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Items: 1 to 50 of 57

1.

Genomic basis for RNA alterations in cancer.

PCAWG Transcriptome Core Group, Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H; PCAWG Transcriptome Working Group, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z; PCAWG Consortium.

Nature. 2020 Feb;578(7793):129-136. doi: 10.1038/s41586-020-1970-0. Epub 2020 Feb 5.

PMID:
32025019
2.

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N; PCAWG Drivers and Functional Interpretation Working Group; PCAWG Structural Variation Working Group, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G; PCAWG Consortium.

Nature. 2020 Feb;578(7793):102-111. doi: 10.1038/s41586-020-1965-x. Epub 2020 Feb 5.

PMID:
32025015
3.

High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.

Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A; PCAWG Transcriptome Working Group; PCAWG Structural Variation Working Group, Creighton CJ; PCAWG Consortium.

Nat Commun. 2020 Feb 5;11(1):736. doi: 10.1038/s41467-019-13885-w.

4.

Current challenges and emerging opportunities of CAR-T cell therapies.

Abreu TR, Fonseca NA, Gonçalves N, Moreira JN.

J Control Release. 2019 Dec 30;319:246-261. doi: 10.1016/j.jconrel.2019.12.047. [Epub ahead of print] Review.

PMID:
31899268
5.

Expression Atlas update: from tissues to single cells.

Papatheodorou I, Moreno P, Manning J, Fuentes AM, George N, Fexova S, Fonseca NA, Füllgrabe A, Green M, Huang N, Huerta L, Iqbal H, Jianu M, Mohammed S, Zhao L, Jarnuczak AF, Jupp S, Marioni J, Meyer K, Petryszak R, Prada Medina CA, Talavera-López C, Teichmann S, Vizcaino JA, Brazma A.

Nucleic Acids Res. 2020 Jan 8;48(D1):D77-D83. doi: 10.1093/nar/gkz947.

PMID:
31665515
6.

A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters.

Demircioğlu D, Cukuroglu E, Kindermans M, Nandi T, Calabrese C, Fonseca NA, Kahles A, Lehmann KV, Stegle O, Brazma A, Brooks AN, Rätsch G, Tan P, Göke J.

Cell. 2019 Sep 5;178(6):1465-1477.e17. doi: 10.1016/j.cell.2019.08.018.

PMID:
31491388
7.

ArrayExpress update - from bulk to single-cell expression data.

Athar A, Füllgrabe A, George N, Iqbal H, Huerta L, Ali A, Snow C, Fonseca NA, Petryszak R, Papatheodorou I, Sarkans U, Brazma A.

Nucleic Acids Res. 2019 Jan 8;47(D1):D711-D715. doi: 10.1093/nar/gky964.

8.

Inferences on specificity recognition at the Malus×domestica gametophytic self-incompatibility system.

Pratas MI, Aguiar B, Vieira J, Nunes V, Teixeira V, Fonseca NA, Iezzoni A, van Nocker S, Vieira CP.

Sci Rep. 2018 Jan 29;8(1):1717. doi: 10.1038/s41598-018-19820-1.

9.

Expression Atlas: gene and protein expression across multiple studies and organisms.

Papatheodorou I, Fonseca NA, Keays M, Tang YA, Barrera E, Bazant W, Burke M, Füllgrabe A, Fuentes AM, George N, Huerta L, Koskinen S, Mohammed S, Geniza M, Preece J, Jaiswal P, Jarnuczak AF, Huber W, Stegle O, Vizcaino JA, Brazma A, Petryszak R.

Nucleic Acids Res. 2018 Jan 4;46(D1):D246-D251. doi: 10.1093/nar/gkx1158.

10.

Targeting cancer stem cells and non-stem cancer cells: the potential of lipid-based nanoparticles.

Cruz AF, Fonseca NA, Moura V, Simoes S, Moreira JN.

Curr Pharm Des. 2017 Nov 14. doi: 10.2174/1381612823666171115105252. [Epub ahead of print]

PMID:
29141533
11.

Two independent modes of chromatin organization revealed by cohesin removal.

