Cathy H. Wu - RankMe

159 papers A* 2A 2B 1C 1Misc 4Journal 107Unranked 37

Year	Rank	Type	Title / Venue / Authors
2023	J	`jnl`	Annotation of biologically relevant ligands in UniProtKB using ChEBI. Bioinform. 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, 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
2023	J	`jnl`	InterPro in 2022. Nucleic Acids Res. Typhaine Paysan-Lafosse, Matthias Blum, Sara Chuguransky, Tiago Grego, Beatriz Lázaro Pinto, Gustavo A. Salazar, Maxwell L. Bileschi, Peer Bork, Alan J. Bridge, Lucy J. Colwell, Julian Gough, Daniel H. Haft, Ivica Letunic, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale, Christine A. Orengo, Arun Prasad Pandurangan, Catherine Rivoire, Christian J. A. Sigrist, Ian Sillitoe, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Alex Bateman
2022	J	`jnl`	A knowledge graph representation learning approach to predict novel kinase-substrate interactions. CoRR Sachin Gavali, Karen Ross, Chuming Chen, Julie Cowart, Cathy H. Wu
2021	J	`jnl`	COVID-19 Knowledge Graph from semantic integration of biomedical literature and databases. Bioinform. Chuming Chen, Karen E. Ross, Sachin Gavali, Julie E. Cowart, Cathy H. Wu
2021	J	`jnl`	The InterPro protein families and domains database: 20 years on. Nucleic Acids Res. Matthias Blum, Hsin-Yu Chang, Sara Chuguransky, Tiago Grego, Swaathi Kandasamy, Alex L. Mitchell, Gift Nuka, Typhaine Paysan-Lafosse, Matloob Qureshi, Shriya Raj, Lorna J. Richardson, Gustavo A. Salazar, Lowri Williams, Peer Bork, Alan J. Bridge, Julian Gough, Daniel H. Haft, Ivica Letunic, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale, Marco Necci, Christine A. Orengo, Arun Prasad Pandurangan, Catherine Rivoire, Christian J. A. Sigrist, Ian Sillitoe, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Alex Bateman, Robert D. Finn
2021	—	`conf`	Understanding the factors related to the opioid epidemic using machine learning. BIBM Sachin Gavali, Chuming Chen, Julie Cowart, Xi Peng, Shanshan Ding, Cathy H. Wu, Tammy Anderson
2021	J	`jnl`	UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res. 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
2019	J	`jnl`	PIRSitePredict for protein functional site prediction using position-specific rules. Database J. Biol. Databases Curation Chuming Chen, Qinghua Wang, Hongzhan Huang, Cholanayakanahalli R. Vinayaka, John S. Garavelli, Cecilia N. Arighi, Darren A. Natale, Cathy H. Wu
2018	J	`jnl`	Automatic gene annotation using GO terms from cellular component domain. BMC Medical Informatics Decis. Mak. Ruoyao Ding, Yingying Qu, Cathy H. Wu, K. Vijay-Shanker
2018	—	`conf`	Cloud-based Semantic Integration and Knowledge Discovery Systems in Precision Medicine. BCB Chuming Chen, Julie E. Cowart, Jia Ren, Sachin Gavali, Yuqi Wang, Hongzhan Huang, Cathy H. Wu, Leslie Arminski, Jian Zhang, Peter B. McGarvey
2018	J	`jnl`	Completing sparse and disconnected protein-protein network by deep learning. BMC Bioinform. Lei Huang, Li Liao, Cathy H. Wu
2018	J	`jnl`	DEXTER: Disease-Expression Relation Extraction from Text. Database J. Biol. Databases Curation Samir Gupta, Hayley Dingerdissen, Karen E. Ross, Yu Hu, Cathy H. Wu, Raja Mazumder, K. Vijay-Shanker
2018	—	`conf`	PENNER: Pattern-enhanced Nested Named Entity Recognition in Biomedical Literature. BIBM Xuan Wang, Yu Zhang, Qi Li, Cathy H. Wu, Jiawei Han
2018	—	`conf`	PTM Knowledge Networks and LINCS Multi-Omics Data for Kinase Inhibitor Drug-Analytics in Lung Cancer. BCB Xu Zhang, Karen E. Ross, Tapan K. Maity, Jake Jaffe, Cathy H. Wu, Udayan Guha
2018	—	`conf`	Pattern Discovery for Wide-Window Open Information Extraction in Biomedical Literature. BIBM Qi Li, Xuan Wang, Yu Zhang, Fei Ling, Cathy H. Wu, Jiawei Han
2018	—	`ed.`	Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2018, Washington, DC, USA, August 29 - September 01, 2018 BCB Amarda Shehu, Cathy H. Wu, Christina Boucher, Jing Li, Hongfang Liu, Mihai Pop
2018	—	`conf`	Protein Complex Mention Recognition with Web-Based Knowledge Learning. SETE@ICWL Ruoyao Ding, Xiaoyi Pan, Yingying Qu, Cathy H. Wu, K. Vijay-Shanker
2018	—	`conf`	RESTful API for iPTMnet: An Integrated Resource for Protein Post-translational Modification Network Discovery. BCB Sachin Gavali, Julie Cowart, Chuming Chen, Karen Ross, Cathy H. Wu
2018	J	`jnl`	iPTMnet: an integrated resource for protein post-translational modification network discovery. Nucleic Acids Res. Hongzhan Huang, Cecilia N. Arighi, Karen E. Ross, Jia Ren, Gang Li, Sheng-Chih Chen, Qinghua Wang, Julie Cowart, K. Vijay-Shanker, Cathy H. Wu
2018	J	`jnl`	iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature. Database J. Biol. Databases Curation Jia Ren, Gang Li, Karen Ross, Cecilia N. Arighi, Peter B. McGarvey, Shruti Rao, Julie Cowart, Subha Madhavan, K. Vijay-Shanker, Cathy H. Wu
