NF
Nuno A. Fonseca
Gene Expression ProfilingSoftwareDatabases, GeneticDNA barcodebioinformaticscontinental PortugalEvolution, MolecularGene Expression Regulation, Neoplasticoccurrence recordsBiological Evolution
On Valency
published · living versionsW_26xzgw86·v1 · currentpublished
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
with Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay +86
1 version
Preprints & journals
71 papers in the corpus · 2008–2024MIMt: a curated 16S rRNA reference database with less redundancy and higher accuracy at species-level identification.39522045 · Cabezas, M Pilar, Fonseca, Nuno A, Muñoz-Mérida, Antonio2024 · 24 citationsEnvironmental microbiome. 2024;19(1):88
The leaf idioblastome of the medicinal plant Catharanthus roseus is associated with stress resistance and alkaloid metabolism.37804484 · Guedes, Joana G, Ribeiro, Rogério, Carqueijeiro, Inês et al.2023 · 22 citationsJournal of experimental botany. 2024;75(1):274-299
Idioblasts accumulating anticancer alkaloids in Catharanthus roseus leaves are a unique cell type10.1101/2023.02.24.529939v1 · Guedes, J. G., Ribeiro, R., Carqueijeiro, I. et al.2023 · 1 citationbioRxiv
Author Correction: Genomic basis for RNA alterations in cancer.36697831 · PCAWG Transcriptome Core Group, Calabrese, Claudia, Davidson, Natalie R et al.2023 · 1 citationNature. 2023;614(7948):E37
Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.36697832 · Rheinbay, Esther, Nielsen, Morten Muhlig, Abascal, Federico et al.2023 · 12 citationsNature. 2023;614(7948):E40
The InBIO barcoding initiative database: DNA barcodes of Iberian Trichoptera, documenting biodiversity for freshwater biomonitoring in a Mediterranean hotspot.38327295 · Pauperio, Joana, Gonzalez, Luis Martin, Martinez, Jesus et al.2024 · 6 citationsBiodiversity data journal. 2023;11:e97484
Author Correction: High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.36481652 · Zhang, Yiqun, Chen, Fengju, Fonseca, Nuno A et al.2022 · 0 citationsNature communications. 2022;13(1):7572
Author Correction: Tumour gene expression signature in primary melanoma predicts long-term outcomes.35581257 · Garg, Manik, Couturier, Dominique-Laurent, Nsengimana, Jérémie et al.2025 · 1 citationNature communications. 2022;13(1):2841
Speeding up the detection of invasive bivalve species using environmental DNA: A Nanopore and Illumina sequencing comparison.35305077 · Egeter, Bastian, Veríssimo, Joana, Lopes-Lima, Manuel et al.2022 · 63 citationsMolecular ecology resources. 2022;22(6):2232-2247
DNA Barcoding of Portuguese Lacewings (Neuroptera) and Snakeflies (Raphidioptera) (Insecta, Neuropterida).34393563 · Oliveira, Daniel, Chaves, Cátia, Pinto, Joana et al.2024 · 3 citationsZooKeys. 2021;1054:67-84
Comparative Genomics of Xanthomonas euroxanthea and Xanthomonas arboricola pv. juglandis Strains Isolated from a Single Walnut Host Tree.33803052 · Fernandes, Camila, Martins, Leonor, Teixeira, Miguel et al.2021 · 20 citationsMicroorganisms. 2021;9(3)
Complete Genome Sequence Obtained by Nanopore and Illumina Hybrid Assembly of Xanthomonas arboricola pv. juglandis CPBF 427, Isolated from Buds of a Walnut Tree.33707324 · Teixeira, Miguel, Fernandes, Camila, Chaves, Cátia et al.2021 · 4 citationsMicrobiology resource announcements. 2021;10(10)
Tumour gene expression signature in primary melanoma predicts long-term outcomes.33602918 · Garg, Manik, Couturier, Dominique-Laurent, Nsengimana, Jérémie et al.2021 · 70 citationsNature communications. 2021;12(1):1137
Shedding Light on the African Enigma: In Vitro Testing of Homo sapiens-Helicobacter pylori Coevolution.33503840 · Cavadas, Bruno, Leite, Marina, Pedro, Nicole et al.2021 · 15 citationsMicroorganisms. 2021;9(2)
