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ORCIDCathy H. Wu
Cathy Wu 0001
Person information
- affiliation: University of Delaware, Newark, DE, USA
Other persons with the same name
- Cathy Wu 0002
![[0000-0001-8594-303X]](https://dblp.dagstuhl.de/img/orcid-mark.12x12.png "0000-0001-8594-303X")
— MIT, Cambridge, MA, USA (and 1 more)
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2020 – today
- 2023
[j108]Typhaine Paysan-Lafosse, Matthias Blum, Sara Chuguransky, Tiago Grego, Beatriz Lázaro Pinto, Gustavo A. Salazar, Maxwell L. Bileschi, Peer Bork, Alan 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:
InterPro in 2022. Nucleic Acids Res. 51(D1): 418-427 (2023)- 2022
- [i3]Sachin Gavali, Karen Ross, Chuming Chen, Julie Cowart, Cathy H. Wu:
A knowledge graph representation learning approach to predict novel kinase-substrate interactions. CoRR abs/2206.02290 (2022) - 2021
- [j107]Chuming Chen, Karen E. Ross, Sachin Gavali, Julie E. Cowart, Cathy H. Wu:
COVID-19 Knowledge Graph from semantic integration of biomedical literature and databases. Bioinform. 37(23): 4597-4598 (2021) - [j106]Seth Carbon, Eric Douglass, Benjamin M. Good, Deepak R. Unni, Nomi L. Harris, Christopher J. Mungall, Siddartha Basu, Rex L. Chisholm, Robert J. Dodson, Eric Hartline, Petra Fey, Paul D. Thomas, Laurent-Philippe Albou, Dustin Ebert, Michael J. Kesling, Huaiyu Mi, Anushya Muruganujan, Xiaosong Huang, Tremayne Mushayahama, Sandra A. LaBonte, Deborah A. Siegele, Giulia Antonazzo, Helen Attrill, Nick H. Brown, Phani V. Garapati, Steven J. Marygold, Vitor Trovisco, Gilberto dos Santos, Kathleen Falls, Christopher J. Tabone, Pinglei Zhou, Joshua L. Goodman, Victor B. Strelets, Jim Thurmond, Penelope Garmiri, Rizwan Ishtiaq, Milagros Rodríguez-López, Marcio Luis Acencio, Martin Kuiper, Astrid Lægreid, Colin Logie, Ruth C. Lovering, Barbara Kramarz, Shirin C. C. Saverimuttu, Sandra M. Pinheiro, Heather Gunn, Renzhi Su, Katherine E. Thurlow, Marcus C. Chibucos, Michelle G. Giglio, Suvarna Nadendla, James B. Munro, Rebecca C. Jackson, Margaret J. Duesbury, Noemi del-Toro, Birgit H. M. Meldal, Kalpana Paneerselvam, Livia Perfetto, Pablo Porras, Sandra E. Orchard, Anjali Shrivastava, Hsin-Yu Chang, Robert D. Finn, Alex L. Mitchell, Neil D. Rawlings, Lorna J. Richardson, Amaia Sangrador-Vegas, Judith A. Blake, Karen R. Christie, Mary E. Dolan, Harold J. Drabkin, David P. Hill, Li Ni, Dmitry M. Sitnikov, Midori A. Harris, Stephen G. Oliver, Kim Rutherford, Valerie Wood, Jaqueline Hayles, Jürg Bähler, Elizabeth R. Bolton, Jeffrey DePons, Melinda R. Dwinell, G. Thomas Hayman, Mary L. Kaldunski, Anne E. Kwitek, Stanley J. F. Laulederkind, Cody Plasterer, Marek Tutaj, Mahima Vedi, Shur-Jen Wang, Peter D'Eustachio, Lisa Matthews, James P. Balhoff, Suzi A. Aleksander, Michael J. Alexander, J. Michael Cherry, Stacia R. Engel, Felix Gondwe, Kalpana Karra, Stuart R. Miyasato, Robert S. Nash, Matt Simison, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Marc Feuermann, Pascale Gaudet, Anne Morgat, Erica Bakker, Tanya Z. Berardini, Leonore Reiser, Shabari Subramaniam, Eva Huala, Cecilia N. Arighi, Andrea H. Auchincloss, Kristian B. Axelsen, Ghislaine Argoud-Puy, Alex Bateman, Marie-Claude Blatter, Emmanuel Boutet, Emily Bowler, Lionel Breuza, Alan Bridge, Ramona Britto, Hema Bye-A-Jee, Cristina Casals-Casas, Elisabeth Coudert, Paul Denny, Anne Estreicher, Maria