2017	—	`conf`	Identifying Comparative Structures in Biomedical Text. BioNLP Samir Gupta, A. S. M. Ashique Mahmood, Karen Ross, Cathy H. Wu, K. Vijay-Shanker
2017	J	`jnl`	InterPro in 2017 - beyond protein family and domain annotations. Nucleic Acids Res. Robert D. Finn, Teresa K. Attwood, Patricia C. Babbitt, Alex Bateman, Peer Bork, Alan J. Bridge, Hsin-Yu Chang, Zsuzsanna Dosztányi, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft, Gemma L. Holliday, Hongzhan Huang, Xiaosong Huang, Ivica Letunic, Rodrigo Lopez, Shennan Lu, Aron Marchler-Bauer, Huaiyu Mi, Jaina Mistry, Darren A. Natale, Marco Necci, Gift Nuka, Christine A. Orengo, Young Mi Park, Sebastien Pesseat, Damiano Piovesan, Simon C. Potter, Neil D. Rawlings, Nicole Redaschi, Lorna J. Richardson, Catherine Rivoire, Amaia Sangrador-Vegas, Christian J. A. Sigrist, Ian Sillitoe, Ben Smithers, Silvano Squizzato, Granger G. Sutton, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Ioannis Xenarios, Lai-Su L. Yeh, Siew-Yit Yong, Alex L. Mitchell
2017	—	`conf`	Noise Reduction Methods for Distantly Supervised Biomedical Relation Extraction. BioNLP Gang Li, Cathy H. Wu, K. Vijay-Shanker
2017	J	`jnl`	Predicting nsSNPs that Disrupt Protein-Protein Interactions Using Docking. IEEE ACM Trans. Comput. Biol. Bioinform. Norman Goodacre, Nathan Edwards, Mark Danielsen, Peter Uetz, Cathy H. Wu
2017	J	`jnl`	Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. Nucleic Acids Res. 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
2017	—	`conf`	UD_GU_BioTM at TREC 2017: Precision Medicine Track. TREC A. S. M. Ashique Mahmood, Gang Li, Shruti Rao, Peter B. McGarvey, Cathy H. Wu, Subha Madhavan, K. Vijay-Shanker
2017	J	`jnl`	eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality. Database J. Biol. Databases Curation Ruoyao Ding, Emmanuel Boutet, Damien Lieberherr, Michel Schneider, Michael Tognolli, Cathy H. Wu, K. Vijay-Shanker, Cecilia N. Arighi
2016	J	`jnl`	BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph. Database J. Biol. Databases Curation Yifan Peng, Cecilia N. Arighi, Cathy H. Wu, K. Vijay-Shanker
2016	J	`jnl`	BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database J. Biol. Databases Curation Sun Kim, Rezarta Islamaj Dogan, Andrew Chatr-aryamontri, Christie S. Chang, Rose Oughtred, Jennifer M. Rust, Riza Batista-Navarro, Jacob Carter, Sophia Ananiadou, Sérgio Matos, André Santos, David Campos, José Luís Oliveira, Onkar Singh, Jitendra Jonnagaddala, Hong-Jie Dai, Emily Chia-Yu Su, Yung-Chun Chang, Yu-Chen Su, Chun-Han Chu, Chien Chin Chen, Wen-Lian Hsu, Yifan Peng, Cecilia N. Arighi, Cathy H. Wu, K. Vijay-Shanker, Ferhat Aydin, Zehra Melce Hüsünbeyi, Arzucan Özgür, Soo-Yong Shin, Dongseop Kwon, Kara Dolinski, Mike Tyers, W. John Wilbur, Donald C. Comeau
2016	J	`jnl`	Computational clustering for viral reference proteomes. Bioinform. Chuming Chen, Hongzhan Huang, Raja Mazumder, Darren A. Natale, Peter B. McGarvey, Jian Zhang, Shawn W. Polson, Yuqi Wang, Cathy H. Wu
2016	J	`jnl`	Enhancing interacting residue prediction with integrated contact matrix prediction in protein-protein interaction. EURASIP J. Bioinform. Syst. Biol. Tianchuan Du, Li Liao, Cathy H. Wu
2016	J	`jnl`	Inference of protein-protein interaction networks from multiple heterogeneous data. EURASIP J. Bioinform. Syst. Biol. Lei Huang, Li Liao, Cathy H. Wu
2016	J	`jnl`	Overview of the interactive task in BioCreative V. Database J. Biol. Databases Curation Qinghua Wang, Shabbir Syed-Abdul, Lara Almeida, Sophia Ananiadou, Yalbi I. Balderas-Martínez, Riza Batista-Navarro, David Campos, Lucy Chilton, Hui-Jou Chou, Gabriela Contreras, Laurel Cooper, Hong-Jie Dai, Barbra Ferrell, Juliane Fluck, Socorro Gama-Castro, Nancy George, Georgios V. Gkoutos, Afroza Khanam Irin, Lars Juhl Jensen, Silvia Jimenez, Toni Rose Jue, Ingrid M. Keseler, Sumit Madan, Sérgio Matos, Peter McQuilton, Marija Milacic, Matthew E. Mort, Jeyakumar Natarajan, Evangelos Pafilis, Emiliano Pereira, Shruti Rao, Fabio Rinaldi, Karen Rothfels, David Salgado, Raquel M. Silva, Onkar Singh, Raymund Stefancsik, Chu-Hsien Su, Suresh Subramani, Hamsa D. Tadepally, Loukia Tsaprouni, Nicole A. Vasilevsky, Xiaodong Wang, Andrew Chatr-aryamontri, Stanley J. F. Laulederkind, Sherri Matis-Mitchell, Johanna R. McEntyre, Sandra E. Orchard, Sangya Pundir, Raul Rodriguez-Esteban, Kimberly Van Auken, Zhiyong Lu, Mary L. Schaeffer, Cathy H. Wu, Lynette Hirschman, Cecilia N. Arighi
2016	J	`jnl`	Protein-protein interaction prediction based on multiple kernels and partial network with linear programming. BMC Syst. Biol. Lei Huang, Li Liao, Cathy H. Wu
2016	—	`conf`	Scalable Text Mining Assisted Curation of PTM Proteoforms in the Protein Ontology. ICBO/BioCreative Karen E. Ross, Darren A. Natale, Cecilia N. Arighi, Sheng-Chih Chen, Hongzhan Huang, Gang Li, Jia Ren, Michael Wang, K. Vijay-Shanker, Cathy H. Wu
