A Web Interface for Nessus Network Security Scanner. - Chuming Chen; Manton M. Matthews (International Conference on Internet Computing, 2004)

A Dual Authentication Protocol for IEEE 802.11 Wireless LANs. - Xinliang Zheng; Chuming Chen; Chin-Tser Huang; Manton M. Matthews; N. Santhapuri (ISWCS, 2005)

AGML Central: web based gel proteomic infrastructure. - Romesh Stanislaus; Chuming Chen; Jennifer Franklin; John M. Arthur; Jonas S. Almeida (Bioinform., 2005)

Extending Description Logic for Reasoning about Ontology Evolution. - Chuming Chen; Manton M. Matthews (Web Intelligence, 2007)

A New Approach to Managing the Evolution of OWL Ontologies. - Chuming Chen; Manton M. Matthews (SWWS, 2008)

Metrics for Evaluating the Semantic Implications of Changes in Evolving Ontologies. - Chuming Chen; Manton M. Matthews (SWWS, 2008)

Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data. - Chuming Chen; Peter B. McGarvey; Hongzhan Huang; Cathy H. Wu (Adv. Bioinformatics, 2010)

Community annotation and bioinformatics workforce development in concert - Little Skate Genome Annotation Workshops and Jamborees. - Qinghua Wang 003; Cecilia N. Arighi; Benjamin L. King; Shawn W. Polson; James Vincent; Chuming Chen; Hongzhan Huang; Brewster F. Kingham; Shallee T. Page; Marc Farnum Rendino; William Kelley Thomas; Daniel W. Udwary; et al. (Database J. Biol. Databases Curation, 2012)

An Integrated Approach for Interpretation of Clinical NGS Genomic Variant Data. - Erin L. Crowgey; Chuming Chen; Shawn W. Polson; Hongzhan Huang; Cathy H. Wu (AMIA, 2013)

ngsShoRT: A Software for Pre-processing Illumina Short Read Sequences for De Novo Genome Assembly. - Chuming Chen; Sari S. Khaleel; Hongzhan Huang; Cathy H. Wu (BCB, 2013)

A fast Peptide Match service for UniProt Knowledgebase. - Chuming Chen; Zhiwen Li; Hongzhan Huang; Baris E. Suzek; Cathy H. Wu (Bioinform., 2013)

Software for pre-processing Illumina next-generation sequencing short read sequences. - Chuming Chen; Sari S. Khaleel; Hongzhan Huang; Cathy H. Wu (Source Code Biol. Medicine, 2014)

Computational clustering for viral reference proteomes. - Chuming Chen; Hongzhan Huang; Raja Mazumder; Darren A. Natale; Peter B. McGarvey; Jian Zhang 051; Shawn W. Polson; Yuqi Wang; Cathy H. Wu (Bioinform., 2016)

Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. - Darren A. Natale; Cecilia N. Arighi; Judith A. Blake; Jonathan P. Bona; Chuming Chen; Sheng-Chih Chen; Karen R. Christie; Julie Cowart; Peter D'Eustachio; Alexander D. Diehl; Harold J. Drabkin; William D. Duncan; et al. (Nucleic Acids Res., 2017)

Cloud-based Semantic Integration and Knowledge Discovery Systems in Precision Medicine. - Chuming Chen; Julie E. Cowart; Jia Ren; Sachin Gavali; Yuqi Wang; Hongzhan Huang; Cathy H. Wu; Leslie Arminski; Jian Zhang 051; Peter B. McGarvey (BCB, 2018)

RESTful API for iPTMnet: An Integrated Resource for Protein Post-translational Modification Network Discovery. - Sachin Gavali; Julie Cowart; Chuming Chen; Karen Ross; Cathy H. Wu (BCB, 2018)

PIRSitePredict for protein functional site prediction using position-specific rules. - Chuming Chen; Qinghua Wang 003; Hongzhan Huang; Cholanayakanahalli R. Vinayaka; John S. Garavelli; Cecilia N. Arighi; Darren A. Natale; Cathy H. Wu (Database J. Biol. Databases Curation, 2019)

piNET: a versatile web platform for downstream analysis and visualization of proteomics data. - Behrouz Shamsaei; Szymon Chojnacki; Marcin Pilarczyk; Mehdi Fazel-Najafabadi; Wen Niu; Chuming Chen; Karen Ross; Andrea Matlock; Jeremy Muhlich; Somchai Chutipongtanate; Jie Zheng 001; John Turner; et al. (Nucleic Acids Res., 2020)

Understanding the factors related to the opioid epidemic using machine learning. - Sachin Gavali; Chuming Chen; Julie Cowart; Xi Peng 005; Shanshan Ding; Cathy H. Wu; Tammy Anderson (BIBM, 2021)

COVID-19 Knowledge Graph from semantic integration of biomedical literature and databases. - Chuming Chen; Karen E. Ross; Sachin Gavali; Julie E. Cowart; Cathy H. Wu (Bioinform., 2021)

UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase. - Alistair MacDougall; Vladimir Volynkin; Rabie Saidi; Diego Poggioli; Hermann Zellner; Emma Hatton-Ellis; Vishal Joshi; Claire O'Donovan; Sandra E. Orchard; Andrea H. Auchincloss; Delphine Baratin; Jerven T. Bolleman; et al. (Bioinform., 2021)

Understanding the factors driving the opioid epidemic using machine learning. - Sachin Gavali; Chuming Chen; Julie Cowart; Xi Peng 005; Shanshan Ding; Cathy Wu 001; Tammy Anderson (CoRR, 2021)

UniProt: the universal protein knowledgebase in 2021. - Alex Bateman; Maria Jesus Martin; Sandra E. Orchard; Michele Magrane; Rahat Agivetova; Shadab Ahmad; Emanuele Alpi; Emily H. Bowler-Barnett; Ramona Britto; Borisas Bursteinas; Hema Bye-A-Jee; Ray Coetzee; et al. (Nucleic Acids Res., 2021)

A knowledge graph representation learning approach to predict novel kinase-substrate interactions. - Sachin Gavali; Karen Ross; Chuming Chen; Julie Cowart; Cathy H. Wu (CoRR, 2022)

Annotation of biologically relevant ligands in UniProtKB using ChEBI. - Elisabeth Coudert; Sebastien Gehant; Edouard De Castro; Monica Pozzato; Delphine Baratin; Teresa Batista Neto; Christian J. A. Sigrist; Nicole Redaschi; Alan J. Bridge; Lucila Aimo; Ghislaine Argoud-Puy; Andrea H. Auchincloss; et al. (Bioinform., 2023)