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2020 – today
- 2024
[j19]Marija Orlic-Milacic
, Karen Rothfels, Lisa Matthews, Adam J. Wright, Bijay Jassal, Veronica Shamovsky, Quang M. Trinh, Marc Gillespie, Cristoffer Sevilla, Krishna Tiwari, Eliot Ragueneau, Chuqiao Gong, Ralf Stephan, Bruce May, Robin Haw, Joel Weiser, Deidre Beavers, Patrick Conley, Henning Hermjakob, Lincoln D. Stein, Peter D'Eustachio, Guanming Wu:
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes. Database J. Biol. Databases Curation 2024 (2024)- [i4]Nathaniel J. Evans, Gordon B. Mills, Guanming Wu, Xubo Song, Shannon K. McWeeney:
Data Valuation with Gradient Similarity. CoRR abs/2405.08217 (2024) - 2023
- [j18]Joshua G. Burkhart, Guanming Wu, Xubo Song, Francesco Raimondi, Shannon K. McWeeney, Melissa H. Wong, Youping Deng:
Biology-inspired graph neural network encodes reactome and reveals biochemical reactions of disease. Patterns 4(7): 100758 (2023) - [c2]Anthony Huffman, Edison Ong, Timothy Brunson, Nasim Sanati, Jie Zheng, Anna Maria Masci, Guanming Wu, Yongqun He:
Ontology-based Representation and Analysis of Conditional Vaccine Immune Responses Using Omics Data. ICBO 2023: 1-12 - 2022
- [j17]Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek M. Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary D. Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio:
The reactome pathway knowledgebase 2022. Nucleic Acids Res. 50(D1): 687-692 (2022) - 2021
- [j16]Anthony Huffman, Anna Maria Masci, Jie Zheng, Nasim Sanati, Timothy Brunson, Guanming Wu, Yongqun He:
CIDO ontology updates and secondary analysis of host responses to COVID-19 infection based on ImmPort reports and literature. J. Biomed. Semant. 12(1): 18 (2021) - [i3]Francesco Raimondi, Joshua G. Burkhart, Matthew J. Betts, Robert B. Russell, Guanming Wu:
Leveraging biochemical reactions to unravel functional impacts of cancer somatic variants affecting protein interaction interfaces. F1000Research 10: 1111 (2021) - 2020
- [j15]Bijay Jassal, Lisa Matthews, Guilherme Viteri, Chuqiao Gong, Pascual Lorente, Antonio Fabregat, Konstantinos Sidiropoulos, Justin Cook, Marc Gillespie, Robin Haw, Fred Loney, Bruce May, Marija Milacic, Karen Rothfels, Cristoffer Sevilla, Veronica Shamovsky, Solomon Shorser, Thawfeek M. Varusai, Joel Weiser, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio:
The reactome pathway knowledgebase. Nucleic Acids Res. 48(Database-Issue): D498-D503 (2020) - [j14]Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah Wala, Ofer Shapira, Grace Tiao, Henrik Hornshøj, Julian M. Hess, Randi Istrup Juul, Ziao Lin, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel Gonzalez-Perez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, André Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uusküla-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jüri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Núria López-Bigas, Gary D. Bader, Jonathan Barenboim, Rameen Beroukhim, Søren Brunak, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, J. Lynn Fink, Joan Frigola, Carlo Gambacorti Passerini, Dale W. Garsed, Gad Getz, Ivo Glynne Gut, David Haan, Arif Ozgun Harmanci, Mohamed Helmy, Ermin Hodzic, José M. G. Izarzugaza, Jong K. Kim, Jan O. Korbel, Erik Larsson, Shantao Li, Xiaotong Li, Shaoke Lou, Kathleen Marchal, Iñigo Martincorena, Alexander Martínez-Fundichely, Patrick D. McGillivray, William Meyerson, Ferran Muiños, Marta Paczkowska, Kiejung Park, Jakob Skou Pedersen, Tirso