2016	J	`jnl`	miRiaD: A Text Mining Tool for Detecting Associations of microRNAs with Diseases. J. Biomed. Semant. Samir Gupta, Karen E. Ross, Catalina O. Tudor, Cathy H. Wu, Carl J. Schmidt, K. Vijay-Shanker
2015	—	`conf`	An extended dependency graph for relation extraction in biomedical texts. BioNLP@IJCNLP Yifan Peng, Samir Gupta, Cathy H. Wu, K. Vijay-Shanker
2015	J	`jnl`	Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system. Database J. Biol. Databases Curation Catalina O. Tudor, Karen E. Ross, Gang Li, K. Vijay-Shanker, Cathy H. Wu, Cecilia N. Arighi
2015	J	`jnl`	Evolutionary Model Selection and Parameter Estimation for Protein-Protein Interaction Network Based on Differential Evolution Algorithm. IEEE ACM Trans. Comput. Biol. Bioinform. Lei Huang, Li Liao, Cathy H. Wu
2015	—	`conf`	Inference of protein-protein interaction networks from multiple heterogeneous data. BCB Lei Huang, Li Liao, Cathy H. Wu
2015	—	`conf`	Protein-protein interaction network inference from multiple kernels with optimization based on random walk by linear programming. BIBM Lei Huang, Li Liao, Cathy H. Wu
2015	J	`jnl`	RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information. IEEE ACM Trans. Comput. Biol. Bioinform. Manabu Torii, Cecilia N. Arighi, Gang Li, Qinghua Wang, Cathy H. Wu, K. Vijay-Shanker
2015	J	`jnl`	The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. Alex L. Mitchell, Hsin-Yu Chang, Louise C. Daugherty, Matthew Fraser, Sarah Hunter, Rodrigo Lopez, Craig McAnulla, Conor McMenamin, Gift Nuka, Sebastien Pesseat, Amaia Sangrador-Vegas, Maxim Scheremetjew, Claudia Rato, Siew-Yit Yong, Alex Bateman, Marco Punta, Teresa K. Attwood, Christian J. A. Sigrist, Nicole Redaschi, Catherine Rivoire, Ioannis Xenarios, Daniel Kahn, Dominique Guyot, Peer Bork, Ivica Letunic, Julian Gough, Matt E. Oates, Daniel H. Haft, Hongzhan Huang, Darren A. Natale, Cathy H. Wu, Christine A. Orengo, Ian Sillitoe, Huaiyu Mi, Paul D. Thomas, Robert D. Finn
2015	J	`jnl`	UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. Bioinform. Baris E. Suzek, Yuqi Wang, Hongzhan Huang, Peter B. McGarvey, Cathy H. Wu
2015	J	`jnl`	miRTex: A Text Mining System for miRNA-Gene Relation Extraction. PLoS Comput. Biol. Gang Li, Karen E. Ross, Cecilia N. Arighi, Yifan Peng, Cathy H. Wu, K. Vijay-Shanker
2014	J	`jnl`	A Generalizable NLP Framework for Fast Development of Pattern-based Biomedical Relation Extraction Systems. BMC Bioinform. Yifan Peng, Manabu Torii, Cathy H. Wu, K. Vijay-Shanker
2014	J	`jnl`	BioC interoperability track overview. Database J. Biol. Databases Curation Donald C. Comeau, Riza Theresa Batista-Navarro, Hong-Jie Dai, Rezarta Islamaj Dogan, Antonio Jimeno-Yepes, Ritu Khare, Zhiyong Lu, Hernani Marques, Carolyn J. Mattingly, Mariana L. Neves, Yifan Peng, Rafal Rak, Fabio Rinaldi, Richard Tzong-Han Tsai, Karin Verspoor, Thomas C. Wiegers, Cathy H. Wu, W. John Wilbur
2014	J	`jnl`	BioCreative-IV virtual issue. Database J. Biol. Databases Curation Cecilia N. Arighi, Cathy H. Wu, Kevin Bretonnel Cohen, Lynette Hirschman, Martin Krallinger, Alfonso Valencia, Zhiyong Lu, W. John Wilbur, Thomas C. Wiegers
2014	—	`conf`	DDI2PPI: an integrated web server for protein-protein interaction and residue contact matrix predictions. BCB Tianchuan Du, Alvaro J. González, Qinghua Wang, Hongzhan Huang, Li Liao, Cathy H. Wu
2014	—	`conf`	Docking features for predicting binding loss due to protein mutation. BCB Norman Goodacre, Nathan Edwards, Mark Danielsen, Peter Uetz, Cathy H. Wu
2014	—	`conf`	Knowledge Representation of Protein PTMs and Complexes in the Protein Ontology: Application to Multi-Faceted Disease Analysis. ICBO Karen Ross, Catalina O. Tudor, Gang Li, Ruoyao Ding, Irem Çelen, Julie Cowart, Cecilia N. Arighi, Darren A. Natale, Cathy H. Wu
2014	J	`jnl`	Protein Ontology: a controlled structured network of protein entities. Nucleic Acids Res. 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, Jia Ren, Natalia V. Roberts, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Meher Shruti Yerramalla, Jian Zhang, Aisha AlJanahi, Irem Çelen, Cynthia Gan, Mengxi Lv, Emily Schuster-Lezell, Cathy H. Wu
2014	J	`jnl`	RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information. Database J. Biol. Databases Curation Manabu Torii, Gang Li, Zhiwen Li, Rose Oughtred, Francesca Diella, Irem Çelen, Cecilia N. Arighi, Hongzhan Huang, K. Vijay-Shanker, Cathy H. Wu
2014	J	`jnl`	Software for pre-processing Illumina next-generation sequencing short read sequences. Source Code Biol. Medicine Chuming Chen, Sari S. Khaleel, Hongzhan Huang, Cathy H. Wu
2014	J	`jnl`	iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system. Database J. Biol. Databases Curation Yifan Peng, Catalina O. Tudor, Manabu Torii, Cathy H. Wu, K. Vijay-Shanker
2013	J	`jnl`	A fast Peptide Match service for UniProt Knowledgebase. Bioinform. Chuming Chen, Zhiwen Li, Hongzhan Huang, Baris E. Suzek, Cathy H. Wu
