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Works (46)

A general strategy for generating expert-guided, simplified views of ontologies

2024-12-18 | Preprint
DOI: 10.1101/2024.12.13.628309
Contributors: Anita R. Caron; Aleix Puig-Barbe; Ellen M. Quardokus; James P. Balhoff; Jasmine Belfiore; Nana-Jane Chipampe; Josef Hardi; Bruce W. Herr, II; Huseyin Kir; Paola Roncaglia et al.
Source: check_circle
Crossref

Toward a minimal information reporting standard about new cell types

2022 | Preprint
DOI: 10.48550/ARXIV.2204.09673
Source: Self-asserted source
Paola Roncaglia

A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology.

Journal of biomedical semantics
2022-10-21 | Journal article
DOI: 10.1186/s13326-022-00279-z
PMID: 36271389
Contributors: Paola Roncaglia; He Y; Yu H; Huffman A; Lin AY; Natale DA; Beverley J; Zheng L; Perl Y; Wang Z et al.
Source: Self-asserted source
Paola Roncaglia

Mondo: Unifying diseases for the world, by the world

2022-04 | Preprint
DOI: 10.1101/2022.04.13.22273750
PPR: PPR482735
Contributors: Vasilevsky NA; Matentzoglu NA; Toro S; Flack JE; Hegde H; Unni DR; Alyea GF; Amberger JS; Babb L; Balhoff JP et al.
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics.

Nucleic acids research
2021-01-01 | Journal article
DOI: 10.1093/nar/gkaa840
PMID: 33045747
PMC: PMC7778936
Source: Self-asserted source
Paola Roncaglia

Gene Ontology Curation of Neuroinflammation Biology Improves the Interpretation of Alzheimer's Disease Gene Expression Data.

Journal of Alzheimer's disease : JAD
2020-05 | Journal article
DOI: 10.3233/jad-200207
PMID: 32417785
Contributors: Kramarz B; Huntley RP; Rodríguez-López M; Roncaglia P; Saverimuttu SCC; Parkinson H; Bandopadhyay R; Martin MJ; Orchard S; Hooper NM et al.
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.

Nucleic acids research
2019-11 | Journal article
DOI: 10.1093/nar/gkz997
PMID: 31701156
Contributors: Shefchek KA; Harris NL; Gargano M; Matentzoglu N; Unni D; Brush M; Keith D; Conlin T; Vasilevsky N; Zhang XA et al.
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer’s Disease Data

Genes
2018-11 | Journal article | Author
DOI: 10.3390/genes9120593
Contributors: Barbara Kramarz; Paola Roncaglia; Birgit Meldal; Huntley R P; Maria J. Martin ; Sandra Orchard; Helen Parkinson; David Brough; Rina Bandopadhyay; Nigel Hooper et al.
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Multidisciplinary Digital Publishing Institute
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Preferred source (of 2)‎

The Gene Ontology Resource: 20 years and still GOing strong.

Nucleic acids research
2018-11 | Journal article
DOI: 10.1093/nar/gky1055
PMID: 30395331
Contributors: The Gene Ontology Consortium
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Exploring autophagy with Gene Ontology

Autophagy
2018-03-04 | Journal article
DOI: 10.1080/15548627.2017.1415189
Contributors: Paul Denny; Marc Feuermann; David P. Hill; Ruth C. Lovering; Helene Plun-Favreau; Paola Roncaglia
Source: check_circle
Crossref

Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology.

Circulation. Genomic and precision medicine
2018-02 | Journal article
DOI: 10.1161/circgen.117.001813
PMID: 29440116
Contributors: Lovering RC; Roncaglia P; Howe DG; Laulederkind SJF; Khodiyar VK; Berardini TZ; Tweedie S; Foulger RE; Osumi-Sutherland D; Campbell NH et al.
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

The Gene Ontology of eukaryotic cilia and flagella

Cilia
2017-12 | Journal article
DOI: 10.1186/s13630-017-0054-8
Contributors: Paola Roncaglia; Teunis J. P. van Dam; Karen R. Christie; Lora Nacheva; Grischa Toedt; Martijn A. Huynen; Rachael P. Huntley; Toby J. Gibson; Jane Lomax
Source: check_circle
Crossref

Expansion of the Gene Ontology knowledgebase and resources.

