Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy.
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Database J. Biol. Databases Curation, January, 2024
Enhancing Scientific Reproducibility Through Automated BioCompute Object Creation Using Retrieval-Augmented Generation from Publications.
CoRR, 2024
Data Harmonization through Use of Community Standards in the Common Fund Data Ecosystem.
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Proceedings of the International Conference on Biomedical Ontology 2022 (ICBO), Ann Arbor, Michigan, USA, September 25, 2022
Bioinformatics tools developed to support BioCompute Objects.
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Database J. Biol. Databases Curation, 2021
Scanning window analysis of non-coding regions within normal-tumor whole-genome sequence samples.
Briefings Bioinform., 2021
COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model.
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Briefings Bioinform., 2021
Analysis of Biomarker Data Towards Development of a Molecular Biomarker Ontology.
Proceedings of the International Conference on Biomedical Ontologies 2021 co-located with the Workshop on Ontologies for the Behavioural and Social Sciences (OntoBess 2021) as part of the Bolzano Summer of Knowledge (BOSK 2021), 2021
<i>miCloud: </i> A Plug-n-Play, Extensible, On-Premises Bioinformatics Cloud for Seamless Execution of Complex Next-Generation Sequencing Data Analysis Pipelines.
J. Comput. Biol., 2019
OncoMX: an Integrated Cancer Mutation and Expression Knowledgebase for Biomarker Evaluation and Discovery.
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Proceedings of the AMIA 2019, 2019
BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery.
Nucleic Acids Res., 2018
Identification of key differentially expressed MicroRNAs in cancer patients through pan-cancer analysis.
Comput. Biol. Medicine, 2018
DEXTER: Disease-Expression Relation Extraction from Text.
Database J. Biol. Databases Curation, 2018
Pubcast and Genecast: Browsing and Exploring Publications and Associated Curated Content in Biology Through Mobile Devices.
IEEE ACM Trans. Comput. Biol. Bioinform., 2017
Computational clustering for viral reference proteomes.
Bioinform., 2016
High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis.
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Database J. Biol. Databases Curation, 2016
Advantages of distributed and parallel algorithms that leverage Cloud Computing platforms for large-scale genome assembly.
F1000Research, 2015
Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis.
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Database J. Biol. Databases Curation, 2015
BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis.
Database J. Biol. Databases Curation, 2015
Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data.
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BMC Bioinform., 2014
A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE).
Database J. Biol. Databases Curation, 2014
Structure-based Comparative Analysis and Prediction of N-linked Glycosylation Sites in Evolutionarily Distant Eukaryotes.
Genom. Proteom. Bioinform., 2013
SNVDis: A Proteome-wide Analysis Service for Evaluating nsSNVs in Protein Functional Sites and Pathways.
Genom. Proteom. Bioinform., 2013
Biocuration Virtual Issue 2012.
Database J. Biol. Databases Curation, 2012
Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference.
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Database J. Biol. Databases Curation, 2012
A comprehensive protein-centric ID mapping service for molecular data integration.
Bioinform., 2011
Structure-Guided Comparative Analysis of Proteins: Principles, Tools, and Applications for Predicting Function.
PLoS Comput. Biol., 2008
An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data.
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Nucleic Acids Res., 2008
UniRef: comprehensive and non-redundant UniProt reference clusters.
Bioinform., 2007
The Universal Protein Resource (UniProt): an expanding universe of protein information.
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Nucleic Acids Res., 2006
Computational identification of strain-, species- and genus-specific proteins.
BMC Bioinform., 2005
GeneOrder3.0: Software for comparing the order of genes in pairs of small bacterial genomes.
BMC Bioinform., 2004
Application of global computational tools GeneOrder and CoreGenes to the comparative analyses of chordopoxvirus genomes.
Inf. Sci., 2002
CoreGenes: A computational tool for identifying and cataloging "core" genes in a set of small genomes.
BMC Bioinform., 2002
Application of Global Computational Tools GeneOrder and OrthologLocator to the Comparative Analyses of Chordopoxvirus Genomes.
Proceedings of the 6th Joint Conference on Information Science, 2002
GeneOrder: comparing the order of genes in small genomes.
Bioinform., 2001