2013	J	`jnl`	A framework for biomedical figure segmentation towards image-based document retrieval. BMC Syst. Biol. Luis D. Lopez, Jingyi Yu, Cecilia N. Arighi, Catalina O. Tudor, Manabu Torii, Hongzhan Huang, K. Vijay-Shanker, Cathy H. Wu
2013	—	`conf`	An Image-Text Approach for Extracting Experimental Evidence of Protein-Protein Interactions in the Biomedical Literature. BCB Luis D. Lopez, Jingyi Yu, Cecilia N. Arighi, Manabu Torii, K. Vijay-Shanker, Hongzhan Huang, Cathy H. Wu
2013	Misc	`conf`	An Integrated Approach for Interpretation of Clinical NGS Genomic Variant Data. AMIA Erin L. Crowgey, Chuming Chen, Shawn W. Polson, Hongzhan Huang, Cathy H. Wu
2013	J	`jnl`	An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database J. Biol. Databases Curation Cecilia N. Arighi, Ben Carterette, K. Bretonnel Cohen, Martin Krallinger, W. John Wilbur, Petra Fey, Robert J. Dodson, Laurel Cooper, Ceri E. Van Slyke, Wasila M. Dahdul, Paula M. Mabee, Donghui Li, Bethany R. Harris, Marc Gillespie, Silvia Jimenez, Phoebe M. Roberts, Lisa Matthews, Kevin G. Becker, Harold J. Drabkin, Susan M. Bello, Luana Licata, Andrew Chatr-aryamontri, Mary L. Schaeffer, Julie Park, Melissa A. Haendel, Kimberly Van Auken, Yuling Li, Juancarlos Chan, Hans-Michael Müller, Hong Cui, James P. Balhoff, Chi-Yang Wu, Zhiyong Lu, Chih-Hsuan Wei, Catalina O. Tudor, Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan, Juan Miguel Cejuela, Pratibha Dubey, Cathy H. Wu
2013	J	`jnl`	BioC: a minimalist approach to interoperability for biomedical text processing. Database J. Biol. Databases Curation Donald C. Comeau, Rezarta Islamaj Dogan, Paolo Ciccarese, Kevin Bretonnel Cohen, Martin Krallinger, Florian Leitner, Zhiyong Lu, Yifan Peng, Fabio Rinaldi, Manabu Torii, Alfonso Valencia, Karin Verspoor, Thomas C. Wiegers, Cathy H. Wu, W. John Wilbur
2013	J	`jnl`	Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint. Database J. Biol. Databases Curation Karen Ross, Cecilia N. Arighi, Jia Ren, Hongzhan Huang, Cathy H. Wu
2013	J	`jnl`	Prediction of contact matrix for protein-protein interaction. Bioinform. Alvaro J. González, Li Liao, Cathy H. Wu
2013	—	`conf`	Text Mining of Protein Phosphorylation Information Using a Generalizable Rule-Based Approach. BCB Manabu Torii, Cecilia N. Arighi, Qinghua Wang, Cathy H. Wu, K. Vijay-Shanker
2013	J	`jnl`	Transcription factors and genetic circuits orchestrating the complex, multilayered response of Clostridium acetobutylicum to butanol and butyrate stress. BMC Syst. Biol. Qinghua Wang, Keerthi Venkataramanan, Hongzhan Huang, Eleftherios T. Papoutsakis, Cathy H. Wu
2013	—	`conf`	ngsShoRT: A Software for Pre-processing Illumina Short Read Sequences for De Novo Genome Assembly. BCB Chuming Chen, Sari S. Khaleel, Hongzhan Huang, Cathy H. Wu
2012	J	`jnl`	BioCreative-2012 Virtual Issue. Database J. Biol. Databases Curation Cathy H. Wu, Cecilia N. Arighi, Kevin Bretonnel Cohen, Lynette Hirschman, Martin Krallinger, Zhiyong Lu, Carolyn J. Mattingly, Alfonso Valencia, Thomas C. Wiegers, W. John Wilbur
2012	—	`conf`	Building a classifier for identifying sentences pertaining to disease-drug relationships in tardive dyskinesia. BIBM Xia Bi, Hongzhan Huang, Sherri Matis-Mitchell, Peter B. McGarvey, Manabu Torii, Hagit Shatkay, Cathy H. Wu
2012	J	`jnl`	Community annotation and bioinformatics workforce development in concert - Little Skate Genome Annotation Workshops and Jamborees. Database J. Biol. Databases Curation 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
2012	J	`jnl`	InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. Sarah Hunter, Philip Jones, Alex L. Mitchell, Rolf Apweiler, Teresa K. Attwood, Alex Bateman, Thomas Bernard, David Binns, Peer Bork, Sarah W. Burge, Edouard De Castro, Penny C. Coggill, Matthew Corbett, Ujjwal Das, Louise C. Daugherty, Lauranne Duquenne, Robert D. Finn, Matthew Fraser, Julian Gough, Daniel H. Haft, Nicolas Hulo, Daniel Kahn, Elizabeth Kelly, Ivica Letunic, David Lonsdale, Rodrigo Lopez, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Conor McMenamin, Huaiyu Mi, Prudence Mutowo-Meullenet, Nicola J. Mulder, Darren A. Natale, Christine A. Orengo, Sebastien Pesseat, Marco Punta, Antony F. Quinn, Catherine Rivoire, Amaia Sangrador-Vegas, Jeremy D. Selengut, Christian J. A. Sigrist, Maxim Scheremetjew, John G. Tate, Manjulapramila Thimmajanarthanan, Paul D. Thomas, Cathy H. Wu, Corin Yeats, Siew-Yit Yong
2012	—	`conf`	Pathway curation: Application of text-mining tools eGIFT and RLIMS-P. BIBM Workshops Carl J. Schmidt, Liang Sun, Cecilia N. Arighi, Keith Decker, K. Vijay-Shanker, Manabu Torii, Catalina O. Tudor, Cathy H. Wu, Peter D'Eustachio
2012	J	`jnl`	Predicting Ligand Binding Residues and Functional Sites Using Multipositional Correlations with Graph Theoretic Clustering and Kernel CCA. IEEE ACM Trans. Comput. Biol. Bioinform. Alvaro J. González, Li Liao, Cathy H. Wu
