Chuming Chen

According to our database, Chuming Chen authored at least 25 papers between 2004 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

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 Bridge, Alan J. Bridge, Lucila Aimo, Ghislaine Argoud-Puy, Andrea H. Auchincloss, Kristian B. Axelsen, Parit Bansal, Marie-Claude Blatter, Jerven T. Bolleman, Emmanuel Boutet, Lionel Breuza, Blanca Cabrera Gil, Cristina Casals-Casas, Kamal Chikh Echioukh, Béatrice A. Cuche, Anne Estreicher, Maria Livia Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Pascale Gaudet, Vivienne Baillie Gerritsen, Arnaud Gos, Nadine Gruaz-Gumowski, Chantal Hulo, Nevila Hyka-Nouspikel, Florence Jungo, Arnaud Kerhornou, Philippe Le Mercier, Damien Lieberherr, Patrick Masson, Anne Morgat, Venkatesh Muthukrishnan, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Sylvain Poux, Manuela Pruess, Catherine Rivoire, Karin Sonesson, Shyamala Sundaram, Alex Bateman, Maria Jesus Martin, Sandra E. Orchard, Michele Magrane, Shadab Ahmad, Emanuele Alpi, Emily H. Bowler-Barnett, Ramona Britto, Hema Bye-A-Jee, Austra Cukura, Paul Denny, Tunca Dogan, Thankgod Ebenezer, Jun Fan, Penelope Garmiri, Leonardo Jose da Costa Gonzales, Emma Hatton-Ellis, Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Vishal Joshi, Dushyanth Jyothi, Swaathi Kandasamy, Antonia Lock, Aurelien Luciani, Marija Lugaric, Jie Luo, Yvonne Lussi, Alistair MacDougall, Fábio Madeira, Mahdi Mahmoudy, Alok Mishra, Katie Moulang, Andrew Nightingale, Sangya Pundir, Guoying Qi, Shriya Raj, Pedro Raposo, Daniel Rice, Rabie Saidi, Rafael Santos, Elena Speretta, James D. Stephenson, Prabhat Totoo, Edward Turner, Nidhi Tyagi, Preethi Vasudev, Kate Warner, Xavier Watkins, Rossana Zaru, Hermann Zellner, Cathy H. Wu, Cecilia N. Arighi, Leslie Arminski, Chuming Chen, Yongxing Chen, Hongzhan Huang, Kati Laiho, Peter B. McGarvey, Darren A. Natale, Karen Ross, C. R. Vinayaka, Qinghua Wang, Yuqi Wang

Bioinform., January, 2023

2022

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

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, Austra Cukura, Alan W. Sousa da Silva, Paul Denny, Tunca Dogan, Thankgod Ebenezer, Jun Fan, Leyla Jael García Castro, Penelope Garmiri, George E. Georghiou, Leonardo Gonzales, Emma Hatton-Ellis, Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Petteri Jokinen, Vishal Joshi, Dushyanth Jyothi, Antonia Lock, Rodrigo Lopez, Aurelien Luciani, Jie Luo, Yvonne Lussi, Alistair MacDougall, Fábio Madeira, Mahdi Mahmoudy, Manuela Menchi, Alok Mishra, Katie Moulang, Andrew Nightingale, Carla Susana Oliveira, Sangya Pundir, Guoying Qi, Shriya Raj, Daniel Rice, Milagros Rodríguez-López, Rabie Saidi, Joseph Sampson, Tony Sawford, Elena Speretta, Edward Turner, Nidhi Tyagi, Preethi Vasudev, Vladimir Volynkin, Kate Warner, Xavier Watkins, Rossana Zaru, Hermann Zellner, Alan J. Bridge, Sylvain Poux, Nicole Redaschi, Lucila Aimo, Ghislaine Argoud-Puy, Andrea H. Auchincloss, Kristian B. Axelsen, Parit Bansal, Delphine Baratin, Marie-Claude Blatter, Jerven T. Bolleman, Emmanuel Boutet, Lionel Breuza, Cristina Casals-Casas, Edouard De Castro, Kamal Chikh Echioukh, Elisabeth Coudert, Béatrice A. Cuche, Mikael Doche, Dolnide Dornevil, Anne Estreicher, Maria Livia Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Sebastien Gehant, Vivienne Baillie Gerritsen, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Chantal Hulo, Nevila Hyka-Nouspikel, Florence Jungo, Guillaume Keller, Arnaud Kerhornou, Vicente Lara, Philippe Le Mercier, Damien Lieberherr, Thierry Lombardot, Xavier Martin, Patrick Masson, Anne Morgat, Teresa Batista Neto, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Monica Pozzato, Manuela Pruess, Catherine Rivoire, Christian J. A. Sigrist, Karin Sonesson, Andre Stutz, Shyamala Sundaram, Michael Tognolli, Laure Verbregue, Cathy H. Wu, Cecilia N. Arighi, Leslie Arminski, Chuming Chen, Yongxing Chen, John S. Garavelli, Hongzhan Huang, Kati Laiho, Peter B. McGarvey, Darren A. Natale, Karen Ross, C. R. Vinayaka, Qinghua Wang, Yuqi Wang, Lai-Su Yeh, Jian Zhang, Patrick Ruch, Douglas Teodoro

Nucleic Acids Res., 2021

Understanding the factors driving the opioid epidemic using machine learning.

