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1. Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0

Author

Rougny Adrien, Touré Vasundra, Moodie Stuart, Balaur Irina, Czauderna Tobias, Borlinghaus Hanna, Dogrusoz Ugur, Mazein Alexander, Dräger Andreas, Blinov Michael L., Villéger Alice, Haw Robin, Demir Emek, Mi Huaiyu, Sorokin Anatoly, Schreiber Falk, and Luna Augustin

Subjects
biological network, circuit diagram, sbgn, standard, systems biology, visualisation, Biotechnology, TP248.13-248.65
Abstract

The Systems Biology Graphical Notation (SBGN) is an international community effort that aims to standardise the visualisation of pathways and networks for readers with diverse scientific backgrounds as well as to support an efficient and accurate exchange of biological knowledge between disparate research communities, industry, and other players in systems biology. SBGN comprises the three languages Entity Relationship, Activity Flow, and Process Description (PD) to cover biological and biochemical systems at distinct levels of detail. PD is closest to metabolic and regulatory pathways found in biological literature and textbooks. Its well-defined semantics offer a superior precision in expressing biological knowledge. PD represents mechanistic and temporal dependencies of biological interactions and transformations as a graph. Its different types of nodes include entity pools (e.g. metabolites, proteins, genes and complexes) and processes (e.g. reactions, associations and influences). The edges describe relationships between the nodes (e.g. consumption, production, stimulation and inhibition). This document details Level 1 Version 2.0 of the PD specification, including several improvements, in particular: 1) the addition of the equivalence operator, subunit, and annotation glyphs, 2) modification to the usage of submaps, and 3) updates to clarify the use of various glyphs (i.e. multimer, empty set, and state variable).

Published
2019
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2. Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2

Author

Mi Huaiyu, Schreiber Falk, Moodie Stuart, Czauderna Tobias, Demir Emek, Haw Robin, Luna Augustin, Le Novère Nicolas, Sorokin Anatoly, and Villéger Alice

Subjects
Biotechnology, TP248.13-248.65
Abstract

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail.

Published
2015
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3. Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2

Author

Sorokin Anatoly, Le Novère Nicolas, Luna Augustin, Czauderna Tobias, Demir Emek, Haw Robin, Mi Huaiyu, Moodie Stuart, Schreiber Falk, and Villéger Alice

Subjects
Biotechnology, TP248.13-248.65
Abstract

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail.

Published
2015
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4. JBrowse 2: a modular genome browser with views of synteny and structural variation

Author

Diesh, Colin, Stevens, Garrett J, Xie, Peter, De Jesus Martinez, Teresa, Hershberg, Elliot A, Leung, Angel, Guo, Emma, Dider, Shihab, Zhang, Junjun, Bridge, Caroline, Hogue, Gregory, Duncan, Andrew, Morgan, Matthew, Flores, Tia, Bimber, Benjamin N, Haw, Robin, Cain, Scott, Buels, Robert M, Stein, Lincoln D, and Holmes, Ian H

Subjects
Information and Computing Sciences, Biological Sciences, Genetics, Bioengineering, Human Genome, Generic health relevance, Genomics, Software, Synteny, Genome, Biological Evolution, Web Browser, Internet, Environmental Sciences, Bioinformatics
Abstract

We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. It retains core features of JBrowse while adding new views for synteny, dotplots, breakpoints, gene fusions, and whole-genome overviews. It allows users to share sessions, open multiple genomes, and navigate between views. It can be embedded in a web page, used as a standalone application, or run from Jupyter notebooks or R sessions. These improvements are enabled by a ground-up redesign using modern web technology. We describe application functionality, use cases, performance benchmarks, and implementation notes for web administrators and developers.