Pons, Sergio Pulido-Tamayo, Iker Reyes-Salazar, Matthew A. Reyna, Carlota Rubio-Perez, Süleyman Cenk Sahinalp, Leonidas Salichos, Mark Shackleton, Raunak Shrestha, Alfonso Valencia, Miguel Vazquez, Lieven P. C. Verbeke, Jiayin Wang, Jonathan Warrell, Sebastian M. Waszak, Joachim Weischenfeldt, Guanming Wu, Jun Yu, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Lihua Zou, Kadir C. Akdemir, Eva G. Alvarez, Adrian Baez-Ortega, Paul C. Boutros, David D. L. Bowtell, Benedikt Brors, Kathleen H. Burns, Kin Chan, Isidro Cortés-Ciriano, Ana Dueso-Barroso, Andrew J. Dunford, Paul A. Edwards, Xavier Estivill, Dariush Etemadmoghadam, Milana Frenkel-Morgenstern, Dmitry A. Gordenin, Barbara Hutter, David T. W. Jones, Young Seok Ju, Marat D. Kazanov, Leszek J. Klimczak, Youngil Koh, Eunjung Alice Lee, Jake June-Koo Lee, Andy G. Lynch, Geoff MacIntyre, Florian Markowetz, Matthew Meyerson, Satoru Miyano, Fabio C. P. Navarro, Stephan Ossowski, Peter J. Park, John V. Pearson, Montserrat Puiggròs, Karsten Rippe, Steven A. Roberts, Bernardo Rodriguez-Martin, Ralph Scully, David Torrents, Izar Villasante, Nicola Waddell, Jeremiah A. Wala, Lixing Yang, Sung-Soo Yoon, Jorge Zamora:
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578(7793): 102-111 (2020) - [p1]Robin Haw, Fred Loney, Edison Ong, Yongqun He, Guanming Wu:
Perform Pathway Enrichment Analysis Using ReactomeFIViz. Protein-Protein Interaction Networks 2020: 165-179
2010 – 2019
- 2019
- [j13]Guilherme Viteri, Lisa Matthews, Thawfeek M. Varusai, Marc Gillespie, Marija Milacic, Justin Cook, Joel Weiser, Solomon Shorser, Konstantinos Sidiropoulos, Antonio Fabregat, Robin Haw, Guanming Wu, Lincoln Stein, Peter D'Eustachio, Henning Hermjakob:
Reactome and ORCID - fine-grained credit attribution for community curation. Database J. Biol. Databases Curation 2019: baz123 (2019) - [j12]Edison Ong, Peter Sun, Kimberly Berke, Jie Zheng, Guanming Wu, Yongqun He:
VIO: ontology classification and study of vaccine responses given various experimental and analytical conditions. BMC Bioinform. 20-S(21): 704 (2019) - 2018
- [j11]Antonio Fabregat, Steven Jupe, Lisa Matthews, Konstantinos Sidiropoulos, Marc Gillespie, Phani V. Garapati, Robin Haw, Bijay Jassal, Florian Korninger, Bruce May, Marija Milacic, Corina Duenas, Karen Rothfels, Cristoffer Sevilla, Veronica Shamovsky, Solomon Shorser, Thawfeek M. Varusai, Guilherme Viteri, Joel Weiser, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio:
The Reactome Pathway Knowledgebase. Nucleic Acids Res. 46(Database-Issue): D649-D655 (2018) - [j10]Antonio Fabregat, Florian Korninger, Guilherme Viteri, Konstantinos Sidiropoulos, Pablo Marín-García, Peipei Ping, Guanming Wu, Lincoln Stein, Peter D'Eustachio, Henning Hermjakob:
Reactome graph database: Efficient access to complex pathway data. PLoS Comput. Biol. 14(1) (2018) - [i2]Fred Loney, Guanming Wu:
Automation of ReactomeFIViz via CyREST API. F1000Research 7: 531 (2018) - 2017
- [j9]Sushma Naithani, Justin Preece, Peter D'Eustachio, Parul Gupta, Vindhya Amarasinghe, Palitha Dharmawardhana, Guanming Wu, Antonio Fabregat, Justin Elser, Joel Weiser, Maria Keays, Alfonso Muñoz-Pomer Fuentes, Robert Petryszak, Lincoln D. Stein, Doreen Ware, Pankaj Jaiswal:
Plant Reactome: a resource for plant pathways and comparative analysis. Nucleic Acids Res. 45(Database-Issue): D1029-D1039 (2017) - 2016