2017-01 | Journal article
DOI: 10.1093/nar/gkw1108
PMID: 27899567
PMC: PMC5210579
Contributors: The Gene Ontology Consortium
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Effects of Pin1 Loss in Hdh(Q111) Knock-in Mice.

2016 | Journal article
DOI: 10.3389/fncel.2016.00110
PMID: 27199664
Contributors: Agostoni E; Michelazzi S; Maurutto M; Carnemolla A; Ciani Y; Vatta P; Roncaglia P; Zucchelli S; Leanza G; Mantovani F et al.
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Extending gene ontology in the context of extracellular RNA and vesicle communication.

2016 | Journal article
PMC: PMC4830068
Contributors: Cheung K; Keerthikumar S; Roncaglia P; Subramanian SL; Roth ME; Samuel M; Anand S; Gangoda L; Gould S; Alexander R et al.
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Extending gene ontology in the context of extracellular RNA and vesicle communication.

2016 | Journal article
DOI: 10.1186/s13326-016-0061-5
PMID: 27076901
Contributors: Cheung KH; Keerthikumar S; Roncaglia P; Subramanian SL; Roth ME; Samuel M; Anand S; Gangoda L; Gould S; Alexander R et al.
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Blood transcriptomics of drug-naive sporadic Parkinson's disease patients.

2015 | Journal article
DOI: 10.1186/s12864-015-2058-3
PMID: 26510930
PMC: PMC4625854
Contributors: Calligaris R; Banica M; Roncaglia P; Robotti E; Finaurini S; Vlachouli C; Antonutti L; Iorio F; Carissimo A; Cattaruzza T et al.
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Using Gene Ontology to describe the role of the neurexin-neuroligin-SHANK complex in human, mouse and rat and its relevance to autism.

2015 | Journal article
DOI:

10.1186/s12859-015-0622-0

PMID:

26047810

PMC:

PMC4458007
Contributors: Patel S; Roncaglia P; Lovering RC
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Tools and data services registry: a community effort to document bioinformatics resources.

2015-11 | Journal article
PMID: 26538599
Contributors: Ison J; Rapacki K; Ménager H; Kalaš M; Rydza E; Chmura P; Anthon C; Beard N; Berka K; Bolser D et al.
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Gene Ontology Consortium: going forward.

2015-01 | Journal article
DOI:

10.1093/nar/gku1179

PMID:

25428369

PMC:

PMC4383973
Contributors: Gene Ontology Consortium
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules.

2014 | Journal article
DOI:

10.1186/1471-2164-15-729

PMID:

25164183

PMC:

PMC4161876
Contributors: Grison A; Zucchelli S; Urzì A; Zamparo I; Lazarevic D; Pascarella G; Roncaglia P; Giorgetti A; Garcia-Esparcia P; Vlachouli C et al.
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

TermGenie - a web-application for pattern-based ontology class generation.

2014 | Journal article
DOI:

10.1186/2041-1480-5-48

PMID:

25937883

PMC:

PMC4417543
Contributors: Dietze H; Berardini TZ; Foulger RE; Hill DP; Lomax J; Osumi-Sutherland D; Roncaglia P; Mungall CJ
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Dissecting the transcriptional phenotype of ribosomal protein deficiency: implications for Diamond-Blackfan Anemia.

Gene
2014-05 | Journal article
DOI: 10.1016/j.gene.2014.04.077
PMID: 24835311
PMC: PMC4058751
Contributors: Aspesi A; Pavesi E; Robotti E; Crescitelli R; Boria I; Avondo F; Moniz H; Da Costa L; Mohandas N; Roncaglia P et al.
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments.