Published
2023

5. Erratum To: COVID‐19 Disease Map, a computational knowledge repository of virus‐host interaction mechanisms

Author

Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert, Orta‐Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Fobo, Gisela, Montrone, Corinna, Brauner, Barbara, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Kumar Gupta, Shailendra, Scheel, Julia, Borlinghaus, Hanna, Czauderna, Tobias, Schreiber, Falk, Montagud, Arnau, Ponce de Leon, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G, Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Ackerman, Emily E, Shoemaker, Jason E, Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yağmur, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Eijssen, Lars, Ehrhart, Friederike, Rex, D A B, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Orlic‐Milacic, Marija, Senff‐Ribeiro, Andrea, Rothfels, Karen, Shamovsky, Veronica, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean‐Marie, Fraser, Rupsha, Ortseifen, Vera, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Hu, Xiaoming, Overall, Rupert W, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M, Bachman, John A, Vega, Carlos, Grouès, Valentin, Vazquez, Miguel, Porras, Pablo, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, de Waard, Anita, Turei, Denes, Luna, Augustin, Babur, Ozgun, Soliman, Sylvain, Valdeolivas, Alberto, Esteban‐Medina, Marina, Peña‐Chilet, Maria, Rian, Kinza, Helikar, Tomáš, Puniya, Bhanwar Lal, Modos, Dezso, Treveil, Agatha, Olbei, Marton, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurélien, Naldi, Aurélien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C, Augé, Franck, Beckmann, Jacques S, Hasenauer, Jan, Wolkenhauer, Olaf, Willighagen, Egon L, Pico, Alexander R, Evelo, Chris T, Gillespie, Marc E, Stein, Lincoln D, Hermjakob, Henning, D'Eustachio, Peter, Saez‐Rodriguez, Julio, Dopazo, Joaquin, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, and Schneider, Reinhard

Published
2021
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6. COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

Author

Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert, Orta‐Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Fobo, Gisela, Montrone, Corinna, Brauner, Barbara, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Kumar Gupta, Shailendra, Scheel, Julia, Borlinghaus, Hanna, Czauderna, Tobias, Schreiber, Falk, Montagud, Arnau, Ponce de Leon, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G, Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Ackerman, Emily E, Shoemaker, Jason E, Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yağmur, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Eijssen, Lars, Ehrhart, Friederike, Rex, Devasahayam Arokia Balaya, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Orlic‐Milacic, Marija, Senff-Ribeiro, Andrea, Rothfels, Karen, Shamovsky, Veronica, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean‐Marie, Fraser, Rupsha, Ortseifen, Vera, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Hu, Xiaoming, Overall, Rupert W, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M, Bachman, John A, Vega, Carlos, Grouès, Valentin, Vazquez, Miguel, Porras, Pablo, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, de Waard, Anita, Turei, Denes, Luna, Augustin, Babur, Ozgun, Soliman, Sylvain, Valdeolivas, Alberto, Esteban‐Medina, Marina, Peña‐Chilet, Maria, Rian, Kinza, Helikar, Tomáš, Puniya, Bhanwar Lal, Modos, Dezso, Treveil, Agatha, Olbei, Marton, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurélien, Naldi, Aurélien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C, Augé, Franck, Beckmann, Jacques S, Hasenauer, Jan, Wolkenhauer, Olaf, Willighagen, Egon L, Pico, Alexander R, Evelo, Chris T, Gillespie, Marc E, Stein, Lincoln D, Hermjakob, Henning, D'Eustachio, Peter, Saez‐Rodriguez, Julio, Dopazo, Joaquin, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, and Schneider, Reinhard

Published
2021
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7. The Reactome Pathway Knowledgebase 2024

Author

Milacic, Marija, primary, Beavers, Deidre, additional, Conley, Patrick, additional, Gong, Chuqiao, additional, Gillespie, Marc, additional, Griss, Johannes, additional, Haw, Robin, additional, Jassal, Bijay, additional, Matthews, Lisa, additional, May, Bruce, additional, Petryszak, Robert, additional, Ragueneau, Eliot, additional, Rothfels, Karen, additional, Sevilla, Cristoffer, additional, Shamovsky, Veronica, additional, Stephan, Ralf, additional, Tiwari, Krishna, additional, Varusai, Thawfeek, additional, Weiser, Joel, additional, Wright, Adam, additional, Wu, Guanming, additional, Stein, Lincoln, additional, Hermjakob, Henning, additional, and D’Eustachio, Peter, additional

