Nuno A Fonseca

Nuno A Fonseca

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Nuno A Fonseca

Nuno A Fonseca

Publications by authors named "Nuno A Fonseca"

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

J Control Release 2020 Mar 30;319:246-261. Epub 2019 Dec 30.

CNC - Center for Neurosciences and Cell Biology, University of Coimbra, Faculty of Medicine (Polo 1), Rua Larga, 3004-504 Coimbra, Portugal; FFUC - Faculty of Pharmacy, University of Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal. Electronic address:

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http://dx.doi.org/10.1016/j.jconrel.2019.12.047DOI Listing
March 2020

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

Nature 2020 02 5;578(7793):102-111. Epub 2020 Feb 5.

The Broad Institute of MIT and Harvard, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/s41586-020-1965-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7054214PMC
February 2020

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

Cell 2019 Sep;178(6):1465-1477.e17

Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore; Cellular and Molecular Research, National Cancer Centre, Singapore 169610, Singapore. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.08.018DOI Listing
September 2019

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

Nucleic Acids Res 2019 Jan;47(D1):D711-D715

European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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https://academic.oup.com/nar/advance-article/doi/10.1093/nar
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http://dx.doi.org/10.1093/nar/gky964DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323929PMC
January 2019

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

Sci Rep 2018 01 29;8(1):1717. Epub 2018 Jan 29.

Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.

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http://dx.doi.org/10.1038/s41598-018-19820-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5788982PMC
January 2018

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

Bioinformatics 2017 Jul;33(14):2218-2220

Functional Genomics Group, European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK.

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http://dx.doi.org/10.1093/bioinformatics/btx143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870697PMC
July 2017

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

Crit Rev Oncol Hematol 2017 May 16;113:111-121. Epub 2017 Mar 16.

CNC - Center for Neurosciences and Cell Biology, University of Coimbra, Faculty of Medicine (Polo 1), Rua Larga, 3004-504 Coimbra, Portugal; FFUC - Faculty of Pharmacy, University of Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal. Electronic address:

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http://dx.doi.org/10.1016/j.critrevonc.2017.03.016DOI Listing
May 2017

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

PLoS One 2015 19;10(5):e0126138. Epub 2015 May 19.

Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126138PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4438004PMC
April 2016

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

Biomaterials 2015 Nov 6;69:76-88. Epub 2015 Aug 6.

CNC - Center for Neurosciences and Cell Biology, University of Coimbra, Faculty of Medicine (Polo I), Rua Larga, Coimbra 3004-504, Portugal; FFUC - Faculty of Pharmacy, University of Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, Coimbra 3000-548, Portugal. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S01429612150065
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http://dx.doi.org/10.1016/j.biomaterials.2015.08.007DOI Listing
November 2015

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

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

3Bs Research Group - Biomaterials, Biodegradables and Biomimetics, Department of Polymer Engineering, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Zona Industrial da Gandra S. Cláudio do Barco, 4806-909, Caldas das Taipas, Guimarães, Portugal.

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http://dx.doi.org/10.1002/term.1817DOI Listing
September 2015

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

PLoS One 2014 30;9(9):e107026. Epub 2014 Sep 30.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0107026PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4182317PMC
June 2015

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

Acta Biomater 2015 May 5;18:196-205. Epub 2015 Mar 5.

3B's Research Group - Biomaterials, Biodegradables and Biomimetics, Department of Polymer Engineering, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Zona Industrial da Gandra S. Cláudio do Barco, 4806-909 Caldas das Taipas, Guimarães, Portugal; ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal. Electronic address:

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http://dx.doi.org/10.1016/j.actbio.2015.02.018DOI Listing
May 2015

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

J Control Release 2014 Dec 11;196:122-31. Epub 2014 Oct 11.

CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Largo Marquês de Pombal, 3004-517 Coimbra, Portugal; FFUC-Faculty of Pharmacy, University of Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal. Electronic address:

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http://dx.doi.org/10.1016/j.jconrel.2014.09.024DOI Listing
December 2014

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

Nat Genet 2014 Jul 25;46(7):753-8. Epub 2014 May 25.

Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.

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http://dx.doi.org/10.1038/ng.2971DOI Listing
July 2014

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

Cancer Treat Rev 2014 Jun 22;40(5):626-35. Epub 2014 Feb 22.

CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Largo Marquês de Pombal, 3004-517 Coimbra, Portugal; FFUC - Faculty of Pharmacy, University of Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal. Electronic address:

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http://dx.doi.org/10.1016/j.ctrv.2014.02.002DOI Listing
June 2014

Improving the performance of Transposable Elements detection tools.

J Integr Bioinform 2013 Nov 14;10(3):231. Epub 2013 Nov 14.

DEI & Faculdade de Engenharia, Universidade do Porto, Portugal.