Sachin Gavali, Chuming Chen, Julie Cowart, Xi Peng, Shanshan Ding, Cathy Wu, Tammy Anderson

CoRR, 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, Elisabeth Coudert, Edouard De Castro, Chantal Hulo, Patrick Masson, Ivo Pedruzzi, Catherine Rivoire, Cecilia N. Arighi, Qinghua Wang, Chuming Chen, Hongzhan Huang, John Garavelli, C. R. Vinayaka, Lai-Su Yeh, Darren A. Natale, Kati Laiho, Maria Jesus Martin, Alexandre Renaux, Klemens Pichler

Bioinform., 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

Understanding the factors related to the opioid epidemic using machine learning.

Sachin Gavali, Chuming Chen, Julie Cowart, Xi Peng, Shanshan Ding, Cathy H. Wu, Tammy Anderson

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

2020

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, John Turner, Dusica Vidovic, Jake Jaffe, Michael J. MacCoss, Cathy Wu, Ajay Pillai, Avi Ma'ayan, Stephan C. Schürer, Michal Kouril, Mario Medvedovic, Jarek Meller

Nucleic Acids Res., 2020

2019

PIRSitePredict for protein functional site prediction using position-specific rules.

Chuming Chen, Qinghua Wang, Hongzhan Huang, Cholanayakanahalli R. Vinayaka, John S. Garavelli, Cecilia N. Arighi, Darren A. Natale, Cathy H. Wu

Database J. Biol. Databases Curation, 2019

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

Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

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, Peter B. McGarvey

Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

2017

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, Hongzhan Huang, Jia Ren, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Qinghua Wang, Jian Zhang, Abdelrahman Elsayed, Cathy H. Wu

Nucleic Acids Res., 2017

2016

Computational clustering for viral reference proteomes.

Chuming Chen, Hongzhan Huang, Raja Mazumder, Darren A. Natale, Peter B. McGarvey, Jian Zhang, Shawn W. Polson, Yuqi Wang, Cathy H. Wu

Bioinform., 2016

2014

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

2013

A fast Peptide Match service for UniProt Knowledgebase.

Chuming Chen, Zhiwen Li, Hongzhan Huang, Baris E. Suzek, Cathy H. Wu

Bioinform., 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

Proceedings of the ACM Conference on Bioinformatics, 2013

An Integrated Approach for Interpretation of Clinical NGS Genomic Variant Data.

Erin L. Crowgey, Chuming Chen, Shawn W. Polson, Hongzhan Huang, Cathy H. Wu

Proceedings of the AMIA 2013, 2013

2012

Community annotation and bioinformatics workforce development in concert - Little Skate Genome Annotation Workshops and Jamborees.

Qinghua Wang, 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, Cathy H. Wu

Database J. Biol. Databases Curation, 2012

2010

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

2008

Metrics for Evaluating the Semantic Implications of Changes in Evolving Ontologies.

Chuming Chen, Manton M. Matthews

Proceedings of the 2008 International Conference on Semantic Web & Web Services, 2008

A New Approach to Managing the Evolution of OWL Ontologies.

Chuming Chen, Manton M. Matthews

Proceedings of the 2008 International Conference on Semantic Web & Web Services, 2008

2007

Extending Description Logic for Reasoning about Ontology Evolution.

Chuming Chen, Manton M. Matthews

Proceedings of the 2007 IEEE / WIC / ACM International Conference on Web Intelligence, 2007

2005

AGML Central: web based gel proteomic infrastructure.

Romesh Stanislaus, Chuming Chen, Jennifer Franklin, John M. Arthur, Jonas S. Almeida

Bioinform., 2005

A Dual Authentication Protocol for IEEE 802.11 Wireless LANs.

Xinliang Zheng, Chuming Chen, Chin-Tser Huang, Manton M. Matthews, N. Santhapuri

Proceedings of the 2nd IEEE International Symposium on Wireless Communication Systems, 2005

2004

A Web Interface for Nessus Network Security Scanner.

Chuming Chen, Manton M. Matthews

Proceedings of the International Conference on Internet Computing, 2004