijo-Ferreira F, Guegan F, Pedro Coelho L, Carmo-Fonseca M, Barbosa-Morais NL, Figueiredo LM.

Mol Microbiol. 2014 Aug;93(4):645-63. doi: 10.1111/mmi.12677. Epub 2014 Jul 14.


Reciprocal regulatory links between cotranscriptional splicing and chromatin.

de Almeida SF, Carmo-Fonseca M.

Semin Cell Dev Biol. 2014 Aug;32:2-10. doi: 10.1016/j.semcdb.2014.03.010. Epub 2014 Mar 19. Review.


The timing of pre-mRNA splicing visualized in real-time.

Carmo-Fonseca M, Kirchhausen T.

Nucleus. 2014 Jan-Feb;5(1):11-4. doi: 10.4161/nucl.28056. Epub 2014 Jan 30.


Live-cell visualization of pre-mRNA splicing with single-molecule sensitivity.

Martin RM, Rino J, Carvalho C, Kirchhausen T, Carmo-Fonseca M.

Cell Rep. 2013 Sep 26;4(6):1144-55. doi: 10.1016/j.celrep.2013.08.013. Epub 2013 Sep 12.


Imaging dynamic interactions between spliceosomal proteins and pre-mRNA in living cells.

Rino J, Martin RM, Carvalho T, Carmo-Fonseca M.

Methods. 2014 Feb;65(3):359-66. doi: 10.1016/j.ymeth.2013.08.010. Epub 2013 Aug 19.


Histone methyltransferase SETD2 coordinates FACT recruitment with nucleosome dynamics during transcription.

Carvalho S, Raposo AC, Martins FB, Grosso AR, Sridhara SC, Rino J, Carmo-Fonseca M, de Almeida SF.

Nucleic Acids Res. 2013 Mar 1;41(5):2881-93. doi: 10.1093/nar/gks1472. Epub 2013 Jan 15.


Alternative splicing and cancer.

Auboeuf D, Carmo-Fonseca M, Valcarcel J, Biamonti G.

J Nucleic Acids. 2012;2012:363809. doi: 10.1155/2012/363809. Epub 2012 May 20. No abstract available.


Dynamic transitions in RNA polymerase II density profiles during transcription termination.

Grosso AR, de Almeida SF, Braga J, Carmo-Fonseca M.

Genome Res. 2012 Aug;22(8):1447-56. doi: 10.1101/gr.138057.112. Epub 2012 Jun 8.


Design principles of interconnections between chromatin and pre-mRNA splicing.

de Almeida SF, Carmo-Fonseca M.

Trends Biochem Sci. 2012 Jun;37(6):248-53. doi: 10.1016/j.tibs.2012.02.002. Epub 2012 Mar 5. Review.


Spliceosome assembly is coupled to RNA polymerase II dynamics at the 3' end of human genes.

Martins SB, Rino J, Carvalho T, Carvalho C, Yoshida M, Klose JM, de Almeida SF, Carmo-Fonseca M.

Nat Struct Mol Biol. 2011 Sep 4;18(10):1115-23. doi: 10.1038/nsmb.2124.


Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36.

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.

Nat Struct Mol Biol. 2011 Jul 26;18(9):977-83. doi: 10.1038/nsmb.2123.


TAL1/SCL is downregulated upon histone deacetylase inhibition in T-cell acute lymphoblastic leukemia cells.

Cardoso BA, de Almeida SF, Laranjeira AB, Carmo-Fonseca M, Yunes JA, Coffer PJ, Barata JT.

Leukemia. 2011 Oct;25(10):1578-86. doi: 10.1038/leu.2011.140. Epub 2011 Jun 7.


RNA seeds nuclear bodies.

Carmo-Fonseca M, Rino J.

Nat Cell Biol. 2011 Feb;13(2):110-2. doi: 10.1038/ncb0211-110.


A link between nuclear RNA surveillance, the human exosome and RNA polymerase II transcriptional termination.

de Almeida SF, García-Sacristán A, Custódio N, Carmo-Fonseca M.

Nucleic Acids Res. 2010 Dec;38(22):8015-26. doi: 10.1093/nar/gkq703. Epub 2010 Aug 10.


Follow that messenger: live-imaging a journey out of the nucleus.

Carmo-Fonseca M.

Dev Cell. 2010 Jun 15;18(6):880-2. doi: 10.1016/j.devcel.2010.05.021.


N-glycosylation is important for the correct intracellular localization of HFE and its ability to decrease cell surface transferrin binding.

Bhatt L, Murphy C, O'Driscoll LS, Carmo-Fonseca M, McCaffrey MW, Fleming JV.

FEBS J. 2010 Aug;277(15):3219-34. doi: 10.1111/j.1742-4658.2010.07727.x. Epub 2010 Jul 5.


Orphan nuclear bodies.

Carmo-Fonseca M, Berciano MT, Lafarga M.

Cold Spring Harb Perspect Biol. 2010 Sep;2(9):a000703. doi: 10.1101/cshperspect.a000703. Epub 2010 Jul 7. Review.


Cotranscriptional RNA checkpoints.

de Almeida SF, Carmo-Fonseca M.

Epigenomics. 2010 Jun;2(3):449-55. doi: 10.2217/epi.10.21. Review.


Unconstrained mining of transcript data reveals increased alternative splicing complexity in the human transcriptome.

Mollet IG, Ben-Dov C, Felício-Silva D, Grosso AR, Eleutério P, Alves R, Staller R, Silva TS, Carmo-Fonseca M.

Nucleic Acids Res. 2010 Aug;38(14):4740-54. doi: 10.1093/nar/gkq197. Epub 2010 Apr 12.


Hsp70 chaperones and type I PRMTs are sequestered at intranuclear inclusions caused by polyalanine expansions in PABPN1.

Tavanez JP, Bengoechea R, Berciano MT, Lafarga M, Carmo-Fonseca M, Enguita FJ.

PLoS One. 2009 Jul 29;4(7):e6418. doi: 10.1371/journal.pone.0006418.


The spliceosome: a self-organized macromolecular machine in the nucleus?

Rino J, Carmo-Fonseca M.

Trends Cell Biol. 2009 Aug;19(8):375-84. doi: 10.1016/j.tcb.2009.05.004. Epub 2009 Jul 17. Review.


Frontiers in fluorescence microscopy.

Rino J, Braga J, Henriques R, Carmo-Fonseca M.

Int J Dev Biol. 2009;53(8-10):1569-79. doi: 10.1387/ijdb.072351jr.


The emerging role of splicing factors in cancer.

Grosso AR, Martins S, Carmo-Fonseca M.

EMBO Rep. 2008 Nov;9(11):1087-93. doi: 10.1038/embor.2008.189. Epub 2008 Oct 10.


Tissue-specific splicing factor gene expression signatures.

Grosso AR, Gomes AQ, Barbosa-Morais NL, Caldeira S, Thorne NP, Grech G, von Lindern M, Carmo-Fonseca M.

Nucleic Acids Res. 2008 Sep;36(15):4823-32. doi: 10.1093/nar/gkn463. Epub 2008 Jul 24.

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