Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint. - Karen Ross; Cecilia N. Arighi; Jia Ren; Hongzhan Huang; Cathy H. Wu (Database J. Biol. Databases Curation, 2013)

Knowledge Representation of Protein PTMs and Complexes in the Protein Ontology: Application to Multi-Faceted Disease Analysis. - Karen Ross; Catalina O. Tudor; Gang Li 021; Ruoyao Ding; Irem Çelen; Julie Cowart; Cecilia N. Arighi; Darren A. Natale; Cathy H. Wu (ICBO, 2014)

Protein Ontology: a controlled structured network of protein entities. - Darren A. Natale; Cecilia N. Arighi; Judith A. Blake; Carol J. Bult; Karen R. Christie; Julie Cowart; Peter D'Eustachio; Alexander D. Diehl; Harold J. Drabkin; Olivia Helfer; Hongzhan Huang; Anna Maria Masci; et al. (Nucleic Acids Res., 2014)

Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system. - Catalina O. Tudor; Karen E. Ross; Gang Li 021; K. Vijay-Shanker; Cathy H. Wu; Cecilia N. Arighi (Database J. Biol. Databases Curation, 2015)

miRTex: A Text Mining System for miRNA-Gene Relation Extraction. - Gang Li 021; Karen E. Ross; Cecilia N. Arighi; Yifan Peng 002; Cathy H. Wu; K. Vijay-Shanker (PLoS Comput. Biol., 2015)

Scalable Text Mining Assisted Curation of PTM Proteoforms in the Protein Ontology. - Karen E. Ross; Darren A. Natale; Cecilia N. Arighi; Sheng-Chih Chen; Hongzhan Huang; Gang Li 021; Jia Ren; Michael Wang; K. Vijay-Shanker; Cathy H. Wu (ICBO/BioCreative, 2016)

miRiaD: A Text Mining Tool for Detecting Associations of microRNAs with Diseases. - Samir Gupta; Karen E. Ross; Catalina O. Tudor; Cathy H. Wu; Carl J. Schmidt; K. Vijay-Shanker (J. Biomed. Semant., 2016)

Identifying Comparative Structures in Biomedical Text. - Samir Gupta; A. S. M. Ashique Mahmood; Karen Ross; Cathy H. Wu; K. Vijay-Shanker (BioNLP, 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; et al. (Nucleic Acids Res., 2017)

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)

PTM Knowledge Networks and LINCS Multi-Omics Data for Kinase Inhibitor Drug-Analytics in Lung Cancer. - Xu Zhang; Karen E. Ross; Tapan K. Maity; Jake Jaffe; Cathy H. Wu; Udayan Guha (BCB, 2018)

DEXTER: Disease-Expression Relation Extraction from Text. - Samir Gupta; Hayley Dingerdissen; Karen E. Ross; Yu Hu 015; Cathy H. Wu; Raja Mazumder; K. Vijay-Shanker (Database J. Biol. Databases Curation, 2018)

iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature. - Jia Ren; Gang Li 021; Karen Ross; Cecilia N. Arighi; Peter B. McGarvey; Shruti Rao; Julie Cowart; Subha Madhavan; K. Vijay-Shanker; Cathy H. Wu (Database J. Biol. Databases Curation, 2018)

iPTMnet: an integrated resource for protein post-translational modification network discovery. - Hongzhan Huang; Cecilia N. Arighi; Karen E. Ross; Jia Ren; Gang Li 021; Sheng-Chih Chen; Qinghua Wang 003; Julie Cowart; K. Vijay-Shanker; Cathy H. Wu (Nucleic Acids Res., 2018)

GlyGen data model and processing workflow. - Robel Y. Kahsay; Jeet Vora; Rahi Navelkar; Reza Mousavi; Brian C. Fochtman; Xavier Holmes; Nagarajan Pattabiraman; René Ranzinger; Rupali Mahadik; Tatiana Williamson; Sujeet Kulkarni; Gaurav Agarwal; et al. (Bioinform., 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 001; John Turner; et al. (Nucleic Acids Res., 2020)

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)

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)

Overview of the COVID-19 text mining tool interactive demonstration track in BioCreative VII. - Andrew Chatr-aryamontri; Lynette Hirschman; Karen E. Ross; Rose Oughtred; Martin Krallinger; Kara Dolinski; Mike Tyers; Tonia Korves; Cecilia N. Arighi (Database J. Biol. Databases Curation, 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)

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)

Network models of protein phosphorylation, acetylation, and ubiquitination connect metabolic and cell signaling pathways in lung cancer. - Karen E. Ross; Guolin Zhang; Cuneyt Akcora; Yu Lin; Bin Fang; John M. Koomen; Eric B. Haura; Mark Grimes (PLoS Comput. Biol., 2023)