Complete Genome Sequences of Walnut-Associated Xanthomonas euroxanthea Strains CPBF 367 and CPBF 426 Obtained by Illumina/Nanopore Hybrid Assembly.33154004 · Teixeira, Miguel, Martins, Leonor, Fernandes, Camila et al.2020 · 5 citationsMicrobiology resource announcements. 2020;9(45)
Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci.32781641 · Cavadas, Bruno, Camacho, Rui, Ferreira, Joana C et al.2020 · 19 citationsMicroorganisms. 2020;8(8)
Tumors induce de novo steroid biosynthesis in T cells to evade immunity.32680985 · Mahata, Bidesh, Pramanik, Jhuma, van der Weyden, Louise et al.2020 · 326 citationsNature communications. 2020;11(1):3588
An RNA-seq Based Machine Learning Approach Identifies Latent Tuberculosis Patients With an Active Tuberculosis Profile.32760401 · Estévez, Olivia, Anibarro, Luis, Garet, Elina et al.2021 · 45 citationsFrontiers in immunology. 2020;11:1470
A user guide for the online exploration and visualization of PCAWG data.32636365 · Goldman, Mary J, Zhang, Junjun, Fonseca, Nuno A et al.2020 · 43 citationsNature communications. 2020;11(1):3400
The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of Iberian Plecoptera.32821214 · Ferreira, Sonia, Tierno de Figueroa, José Manuel, Martins, Filipa Ms et al.2024 · 17 citationsBiodiversity data journal. 2020;8:e55137
Speeding up the detection of invasive aquatic species using environmental DNA and nanopore sequencing10.1101/2020.06.09.142521v1 · Egeter, B., Verissimo, J., Lopes_Lima, M. et al.2020 · 12 citationsbioRxiv
The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Diptera 01.32256158 · Ferreira, Sonia A, Andrade, Rui, Gonçalves, Ana R et al.2022 · 13 citationsBiodiversity data journal. 2020;8:e49985
High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.32024823 · Zhang, Yiqun, Chen, Fengju, Fonseca, Nuno A et al.2020 · 77 citationsNature communications. 2020;11(1):736
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.32025015 · Rheinbay, Esther, Nielsen, Morten Muhlig, Abascal, Federico et al.2020 · 629 citationsNature. 2020;578(7793):102-111
Genomic basis for RNA alterations in cancer.32025019 · PCAWG Transcriptome Core Group, Calabrese, Claudia, Davidson, Natalie R et al.2020 · 399 citationsNature. 2020;578(7793):129-136
Expression Atlas update: from tissues to single cells.31665515 · Papatheodorou, Irene, Moreno, Pablo, Manning, Jonathan et al.2020 · 503 citationsNucleic acids research. 2020;48(D1):D77-D83
A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters.31491388 · Demircioğlu, Deniz, Cukuroglu, Engin, Kindermans, Martin et al.2020 · 250 citationsCell. 2019;178(6):1465-1477.e17
ArrayExpress update - from bulk to single-cell expression data.30357387 · Athar, Awais, Füllgrabe, Anja, George, Nancy et al.2020 · 606 citationsNucleic acids research. 2019;47(D1):D711-D715
Inferences on specificity recognition at the Malus×domestica gametophytic self-incompatibility system.29379047 · Pratas, Maria I, Aguiar, Bruno, Vieira, Jorge et al.2018 · 34 citationsScientific reports. 2018;8(1):1717
Gramene 2018: unifying comparative genomics and pathway resources for plant research.29165610 · Tello-Ruiz, Marcela K, Naithani, Sushma, Stein, Joshua C et al.2019 · 172 citationsNucleic acids research. 2018;46(D1):D1181-D1189
Expression Atlas: gene and protein expression across multiple studies and organisms.29165655 · Papatheodorou, Irene, Fonseca, Nuno A, Keays, Maria et al.2019 · 419 citationsNucleic acids research. 2018;46(D1):D246-D251
Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer.29229604 · Garcia-Alonso, Luz, Iorio, Francesco, Matchan, Angela et al.2019 · 203 citationsCancer research. 2018;78(3):769-780
