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Page 1
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. Earl D, et al. Among authors: fonseca na. Genome Res. 2011 Dec;21(12):2224-41. doi: 10.1101/gr.126599.111. Epub 2011 Sep 16. Genome Res. 2011. PMID: 21926179 Free PMC article.
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. Bradnam KR, et al. Among authors: fonseca na. Gigascience. 2013 Jul 22;2(1):10. doi: 10.1186/2047-217X-2-10. Gigascience. 2013. PMID: 23870653 Free PMC article.
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. PCAWG Transcriptome Core Group, et al. Among authors: fonseca na. Nature. 2020 Feb;578(7793):129-136. doi: 10.1038/s41586-020-1970-0. Epub 2020 Feb 5. Nature. 2020. PMID: 32025019 Free PMC article.
Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer.
Garcia-Alonso L, Iorio F, Matchan A, Fonseca N, Jaaks P, Peat G, Pignatelli M, Falcone F, Benes CH, Dunham I, Bignell G, McDade SS, Garnett MJ, Saez-Rodriguez J. Garcia-Alonso L, et al. Cancer Res. 2018 Feb 1;78(3):769-780. doi: 10.1158/0008-5472.CAN-17-1679. Epub 2017 Dec 11. Cancer Res. 2018. PMID: 29229604 Free PMC article.
Cell surface Nucleolin represents a novel cellular target for neuroblastoma therapy.
Brignole C, Bensa V, Fonseca NA, Del Zotto G, Bruno S, Cruz AF, Malaguti F, Carlini B, Morandi F, Calarco E, Perri P, Moura V, Emionite L, Cilli M, De Leonardis F, Tondo A, Amoroso L, Conte M, Garaventa A, Sementa AR, Corrias MV, Ponzoni M, Moreira JN, Pastorino F. Brignole C, et al. Among authors: fonseca na. J Exp Clin Cancer Res. 2021 Jun 2;40(1):180. doi: 10.1186/s13046-021-01993-9. J Exp Clin Cancer Res. 2021. PMID: 34078433 Free PMC article.
The Enhanced Efficacy of Intracellular Delivery of Doxorubicin/C6-Ceramide Combination Mediated by the F3 Peptide/Nucleolin System Is Supported by the Downregulation of the PI3K/Akt Pathway.
Cruz AF, Caleiras MB, Fonseca NA, Gonçalves N, Mendes VM, Sampaio SF, Moura V, Melo JB, Almeida RD, Manadas B, Simões S, Moreira JN. Cruz AF, et al. Among authors: fonseca na. Cancers (Basel). 2021 Jun 18;13(12):3052. doi: 10.3390/cancers13123052. Cancers (Basel). 2021. PMID: 34207464 Free PMC article.
Nucleolin Overexpression Predicts Patient Prognosis While Providing a Framework for Targeted Therapeutic Intervention in Lung Cancer.
Valério-Fernandes Â, Fonseca NA, Gonçalves N, Cruz AF, Pereira MI, Gregório AC, Moura V, Ladeirinha AF, Alarcão A, Gonçalves J, Abrunhosa A, Melo JB, Carvalho L, Simões S, Moreira JN. Valério-Fernandes Â, et al. Among authors: fonseca na. Cancers (Basel). 2022 Apr 29;14(9):2217. doi: 10.3390/cancers14092217. Cancers (Basel). 2022. PMID: 35565346 Free PMC article.
Nucleolin expression has prognostic value in neuroblastoma patients.
Cangelosi D, Brignole C, Bensa V, Tamma R, Malaguti F, Carlini B, Giusto E, Calarco E, Perri P, Ribatti D, Fonseca NA, Moreira JN, Eva A, Amoroso L, Conte M, Garaventa A, Sementa AR, Corrias MV, Ponzoni M, Pastorino F. Cangelosi D, et al. Among authors: fonseca na. EBioMedicine. 2022 Nov;85:104300. doi: 10.1016/j.ebiom.2022.104300. Epub 2022 Oct 6. EBioMedicine. 2022. PMID: 36209521 Free PMC article.
128 results