2013-10 | Journal article
PMID:

24093723
Contributors: Roncaglia P; Martone ME; Hill DP; Berardini TZ; Foulger RE; Imam FT; Drabkin H; Mungall CJ; Lomax J
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Adhesion to carbon nanotube conductive scaffolds forces action-potential appearance in immature rat spinal neurons.

2013 | Journal article
DOI:

10.1371/journal.pone.0073621

PMID:

23951361

PMC:

PMC3741175
Contributors: Fabbro A; Sucapane A; Toma FM; Calura E; Rizzetto L; Carrieri C; Roncaglia P; Martinelli V; Scaini D; Masten L et al.
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

DNA Damage in Mammalian Neural Stem Cells Leads to Astrocytic Differentiation Mediated by BMP2 Signaling through JAK-STAT.

2013 | Journal article
DOI:

10.1016/j.stemcr.2013.06.004

PMID:

24052948

PMC:

PMC3757751
Contributors: Schneider L; Pellegatta S; Favaro R; Pisati F; Roncaglia P; Testa G; Nicolis SK; Finocchiaro G; d'Adda di Fagagna F
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.

2013 | Journal article
DOI:

10.1186/1471-2164-14-513

PMID:

23895341

PMC:

PMC3733925
Contributors: Hill DP; Adams N; Bada M; Batchelor C; Berardini TZ; Dietze H; Drabkin HJ; Ennis M; Foulger RE; Harris MA et al.
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Genome-wide expression profiling and functional characterization of SCA28 lymphoblastoid cell lines reveal impairment in cell growth and activation of apoptotic pathways.

2013 | Journal article
DOI:

10.1186/1755-8794-6-22

PMID:

23777634

PMC:

PMC3689607
Contributors: Mancini C; Roncaglia P; Brussino A; Stevanin G; Lo Buono N; Krmac H; Maltecca F; Gazzano E; Bartoletti Stella A; Calvaruso MA et al.
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Gene Ontology annotations and resources.

Nucleic acids research
2012-11 | Journal article
DOI: 10.1093/nar/gks1050
PMID: 23161678
PMC: PMC3531070
Contributors: Gene Ontology Consortium; Blake JA; Dolan M; Drabkin H; Hill DP; Li N; Sitnikov D; Bridges S; Burgess S; Buza T et al.
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Motor neuron impairment mediated by a sumoylated fragment of the glial glutamate transporter EAAT2.

2011-11 | Journal article
DOI:

10.1002/glia.21218

PMID:

21769946
Contributors: Foran E; Bogush A; Goffredo M; Roncaglia P; Gustincich S; Pasinelli P; Trotti D
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

The Gene Ontology: enhancements for 2011.

Nucleic acids research
2011-11 | Journal article
DOI: 10.1093/nar/gkr1028
PMID: 22102568
PMC: PMC3245151
Contributors: Gene Ontology Consortium
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Direct generation of functional dopaminergic neurons from mouse and human fibroblasts.

2011-08 | Journal article
DOI:

10.1038/nature10284

PMID:

21725324
Contributors: Caiazzo M; Dell'Anno MT; Dvoretskova E; Lazarevic D; Taverna S; Leo D; Sotnikova TD; Menegon A; Roncaglia P; Colciago G et al.
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Developmental influence of the cellular prion protein on the gene expression profile in mouse hippocampus.

2011-06 | Journal article
DOI:

10.1152/physiolgenomics.00205.2010

PMID:

21406608
Contributors: Benvegnù S; Roncaglia P; Agostini F; Casalone C; Corona C; Gustincich S; Legname G
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Parkinson disease-associated DJ-1 is required for the expression of the glial cell line-derived neurotrophic factor receptor RET in human neuroblastoma cells.

2010-06 | Journal article
DOI:

10.1074/jbc.M109.088294

PMID:

20395301

PMC:

PMC2881782
Contributors: Foti R; Zucchelli S; Biagioli M; Roncaglia P; Vilotti S; Calligaris R; Krmac H; Girardini JE; Del Sal G; Gustincich S
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Characterization of caspase-dependent and caspase-independent deaths in glioblastoma cells treated with inhibitors of the ubiquitin-proteasome system.

