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Predicting malignancy from mammography findings and image-guided core biopsies.

Ferreira P, Fonseca NA, Dutra I, Woods R, Burnside E.

Int J Data Min Bioinform. 2015;11(3):257-76.


Nucleolin overexpression in breast cancer cell sub-populations with different stem-like phenotype enables targeted intracellular delivery of synergistic drug combination.

Fonseca NA, Rodrigues AS, Rodrigues-Santos P, Alves V, Gregório AC, Valério-Fernandes Â, Gomes-da-Silva LC, Rosa MS, Moura V, Ramalho-Santos J, Simões S, Moreira JN.

Biomaterials. 2015 Nov;69:76-88. doi: 10.1016/j.biomaterials.2015.08.007. Epub 2015 Aug 6.


Convergent evolution at the gametophytic self-incompatibility system in Malus and Prunus.

Aguiar B, Vieira J, Cunha AE, Fonseca NA, Iezzoni A, van Nocker S, Vieira CP.

PLoS One. 2015 May 19;10(5):e0126138. doi: 10.1371/journal.pone.0126138. eCollection 2015.


Antibacterial activity of chitosan nanofiber meshes with liposomes immobilized releasing gentamicin.

Monteiro N, Martins M, Martins A, Fonseca NA, Moreira JN, Reis RL, Neves NM.

Acta Biomater. 2015 May;18:196-205. doi: 10.1016/j.actbio.2015.02.018. Epub 2015 Mar 5.


Simultaneous active intracellular delivery of doxorubicin and C6-ceramide shifts the additive/antagonistic drug interaction of non-encapsulated combination.

Fonseca NA, Gomes-da-Silva LC, Moura V, Simões S, Moreira JN.

J Control Release. 2014 Dec 28;196:122-31. doi: 10.1016/j.jconrel.2014.09.024. Epub 2014 Oct 11.


RNA-Seq gene profiling--a systematic empirical comparison.

Fonseca NA, Marioni J, Brazma A.

PLoS One. 2014 Sep 30;9(9):e107026. doi: 10.1371/journal.pone.0107026. eCollection 2014.


High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.

Schmitt BM, Rudolph KL, Karagianni P, Fonseca NA, White RJ, Talianidis I, Odom DT, Marioni JC, Kutter C.

Genome Res. 2014 Nov;24(11):1797-807. doi: 10.1101/gr.176784.114. Epub 2014 Aug 13.


Instructive nanofibrous scaffold comprising runt-related transcription factor 2 gene delivery for bone tissue engineering.

Monteiro N, Ribeiro D, Martins A, Faria S, Fonseca NA, Moreira JN, Reis RL, Neves NM.

ACS Nano. 2014 Aug 26;8(8):8082-94.


Long-range enhancers regulating Myc expression are required for normal facial morphogenesis.

Uslu VV, Petretich M, Ruf S, Langenfeld K, Fonseca NA, Marioni JC, Spitz F.

Nat Genet. 2014 Jul;46(7):753-8. doi: 10.1038/ng.2971. Epub 2014 May 25.


Bridging cancer biology and the patients' needs with nanotechnology-based approaches.

Fonseca NA, Gregório AC, Valério-Fernandes A, Simões S, Moreira JN.

Cancer Treat Rev. 2014 Jun;40(5):626-35. doi: 10.1016/j.ctrv.2014.02.002. Epub 2014 Feb 22. Review.


Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.

Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, McMurry J, Marioni JC, Malone J, Megy K, Rustici G, Tang AY, Taubert J, Williams E, Mannion O, Parkinson HE, Brazma A.

Nucleic Acids Res. 2014 Jan;42(Database issue):D926-32. doi: 10.1093/nar/gkt1270. Epub 2013 Dec 4.


Improving the performance of Transposable Elements detection tools.

Loureiro T, Camacho R, Vieira J, Fonseca NA.

J Integr Bioinform. 2013 Nov 14;10(3):231. doi: 10.2390/biecoll-jib-2013-231.


On the use of dexamethasone-loaded liposomes to induce the osteogenic differentiation of human mesenchymal stem cells.

Monteiro N, Martins A, Ribeiro D, Faria S, Fonseca NA, Moreira JN, Reis RL, Neves NM.

J Tissue Eng Regen Med. 2015 Sep;9(9):1056-66. doi: 10.1002/term.1817. Epub 2013 Oct 7.


Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF.

Gigascience. 2013 Jul 22;2(1):10. doi: 10.1186/2047-217X-2-10.


The Drosophila melanogaster methuselah gene: a novel gene with ancient functions.

Araújo AR, Reis M, Rocha H, Aguiar B, Morales-Hojas R, Macedo-Ribeiro S, Fonseca NA, Reboiro-Jato D, Reboiro-Jato M, Fdez-Riverola F, Vieira CP, Vieira J.

PLoS One. 2013 May 16;8(5):e63747. doi: 10.1371/journal.pone.0063747. Print 2013.


Patterns of evolution at the gametophytic self-incompatibility Sorbus aucuparia (Pyrinae) S pollen genes support the non-self recognition by multiple factors model.

Aguiar B, Vieira J, Cunha AE, Fonseca NA, Reboiro-Jato D, Reboiro-Jato M, Fdez-Riverola F, Raspé O, Vieira CP.

J Exp Bot. 2013 May;64(8):2423-34. doi: 10.1093/jxb/ert098. Epub 2013 Apr 19.


Drosophila americana as a model species for comparative studies on the molecular basis of phenotypic variation.

Fonseca NA, Morales-Hojas R, Reis M, Rocha H, Vieira CP, Nolte V, Schlötterer C, Vieira J.

Genome Biol Evol. 2013;5(4):661-79. doi: 10.1093/gbe/evt037.


Predicting the secondary structure of proteins using machine learning algorithms.

Camacho R, Ferreira R, Rosa N, Guimarães V, Fonseca NA, Costa VS, de Sousa M, Magalhães A.

Int J Data Min Bioinform. 2012;6(6):571-84.


Tools for mapping high-throughput sequencing data.

Fonseca NA, Rung J, Brazma A, Marioni JC.

Bioinformatics. 2012 Dec 15;28(24):3169-77. doi: 10.1093/bioinformatics/bts605. Epub 2012 Oct 11.


ADOPS--Automatic Detection Of Positively Selected Sites.

Reboiro-Jato D, Reboiro-Jato M, Fdez-Riverola F, Vieira CP, Fonseca NA, Vieira J.

J Integr Bioinform. 2012 Jul 24;9(3):200. doi: 10.2390/biecoll-jib-2012-200.

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