2012	J	`jnl`	Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference. Database J. Biol. Databases Curation Pascale Gaudet, Cecilia N. Arighi, Frederic B. Bastian, Alex Bateman, Judith A. Blake, J. Michael Cherry, Peter D'Eustachio, Robert D. Finn, Michelle G. Giglio, Lynette Hirschman, Renate Kania, William Klimke, Maria Jesus Martin, Ilene Karsch-Mizrachi, Monica C. Munoz-Torres, Darren A. Natale, Claire O'Donovan, B. F. Francis Ouellette, Kim D. Pruitt, Marc Robinson-Rechavi, Susanna-Assunta Sansone, Paul N. Schofield, Granger G. Sutton, Kimberly Van Auken, Sona Vasudevan, Cathy H. Wu, Jasmine Young, Raja Mazumder
2012	—	`conf`	Robust segmentation of biomedical figures for image-based document retrieval. BIBM Luis D. Lopez, Jingyi Yu, Catalina O. Tudor, Cecilia N. Arighi, Hongzhan Huang, K. Vijay-Shanker, Cathy H. Wu
2012	J	`jnl`	Text mining for the biocuration workflow. Database J. Biol. Databases Curation Lynette Hirschman, Gully A. P. C. Burns, Martin Krallinger, Cecilia N. Arighi, K. Bretonnel Cohen, Alfonso Valencia, Cathy H. Wu, Andrew Chatr-aryamontri, Karen G. Dowell, Eva Huala, Anália Lourenço, Robert S. Nash, Anne-Lise Veuthey, Thomas C. Wiegers, Andrew G. Winter
2012	J	`jnl`	The eFIP system for text mining of protein interaction networks of phosphorylated proteins. Database J. Biol. Databases Curation Catalina O. Tudor, Cecilia N. Arighi, Qinghua Wang, Cathy H. Wu, K. Vijay-Shanker
2012	—	`conf`	iSimp: A sentence simplification system for biomedicail text. BIBM Yifan Peng, Catalina O. Tudor, Manabu Torii, Cathy H. Wu, K. Vijay-Shanker
2011	J	`jnl`	A comprehensive protein-centric ID mapping service for molecular data integration. Bioinform. Hongzhan Huang, Peter B. McGarvey, Baris E. Suzek, Raja Mazumder, Jian Zhang, Yongxing Chen, Cathy H. Wu
2011	—	`conf`	An Automatic System for Extracting Figures and Captions in Biomedical PDF Documents. BIBM Luis D. Lopez, Jingyi Yu, Cecilia N. Arighi, Hongzhan Huang, Hagit Shatkay, Cathy H. Wu
2011	J	`jnl`	BioCreative III interactive task: an overview. BMC Bioinform. Cecilia N. Arighi, Phoebe M. Roberts, Shashank Agarwal, Sanmitra Bhattacharya, Gianni Cesareni, Andrew Chatr-aryamontri, Simon Clematide, Pascale Gaudet, Michelle G. Giglio, Ian Harrow, Eva Huala, Martin Krallinger, Ulf Leser, Donghui Li, Feifan Liu, Zhiyong Lu, Lois J. Maltais, Naoaki Okazaki, Livia Perfetto, Fabio Rinaldi, Rune Sætre, David Salgado, Padmini Srinivasan, Philippe E. Thomas, Luca Toldo, Lynette Hirschman, Cathy H. Wu
2011	J	`jnl`	Overview of the BioCreative III Workshop. BMC Bioinform. Cecilia N. Arighi, Zhiyong Lu, Martin Krallinger, Kevin Bretonnel Cohen, W. John Wilbur, Alfonso Valencia, Lynette Hirschman, Cathy H. Wu
2011	—	`conf`	Protein-Centric Connection of Biomedical Knowledge: Protein Ontology (PRO) Research and Annotation Tools. ICBO Cecilia N. Arighi, Darren A. Natale, Judith A. Blake, Carol J. Bult, Michael Caudy, Alexander D. Diehl, Harold J. Drabkin, Peter D'Eustachio, Alexei V. Evsikov, Hongzhan Huang, Natalia V. Roberts, Alan Ruttenberg, Barry Smith, Jian Zhang, Cathy H. Wu
2011	J	`jnl`	The Protein Ontology: a structured representation of protein forms and complexes. Nucleic Acids Res. Darren A. Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Carol J. Bult, Michael Caudy, Harold J. Drabkin, Peter D'Eustachio, Alexei V. Evsikov, Hongzhan Huang, Jules Nchoutmboube, Natalia V. Roberts, Barry Smith, Jian Zhang, Cathy H. Wu
2011	J	`jnl`	The Representation of Protein Complexes in the Protein Ontology (PRO). BMC Bioinform. Carol J. Bult, Harold J. Drabkin, Alexei V. Evsikov, Darren A. Natale, Cecilia N. Arighi, Natalia V. Roberts, Alan Ruttenberg, Peter D'Eustachio, Barry Smith, Judith A. Blake, Cathy H. Wu
2010	J	`jnl`	Document classification for mining host pathogen protein-protein interactions. Artif. Intell. Medicine Lanlan Yin, Guixian Xu, Manabu Torii, Zhendong Niu, José M. Maisog, Cathy H. Wu, Zhang-Zhi Hu, Hongfang Liu
2010	—	`conf`	Predicting Functional Sites in Biological Sequences Using Canonical Correlation Analysis. BIOCOMP Alvaro J. González, Li Liao, Cathy H. Wu
2010	—	`conf`	Predicting ligand binding residues using multi-positional correlations and kernel canonical correlation analysis. BIBM Alvaro J. González, Li Liao, Cathy H. Wu
2010	C	`conf`	Prediction of Catalytic Residues in Proteins Using a Consensus of Prediction (CoP) Approach. BIBE Natalia V. Petrova, Cathy H. Wu
2010	J	`jnl`	Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data. Adv. Bioinformatics Chuming Chen, Peter B. McGarvey, Hongzhan Huang, Cathy H. Wu
2009	—	`ch.`	Information Extraction of Protein Phosphorylation from Biomedical Literature. Information Retrieval in Biomedicine Meenakshi Narayanaswamy, K. E. Ravikumar, Zhang-Zhi Hu, K. Vijay-Shanker, Cathy H. Wu