2009-11 | Journal article
DOI:

10.1158/1535-7163.MCT-09-0431

PMID:

19887551
Contributors: Foti C; Florean C; Pezzutto A; Roncaglia P; Tomasella A; Gustincich S; Brancolini C
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Unexpected expression of alpha- and beta-globin in mesencephalic dopaminergic neurons and glial cells.

2009-09 | Journal article
DOI:

10.1073/pnas.0813216106

PMID:

19717439

PMC:

PMC2732704
Contributors: Biagioli M; Pinto M; Cesselli D; Zaninello M; Lazarevic D; Roncaglia P; Simone R; Vlachouli C; Plessy C; Bertin N et al.
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

A transcriptome analysis identifies molecular effectors of unconjugated bilirubin in human neuroblastoma SH-SY5Y cells.

2009 | Journal article
DOI:

10.1186/1471-2164-10-543

PMID:

19925663

PMC:

PMC2789749
Contributors: Calligaris R; Bellarosa C; Foti R; Roncaglia P; Giraudi P; Krmac H; Tiribelli C; Gustincich S
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer.

2009 | Journal article
DOI:

10.1186/1471-2164-10-442

PMID:

19765279

PMC:

PMC2760583
Contributors: Avondo F; Roncaglia P; Crescenzio N; Krmac H; Garelli E; Armiraglio M; Castagnoli C; Campagnoli MF; Ramenghi U; Gustincich S et al.
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Large differences in aging phenotype between strains of the short-lived annual fish Nothobranchius furzeri.

2008 | Journal article
DOI:

10.1371/journal.pone.0003866

PMID:

19052641

PMC:

PMC2585814
Contributors: Terzibasi E; Valenzano DR; Benedetti M; Roncaglia P; Cattaneo A; Domenici L; Cellerino A
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Annual fishes of the genus Nothobranchius as a model system for aging research.

2005-10 | Journal article
DOI:

10.1111/j.1474-9726.2005.00165.x

PMID:

16164422
Contributors: Genade T; Benedetti M; Terzibasi E; Roncaglia P; Valenzano DR; Cattaneo A; Cellerino A
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans.

2005-02 | Journal article
DOI:

10.1126/science.1103773

PMID:

15653466

PMC:

PMC3520129
Contributors: Loftus BJ; Fung E; Roncaglia P; Rowley D; Amedeo P; Bruno D; Vamathevan J; Miranda M; Anderson IJ; Fraser JA et al.
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

The genome of the protist parasite Entamoeba histolytica.

2005-02 | Journal article
DOI:

10.1038/nature03291

PMID:

15729342
Contributors: Loftus B; Anderson I; Davies R; Alsmark UC; Samuelson J; Amedeo P; Roncaglia P; Berriman M; Hirt RP; Mann BJ et al.
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Genomic organization and expression of 23 new genes from MATalpha locus of Cryptococcus neoformans var. gattii.

2005-01 | Journal article
DOI:

10.1016/j.bbrc.2004.11.017

PMID:

15567176
Contributors: Ren P; Roncaglia P; Springer DJ; Fan J; Chaturvedi V
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Pore topology of the hyperpolarization-activated cyclic nucleotide-gated channel from sea urchin sperm.

2002-10 | Journal article
DOI:

10.1016/S0006-3495(02)73957-X

PMID:

12324414

PMC:

PMC1302285
Contributors: Roncaglia P; Mistrík P; Torre V
Source: Self-asserted source
Paola Roncaglia via Europe PubMed Central

Cyclic-nucleotide-gated channels: pore topology in desensitizing E19A mutants.

2001 | Journal article
PMID: 11316260
Source: Self-asserted source
Paola Roncaglia

Cyclic nucleotide-gated channels: intra- and extracellular accessibility to Cd2+ of substituted cysteine residues within the P-loop.

2000 | Journal article
DOI: 10.1007/s004240000324
PMID: 10958339
Source: Self-asserted source
Paola Roncaglia
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