Published
2023
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8. Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes

Author

Orlic-Milacic, Marija, primary, Rothfels, Karen, additional, Matthews, Lisa, additional, Wright, Adam, additional, Jassal, Bijay, additional, Shamovsky, Veronica, additional, Trinh, Quang, additional, Gillespie, Marc, additional, Sevilla, Cristoffer, additional, Tiwari, Krishna, additional, Ragueneau, Eliot, additional, Gong, Chuqiao, additional, Stephan, Ralf, additional, May, Bruce, additional, Haw, Robin, additional, Weiser, Joel, additional, Beavers, Deidre, additional, Conley, Patrick, additional, Hermjakob, Henning, additional, Stein, Lincoln D., additional, D’Eustachio, Peter, additional, and Wu, Guanming, additional

Published
2023
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9. BioMart Central Portal: an open database network for the biological community

Author

Guberman, Jonathan M, Ai, J, Arnaiz, O, Baran, Joachim, Blake, Andrew, Baldock, Richard, Chelala, Claude, Croft, David, Cros, Anthony, Cutts, Rosalind J, Di Génova, A, Forbes, Simon, Fujisawa, T, Gadaleta, E, Goodstein, DM, Gundem, Gunes, Haggarty, Bernard, Haider, Syed, Hall, Matthew, Harris, Todd, Haw, Robin, Hu, S, Hubbard, Simon, Hsu, Jack, Iyer, Vivek, Jones, Philip, Katayama, Toshiaki, Kinsella, R, Kong, Lei, Lawson, Daniel, Liang, Yong, Lopez-Bigas, Nuria, Luo, J, Lush, Michael, Mason, Jeremy, Moreews, Francois, Ndegwa, Nelson, Oakley, Darren, Perez-Llamas, Christian, Primig, Michael, Rivkin, Elena, Rosanoff, S, Shepherd, Rebecca, Simon, Reinhard, Skarnes, B, Smedley, Damian, Sperling, Linda, Spooner, William, Stevenson, Peter, Stone, Kevin, Teague, J, Wang, Jun, Wang, Jianxin, Whitty, Brett, Wong, DT, Wong-Erasmus, Marie, Yao, L, Youens-Clark, Ken, Yung, Christina, Zhang, Junjun, and Kasprzyk, Arek

Subjects
Networking and Information Technology R&D (NITRD), Aetiology, 2.6 Resources and infrastructure (aetiology), Animals, Bacteria, Biomedical Research, Database Management Systems, Databases, Factual, Fungi, Genome, Humans, International Cooperation, Internet, User-Computer Interface, Viruses, Data Format, Library and Information Studies
Abstract

BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities.

Published
2011

10. Illuminate the Functions of Dark Proteins Using the Reactome‐IDG Web Portal

Author

Beavers, Deidre, primary, Brunson, Timothy, additional, Sanati, Nasim, additional, Matthews, Lisa, additional, Haw, Robin, additional, Shorser, Solomon, additional, Sevilla, Cristoffer, additional, Viteri, Guilherme, additional, Conley, Patrick, additional, Rothfels, Karen, additional, Hermjakob, Henning, additional, Stein, Lincoln, additional, D'Eustachio, Peter, additional, and Wu, Guanming, additional

Published
2023
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11. The Reactome Pathway Knowledgebase 2024.

