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The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study

Database
2025-01-13 | Journal article
DOI: 10.1093/database/baad066
Contributors: Simona Panni; Kalpana Panneerselvam; Pablo Porras; Margaret Duesbury; Livia Perfetto; Luana Licata; Henning Hermjakob; Sandra Orchard
Source: check_circle
Crossref

An atlas of protein-protein associations of human tissues prioritizes candidate disease genes

2024-05 | Preprint
DOI: 10.1101/2024.05.15.594301
PPR: PPR854055
Contributors: Laman Trip DS; van Oostrum M; Memon D; Frommelt F; Baptista D; Panneerselvam K; Bradley G; Licata L; Hermjakob H; Orchard S et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

The landscape of cancer-rewired GPCR signaling axes.

Cell genomics
2024-05 | Journal article
DOI: 10.1016/j.xgen.2024.100557
PMID: 38723607
PMC: PMC11099383
Contributors: Arora C; Matic M; Bisceglia L; Di Chiaro P; De Oliveira Rosa N; Carli F; Clubb L; Nemati Fard LA; Kargas G; Diaferia GR et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

Correction: Curation of causal interactions mediated by genes associated with autism accelerates the understanding of gene-phenotype relationships underlying neurodevelopmental disorders.

Molecular psychiatry
2024-01 | Journal article
DOI: 10.1038/s41380-024-02432-9
PMID: 38267621
PMC: PMC11078712
Contributors: Iannuccelli M; Vitriolo A; Licata L; Lo Surdo P; Contino S; Cheroni C; Capocefalo D; Castagnoli L; Testa G; Cesareni G et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

Curation of causal interactions mediated by genes associated with autism accelerates the understanding of gene-phenotype relationships underlying neurodevelopmental disorders.

Molecular psychiatry
2023-12 | Journal article
DOI: 10.1038/s41380-023-02317-3
PMID: 38102483
PMC: PMC11078740
Contributors: Iannuccelli M; Vitriolo A; Licata L; Lo Surdo P; Contino S; Cheroni C; Capocefalo D; Castagnoli L; Testa G; Cesareni G et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

The landscape of microRNA interactions annotation: analysis of three rare disorders as case study

2023-06 | Preprint
DOI: 10.1101/2023.06.20.545695
PPR: PPR679890
Contributors: Simona P; Panneerselvam K; Porras P; Duesbury M; Perfetto L; Licata L; Hermjakob H; Orchard S
Source: Self-asserted source
Luana Licata via Europe PubMed Central

Resources and tools for rare disease variant interpretation.

Frontiers in molecular biosciences
2023-05 | Journal article
DOI: 10.3389/fmolb.2023.1169109
PMID: 37234922
PMC: PMC10206239
Contributors: Licata L; Via A; Turina P; Babbi G; Benevenuta S; Carta C; Casadio R; Cicconardi A; Facchiano A; Fariselli P et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

The landscape of cancer rewired GPCR signaling axes

2023-03 | Preprint
DOI: 10.1101/2023.03.13.532291
PPR: PPR629892
Contributors: Arora C; Matic M; DiChiaro P; Rosa NDO; Carli F; Clubb L; Fard LAN; Kargas G; Diaferia G; Vukotic R et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

Curation of causal interactions mediated by genes associated to autism accelerates the understanding of gene-phenotype relationships underlying neurodevelopmental disorders

2023-01-09 | Preprint
DOI: 10.1101/2023.01.09.523265
Contributors: Marta Iannuccelli; Alessandro Vitriolo; Luana Licata; Cristina Cheroni; Luisa Castagnoli; Giuseppe Testa; Gianni Cesareni; Livia Perfetto
Source: check_circle
Crossref

SIGNOR 3.0, the SIGnaling network open resource 3.0: 2022 update

Nucleic Acids Research
2023-01-06 | Journal article
DOI: 10.1093/nar/gkac883
Contributors: Prisca Lo Surdo; Marta Iannuccelli; Silvia Contino; Luisa Castagnoli; Luana Licata; Gianni Cesareni; Livia Perfetto
Source: check_circle
Crossref

The RD-Connect Genome-Phenome Analysis Platform: Accelerating diagnosis, research, and gene discovery for rare diseases.

