2024
Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy.
Database J. Biol. Databases Curation, January, 2024

Enhancing Scientific Reproducibility Through Automated BioCompute Object Creation Using Retrieval-Augmented Generation from Publications.
CoRR, 2024

2022
Data Harmonization through Use of Community Standards in the Common Fund Data Ecosystem.
Proceedings of the International Conference on Biomedical Ontology 2022 (ICBO), Ann Arbor, Michigan, USA, September 25, 2022

2021
Bioinformatics tools developed to support BioCompute Objects.
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.
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

2020
GlyGen data model and processing workflow.
Bioinform., 2020

2019
<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.
Proceedings of the AMIA 2019, 2019

2018
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

2017
Pubcast and Genecast: Browsing and Exploring Publications and Associated Curated Content in Biology Through Mobile Devices.
IEEE ACM Trans. Comput. Biol. Bioinform., 2017

2016
Computational clustering for viral reference proteomes.
Bioinform., 2016

High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis.
Database J. Biol. Databases Curation, 2016

2015
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.
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

2014
Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data.
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

2013
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

2012
Biocuration Virtual Issue 2012.
Database J. Biol. Databases Curation, 2012

Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference.
Database J. Biol. Databases Curation, 2012

2011
A comprehensive protein-centric ID mapping service for molecular data integration.
Bioinform., 2011

2008
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.
Nucleic Acids Res., 2008

2007
UniRef: comprehensive and non-redundant UniProt reference clusters.
Bioinform., 2007

2006
The Universal Protein Resource (UniProt): an expanding universe of protein information.
Nucleic Acids Res., 2006

2005
Computational identification of strain-, species- and genus-specific proteins.
BMC Bioinform., 2005

2004
PIRSF: family classification system at the Protein Information Resource.
Nucleic Acids Res., 2004

GeneOrder3.0: Software for comparing the order of genes in pairs of small bacterial genomes.
BMC Bioinform., 2004

2003
CDD: a curated Entrez database of conserved domain alignments.
Nucleic Acids Res., 2003

MMDB: Entrez's 3D-structure database.
Nucleic Acids Res., 2003

The COG database: an updated version includes eukaryotes.
BMC Bioinform., 2003

2002
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

2001
GeneOrder: comparing the order of genes in small genomes.
Bioinform., 2001