Author

Milacic, Marija, Beavers, Deidre, Conley, Patrick, Gong, Chuqiao, Gillespie, Marc, Griss, Johannes, Haw, Robin, Jassal, Bijay, Matthews, Lisa, May, Bruce, Petryszak, Robert, Ragueneau, Eliot, Rothfels, Karen, Sevilla, Cristoffer, Shamovsky, Veronica, Stephan, Ralf, Tiwari, Krishna, Varusai, Thawfeek, Weiser, Joel, and Wright, Adam

Published
2024
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14. Illuminating Dark Proteins using Reactome Pathways

Author

Brunson, Timothy, primary, Sanati, Nasim, additional, Matthews, Lisa, additional, Haw, Robin, additional, Beavers, Deidre, additional, Shorser, Solomon, additional, Sevilla, Cristoffer, additional, Viteri, Guilherme, additional, Conley, Patrick, additional, Rothfels, Karen, additional, Hermjakob, Henning, additional, Stein, Lincoln, additional, D’Eustachio, Peter, additional, and Wu, Guanming, additional

Published
2023
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15. Using the Reactome Database

Author

Rothfels, Karen, primary, Milacic, Marija, additional, Matthews, Lisa, additional, Haw, Robin, additional, Sevilla, Cristoffer, additional, Gillespie, Marc, additional, Stephan, Ralf, additional, Gong, Chuqiao, additional, Ragueneau, Eliot, additional, May, Bruce, additional, Shamovsky, Veronica, additional, Wright, Adam, additional, Weiser, Joel, additional, Beavers, Deidre, additional, Conley, Patrick, additional, Tiwari, Krishna, additional, Jassal, Bijay, additional, Griss, Johannes, additional, Senff‐Ribeiro, Andrea, additional, Brunson, Timothy, additional, Petryszak, Robert, additional, Hermjakob, Henning, additional, D'Eustachio, Peter, additional, Wu, Guanming, additional, and Stein, Lincoln, additional

Published
2023
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16. Functional Annotation of Disease Variants in Reactome

Author

Orlic-Milacic, Marija, Rothfels, Karen, Matthews, Lisa, Wright, Adam, Jassal, Bijay, Shamovsky, Veronica, Trinh, Quang, Gillespie, Marc, Sevilla, Cristoffer, Tiwari, Krishna, Ragueneau, Eliot, Gong, Chuqiao, Stephan, Ralf, May, Bruce, Haw, Robin, Weiser, Joel, Beavers, Deidre, Conley, Patrick, Hermjakob, Henning, Stein, Lincoln D., D'Eustachio, Peter, and Wu, Guanming

Abstract

Supplementary Tables and Supplementary Methods for the research article "Functional Annotation of Disease Variants in Reactome".

Published
2023
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17. Illuminating Dark Proteins using Reactome Pathways

Author

Brunson, Timothy, Sanati, Nasim, Matthews, Lisa, Haw, Robin, Beavers, Deidre, Shorser, Solomon, Sevilla, Cristoffer, Conley, Patrick, Rothfels, Karen, Hermjakob, Henning, Stein, Lincoln, D'Eustachio, Peter, and Wu, Guanming

Subjects
dark proteins, Reactome, pathways, random forest, fuzzy logic simulation, interacting pathways, BERT, NLP, scRNA-seq
Abstract

Limited knowledge about a substantial portion of protein coding genes, known as "dark" proteins, hinders our understanding of their functions and potential therapeutic applications. To address this, we leveraged Reactome, the most comprehensive, open source, open-access pathway knowledgebase, to contextualize dark proteins within biological pathways. By integrating multiple resources and employing a Random Forest classifier trained on 106 protein/gene pairwise features, we predicted functional interactions between dark proteins and Reactome-annotated proteins. We then developed three scores to measure the interactions between dark proteins and Reactome pathways, utilizing enrichment analysis and fuzzy logic simulations. Correlation analysis of these scores with an independent single-cell RNA sequencing dataset provided supporting evidence for this approach. Furthermore, systematic natural language processing (NLP) analysis of over 22 million PubMed abstracts and manual checking of the literature associated with 20 randomly selected dark proteins reinforced the predicted interactions between proteins and pathways. To enhance the visualization and exploration of dark proteins within Reactome pathways, we developed the Reactome IDG portal, deployed athttps://idg.reactome.org, a web application featuring tissue-specific protein and gene expression overlay, as well as drug interactions. Our integrated computational approach, together with the user-friendly web platform, offers a valuable resource for uncovering potential biological functions and therapeutic implications of dark proteins.