Human mutation
2022-06 | Journal article
DOI: 10.1002/humu.24353
PMID: 35178824
PMC: PMC9324157
Contributors: Laurie S; Piscia D; Matalonga L; Corvó A; Fernández-Callejo M; Garcia-Linares C; Hernandez-Ferrer C; Luengo C; Martínez I; Papakonstantinou A et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

A Resource to Infer Molecular Paths Linking Cancer Mutations to Perturbation of Cell Metabolism.

Frontiers in molecular biosciences
2022-05 | Journal article
DOI: 10.3389/fmolb.2022.893256
PMID: 35664677
PMC: PMC9158333
Contributors: Iannuccelli M; Lo Surdo P; Licata L; Castagnoli L; Cesareni G; Perfetto L
Source: Self-asserted source
Luana Licata via Europe PubMed Central

The Intricacy of the Viral-Human Protein Interaction Networks: Resources, Data, and Analyses.

Frontiers in microbiology
2022-04 | Journal article
DOI: 10.3389/fmicb.2022.849781
PMID: 35531299
PMC: PMC9069133
Contributors: Saha D; Iannuccelli M; Brun C; Zanzoni A; Licata L
Source: Self-asserted source
Luana Licata via Europe PubMed Central

IMEx Databases: Displaying Molecular Interactions into a Single, Standards-Compliant Dataset.

Methods in molecular biology (Clifton, N.J.)
2022-01 | Journal article
DOI: 10.1007/978-1-0716-2095-3_2
PMID: 35507258
Contributors: Porras P; Orchard S; Licata L
Source: Self-asserted source
Luana Licata via Europe PubMed Central

The IntAct database: efficient access to fine-grained molecular interaction data.

Nucleic acids research
2022-01 | Journal article
DOI: 10.1093/nar/gkab1006
PMID: 34761267
PMC: PMC8728211
Contributors: Del Toro N; Shrivastava A; Ragueneau E; Meldal B; Combe C; Barrera E; Perfetto L; How K; Ratan P; Shirodkar G et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

Molecular systems biology
2021-12 | Journal article
DOI: 10.15252/msb.202110851
PMID: 34939300
PMC: PMC8696085
Contributors: Ostaszewski M; Niarakis A; Mazein A; Kuperstein I; Phair R; Orta-Resendiz A; Singh V; Aghamiri SS; Acencio ML; Glaab E et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

Molecular systems biology
2021-10 | Journal article
DOI: 10.15252/msb.202110387
PMID: 34664389
PMC: PMC8524328
Contributors: Ostaszewski M; Niarakis A; Mazein A; Kuperstein I; Phair R; Orta-Resendiz A; Singh V; Aghamiri SS; Acencio ML; Glaab E et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

The gene regulation knowledge commons: the action area of GREEKC.

Biochimica et biophysica acta. Gene regulatory mechanisms
2021-10 | Journal article
DOI: 10.1016/j.bbagrm.2021.194768
PMID: 34757206
Contributors: Kuiper M; Bonello J; Fernández-Breis JT; Bucher P; Futschik ME; Gaudet P; Kulakovskiy IV; Licata L; Logie C; Lovering RC et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

Phosphomatics: interactive interrogation of substrate-kinase networks in global phosphoproteomics datasets.

