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Author Details

Nuno A Fonseca
European Bioinformatics Institute
2008
55
23
PMIDPaper TitleJournal TitlePublished Year
36697831Author Correction: Genomic basis for RNA alterations in cancer.Nature2023
36697832Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.Nature2023
36481652Author Correction: High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.Nat Commun2022
35581257Author Correction: Tumour gene expression signature in primary melanoma predicts long-term outcomes.Nat Commun2022
33803052Comparative Genomics of <i>Xanthomonas euroxanthea</i> and <i>Xanthomonas arboricola</i> pv. <i>juglandis</i> Strains Isolated from a Single Walnut Host Tree.Microorganisms2021
33602918Tumour gene expression signature in primary melanoma predicts long-term outcomes.Nat Commun2021
33707324Complete Genome Sequence Obtained by Nanopore and Illumina Hybrid Assembly of Xanthomonas arboricola pv. juglandis CPBF 427, Isolated from Buds of a Walnut Tree.Microbiol Resour Announc2021
33503840Shedding Light on the African Enigma: In Vitro Testing of <i>Homo sapiens-Helicobacter pylori</i> Coevolution.Microorganisms2021
32256158The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Diptera 01.Biodivers Data J2020
31665515Expression Atlas update: from tissues to single cells.Nucleic Acids Res2020
33154004Complete Genome Sequences of Walnut-Associated <i>Xanthomonas euroxanthea</i> Strains CPBF 367 and CPBF 426 Obtained by Illumina/Nanopore Hybrid Assembly.Microbiol Resour Announc2020
32636365A user guide for the online exploration and visualization of PCAWG data.Nat Commun2020
32680985Tumors induce de novo steroid biosynthesis in T cells to evade immunity.Nat Commun2020
32821214The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of Iberian Plecoptera.Biodivers Data J2020
32760401An RNA-seq Based Machine Learning Approach Identifies Latent Tuberculosis Patients With an Active Tuberculosis Profile.Front Immunol2020
32781641Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci.Microorganisms2020
30357387ArrayExpress update - from bulk to single-cell expression data.Nucleic Acids Res2019
31491388A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters.Cell2019
29165610Gramene 2018: unifying comparative genomics and pathway resources for plant research.Nucleic Acids Res2018
29379047Inferences on specificity recognition at the Malusÿdomestica gametophytic self-incompatibility system.Sci Rep2018
29229604Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer.Cancer Res2018
29165655Expression Atlas: gene and protein expression across multiple studies and organisms.Nucleic Acids Res2018
29094699Two independent modes of chromatin organization revealed by cohesin removal.Nature2017
28369191The RNASeq-er API-a gateway to systematically updated analysis of public RNA-seq data.Bioinformatics2017
26553803Gramene 2016: comparative plant genomics and pathway resources.Nucleic Acids Res2016
26481351Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.Nucleic Acids Res2016
25993016Convergent evolution at the gametophytic self-incompatibility system in Malus and Prunus.PLoS One2015
26333262Predicting malignancy from mammography findings and image-guided core biopsies.Int J Data Min Bioinform2015
26110515Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.BMC Genomics2015
24304889Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.Nucleic Acids Res2014
25268973RNA-Seq gene profiling--a systematic empirical comparison.PLoS One2014
25122613High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.Genome Res2014
24859337Long-range enhancers regulating Myc expression are required for normal facial morphogenesis.Nat Genet2014
23493635Drosophila americana as a model species for comparative studies on the molecular basis of phenotypic variation.Genome Biol Evol2013
24231145Improving the performance of Transposable Elements detection tools.J Integr Bioinform2013
23870653Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.Gigascience2013
23696853The Drosophila melanogaster methuselah gene: a novel gene with ancient functions.PLoS One2013
23606363Patterns of evolution at the gametophytic self-incompatibility Sorbus aucuparia (Pyrinae) S pollen genes support the non-self recognition by multiple factors model.J Exp Bot2013
22561870The DAIBAM MITE element is involved in the origin of one fixed and two polymorphic Drosophila virilis phylad inversions.Fly (Austin)2012
23356008Predicting the secondary structure of proteins using machine learning algorithms.Int J Data Min Bioinform2012
23060614Tools for mapping high-throughput sequencing data.Bioinformatics2012
22829571ADOPS--Automatic Detection Of Positively Selected Sites.J Integr Bioinform2012
20552217PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile.Int J Legal Med2011
24363962Predicting Malignancy from Mammography Findings and Surgical Biopsies.Proceedings (IEEE Int Conf Bioinformatics Biomed)2011
21926445A relational learning approach to Structure-Activity Relationships in drug design toxicity studies.J Integr Bioinform2011
21926179Assemblathon 1: a competitive assessment of de novo short read assembly methods.Genome Res2011
21130100Amino acid pair- and triplet-wise groupings in the interior of α-helical segments in proteins.J Theor Biol2011
20108322Phylogeny of the teashirt-related zinc finger (tshz) gene family and analysis of the developmental expression of tshz2 and tshz3b in the zebrafish.Dev Dyn2010
20584298Evolutionary patterns at the RNase based gametophytic self - incompatibility system in two divergent Rosaceae groups (Maloideae and Prunus).BMC Evol Biol2010
19484130Gene classification based on amino acid motifs and residues: the DLX (distal-less) test case.PLoS One2009
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Collaborators

Alvis Brazma
European Bioinformatics Institute
Co-authored papers 15
Robert Petryszak
Oregon Health and Science University
Co-authored papers 10
Laura Huerta
Co-authored papers 7
Maria Keays
Wellcome Sanger Institute
Co-authored papers 7
Anja Füllgrabe
Co-authored papers 6
John C Marioni
Cancer Research UK Cambridge Institute, University of Cambridge
Co-authored papers 6
Y Amy Tang
Northeastern University
Co-authored papers 5
Irene Papatheodorou
Co-authored papers 5
Wolfgang Huber
Technische Universitat Munchen
Co-authored papers 5
Pankaj Jaiswal
Oregon State University
Co-authored papers 4
Paul Kersey
European Bioinformatics Institute
Co-authored papers 4
Simon Jupp
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 3
David J Adams
Wellcome Sanger Institute
Co-authored papers 3
Lincoln Stein
Ontario Institute for Cancer Research, University Avenue
Co-authored papers 3
Nancy George
Co-authored papers 3
Andr?? Kahles
ETH Zurich
Co-authored papers 3
Helen Parkinson
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Co-authored papers 3
David Haussler
Genomics Institute, University of California Santa Cruz
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Justin Preece
Oregon State University
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Oliver Stegle
Wellcome Sanger Institute
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Karyn Megy
University of Cambridge
Co-authored papers 2
Sante Gnerre
Co-authored papers 2
Marcela K Tello-Ruiz
State University of New York at Old Westbury
Co-authored papers 2
Juan Antonio Vizca??no
EMBL-European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 2
Justin Elser
Oregon State University
Co-authored papers 2
Gunnar R??tsch
ETH Zurich
Co-authored papers 2
Richard A Scolyer
Co-authored papers 2
Rayan Chikhi
Co-authored papers 2
Richard Durbin
University of Cambridge
Co-authored papers 2
James Thomason
USDA-ARS Laboratory at Cold Spring Harbor Laboratory
Co-authored papers 2
Release 1.2