Karen E. Ross

According to our database, Karen E. Ross authored at least 22 papers between 2013 and 2023.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of three.

2023

Network models of protein phosphorylation, acetylation, and ubiquitination connect metabolic and cell signaling pathways in lung cancer.

Karen E. Ross, Guolin Zhang, Cuneyt Akcora, Yu Lin, Bin Fang, John M. Koomen, Eric B. Haura, Mark Grimes

PLoS Comput. Biol., March, 2023

Annotation of biologically relevant ligands in UniProtKB using ChEBI.

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

Bioinform., January, 2023

2022

A knowledge graph representation learning approach to predict novel kinase-substrate interactions.

Sachin Gavali, Karen Ross, Chuming Chen, Julie Cowart, Cathy H. Wu

CoRR, 2022

Overview of the COVID-19 text mining tool interactive demonstration track in BioCreative VII.

Andrew Chatr-aryamontri, Lynette Hirschman, Karen E. Ross, Rose Oughtred, Martin Krallinger, Kara Dolinski, Mike Tyers, Tonia Korves, Cecilia N. Arighi

Database J. Biol. Databases Curation, 2022

2021

UniProt: the universal protein knowledgebase in 2021.

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

Nucleic Acids Res., 2021

COVID-19 Knowledge Graph from semantic integration of biomedical literature and databases.

Chuming Chen, Karen E. Ross, Sachin Gavali, Julie E. Cowart, Cathy H. Wu

Bioinform., 2021

2020

piNET: a versatile web platform for downstream analysis and visualization of proteomics data.

Behrouz Shamsaei, Szymon Chojnacki, Marcin Pilarczyk, Mehdi Fazel-Najafabadi, Wen Niu, Chuming Chen, Karen Ross, Andrea Matlock, Jeremy Muhlich, Somchai Chutipongtanate, Jie Zheng, John Turner, Dusica Vidovic, Jake Jaffe, Michael J. MacCoss, Cathy Wu, Ajay Pillai, Avi Ma'ayan, Stephan C. Schürer, Michal Kouril, Mario Medvedovic, Jarek Meller

Nucleic Acids Res., 2020

GlyGen data model and processing workflow.

Robel Y. Kahsay, Jeet Vora, Rahi Navelkar, Reza Mousavi, Brian C. Fochtman, Xavier Holmes, Nagarajan Pattabiraman, René Ranzinger, Rupali Mahadik, Tatiana Williamson, Sujeet Kulkarni, Gaurav Agarwal, Maria Jesus Martin, Preethi Vasudev, Leyla J. García, Nathan Edwards, Wenjin Zhang, Darren A. Natale, Karen Ross, Kiyoko F. Aoki-Kinoshita, Matthew P. Campbell, William S. York, Raja Mazumder

Bioinform., 2020

2018

iPTMnet: an integrated resource for protein post-translational modification network discovery.

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

Nucleic Acids Res., 2018

iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature.

Jia Ren, Gang Li, Karen Ross, Cecilia N. Arighi, Peter B. McGarvey, Shruti Rao, Julie Cowart, Subha Madhavan, K. Vijay-Shanker, Cathy H. Wu

Database J. Biol. Databases Curation, 2018

DEXTER: Disease-Expression Relation Extraction from Text.

Samir Gupta, Hayley Dingerdissen, Karen E. Ross, Yu Hu, Cathy H. Wu, Raja Mazumder, K. Vijay-Shanker

Database J. Biol. Databases Curation, 2018

PTM Knowledge Networks and LINCS Multi-Omics Data for Kinase Inhibitor Drug-Analytics in Lung Cancer.

Xu Zhang, Karen E. Ross, Tapan K. Maity, Jake Jaffe, Cathy H. Wu, Udayan Guha

Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

RESTful API for iPTMnet: An Integrated Resource for Protein Post-translational Modification Network Discovery.

Sachin Gavali, Julie Cowart, Chuming Chen, Karen Ross, Cathy H. Wu

Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

2017

Protein Ontology (PRO): enhancing and scaling up the representation of protein entities.

Darren A. Natale, Cecilia N. Arighi, Judith A. Blake, Jonathan P. Bona, Chuming Chen, Sheng-Chih Chen, Karen R. Christie, Julie Cowart, Peter D'Eustachio, Alexander D. Diehl, Harold J. Drabkin, William D. Duncan, Hongzhan Huang, Jia Ren, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Qinghua Wang, Jian Zhang, Abdelrahman Elsayed, Cathy H. Wu

Nucleic Acids Res., 2017

Identifying Comparative Structures in Biomedical Text.

Samir Gupta, A. S. M. Ashique Mahmood, Karen Ross, Cathy H. Wu, K. Vijay-Shanker

Proceedings of the BioNLP 2017, Vancouver, Canada, August 4, 2017, 2017

2016

miRiaD: A Text Mining Tool for Detecting Associations of microRNAs with Diseases.

Samir Gupta, Karen E. Ross, Catalina O. Tudor, Cathy H. Wu, Carl J. Schmidt, K. Vijay-Shanker

J. Biomed. Semant., 2016

Scalable Text Mining Assisted Curation of PTM Proteoforms in the Protein Ontology.

Karen E. Ross, Darren A. Natale, Cecilia N. Arighi, Sheng-Chih Chen, Hongzhan Huang, Gang Li, Jia Ren, Michael Wang, K. Vijay-Shanker, Cathy H. Wu

Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

2015

miRTex: A Text Mining System for miRNA-Gene Relation Extraction.

Gang Li, Karen E. Ross, Cecilia N. Arighi, Yifan Peng, Cathy H. Wu, K. Vijay-Shanker

PLoS Comput. Biol., 2015

Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system.

Catalina O. Tudor, Karen E. Ross, Gang Li, K. Vijay-Shanker, Cathy H. Wu, Cecilia N. Arighi

Database J. Biol. Databases Curation, 2015

2014

Protein Ontology: a controlled structured network of protein entities.

Darren A. Natale, Cecilia N. Arighi, Judith A. Blake, Carol J. Bult, Karen R. Christie, Julie Cowart, Peter D'Eustachio, Alexander D. Diehl, Harold J. Drabkin, Olivia Helfer, Hongzhan Huang, Anna Maria Masci, 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

Nucleic Acids Res., 2014

Knowledge Representation of Protein PTMs and Complexes in the Protein Ontology: Application to Multi-Faceted Disease Analysis.

Karen Ross, Catalina O. Tudor, Gang Li, Ruoyao Ding, Irem Çelen, Julie Cowart, Cecilia N. Arighi, Darren A. Natale, Cathy H. Wu

Proceedings of the 5th International Conference on Biomedical Ontology, 2014

2013

Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint.

Karen Ross, Cecilia N. Arighi, Jia Ren, Hongzhan Huang, Cathy H. Wu

Database J. Biol. Databases Curation, 2013