Bioinformatics (Oxford, England)
2021-07 | Journal article
DOI: 10.1093/bioinformatics/btaa916
PMID: 33119075
Contributors: Leeming MG; O'Callaghan S; Licata L; Iannuccelli M; Lo Surdo P; Micarelli E; Ang CS; Nie S; Varshney S; Ameen S et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

A Resource for the Network Representation of Cell Perturbations Caused by SARS-CoV-2 Infection

Genes
2021-03 | Journal article | Author
DOI: 10.3390/genes12030450
Contributors: Livia Perfetto; Elisa Micarelli; Marta Iannuccelli; Prisca Lo Surdo; Giulio Giuliani; Sara Latini; Giusj Monia Pugliese; Giorgia Massacci; Simone Vumbaca; Federica Riccio et al.
Source: check_circle
Multidisciplinary Digital Publishing Institute

Integrating Patient-Specific Information into Logic Models of Complex Diseases: Application to Acute Myeloid Leukemia.

Journal of personalized medicine
2021-02 | Journal article
DOI: 10.3390/jpm11020117
PMID: 33578936
PMC: PMC7916657
Contributors: Palma A; Iannuccelli M; Rozzo I; Licata L; Perfetto L; Massacci G; Castagnoli L; Cesareni G; Sacco F
Source: Self-asserted source
Luana Licata via Europe PubMed Central

Towards a unified open access dataset of molecular interactions.

Nature communications
2020-12 | Journal article
DOI: 10.1038/s41467-020-19942-z
PMID: 33262342
PMC: PMC7708836
Contributors: Porras P; Barrera E; Bridge A; Del-Toro N; Cesareni G; Duesbury M; Hermjakob H; Iannuccelli M; Jurisica I; Kotlyar M et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

2020-10 | Preprint
DOI: 10.1101/2020.10.26.356014
PPR: PPR231819
Contributors: Ostaszewski M; Niarakis A; Mazein A; Kuperstein I; Phair R; Orta-Resendiz A; Singh V; Aghamiri SS; Acencio ML; Glaab E et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST).

Bioinformatics (Oxford, England)
2020-07 | Journal article
DOI: 10.1093/bioinformatics/btaa622
PMID: 32637990
Contributors: Touré V; Vercruysse S; Acencio ML; Lovering RC; Orchard S; Bradley G; Casals-Casas C; Chaouiya C; Del-Toro N; Flobak Å et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions

2020-06-16 | Preprint
DOI: 10.1101/2020.06.16.153817
Contributors: L Perfetto; C Pastrello; N Del-Toro; M Duesbury; M Iannuccelli; M Kotlyar; L Licata; B Meldal; K Panneerselvam; S Panni et al.
Source: check_circle
Crossref

The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences.

Bioinformatics (Oxford, England)
2020-04 | Journal article
DOI: 10.1093/bioinformatics/btz959
PMID: 31950984
PMC: PMC7446027
Contributors: Drysdale R; Cook CE; Petryszak R; Baillie-Gerritsen V; Barlow M; Gasteiger E; Gruhl F; Haas J; Lanfear J; Lopez R et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)

2020-04 | Preprint
DOI: 10.20944/preprints202004.0480.v1
PPR: PPR155987
Contributors: Touré V; Vercruysse S; Acencio ML; Lovering R; Orchard S; Bradley G; Casals-Casas C; Chaouiya C; del-Toro N; Flobak Å et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

Using the MINT Database to Search Protein Interactions.

Current protocols in bioinformatics
2020-03-01 | Journal article
DOI: 10.1002/cpbi.93
PMID: 31945268
Source: Self-asserted source
Luana Licata

CancerGeneNet: linking driver genes to cancer hallmarks

Nucleic Acids Research
2020-01-08 | Journal article
DOI: 10.1093/nar/gkz871
Contributors: Marta Iannuccelli; Elisa Micarelli; Prisca Lo Surdo; Alessandro Palma; Livia Perfetto; Ilaria Rozzo; Luisa Castagnoli; Luana Licata; Gianni Cesareni
Source: check_circle
Crossref

The IMEx coronavirus interactome: an evolving map of Coronaviridae–host molecular interactions

Database
2020-01-01 | Journal article
DOI: 10.1093/database/baaa096
Contributors: L Perfetto; C Pastrello; N del-Toro; M Duesbury; M Iannuccelli; M Kotlyar; L Licata; B Meldal; K Panneerselvam; S Panni et al.
Source: check_circle
Crossref

CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination.