Published
2023
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18. JBrowse Jupyter: a Python interface to JBrowse 2

Author

De Jesus Martinez, Teresa, primary, Hershberg, Elliot A, additional, Guo, Emma, additional, Stevens, Garrett J, additional, Diesh, Colin, additional, Xie, Peter, additional, Bridge, Caroline, additional, Cain, Scott, additional, Haw, Robin, additional, Buels, Robert M, additional, Stein, Lincoln D, additional, and Holmes, Ian H, additional

Published
2023
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20. JBrowse 2: A modular genome browser with views of synteny and structural variation

Author

Diesh, Colin, primary, Stevens, Garrett J, additional, Xie, Peter, additional, De Jesus Martinez, Teresa, additional, Hershberg, Elliot A., additional, Leung, Angel, additional, Guo, Emma, additional, Dider, Shihab, additional, Zhang, Junjun, additional, Bridge, Caroline, additional, Hogue, Gregory, additional, Duncan, Andrew, additional, Morgan, Matthew, additional, Flores, Tia, additional, Bimber, Benjamin N., additional, Haw, Robin, additional, Cain, Scott, additional, Buels, Robert M., additional, Stein, Lincoln D., additional, and Holmes, Ian H., additional

Published
2022
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21. Abstract LB503: Using JBrowse 2 plugins to visualize cancer genomic data

Author

Haw, Robin Andrew, primary, Diesh, Colin, additional, Bridge, Caroline, additional, Buels, Rob, additional, Stevens, Garrett, additional, Xie, Peter, additional, Martinez, Teresa, additional, Hershberg, Elliot, additional, Zhang, Junjun, additional, Dider, Shihab, additional, Cain, Scott, additional, Stein, Lincoln, additional, and Holmes, Ian, additional

Published
2022
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23. JBrowse Jupyter: A Python interface to JBrowse 2

Author

Martinez, Teresa De Jesus, primary, Hershberg, Elliot A., additional, Guo, Emma, additional, Stevens, Garrett J, additional, Diesh, Colin, additional, Xie, Peter, additional, Bridge, Caroline, additional, Cain, Scott, additional, Haw, Robin, additional, Buels, Robert M., additional, Stein, Lincoln D., additional, and Holmes, Ian H., additional

Published
2022
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25. The reactome pathway knowledgebase 2022

Author

Gillespie, Marc, primary, Jassal, Bijay, additional, Stephan, Ralf, additional, Milacic, Marija, additional, Rothfels, Karen, additional, Senff-Ribeiro, Andrea, additional, Griss, Johannes, additional, Sevilla, Cristoffer, additional, Matthews, Lisa, additional, Gong, Chuqiao, additional, Deng, Chuan, additional, Varusai, Thawfeek, additional, Ragueneau, Eliot, additional, Haider, Yusra, additional, May, Bruce, additional, Shamovsky, Veronica, additional, Weiser, Joel, additional, Brunson, Timothy, additional, Sanati, Nasim, additional, Beckman, Liam, additional, Shao, Xiang, additional, Fabregat, Antonio, additional, Sidiropoulos, Konstantinos, additional, Murillo, Julieth, additional, Viteri, Guilherme, additional, Cook, Justin, additional, Shorser, Solomon, additional, Bader, Gary, additional, Demir, Emek, additional, Sander, Chris, additional, Haw, Robin, additional, Wu, Guanming, additional, Stein, Lincoln, additional, Hermjakob, Henning, additional, and D’Eustachio, Peter, additional

Published
2021
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26. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