2009	J	`jnl`	InterPro: the integrative protein signature database. Nucleic Acids Res. Sarah Hunter, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Peer Bork, Ujjwal Das, Louise C. Daugherty, Lauranne Duquenne, Robert D. Finn, Julian Gough, Daniel H. Haft, Nicolas Hulo, Daniel Kahn, Elizabeth Kelly, Aurélie Laugraud, Ivica Letunic, David Lonsdale, Rodrigo Lopez, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Jaina Mistry, Alex L. Mitchell, Nicola J. Mulder, Darren A. Natale, Christine A. Orengo, Antony F. Quinn, Jeremy D. Selengut, Christian J. A. Sigrist, Manjula Thimma, Paul D. Thomas, Franck Valentin, Derek Wilson, Cathy H. Wu, Corin Yeats
2009	J	`jnl`	Research Paper: BioTagger-GM: A Gene/Protein Name Recognition System. J. Am. Medical Informatics Assoc. Manabu Torii, Zhang-Zhi Hu, Cathy H. Wu, Hongfang Liu
2009	J	`jnl`	TGF-beta signaling proteins and the Protein Ontology. BMC Bioinform. Cecilia N. Arighi, Hongfang Liu, Darren A. Natale, Winona C. Barker, Harold J. Drabkin, Judith A. Blake, Barry Smith, Cathy H. Wu
2008	J	`jnl`	An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data. Nucleic Acids Res. C. Zhang, Oswald Crasta, Stephen A. Cammer, Rebecca Will, Ron Kenyon, Daniel E. Sullivan, Q. Yu, W. Sun, R. Jha, D. Liu, Tian Xue, Y. Zhang, M. Moore, Peter B. McGarvey, Hongzhan Huang, Yongxing Chen, J. Zhang, Raja Mazumder, Cathy H. Wu, Bruno W. S. Sobral
2008	—	`ch.`	Bioinformatic Databases. Wiley Encyclopedia of Computer Science and Engineering Katherine G. Herbert, Junilda Spirollari, Jason Tsong-Li Wang, William H. Piel, John D. Westbrook, Winona C. Barker, Zhang-Zhi Hu, Cathy H. Wu
2008	—	`conf`	Document Classification for Mining Host Pathogen Protein-Protein Interactions. BIBM Guixian Xu, Lanlan Yin, Manabu Torii, Zhendong Niu, Cathy H. Wu, Zhang-Zhi Hu, Hongfang Liu
2008	—	`conf`	Functional Annotation of Protein Isoforms and Modified Forms. BIOCOMP Harold J. Drabkin, Cecilia N. Arighi, Cathy H. Wu, Judith A. Blake
2008	—	`conf`	iProLINK: A Framework for Linking Text Mining with Ontology and Systems Biology. BIBM Zhang-Zhi Hu, K. Bretonnel Cohen, Lynette Hirschman, Alfonso Valencia, Hongfang Liu, Michelle G. Giglio, Cathy H. Wu
2007	J	`jnl`	A comparison study on algorithms of detecting long forms for short forms in biomedical text. BMC Bioinform. Manabu Torii, Zhang-Zhi Hu, Min Song, Cathy H. Wu, Hongfang Liu
2007	J	`jnl`	Dependence network modeling for biomarker identification. Bioinform. Peng Qiu, Z. Jane Wang, K. J. Ray Liu, Zhang-Zhi Hu, Cathy H. Wu
2007	J	`jnl`	Framework for a Protein Ontology. BMC Bioinform. Darren A. Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Ti-Cheng Chang, Zhang-Zhi Hu, Hongfang Liu, Barry Smith, Cathy H. Wu
2007	—	`conf`	Mapping Gene/Protein Names in Free Text to Biomedical Databases. ICDM Workshops Hongfang Liu, Manabu Torii, Zhang-Zhi Hu, Cathy H. Wu
2007	J	`jnl`	New developments in the InterPro database. Nucleic Acids Res. Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Peer Bork, Virginie Buillard, Lorenzo Cerutti, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Louise C. Daugherty, Mark Dibley, Robert D. Finn, Wolfgang Fleischmann, Julian Gough, Daniel H. Haft, Nicolas Hulo, Sarah Hunter, Daniel Kahn, Alexander Kanapin, Anish Kejariwal, Alberto Labarga, Petra S. Langendijk-Genevaux, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Jaina Mistry, Alex L. Mitchell, Anastasia N. Nikolskaya, Sandra E. Orchard, Christine A. Orengo, Robert Petryszak, Jeremy D. Selengut, Christian J. A. Sigrist, Paul D. Thomas, Franck Valentin, Derek Wilson, Cathy H. Wu, Corin Yeats
2007	J	`jnl`	UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinform. Baris E. Suzek, Hongzhan Huang, Peter B. McGarvey, Raja Mazumder, Cathy H. Wu
2006	J	`jnl`	An online literature mining tool for protein phosphorylation. Bioinform. X. Yuan, Zhang-Zhi Hu, H. T. Wu, Manabu Torii, Meenakshi Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker, Cathy H. Wu
2006	J	`jnl`	BioThesaurus: a web-based thesaurus of protein and gene names. Bioinform. Hongfang Liu, Zhang-Zhi Hu, Jian Zhang, Cathy H. Wu
2006	J	`jnl`	Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties. BMC Bioinform. Natalia V. Petrova, Cathy H. Wu
2006	J	`jnl`	Research Paper: Quantitative Assessment of Dictionary-based Protein Named Entity Tagging. J. Am. Medical Informatics Assoc. Hongfang Liu, Zhang-Zhi Hu, Manabu Torii, Cathy H. Wu, Carol Friedman
2006	J	`jnl`	Substring selection for biomedical document classification. Bioinform. Bo Han, Zoran Obradovic, Zhang-Zhi Hu, Cathy H. Wu, Slobodan Vucetic
2006	J	`jnl`	The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res. Cathy H. Wu, Rolf Apweiler, Amos Bairoch, Darren A. Natale, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, Maria Jesus Martin, Raja Mazumder, Claire O'Donovan, Nicole Redaschi, Baris E. Suzek