Bioinformatics (Oxford, England)
2019-10 | Journal article
DOI: 10.1093/bioinformatics/btz132
PMID: 30793173
Contributors: Perfetto L; Acencio ML; Bradley G; Cesareni G; Del Toro N; Fazekas D; Hermjakob H; Korcsmaros T; Kuiper M; Lægreid A et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update

Nucleic Acids Research
2019-10-29 | Journal article
DOI: 10.1093/nar/gkz949
Contributors: Luana Licata; Prisca Lo Surdo; Marta Iannuccelli; Alessandro Palma; Elisa Micarelli; Livia Perfetto; Daniele Peluso; Alberto Calderone; Luisa Castagnoli; Gianni Cesareni
Source: check_circle
Crossref

Myo-REG: A Portal for Signaling Interactions in Muscle Regeneration.

Frontiers in physiology
2019-09 | Journal article
DOI: 10.3389/fphys.2019.01216
PMID: 31611808
PMC: PMC6776608
Contributors: Palma A; Perpetuini AC; Ferrentino F; Fuoco C; Gargioli C; Giuliani G; Iannuccelli M; Licata L; Micarelli E; Paoluzi S et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

Myo-REG: a portal for signaling interactions in muscle regeneration

2019-07 | Other
DOI: 10.1101/711168
OTHER-ID:

PPR86610
Contributors: Palma A; Calderone A; Perpetuini AC; Ferrentino F; Fuoco C; Gargioli C; Giuliani G; Iannuccelli M; Licata L; Micarelli E et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

Publisher Correction: Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.

Nature communications
2019-03 | Journal article
DOI: 10.1038/s41467-019-08814-w
PMID: 30833551
PMC: PMC6399256
Contributors: IMEx Consortium contributing authors; Del-Toro N; Duesbury M; Koch M; Perfetto L; Shrivastava A; Ochoa D; Wagih O; Piñero J; Kotlyar M et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.

Nature communications
2019-01 | Journal article
DOI: 10.1038/s41467-018-07709-6
PMID: 30602777
PMC: PMC6315030
Contributors: IMEx Consortium Curators; Del-Toro N; Duesbury M; Koch M; Koch M; Perfetto L; Shrivastava A; Ochoa D; Wagih O; Piñero J et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

CausalTab: PSI-MITAB 2.8 updated format for signaling data representation and dissemination

2018-08 | Other
DOI: 10.1101/385773
OTHER-ID:

PPR46518
Contributors: Perfetto L; Acencio M; Bradley G; Cesareni G; Toro N; Fazekas D; Hermjakob H; Korcsmaros T; Kuiper M; Lægreid A et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.

BMC bioinformatics
2018-04 | Journal article
DOI: 10.1186/s12859-018-2118-1
PMID: 29642841
PMC: PMC5896046
Contributors: Sivade Dumousseau M; Alonso-López D; Ammari M; Bradley G; Campbell NH; Ceol A; Cesareni G; Combe C; De Las Rivas J; Del-Toro N et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

DISNOR: a disease network open resource.

Nucleic acids research
2018-01 | Journal article
DOI: 10.1093/nar/gkx876
PMID: 29036667
PMC: PMC5753342
Contributors: Lo Surdo P; Calderone A; Iannuccelli M; Licata L; Peluso D; Castagnoli L; Cesareni G; Perfetto L
Source: Self-asserted source
Luana Licata via Europe PubMed Central

The MIntAct Project and Molecular Interaction Databases.