Schwarzer W, Abdennur N, Goloborodko A, Pekowska A, Fudenberg G, Loe-Mie Y, Fonseca NA, Huber W, Haering CH, Mirny L, Spitz F.

Nature. 2017 Nov 2;551(7678):51-56. doi: 10.1038/nature24281. Epub 2017 Sep 27.

12.

The cancer stem cell phenotype as a determinant factor of the heterotypic nature of breast tumors.

Fonseca NA, Cruz AF, Moura V, Simões S, Moreira JN.

Crit Rev Oncol Hematol. 2017 May;113:111-121. doi: 10.1016/j.critrevonc.2017.03.016. Epub 2017 Mar 16. Review.

PMID:
28427501
13.

The RNASeq-er API-a gateway to systematically updated analysis of public RNA-seq data.

Petryszak R, Fonseca NA, Füllgrabe A, Huerta L, Keays M, Tang YA, Brazma A.

Bioinformatics. 2017 Jul 15;33(14):2218-2220. doi: 10.1093/bioinformatics/btx143.

14.

Inoculated Cell Density as a Determinant Factor of the Growth Dynamics and Metastatic Efficiency of a Breast Cancer Murine Model.

Gregório AC, Fonseca NA, Moura V, Lacerda M, Figueiredo P, Simões S, Dias S, Moreira JN.

PLoS One. 2016 Nov 7;11(11):e0165817. doi: 10.1371/journal.pone.0165817. eCollection 2016.

15.

Gramene 2016: comparative plant genomics and pathway resources.

Tello-Ruiz MK, Stein J, Wei S, Preece J, Olson A, Naithani S, Amarasinghe V, Dharmawardhana P, Jiao Y, Mulvaney J, Kumari S, Chougule K, Elser J, Wang B, Thomason J, Bolser DM, Kerhornou A, Walts B, Fonseca NA, Huerta L, Keays M, Tang YA, Parkinson H, Fabregat A, McKay S, Weiser J, D'Eustachio P, Stein L, Petryszak R, Kersey PJ, Jaiswal P, Ware D.

Nucleic Acids Res. 2016 Jan 4;44(D1):D1133-40. doi: 10.1093/nar/gkv1179. Epub 2015 Nov 8.

16.

Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.

Petryszak R, Keays M, Tang YA, Fonseca NA, Barrera E, Burdett T, Füllgrabe A, Fuentes AM, Jupp S, Koskinen S, Mannion O, Huerta L, Megy K, Snow C, Williams E, Barzine M, Hastings E, Weisser H, Wright J, Jaiswal P, Huber W, Choudhary J, Parkinson HE, Brazma A.

Nucleic Acids Res. 2016 Jan 4;44(D1):D746-52. doi: 10.1093/nar/gkv1045. Epub 2015 Oct 19.

17.

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.

18.

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.

PMID:
26283155
19.

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.

20.

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.

PMID:
25749293
21.

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.

PMID:
25305563
22.

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.

23.

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.

24.

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.

PMID:
25046548
25.

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.

PMID:
24859337
26.

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.

PMID:
24613464
27.

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.

28.

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.

PMID:
24231145
29.

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.

PMID:
24123949
30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

PMID:
23356008
35.

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.

PMID:
23060614
36.

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.

PMID:
22829571
37.

Effect of holding medium, temperature and time on structural integrity of equine ovarian follicles during the non-breeding season.

Gomes RG, Andrade ER, Lisboa LA, Ciquini A, Barreiros TR, Fonseca NA, Seneda MM.

Theriogenology. 2012 Sep 1;78(4):731-6. doi: 10.1016/j.theriogenology.2012.03.019. Epub 2012 May 23.

PMID:
22626777
38.

Lipid-based nanoparticles for siRNA delivery in cancer therapy: paradigms and challenges.

Gomes-da-Silva LC, Fonseca NA, Moura V, Pedroso de Lima MC, Simões S, Moreira JN.

Acc Chem Res. 2012 Jul 17;45(7):1163-71. doi: 10.1021/ar300048p. Epub 2012 May 8.