Author

Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Fonds National de la Recherche - FnR [sponsor], Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert, Orta-Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Fobo, Gisela, Montrone, Corinna, Brauner, Barbara, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Kumar Gupta, Shailendra, Scheel, Julia, Borlinghaus, Hanna, Czauderna, Tobias, Schreiber, Falk, Montagud, Arnau, Ponce de Leon, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G., Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Ackerman, Emily E., Shoemaker, Jason E., Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yağmur, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Eijssen, Lars, Ehrhart, Friederike, Rex, Devasahayam Arokia Balaya, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Orlic-Milacic, Marija, Senff Ribeiro, Andrea, Rothfels, Karen, Shamovsky, Veronica, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean-Marie, Fraser, Rupsha, Ortseifen, Vera, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Hu, Xiaoming, Overall, Rupert W., Maier, Dieter, Bauch, Angela, Gyori, Benjamin M., Bachman, John A., Vega, Carlos, Groues, Valentin, Vazquez, Miguel, Porras, Pablo, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, de Waard, Anita, Turei, Denes, Luna, Augustin, Babur, Ozgun, Soliman, Sylvain, Valdeolivas, Alberto, Esteban-Medina, Marina, Peña-Chilet, Maria, Rian, Kinza, Helikar, Tomáš, Puniya, Bhanwar Lal, Modos, Dezso, Treveil, Agatha, Olbei, Marton, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurélien, Naldi, Aurélien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C., Augé, Franck, Beckmann, Jacques S., Hasenauer, Jan, Wolkenhauer, Olaf, Wilighagen, Egon L., Pico, Alexander R., Evelo, Chris T., Gillespie, Marc E., Stein, Lincoln D., Hermjakob, Henning, D'Eustachio, Peter, Saez-Rodriguez, Julio, Dopazo, Joaquin, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard, Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], Fonds National de la Recherche - FnR [sponsor], Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert, Orta-Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Fobo, Gisela, Montrone, Corinna, Brauner, Barbara, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Kumar Gupta, Shailendra, Scheel, Julia, Borlinghaus, Hanna, Czauderna, Tobias, Schreiber, Falk, Montagud, Arnau, Ponce de Leon, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G., Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Ackerman, Emily E., Shoemaker, Jason E., Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yağmur, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Eijssen, Lars, Ehrhart, Friederike, Rex, Devasahayam Arokia Balaya, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Orlic-Milacic, Marija, Senff Ribeiro, Andrea, Rothfels, Karen, Shamovsky, Veronica, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean-Marie, Fraser, Rupsha, Ortseifen, Vera, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Hu, Xiaoming, Overall, Rupert W., Maier, Dieter, Bauch, Angela, Gyori, Benjamin M., Bachman, John A., Vega, Carlos, Groues, Valentin, Vazquez, Miguel, Porras, Pablo, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, de Waard, Anita, Turei, Denes, Luna, Augustin, Babur, Ozgun, Soliman, Sylvain, Valdeolivas, Alberto, Esteban-Medina, Marina, Peña-Chilet, Maria, Rian, Kinza, Helikar, Tomáš, Puniya, Bhanwar Lal, Modos, Dezso, Treveil, Agatha, Olbei, Marton, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurélien, Naldi, Aurélien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C., Augé, Franck, Beckmann, Jacques S., Hasenauer, Jan, Wolkenhauer, Olaf, Wilighagen, Egon L., Pico, Alexander R., Evelo, Chris T., Gillespie, Marc E., Stein, Lincoln D., Hermjakob, Henning, D'Eustachio, Peter, Saez-Rodriguez, Julio, Dopazo, Joaquin, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, and Schneider, Reinhard

Abstract

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.