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http://dx.doi.org/10.2390/biecoll-jib-2013-231DOI Listing
November 2013

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

Gigascience 2013 Jul 22;2(1):10. Epub 2013 Jul 22.

Genome Center, UC, Davis, CA 95616, USA.

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http://dx.doi.org/10.1186/2047-217X-2-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3844414PMC
July 2013

Predicting the secondary structure of proteins using machine learning algorithms.

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

LIAAD & DEI-Faculdade de Engenharia da Universidade do Porto, Rua Dr Roberto Frias s/n, 4420-465 Porto, Portugal.

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http://www.dcc.fc.up.pt/~ricroc/homepage/publications/stampa
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http://dx.doi.org/10.1504/ijdmb.2012.050265DOI Listing
April 2013

Tools for mapping high-throughput sequencing data.

Bioinformatics 2012 Dec 11;28(24):3169-77. Epub 2012 Oct 11.

EMBL Outstation, European Bioinformatics Institute (EBI), Hinxton, Cambridge CB10 ISD, UK.

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http://dx.doi.org/10.1093/bioinformatics/bts605DOI Listing
December 2012

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

Fly (Austin) 2012 Apr-Jun;6(2):71-4. Epub 2012 Apr 1.

CRACS-INESC Porto LA, Porto, Portugal.

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http://dx.doi.org/10.4161/fly.19423DOI Listing
October 2012

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

Acc Chem Res 2012 Jul 8;45(7):1163-71. Epub 2012 May 8.

Center for Neurosciences and Cell Biology, University of Coimbra, Portugal.

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http://dx.doi.org/10.1021/ar300048pDOI Listing
July 2012

ADOPS--Automatic Detection Of Positively Selected Sites.

J Integr Bioinform 2012 Jul 24;9(3):200. Epub 2012 Jul 24.

Departamento de Informática, Universidade de Vigo, Spain.

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http://dx.doi.org/10.2390/biecoll-jib-2012-200DOI Listing
July 2012

Predicting Malignancy from Mammography Findings and Surgical Biopsies.

Proceedings (IEEE Int Conf Bioinformatics Biomed) 2011 Nov;2011

University of Wisconsin, Medical School, Madison, WI, USA.

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http://dx.doi.org/10.1109/BIBM.2011.71DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866819PMC
November 2011

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

J Integr Bioinform 2011 Sep 16;8(3):182. Epub 2011 Sep 16.

LIAAD-INESC Porto LA & DEI, FEUP, Universidade do Porto, Portugal.

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http://dx.doi.org/10.2390/biecoll-jib-2011-182DOI Listing
September 2011

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

J Theor Biol 2011 Feb 2;271(1):136-44. Epub 2010 Dec 2.

REQUIMTE/University of Porto, Faculty of Sciences, R. Campo Alegre 687, 4169-007 Porto, Portugal.

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http://dx.doi.org/10.1016/j.jtbi.2010.11.028DOI Listing
February 2011

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

BMC Evol Biol 2010 Jun 28;10:200. Epub 2010 Jun 28.

Instituto de Biologia Molecular e Celular, University of Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal.

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http://dx.doi.org/10.1186/1471-2148-10-200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909234PMC
June 2010

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

J Mol Evol 2009 Jul 4;69(1):32-41. Epub 2009 Jun 4.

Instituto de Biologia Molecular e Celular, University of Porto, Portugal.

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http://dx.doi.org/10.1007/s00239-009-9249-yDOI Listing
July 2009

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

PLoS One 2009 Jun 1;4(6):e5748. Epub 2009 Jun 1.

Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0005748PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2685005PMC
June 2009

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

J Mol Evol 2008 Aug 15;67(2):179-90. Epub 2008 Jul 15.

Molecular Evolution Group, Instituto de Biologia Celular e Molecular (IBMC), University of Porto, Rua do Campo Alegre 823, 4150-180, Porto, Portugal.

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http://dx.doi.org/10.1007/s00239-008-9137-xDOI Listing
August 2008

Protein evolution of ANTP and PRD homeobox genes.

BMC Evol Biol 2008 Jul 11;8:200. Epub 2008 Jul 11.

Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal.

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http://dx.doi.org/10.1186/1471-2148-8-200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2491631PMC
July 2008

The number, age, sharing and relatedness of S-locus specificities in Prunus.

Genet Res (Camb) 2008 Feb;90(1):17-26

Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal.

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http://dx.doi.org/10.1017/S0016672307009044DOI Listing
February 2008

Amino acid pairing at the N- and C-termini of helical segments in proteins.

Proteins 2008 Jan;70(1):188-96

IBMC and LIACC, R. Campo Alegre, 1021/1055, 4169-007 Porto, Portugal.

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http://dx.doi.org/10.1002/prot.21525DOI Listing
January 2008