PMID:
22568781
39.

The DAIBAM MITE element is involved in the origin of one fixed and two polymorphic Drosophila virilis phylad inversions.

Fonseca NA, Vieira CP, Schlötterer C, Vieira J.

Fly (Austin). 2012 Apr-Jun;6(2):71-4. doi: 10.4161/fly.19423. Epub 2012 Apr 1.

PMID:
22561870
40.

Predicting Malignancy from Mammography Findings and Surgical Biopsies.

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

Proceedings (IEEE Int Conf Bioinformatics Biomed). 2011 Nov;2011. doi: 10.1109/BIBM.2011.71.

41.

A relational learning approach to Structure-Activity Relationships in drug design toxicity studies.

Camacho R, Pereira M, Costa VS, Fonseca NA, Adriano C, Simões CJ, Brito RM.

J Integr Bioinform. 2011 Sep 16;8(3):182. doi: 10.2390/biecoll-jib-2011-182.

PMID:
21926445
42.

Assemblathon 1: a competitive assessment of de novo short read assembly methods.

Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B.

Genome Res. 2011 Dec;21(12):2224-41. doi: 10.1101/gr.126599.111. Epub 2011 Sep 16.

43.

Amino acid pair- and triplet-wise groupings in the interior of α-helical segments in proteins.

de Sousa MM, Munteanu CR, Pazos A, Fonseca NA, Camacho R, Magalhães AL.

J Theor Biol. 2011 Feb 21;271(1):136-44. doi: 10.1016/j.jtbi.2010.11.028. Epub 2010 Dec 2.

PMID:
21130100
44.

Evolutionary patterns at the RNase based gametophytic self - incompatibility system in two divergent Rosaceae groups (Maloideae and Prunus).

Vieira J, Ferreira PG, Aguiar B, Fonseca NA, Vieira CP.

BMC Evol Biol. 2010 Jun 28;10:200. doi: 10.1186/1471-2148-10-200.

45.

PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile.

Pereira L, Alshamali F, Andreassen R, Ballard R, Chantratita W, Cho NS, Coudray C, Dugoujon JM, Espinoza M, González-Andrade F, Hadi S, Immel UD, Marian C, Gonzalez-Martin A, Mertens G, Parson W, Perone C, Prieto L, Takeshita H, Rangel Villalobos H, Zeng Z, Zhivotovsky L, Camacho R, Fonseca NA.

Int J Legal Med. 2011 Sep;125(5):629-36. doi: 10.1007/s00414-010-0472-2. Epub 2010 Jun 16.

PMID:
20552217
46.

Phylogeny of the teashirt-related zinc finger (tshz) gene family and analysis of the developmental expression of tshz2 and tshz3b in the zebrafish.

Santos JS, Fonseca NA, Vieira CP, Vieira J, Casares F.

Dev Dyn. 2010 Mar;239(3):1010-8. doi: 10.1002/dvdy.22228.

47.

RNase-based gametophytic self-incompatibility evolution: Questioning the hypothesis of multiple independent recruitments of the S-pollen gene.

Vieira J, Fonseca NA, Vieira CP.

J Mol Evol. 2009 Jul;69(1):32-41. doi: 10.1007/s00239-009-9249-y. Epub 2009 Jun 4.

PMID:
19495553
48.

Gene classification based on amino acid motifs and residues: the DLX (distal-less) test case.

Fonseca NA, Vieira CP, Vieira J.

PLoS One. 2009 Jun 1;4(6):e5748. doi: 10.1371/journal.pone.0005748.

49.

An S-RNase-based gametophytic self-incompatibility system evolved only once in eudicots.

Vieira J, Fonseca NA, Vieira CP.

J Mol Evol. 2008 Aug;67(2):179-90. doi: 10.1007/s00239-008-9137-x. Epub 2008 Jul 15.

PMID:
18626680
50.

Protein evolution of ANTP and PRD homeobox genes.

Fonseca NA, Vieira CP, Holland PW, Vieira J.

BMC Evol Biol. 2008 Jul 11;8:200. doi: 10.1186/1471-2148-8-200.

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