Published
2021

27. COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

Author

Fonds National de la Recherche Luxembourg, European Commission, Federal Ministry of Education and Research (Germany), Ministry of Science, Research and Art Baden-Württemberg, German Center for Infection Research, Netherlands Organisation for Health Research and Development, National Institutes of Health (US), European Molecular Biology Laboratory, Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert, Orta-Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Schreiber, Falk, Montagud, Arnau, Ponce de León, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G., Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Orlic-Milacic, Marija, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Senff Ribeiro, Andrea, Ackerman, Emily E., Shoemaker, Jason E., Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yagmu, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Rothfels, Karen, Eijssen, Lars, Ehrhart, Friederike, Arokia Balaya Rex, Devasahayam, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Shamovsky, Veronic, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean-Marie, Fraser, Rupsha, Ortseifen, Vera, Soliman, Sylvain, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Valdeolivas, Alberto, Hu, Xiaoming, Overall, Rupert W., Maier, Dieter, Bauch, Angela, Gyori, Benjamin M., Bachman, John A., Vega, Carlos, Groues, Valentin, Vázquez, Miguel, Porras, Pablo, Esteban-Medina, Marina, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, Waard, Anita de, Turei, Denes, Luna, Augustín, Babur, Ozgun, Peña-Chilet, María, Rian, Kinza, Helikar, Tomas, Lal Puniya, Bhanwar, Modos, Dezso, Treveil, Agatha, Olbe, Marton, Fobo, Gisela, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurelien, Naldi, Aurelien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C., Montrone, Corinna, Auge, Franck, Beckmann, Jacques S., Hasenauer, Jan, Wolkenhauer, Olaf, Wilighagen, Egon L ., Pico, Alexander R., Evelo, Chris T., Gillespie, Marc E., Stein, Lincoln D., Hermjakob, Henning, Brauner, Barbara, D’Eustachio, Peter, Sáez-Rodríguez, Julio, Dopazo, Joaquín, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Gupta, Shailendra Kumar, Scheel, Julia, Borlinghaus, Hanna, Czauderna, Tobias, Fonds National de la Recherche Luxembourg, European Commission, Federal Ministry of Education and Research (Germany), Ministry of Science, Research and Art Baden-Württemberg, German Center for Infection Research, Netherlands Organisation for Health Research and Development, National Institutes of Health (US), European Molecular Biology Laboratory, Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert, Orta-Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Schreiber, Falk, Montagud, Arnau, Ponce de León, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G., Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Orlic-Milacic, Marija, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Senff Ribeiro, Andrea, Ackerman, Emily E., Shoemaker, Jason E., Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yagmu, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Rothfels, Karen, Eijssen, Lars, Ehrhart, Friederike, Arokia Balaya Rex, Devasahayam, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Shamovsky, Veronic, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean-Marie, Fraser, Rupsha, Ortseifen, Vera, Soliman, Sylvain, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Valdeolivas, Alberto, Hu, Xiaoming, Overall, Rupert W., Maier, Dieter, Bauch, Angela, Gyori, Benjamin M., Bachman, John A., Vega, Carlos, Groues, Valentin, Vázquez, Miguel, Porras, Pablo, Esteban-Medina, Marina, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, Waard, Anita de, Turei, Denes, Luna, Augustín, Babur, Ozgun, Peña-Chilet, María, Rian, Kinza, Helikar, Tomas, Lal Puniya, Bhanwar, Modos, Dezso, Treveil, Agatha, Olbe, Marton, Fobo, Gisela, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurelien, Naldi, Aurelien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C., Montrone, Corinna, Auge, Franck, Beckmann, Jacques S., Hasenauer, Jan, Wolkenhauer, Olaf, Wilighagen, Egon L ., Pico, Alexander R., Evelo, Chris T., Gillespie, Marc E., Stein, Lincoln D., Hermjakob, Henning, Brauner, Barbara, D’Eustachio, Peter, Sáez-Rodríguez, Julio, Dopazo, Joaquín, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Gupta, Shailendra Kumar, Scheel, Julia, Borlinghaus, Hanna, and Czauderna, Tobias

Abstract

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.