Livia Famiglietti, George E. Georghiou, Arnaud Gos, Nadine Gruaz-Gumowski, Emma Hatton-Ellis, Chantal Hulo, Alexandr Ignatchenko, Florence Jungo, Kati Laiho, Philippe Le Mercier, Damien Lieberherr, Antonia Lock, Yvonne Lussi, Alistair MacDougall, Michele Magrane, Maria Jesus Martin, Patrick Masson, Darren A. Natale, Nevila Hyka-Nouspikel, Ivo Pedruzzi, Lucille Pourcel, Sylvain Poux, Sangya Pundir, Catherine Rivoire, Elena Speretta, Shyamala Sundaram, Nidhi Tyagi, Kate Warner, Rossana Zaru, Cathy H. Wu, Alexander D. Diehl, Juancarlos Chan, Christian A. Grove, Raymond Y. N. Lee, Hans-Michael Müller, Daniela Raciti, Kimberly Van Auken, Paul W. Sternberg, Matthew Berriman, Michael Paulini, Kevin L. Howe, Sibyl Gao, Adam Wright, Lincoln Stein, Douglas G. Howe, Sabrina Toro, Monte Westerfield, Pankaj Jaiswal, Laurel Cooper, Justin Elser:
The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res. 49(Database-Issue): D325-D334 (2021) - [j105]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 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:
The InterPro protein families and domains database: 20 years on. Nucleic Acids Res. 49(Database-Issue): D344-D354 (2021) - [j104]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 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:
UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res. 49(Database-Issue): D480-D489 (2021) - [c48]Mengmeng Ma, Jian Ren, Long Zhao, Sergey Tulyakov, Cathy Wu, Xi Peng:
SMIL: Multimodal Learning with Severely Missing Modality. AAAI 2021: 2302-2310 - [c47]Sachin Gavali, Chuming Chen, Julie Cowart, Xi Peng, Shanshan Ding, Cathy H. Wu, Tammy Anderson:
Understanding the factors related to the opioid epidemic using machine learning. BIBM 2021: 1309-1314 - [i2]Mengmeng Ma, Jian Ren, Long Zhao, Sergey Tulyakov, Cathy Wu, Xi Peng:
SMIL: Multimodal Learning with Severely Missing Modality. CoRR abs/2103.05677 (2021) - [i1]Sachin Gavali, Chuming Chen, Julie Cowart, Xi Peng, Shanshan Ding, Cathy Wu, Tammy Anderson:
Understanding the factors driving the opioid epidemic using machine learning. CoRR abs/2108.07301 (2021) - 2020
- [j103]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:
piNET: a versatile web platform for downstream analysis and visualization of proteomics data. Nucleic Acids Res. 48(Webserver-Issue): W85-W93 (2020)
2010 – 2019
- 2019
- [j102]Chuming Chen, Qinghua Wang, Hongzhan Huang, Cholanayakanahalli R. Vinayaka, John S. Garavelli, Cecilia N. Arighi, Darren A. Natale, Cathy H. Wu:
PIRSitePredict for protein functional site prediction using position-specific rules. Database J. Biol. Databases Curation 2019: baz026 (2019) - 2018
- [j101]Samir Gupta, Hayley Dingerdissen, Karen E. Ross, Yu Hu, Cathy H. Wu, Raja Mazumder, K. Vijay-Shanker:
DEXTER: Disease-Expression Relation Extraction from Text. Database J. Biol. Databases Curation 2018: bay045 (2018) - [j100]Jia Ren, Gang Li, Karen Ross, Cecilia N. Arighi, Peter B. McGarvey, Shruti Rao, Julie Cowart, Subha Madhavan, K. Vijay-Shanker, Cathy H. Wu:
iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature. Database J. Biol. Databases Curation 2018: bay128 (2018) - [j99]Lei Huang, Li Liao, Cathy H. Wu:
Completing sparse and disconnected protein-protein network by deep learning. BMC Bioinform. 19(1): 103:1-103:12 (2018) - [j98]Ruoyao Ding, Yingying Qu, Cathy H. Wu, K. Vijay-Shanker:
Automatic gene annotation using GO terms from cellular component domain. BMC Medical Informatics Decis. Mak. 18(S-5): 97-106 (2018) - [j97]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:
iPTMnet: an integrated resource for protein post-translational modification network discovery. Nucleic Acids Res. 46(Database-Issue): D542-D550 (2018) - [c46]Xu Zhang, Karen E. Ross, Tapan K. Maity, Jake Jaffe, Cathy H. Wu, Udayan Guha:
PTM Knowledge Networks and LINCS Multi-Omics Data for Kinase Inhibitor Drug-Analytics in Lung Cancer. BCB 2018: 524 - [c45]Sachin Gavali, Julie Cowart, Chuming Chen, Karen Ross, Cathy H. Wu:
RESTful API for iPTMnet: An Integrated Resource for Protein Post-translational Modification Network Discovery. BCB 2018: 541 - [c44]Chuming Chen, Julie E. Cowart, Jia Ren, Sachin Gavali, Yuqi Wang, Hongzhan Huang, Cathy H. Wu, Leslie Arminski, Jian Zhang, Peter B. McGarvey:
Cloud-based Semantic Integration and Knowledge Discovery Systems in Precision Medicine. BCB 2018: 542 - [c43]Qi Li, Xuan Wang, Yu Zhang, Fei Ling, Cathy H. Wu, Jiawei Han:
Pattern Discovery for Wide-Window Open Information Extraction in Biomedical Literature. BIBM 2018: 420-427 - [c42]Xuan Wang, Yu Zhang, Qi Li, Cathy H. Wu, Jiawei Han:
PENNER: Pattern-enhanced Nested Named Entity Recognition in Biomedical Literature. BIBM 2018: 540-547 - [c41]Ruoyao Ding, Xiaoyi Pan, Yingying Qu, Cathy H. Wu, K. Vijay-Shanker:
Protein Complex Mention Recognition with Web-Based Knowledge Learning. SETE@ICWL 2018: 190-197 - [e2]Amarda Shehu, Cathy H. Wu, Christina Boucher, Jing Li, Hongfang Liu, Mihai Pop:
Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2018, Washington, DC, USA, August 29 - September 01, 2018. ACM 2018 [contents] - 2017
- [j96]Ruoyao Ding, Emmanuel Boutet, Damien Lieberherr, Michel Schneider, Michael Tognolli, Cathy H. Wu, K. Vijay-Shanker, Cecilia N. Arighi:
eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality. Database J. Biol. Databases Curation 2017: bax081 (2017) - [j95]Robert D. Finn, Teresa K. Attwood, Patricia C. Babbitt, Alex Bateman, Peer Bork, Alan 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:
InterPro in 2017 - beyond protein family and domain annotations. Nucleic Acids Res. 45(Database-Issue): D190-D199 (2017) - [j94]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:
Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. Nucleic Acids Res. 45(Database-Issue): D339-D346 (2017) - [j93]Norman Goodacre, Nathan Edwards, Mark Danielsen, Peter Uetz, Cathy H. Wu:
Predicting nsSNPs that Disrupt Protein-Protein Interactions Using Docking. IEEE ACM Trans. Comput. Biol. Bioinform. 14(5): 1082-1093 (2017) - [c40]Gang Li, Cathy H. Wu, K. Vijay-Shanker:
Noise Reduction Methods for Distantly Supervised Biomedical Relation Extraction. BioNLP 2017: 184-193 - [c39]Samir Gupta, A. S. M. Ashique Mahmood, Karen Ross, Cathy H. Wu, K. Vijay-Shanker:
Identifying Comparative Structures in Biomedical Text. BioNLP 2017: 206-215 - [c38]A. S. M. Ashique Mahmood, Gang Li, Shruti Rao, Peter B. McGarvey, Cathy H. Wu, Subha Madhavan, K. Vijay-Shanker:
UD_GU_BioTM at TREC 2017: Precision Medicine Track. TREC 2017 - 2016
- [j92]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:
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database J. Biol. Databases Curation 2016 (2016) - [j91]Yifan Peng, Cecilia N. Arighi, Cathy H. Wu, K. Vijay-Shanker:
BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph. Database J. Biol. Databases Curation 2016 (2016) - [j90]Qinghua Wang, Shabbir S. 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:
Overview of the interactive task in BioCreative V. Database J. Biol. Databases Curation 2016 (2016) - [j89]Chuming Chen, Hongzhan Huang, Raja Mazumder, Darren A. Natale, Peter B. McGarvey, Jian Zhang, Shawn W. Polson, Yuqi Wang, Cathy H. Wu:
Computational clustering for viral reference proteomes. Bioinform. 32(13): 2041-2043 (2016) - [j88]Samir Gupta, Karen E. Ross, Catalina O. Tudor, Cathy H. Wu, Carl J. Schmidt, K. Vijay-Shanker:
miRiaD: A Text Mining Tool for Detecting Associations of microRNAs with Diseases. J. Biomed. Semant. 7: 9 (2016) - [j87]Lei Huang, Li Liao, Cathy H. Wu:
Protein-protein interaction prediction based on multiple kernels and partial network with linear programming. BMC Syst. Biol. 10(S-2): 45 (2016) - [j86]Lei Huang, Li Liao, Cathy H. Wu:
Inference of protein-protein interaction networks from multiple heterogeneous data. EURASIP J. Bioinform. Syst. Biol. 2016: 8 (2016) - [j85]Tianchuan Du, Li Liao, Cathy H. Wu:
Enhancing interacting residue prediction with integrated contact matrix prediction in protein-protein interaction. EURASIP J. Bioinform. Syst. Biol. 2016: 17 (2016) - [c37]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:
Scalable Text Mining Assisted Curation of PTM Proteoforms in the Protein Ontology. ICBO/BioCreative 2016 - 2015
- [j84]Catalina O. Tudor, Karen E. Ross, Gang Li, K. Vijay-Shanker, Cathy H. Wu, Cecilia N. Arighi:
Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system. Database J. Biol. Databases Curation 2015 (2015) - [j83]Baris E. Suzek, Yuqi Wang, Hongzhan Huang, Peter B. McGarvey, Cathy H. Wu:
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. Bioinform. 31(6): 926-932 (2015) - [j82]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:
The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. 43(Database-Issue): 213-221 (2015) - [j81]Gang Li, Karen E. Ross, Cecilia N. Arighi, Yifan Peng, Cathy H. Wu, K. Vijay-Shanker:
miRTex: A Text Mining System for miRNA-Gene Relation Extraction. PLoS Comput. Biol. 11(9) (2015) - [j80]Manabu Torii, Cecilia N. Arighi, Gang Li, Qinghua Wang, Cathy H. Wu, K. Vijay-Shanker:
RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information. IEEE ACM Trans. Comput. Biol. Bioinform. 12(1): 17-29 (2015) - [j79]Lei Huang, Li Liao, Cathy H. Wu:
Evolutionary Model Selection and Parameter Estimation for Protein-Protein Interaction Network Based on Differential Evolution Algorithm. IEEE ACM Trans. Comput. Biol. Bioinform. 12(3): 622-631 (2015) - [c36]Lei Huang, Li Liao, Cathy H. Wu:
Inference of protein-protein interaction networks from multiple heterogeneous data. BCB 2015: 655 - [c35]Lei Huang, Li Liao, Cathy H. Wu:
Protein-protein interaction network inference from multiple kernels with optimization based on random walk by linear programming. BIBM 2015: 201-207 - [c34]Yifan Peng, Samir Gupta, Cathy H. Wu, K. Vijay-Shanker:
An extended dependency graph for relation extraction in biomedical texts. BioNLP@IJCNLP 2015: 21-30 - 2014
- [j78]Cecilia N. Arighi, Cathy H. Wu, Kevin Bretonnel Cohen, Lynette Hirschman, Martin Krallinger, Alfonso Valencia, Zhiyong Lu, W. John Wilbur, Thomas C. Wiegers:
BioCreative-IV virtual issue. Database J. Biol. Databases Curation 2014 (2014) - [j77]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:
BioC interoperability track overview. Database J. Biol. Databases Curation 2014 (2014) - [j76]Yifan Peng, Catalina O. Tudor, Manabu Torii, Cathy H. Wu, K. Vijay-Shanker:
iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system. Database J. Biol. Databases Curation 2014 (2014) - [j75]Manabu Torii, Gang Li, Zhiwen Li, Rose Oughtred, Francesca Diella, Irem Çelen, Cecilia N. Arighi, Hongzhan Huang, K. Vijay-Shanker, Cathy H. Wu:
RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information. Database J. Biol. Databases Curation 2014 (2014) - [j74]Yifan Peng, Manabu Torii, Cathy H. Wu, K. Vijay-Shanker:
A Generalizable NLP Framework for Fast Development of Pattern-based Biomedical Relation Extraction Systems. BMC Bioinform. 15: 285 (2014) - [j73]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:
Protein Ontology: a controlled structured network of protein entities. Nucleic Acids Res. 42(Database-Issue): 415-421 (2014) - [j72]Nguyen T. Nguyen, Xiaolin Zhang, Cathy Wu, Richard A. Lange, Robert J. Chilton, Merry L. Lindsey, Yufang Jin:
Integrative Computational and Experimental Approaches to Establish a Post-Myocardial Infarction Knowledge Map. PLoS Comput. Biol. 10(3) (2014) - [j71]Chuming Chen, Sari S. Khaleel, Hongzhan Huang, Cathy H. Wu:
Software for pre-processing Illumina next-generation sequencing short read sequences. Source Code Biol. Medicine 9: 8 (2014) - [c33]Norman Goodacre, Nathan Edwards, Mark Danielsen, Peter Uetz, Cathy H. Wu:
Docking features for predicting binding loss due to protein mutation. BCB 2014: 23-32 - [c32]Tianchuan Du, Alvaro J. González, Qinghua Wang, Hongzhan Huang, Li Liao, Cathy H. Wu:
DDI2PPI: an integrated web server for protein-protein interaction and residue contact matrix predictions. BCB 2014: 641-642 - [c31]Karen Ross, Catalina O. Tudor, Gang Li, Ruoyao Ding, Irem Çelen, Julie Cowart, Cecilia N. Arighi, Darren A. Natale, Cathy H. Wu:
Knowledge Representation of Protein PTMs and Complexes in the Protein Ontology: Application to Multi-Faceted Disease Analysis. ICBO 2014: 43-46 - 2013
- [j70]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:
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database J. Biol. Databases Curation 2013 (2013) - [j69]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:
BioC: a minimalist approach to interoperability for biomedical text processing. Database J. Biol. Databases Curation 2013 (2013) - [j68]Karen Ross, Cecilia N. Arighi, Jia Ren, Hongzhan Huang, Cathy H. Wu:
Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint. Database J. Biol. Databases Curation 2013 (2013) - [j67]Alvaro J. González, Li Liao, Cathy H. Wu:
Prediction of contact matrix for protein-protein interaction. Bioinform. 29(8): 1018-1025 (2013) - [j66]Chuming Chen, Zhiwen Li, Hongzhan Huang, Baris E. Suzek, Cathy H. Wu:
A fast Peptide Match service for UniProt Knowledgebase. Bioinform. 29(21): 2808-2809 (2013) - [j65]Qinghua Wang, Keerthi Venkataramanan, Hongzhan Huang, Eleftherios T. Papoutsakis, Cathy H. Wu:
Transcription factors and genetic circuits orchestrating the complex, multilayered response of Clostridium acetobutylicum to butanol and butyrate stress. BMC Syst. Biol. 7: 120 (2013) - [j64]Luis D. Lopez, Jingyi Yu, Cecilia N. Arighi, Catalina O. Tudor, Manabu Torii, Hongzhan Huang, K. Vijay-Shanker, Cathy H. Wu:
A framework for biomedical figure segmentation towards image-based document retrieval. BMC Syst. Biol. 7(S-4): S8 (2013) - [c30]Erin L. Crowgey, Chuming Chen, Shawn W. Polson, Hongzhan Huang, Cathy H. Wu:
An Integrated Approach for Interpretation of Clinical NGS Genomic Variant Data. AMIA 2013 - [c29]Manabu Torii, Cecilia N. Arighi, Qinghua Wang, Cathy H. Wu, K. Vijay-Shanker:
Text Mining of Protein Phosphorylation Information Using a Generalizable Rule-Based Approach. BCB 2013: 201 - [c28]Luis D. Lopez, Jingyi Yu, Cecilia N. Arighi, Manabu Torii, K. Vijay-Shanker, Hongzhan Huang, Cathy H. Wu:
An Image-Text Approach for Extracting Experimental Evidence of Protein-Protein Interactions in the Biomedical Literature. BCB 2013: 412 - [c27]Chuming Chen, Sari S. Khaleel, Hongzhan Huang, Cathy H. Wu:
ngsShoRT: A Software for Pre-processing Illumina Short Read Sequences for De Novo Genome Assembly. BCB 2013: 706 - 2012
- [j63]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:
Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference. Database J. Biol. Databases Curation 2012 (2012) - [j62]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:
Text mining for the biocuration workflow. Database J. Biol. Databases Curation 2012 (2012) - [j61]Catalina O. Tudor, Cecilia N. Arighi, Qinghua Wang, Cathy H. Wu, K. Vijay-Shanker:
The eFIP system for text mining of protein interaction networks of phosphorylated proteins. Database J. Biol. Databases Curation 2012 (2012) - [j60]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:
Community annotation and bioinformatics workforce development in concert - Little Skate Genome Annotation Workshops and Jamborees. Database J. Biol. Databases Curation 2012 (2012) - [j59]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:
BioCreative-2012 Virtual Issue. Database J. Biol. Databases Curation 2012 (2012) - [j58]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:
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. 40(Database-Issue): 306-312 (2012) - [j57]Alvaro J. González, Li Liao, Cathy H. Wu:
Predicting Ligand Binding Residues and Functional Sites Using Multipositional Correlations with Graph Theoretic Clustering and Kernel CCA. IEEE ACM Trans. Comput. Biol. Bioinform. 9(4): 992-1001 (2012) - [c26]Xia Bi, Hongzhan Huang, Sherri Matis-Mitchell, Peter B. McGarvey, Manabu Torii, Hagit Shatkay, Cathy H. Wu:
Building a classifier for identifying sentences pertaining to disease-drug relationships in tardive dyskinesia. BIBM 2012: 1-4 - [c25]Luis D. Lopez, Jingyi Yu, Catalina O. Tudor, Cecilia N. Arighi, Hongzhan Huang, K. Vijay-Shanker, Cathy H. Wu:
Robust segmentation of biomedical figures for image-based document retrieval. BIBM 2012: 1-6 - [c24]Yifan Peng, Catalina O. Tudor, Manabu Torii, Cathy H. Wu, K. Vijay-Shanker:
iSimp: A sentence simplification system for biomedicail text. BIBM 2012: 1-6 - [c23]Carl J. Schmidt, Liang Sun, Cecilia N. Arighi, Keith Decker, K. Vijay-Shanker, Manabu Torii, Catalina O. Tudor, Cathy H. Wu, Peter D'Eustachio:
Pathway curation: Application of text-mining tools eGIFT and RLIMS-P. BIBM Workshops 2012: 523-528 - 2011
- [j56]Hongzhan Huang, Peter B. McGarvey, Baris E. Suzek, Raja Mazumder, Jian Zhang, Yongxing Chen, Cathy H. Wu:
A comprehensive protein-centric ID mapping service for molecular data integration. Bioinform. 27(8): 1190-1191 (2011) - [j55]