2005	J	`jnl`	Computational identification of strain-, species- and genus-specific proteins. BMC Bioinform. Raja Mazumder, Darren A. Natale, Sudhir Murthy, Rathi Thiagarajan, Cathy H. Wu
2005	J	`jnl`	DynGO: a tool for visualizing and mining of Gene Ontology and its associations. BMC Bioinform. Hongfang Liu, Zhang-Zhi Hu, Cathy H. Wu
2005	A*	`conf`	Dynamically Generating a Protein Entity Dictionary Using Online Resources. ACL Hongfang Liu, Zhang-Zhi Hu, Cathy H. Wu
2005	J	`jnl`	InterPro, progress and status in 2005. Nucleic Acids Res. Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Paul Bradley, Peer Bork, Phillip Bucher, Lorenzo Cerutti, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Wolfgang Fleischmann, Julian Gough, Daniel H. Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Jennifer McDowall, Alex L. Mitchell, Anastasia N. Nikolskaya, Sandra E. Orchard, Marco Pagni, Chris P. Ponting, Emmanuel Quevillon, Jeremy D. Selengut, Christian J. A. Sigrist, Ville Silventoinen, David J. Studholme, Robert Vaughan, Cathy H. Wu
2005	J	`jnl`	Literature mining and database annotation of protein phosphorylation using a rule-based system. Bioinform. Zhang-Zhi Hu, Meenakshi Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker, Cathy H. Wu
2005	J	`jnl`	The Universal Protein Resource (UniProt). Nucleic Acids Res. Amos Bairoch, Rolf Apweiler, Cathy H. Wu, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, Maria Jesus Martin, Darren A. Natale, Claire O'Donovan, Nicole Redaschi, Lai-Su L. Yeh
2004	J	`jnl`	BIO-AJAX: An Extensible Framework for Biological Data Cleaning. SIGMOD Rec. Katherine G. Herbert, Narain H. Gehani, William H. Piel, Jason Tsong-Li Wang, Cathy H. Wu
2004	J	`jnl`	PIRSF: family classification system at the Protein Information Resource. Nucleic Acids Res. Cathy H. Wu, Anastasia N. Nikolskaya, Hongzhan Huang, Lai-Su L. Yeh, Darren A. Natale, Cholanayakanahalli R. Vinayaka, Zhang-Zhi Hu, Raja Mazumder, Sandeep Kumar, Panagiotis Kourtesis, Robert S. Ledley, Baris E. Suzek, Leslie Arminski, Yongxing Chen, Jian Zhang, Jorge Louie Cardenas, Sehee Chung, Jorge Castro-Alvear, Georgi Dinkov, Winona C. Barker
2004	J	`jnl`	The PIR integrated protein databases and data retrieval system. Data Sci. J. Hongzhan Huang, Zhang-Zhi Hu, Baris E. Suzek, Cathy H. Wu
2004	J	`jnl`	The iProClass integrated database for protein functional analysis. Comput. Biol. Chem. Cathy H. Wu, Hongzhan Huang, Anastasia N. Nikolskaya, Zhang-Zhi Hu, Winona C. Barker
2004	J	`jnl`	UniProt: the Universal Protein knowledgebase. Nucleic Acids Res. Rolf Apweiler, Amos Bairoch, Cathy H. Wu, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, Maria Jesus Martin, Darren A. Natale, Claire O'Donovan, Nicole Redaschi, Lai-Su L. Yeh
2004	J	`jnl`	iProLINK: an integrated protein resource for literature mining. Comput. Biol. Chem. Zhang-Zhi Hu, Inderjeet Mani, Vincent Hermoso, Hongfang Liu, Cathy H. Wu
2003	—	`book`	Computational Biology and Genome Informatics Jason Tsong-Li Wang, Cathy H. Wu, Paul P. Wang
2003	Misc	`conf`	Linking Biomedical Language, Information and Knowledge - Session Introduction. Pacific Symposium on Biocomputing Lynette Hirschman, Carol Friedman, Robin McEntire, Cathy H. Wu
2003	J	`jnl`	Protein family classification and functional annotation. Comput. Biol. Chem. Cathy H. Wu, Hongzhan Huang, Lai-Su L. Yeh, Winona C. Barker
2003	—	`ch.`	The Protein Information Resource for Functional Genomics and Proteomics. Computational Biology and Genome Informatics Cathy H. Wu
2003	J	`jnl`	The Protein Information Resource. Nucleic Acids Res. Cathy H. Wu, Lai-Su L. Yeh, Hongzhan Huang, Leslie Arminski, Jorge Castro-Alvear, Yongxing Chen, Zhang-Zhi Hu, Panagiotis Kourtesis, Robert S. Ledley, Baris E. Suzek, Cholanayakanahalli R. Vinayaka, Jian Zhang, Winona C. Barker
2003	J	`jnl`	iProClass: an integrated database of protein family, function and structure information. Nucleic Acids Res. Hongzhan Huang, Winona C. Barker, Yongxing Chen, Cathy H. Wu
2002	J	`jnl`	Accomplishments and challenges in literature data mining for biology. Bioinform. Lynette Hirschman, Jong-Chan Park, Jun'ichi Tsujii, Limsoon Wong, Cathy H. Wu
2002	Misc	`conf`	Literature Data Mining for Biology - Session Introduction. Pacific Symposium on Biocomputing Lynette Hirschman, Jong C. Park, Jun'ichi Tsujii, Cathy H. Wu, Limsoon Wong
2002	J	`jnl`	The Protein Information Resource: an integrated public resource of functional annotation of proteins. Nucleic Acids Res. Cathy H. Wu, Hongzhan Huang, Leslie Arminski, Jorge Castro-Alvear, Yongxing Chen, Zhang-Zhi Hu, Robert S. Ledley, Kali C. Lewis, Hans-Werner Mewes, Bruce C. Orcutt, Baris E. Suzek, Akira Tsugita, Cholanayakanahalli R. Vinayaka, Lai-Su L. Yeh, Jian Zhang, Winona C. Barker