- [j8]Antonio Fabregat, Konstantinos Sidiropoulos, Phani V. Garapati, Marc Gillespie, Kerstin Hausmann, Robin Haw, Bijay Jassal, Steven Jupe, Florian Korninger, Sheldon J. McKay, Lisa Matthews, Bruce May, Marija Milacic, Karen Rothfels, Veronica Shamovsky, Marissa Webber, Joel Weiser, Mark Williams, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio:
The Reactome pathway Knowledgebase. Nucleic Acids Res. 44(Database-Issue): 481-487 (2016) - [j7]Anwesha Bohler, Guanming Wu, Martina Kutmon, Leontius Adhika Pradhana, Susan L. Coort, Kristina Hanspers, Robin Haw, Alexander R. Pico, Chris T. A. Evelo:
Reactome from a WikiPathways Perspective. PLoS Comput. Biol. 12(5) (2016) - 2014
- [j6]Steven Jupe, Bijay Jassal, Mark Williams, Guanming Wu:
A controlled vocabulary for pathway entities and events. Database J. Biol. Databases Curation 2014 (2014) - [j5]David Croft, Antonio Fabregat Mundo, Robin Haw, Marija Milacic, Joel Weiser, Guanming Wu, Michael Caudy, Phani V. Garapati, Marc Gillespie, Maulik R. Kamdar, Bijay Jassal, Steven Jupe, Lisa Matthews, Bruce May, Stanislav Palatnik, Karen Rothfels, Veronica Shamovsky, Heeyeon Song, Mark Williams, Ewan Birney, Henning Hermjakob, Lincoln Stein, Peter D'Eustachio:
The Reactome pathway knowledgebase. Nucleic Acids Res. 42(Database-Issue): 472-477 (2014) - [j4]Marcela K. Monaco, Joshua C. Stein, Sushma Naithani, Sharon Wei, Palitha Dharmawardhana, Sunita Kumari, Vindhya Amarasinghe, Ken Youens-Clark, James Thomason, Justin Preece, Shiran Pasternak, Andrew Olson, Yinping Jiao, Zhenyuan Lu, Daniel M. Bolser, Arnaud Kerhornou, Daniel M. Staines, Brandon Walts, Guanming Wu, Peter D'Eustachio, Robin Haw, David Croft, Paul J. Kersey, Lincoln Stein, Pankaj Jaiswal, Doreen Ware:
Gramene 2013: comparative plant genomics resources. Nucleic Acids Res. 42(Database-Issue): 1193-1199 (2014) - [i1]Guanming Wu, Eric T. Dawson, Adrian Duong, Robin Haw, Lincoln Stein:
ReactomeFIViz: the Reactome FI Cytoscape app for pathway and network-based data analysis. F1000Research 3: 146 (2014) - 2011
- [j3]David Croft, Gavin O'Kelly, Guanming Wu, Robin Haw, Marc Gillespie, Lisa Matthews, Michael Caudy, Phani V. Garapati, Gopal Gopinath, Bijay Jassal, Steven Jupe, Irina Kalatskaya, Shahana Mahajan, Bruce May, Nelson Ndegwa, Esther Schmidt, Veronica Shamovsky, Christina K. Yung, Ewan Birney, Henning Hermjakob, Peter D'Eustachio, Lincoln Stein:
Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res. 39(Database-Issue): 691-697 (2011)
2000 – 2009
- 2009
- [j2]Lisa Matthews, Gopal Gopinath, Marc Gillespie, Michael Caudy, David Croft, Bernard de Bono, Phani V. Garapati, Jill Hemish, Henning Hermjakob, Bijay Jassal, Alexander Kanapin, Suzanna Lewis, Shahana Mahajan, Bruce May, Esther Schmidt, Imre Vastrik, Guanming Wu, Ewan Birney, Lincoln Stein, Peter D'Eustachio:
Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 37(Database-Issue): 619-622 (2009) - 2007
- [j1]Bernard de Bono, Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Gopal Gopinath, David Croft, Marc Gillespie, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Guanming Wu, Ewan Birney, Lincoln Stein:
Reactome: An integrated expert model of human molecular processes and access toolkit. J. Integr. Bioinform. 4(3) (2007) - 2006
- [c1]Esther Schmidt, Ewan Birney, David Croft, Bernard de Bono, Peter D'Eustachio, Marc Gillespie, Gopal Gopinath, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Lincoln Stein, Imre Vastrik, Guanming Wu:
Reactome - A Knowledgebase of Biological Pathways. OTM Workshops (1) 2006: 710-719
Coauthor Index
aka: Lincoln D. Stein
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