Assessing the Gene Regulatory Landscape in 1,188 Human Tumors10.1101/225441v1 · Calabrese, C., Lehmann, K.-V., Urban, L. et al.2017 · 3 citationsbioRxiv
Two independent modes of chromatin organization revealed by cohesin removal.29094699 · Schwarzer, Wibke, Abdennur, Nezar, Goloborodko, Anton et al.2018 · 1,194 citationsNature. 2017;551(7678):51-56
Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types10.1101/183889v2 · PCAWG Transcriptome Core Group,, Calabrese, C., Davidson, N. R. et al.2017 · 22 citationsbioRxiv
The RNASeq-er API-a gateway to systematically updated analysis of public RNA-seq data.28369191 · Petryszak, Robert, Fonseca, Nuno A, Füllgrabe, Anja et al.2018 · 31 citationsBioinformatics (Oxford, England). 2017;33(14):2218-2220
A user's guide to the online resources for data exploration, visualization, and discovery for the Pan-Cancer Analysis of Whole Genomes project (PCAWG)10.1101/163907v7 · Goldman, M., Zhang, J., Fonseca, N. A. et al.2017 · 4 citationsbioRxiv
Comprehensive genome and transcriptome analysis reveals genetic basis for gene fusions in cancer10.1101/148684v2 · Fonseca, N. A., He, Y., Greger, L. et al.2017 · 6 citationsbioRxiv
New integrative computational approaches unveil the Saccharomyces cerevisiae pheno-metabolomic fermentative profile and allow strain selection for winemaking.27283661 · Franco-Duarte, Ricardo, Umek, Lan, Mendes, Inês et al.2017 · 31 citationsFood chemistry. 2016;211:509-20
Gramene 2016: comparative plant genomics and pathway resources.26553803 · Tello-Ruiz, Marcela K, Stein, Joshua, Wei, Sharon et al.2016 · 131 citationsNucleic acids research. 2016;44(D1):D1133-40
Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.26481351 · Petryszak, Robert, Keays, Maria, Tang, Y Amy et al.2016 · 530 citationsNucleic acids research. 2016;44(D1):D746-52
Convergent evolution at the gametophytic self-incompatibility system in Malus and Prunus.25993016 · Aguiar, Bruno, Vieira, Jorge, Cunha, Ana E et al.2016 · 63 citationsPloS one. 2015;10(5):e0126138
Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.26110515 · Frankish, Adam, Uszczynska, Barbara, Ritchie, Graham R S et al.2016 · 106 citationsBMC genomics. 2015;16 Suppl 8:S2
Predicting malignancy from mammography findings and image-guided core biopsies.26333262 · Ferreira, Pedro, Fonseca, Nuno A, Dutra, Inês et al.2015 · 10 citationsInternational journal of data mining and bioinformatics. 2015;11(3):257-76
RNA-Seq gene profiling--a systematic empirical comparison.25268973 · Fonseca, Nuno A, Marioni, John, Brazma, Alvis2015 · 99 citationsPloS one. 2014;9(9):e107026
High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.25122613 · Schmitt, Bianca M, Rudolph, Konrad L M, Karagianni, Panagiota et al.2015 · 94 citationsGenome research. 2014;24(11):1797-807
iRAP - an integrated RNA-seq Analysis Pipeline10.1101/005991v1 · Nuno A. Fonseca, Robert Petryszak, John Marioni et al.2014 · 33 citationsbioRxiv
Long-range enhancers regulating Myc expression are required for normal facial morphogenesis.24859337 · Uslu, Veli Vural, Petretich, Massimo, Ruf, Sandra et al.2014 · 134 citationsNature genetics. 2014;46(7):753-8
Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.24304889 · Petryszak, Robert, Burdett, Tony, Fiorelli, Benedetto et al.2014 · 344 citationsNucleic acids research. 2014;42(Database issue):D926-32
Improving the performance of Transposable Elements detection tools.24231145 · Loureiro, Tiago, Camacho, Rui, Vieira, Jorge et al.2014 · 20 citationsJournal of integrative bioinformatics. 2013;10(3):231
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