


Остановите войну!
for scientists:


default search action
Cathy H. Wu
Cathy Wu 0001
Person information

- affiliation: University of Delaware, Newark, DE, USA
Other persons with the same name
- Cathy Wu 0002
— MIT, Cambridge, MA, USA (and 1 more)
Refine list

refinements active!
zoomed in on ?? of ?? records
view refined list in
export refined list as
showing all ?? records
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]