2001	J	`jnl`	DNA sequence classification via an expectation maximization algorithm and neural networks: a case study. IEEE Trans. Syst. Man Cybern. Part C Qicheng Ma, Jason Tsong-Li Wang, Dennis E. Shasha, Cathy H. Wu
2001	J	`jnl`	New techniques for extracting features from protein sequences. IBM Syst. J. Jason Tsong-Li Wang, Qicheng Ma, Dennis E. Shasha, Cathy H. Wu
2001	J	`jnl`	Protein Information Resource: a community resource for expert annotation of protein data. Nucleic Acids Res. Winona C. Barker, John S. Garavelli, Zhenglin Hou, Hongzhan Huang, Robert S. Ledley, Peter B. McGarvey, Hans-Werner Mewes, Bruce C. Orcutt, Friedhelm Pfeiffer, Akira Tsugita, Cholanayakanahalli R. Vinayaka, Chunlin Xiao, Lai-Su L. Yeh, Cathy H. Wu
2001	J	`jnl`	iProClass: an integrated, comprehensive and annotated protein classification database. Nucleic Acids Res. Cathy H. Wu, Chunlin Xiao, Zhenglin Hou, Hongzhan Huang, Winona C. Barker
2000	A*	`conf`	Application of neural networks to biological data mining: a case study in protein sequence classification. KDD Jason Tsong-Li Wang, Qicheng Ma, Dennis E. Shasha, Cathy H. Wu
2000	J	`jnl`	PIR: a new resource for bioinformatics. Bioinform. Peter B. McGarvey, Hongzhan Huang, Winona C. Barker, Bruce C. Orcutt, John S. Garavelli, Geetha Y. Srinivasarao, Lai-Su L. Yeh, Chunlin Xiao, Cathy H. Wu
2000	J	`jnl`	ProClass protein family database. Nucleic Acids Res. Hongzhan Huang, Chunlin Xiao, Cathy H. Wu
2000	J	`jnl`	The Protein Information Resource (PIR). Nucleic Acids Res. Winona C. Barker, John S. Garavelli, Hongzhan Huang, Peter B. McGarvey, Bruce C. Orcutt, Geetha Y. Srinivasarao, Chunlin Xiao, Lai-Su L. Yeh, Robert S. Ledley, Joseph F. Janda, Friedhelm Pfeiffer, Hans-Werner Mewes, Akira Tsugita, Cathy H. Wu
1999	J	`jnl`	Gene Family Identification Network Design for Protein Sequence Analysis. Int. J. Artif. Intell. Tools Cathy H. Wu, Hongzhan Huang, Jerry McLarty
1999	J	`jnl`	ProClass Protein Family Database. Nucleic Acids Res. Cathy H. Wu, Sailaja Shivakumar, Hongzhan Huang
1999	J	`jnl`	The PIR-International Protein Sequence Database. Nucleic Acids Res. Winona C. Barker, John S. Garavelli, Peter B. McGarvey, Christopher R. Marzec, Bruce C. Orcutt, Geetha Y. Srinivasarao, Lai-Su L. Yeh, Robert S. Ledley, Hans-Werner Mewes, Friedhelm Pfeiffer, Akira Tsugita, Cathy H. Wu
1998	J	`jnl`	GeneFIND web server for protein family identification and information retrieval. Bioinform. Cathy H. Wu, Sailaja Shivakumar, Chittari V. Shivakumar, Sheng-Chih Chen
1997	J	`jnl`	Artificial Neural Networks for Molecular Sequence Analysis. Comput. Chem. Cathy H. Wu
1997	J	`jnl`	Counter-Propagation Neural Networks for Molecular Sequence Classification: Supervised LVQ and Dynamic Node Allocation. Appl. Intell. Cathy H. Wu, Hsi-Lien Chen, Sheng-Chih Chen
1997	—	`conf`	Motif neural network design for large-scale protein family identification. ICNN Cathy H. Wu, Sheng Zhao, Kevin Simmons, Sailaja Shivakumar
1996	J	`jnl`	A Protein Class Database Organized with ProSite Protein Groups and PIR Superfamilies. J. Comput. Biol. Cathy H. Wu, Sheng Zhao, Hsi-Lien Chen
1996	J	`jnl`	Motif identification neural design for rapid and sensitive protein family search. Comput. Appl. Biosci. Cathy H. Wu, Sheng Zhao, Hsi-Lien Chen, Chin-Ju Lo, Jerry McLarty
1995	J	`jnl`	Gene Classification Artificial Neural System. Int. J. Artif. Intell. Tools Cathy H. Wu, Hsi-Lien Chen, Sheng-Chih Chen
1995	J	`jnl`	Neural Networks for Full-Scale Protein Sequence Classification: Sequence Encoding with Singular Value Decomposition. Mach. Learn. Cathy H. Wu, Michael W. Berry, Sailaja Shivakumar
1993	J	`jnl`	Classification Neural Networks for Rapid Sequence Annotation and Automated Database Organization. Comput. Chem. Cathy H. Wu
1993	A	`conf`	Neural Networks for Molecular Sequence Classification. ISMB Cathy H. Wu, Michael W. Berry, Yuk-Shing Fung, Jerry McLarty
1992	Misc	`conf`	CANS: an interactive neural network system for CRAY supercomputers. SAC George M. Whitson, Cathy H. Wu, John Taylor, Adisorn Ermongkonchai
1992	A	`conf`	Classification Artificial Neural Systems for Genome Research. SC Cathy H. Wu, George M. Whitson, Chun-Tse Hsiao, Cheng-Fu Huang
1991	—	`conf`	Neural networks for molecular sequence database management. ACM Conference on Computer Science Cathy H. Wu, Jerry McLarty, George M. Whitson
1991	—	`conf`	Protein Classification Using a Neural Network Database System. Conference on Analysis of Neural Network Applications Cathy H. Wu, Tzx-Chung Chang
1990	—	`conf`	Artificial Neural System for Gene Classification Using a Domain Database. ACM Conference on Computer Science Cathy H. Wu, George M. Whitson
1990	B	`conf`	PROCANS: a protein classification system using a neural network. IJCNN Cathy H. Wu, George M. Whitson, G. J. Montllor
1990	—	`conf`	Using an Artificial Neural System to Determine the Knowledge Base of an Expert System. SIGSMALL/PC Symposium George M. Whitson, Cathy H. Wu, Pam Taylor