Methods in molecular biology (Clifton, N.J.)
2016-01 | Journal article
DOI: 10.1007/978-1-4939-3572-7_3
PMID: 27115627
Contributors: Licata L; Orchard S
Source: Self-asserted source
Luana Licata via Europe PubMed Central

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

Nucleic acids research
2015-11 | Journal article
DOI: 10.1093/nar/gkv1116
PMID: 26538599
PMC: PMC4702812
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
Luana Licata via Europe PubMed Central

SIGNOR: a database of causal relationships between biological entities.

Nucleic acids research
2015-10 | Journal article
DOI: 10.1093/nar/gkv1048
PMID: 26467481
PMC: PMC4702784
Contributors: Perfetto L; Briganti L; Calderone A; Cerquone Perpetuini A; Iannuccelli M; Langone F; Licata L; Marinkovic M; Mattioni A; Pavlidou T et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

The complex portal--an encyclopaedia of macromolecular complexes.

Nucleic acids research
2014-10 | Journal article
DOI: 10.1093/nar/gku975
PMID: 25313161
PMC: PMC4384031
Contributors: Meldal BH; Forner-Martinez O; Costanzo MC; Dana J; Demeter J; Dumousseau M; Dwight SS; Gaulton A; Licata L; Melidoni AN et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

VirusMentha: a new resource for virus-host protein interactions.

Nucleic acids research
2014-09 | Journal article
DOI: 10.1093/nar/gku830
PMID: 25217587
PMC: PMC4384001
Contributors: Calderone A; Licata L; Cesareni G
Source: Self-asserted source
Luana Licata via Europe PubMed Central

The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.

Nucleic acids research
2013-11 | Journal article
DOI: 10.1093/nar/gkt1115
PMID: 24234451
PMC: PMC3965093
Contributors: Orchard S; Ammari M; Aranda B; Breuza L; Briganti L; Broackes-Carter F; Campbell NH; Chavali G; Chen C; del-Toro N et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task.

Database : the journal of biological databases and curation
2013-01 | Journal article
DOI: 10.1093/database/bas056
PMID: 23327936
PMC: PMC3625048
Contributors: Arighi CN; Carterette B; Cohen KB; Krallinger M; Wilbur WJ; Fey P; Dodson R; Cooper L; Van Slyke CE; Dahdul W et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

MINT, the molecular interaction database: 2012 update.

Nucleic acids research
2011-11 | Journal article
DOI: 10.1093/nar/gkr930
PMID: 22096227
PMC: PMC3244991
Contributors: Licata L; Briganti L; Peluso D; Perfetto L; Iannuccelli M; Galeota E; Sacco F; Palma A; Nardozza AP; Santonico E et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases.

BMC bioinformatics
2011-10 | Journal article
DOI: 10.1186/1471-2105-12-S8-S8
PMID: 22151178
PMC: PMC3269943
Contributors: Chatr-Aryamontri A; Winter A; Perfetto L; Briganti L; Licata L; Iannuccelli M; Castagnoli L; Cesareni G; Tyers M
Source: Self-asserted source
Luana Licata via Europe PubMed Central

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text.

BMC bioinformatics
2011-10 | Journal article
DOI: 10.1186/1471-2105-12-S8-S3
PMID: 22151929
PMC: PMC3269938
Contributors: Krallinger M; Vazquez M; Leitner F; Salgado D; Chatr-Aryamontri A; Winter A; Perfetto L; Briganti L; Licata L; Iannuccelli M et al.
Source: Self-asserted source
Luana Licata via Europe PubMed Central

The FEBS Letters/BioCreative II.5 experiment: making biological information accessible.

Nature biotechnology
2010-09 | Journal article
DOI: 10.1038/nbt0910-897
PMID: 20829821
Contributors: Leitner F; Chatr-aryamontri A; Mardis SA; Ceol A; Krallinger M; Licata L; Hirschman L; Cesareni G; Valencia A
Source: Self-asserted source
Luana Licata via Europe PubMed Central
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