Published
2021

28. Gramene 2013: comparative plant genomics resources

Author

Monaco, Marcela K., Stein, Joshua, Naithani, Sushma, Wei, Sharon, Dharmawardhana, Palitha, Kumari, Sunita, Amarasinghe, Vindhya, Youens-Clark, Ken, Thomason, James, Preece, Justin, Pasternak, Shiran, Olson, Andrew, Jiao, Yinping, Lu, Zhenyuan, Bolser, Dan, Kerhornou, Arnaud, Staines, Dan, Walts, Brandon, Wu, Guanming, DʼEustachio, Peter, Haw, Robin, Croft, David, Kersey, Paul J., Stein, Lincoln, Jaiswal, Pankaj, and Ware, Doreen

Published
2014
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29. The Reactome pathway knowledgebase

Author

Croft, David, Mundo, Antonio Fabregat, Haw, Robin, Milacic, Marija, Weiser, Joel, Wu, Guanming, Caudy, Michael, Garapati, Phani, Gillespie, Marc, Kamdar, Maulik R., Jassal, Bijay, Jupe, Steven, Matthews, Lisa, May, Bruce, Palatnik, Stanislav, Rothfels, Karen, Shamovsky, Veronica, Song, Heeyeon, Williams, Mark, Birney, Ewan, Hermjakob, Henning, Stein, Lincoln, and DʼEustachio, Peter

Published
2014
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31. Reactome: a database of reactions, pathways and biological processes

Author

Croft, David, O’Kelly, Gavin, Wu, Guanming, Haw, Robin, Gillespie, Marc, Matthews, Lisa, Caudy, Michael, Garapati, Phani, Gopinath, Gopal, Jassal, Bijay, Jupe, Steven, Kalatskaya, Irina, Mahajan, Shahana, May, Bruce, Ndegwa, Nelson, Schmidt, Esther, Shamovsky, Veronica, Yung, Christina, Birney, Ewan, Hermjakob, Henning, D’Eustachio, Peter, and Stein, Lincoln

Published
2011
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32. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

Author

Krogan, Nevan J., Cagney, Gerard, Yu, Haiyuan, Zhong, Gouqing, Guo, Xinghua, Ignatchenko, Alexandr, Li, Joyce, Pu, Shuye, Datta, Nira, Tikuisis, Aaron P., Punna, Thanuja, Peregrín-Alvarez, José M., Shales, Michael, Zhang, Xin, Davey, Michael, Robinson, Mark D., Paccanaro, Alberto, Bray, James E., Sheung, Anthony, Beattie, Bryan, Richards, Dawn P., Canadien, Veronica, Lalev, Atanas, Mena, Frank, Wong, Peter, Starostine, Andrei, Canete, Myra M., Vlasblom, James, Wu, Samuel, Orsi, Chris, Collins, Sean R., Chandran, Shamanta, Haw, Robin, Rilstone, Jennifer J., Gandi, Kiran, Thompson, Natalie J., Musso, Gabe, St Onge, Peter, Ghanny, Shaun, Lam, Mandy H. Y., Butland, Gareth, Altaf-Ul, Amin M., Kanaya, Shigehiko, Shilatifard, Ali, O'Shea, Erin, Weissman, Jonathan S., Ingles, C. James, Hughes, Timothy R., Parkinson, John, Gerstein, Mark, Wodak, Shoshana J., Emili, Andrew, and Greenblatt, Jack F.

Published
2006

33. The reactome pathway knowledgebase

Author

Jassal, Bijay, primary, Matthews, Lisa, additional, Viteri, Guilherme, additional, Gong, Chuqiao, additional, Lorente, Pascual, additional, Fabregat, Antonio, additional, Sidiropoulos, Konstantinos, additional, Cook, Justin, additional, Gillespie, Marc, additional, Haw, Robin, additional, Loney, Fred, additional, May, Bruce, additional, Milacic, Marija, additional, Rothfels, Karen, additional, Sevilla, Cristoffer, additional, Shamovsky, Veronica, additional, Shorser, Solomon, additional, Varusai, Thawfeek, additional, Weiser, Joel, additional, Wu, Guanming, additional, Stein, Lincoln, additional, Hermjakob, Henning, additional, and D’Eustachio, Peter, additional

Published
2019
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34. Reactome and ORCID—fine-grained credit attribution for community curation

Author

Viteri, Guilherme, primary, Matthews, Lisa, additional, Varusai, Thawfeek, additional, Gillespie, Marc, additional, Milacic, Marija, additional, Cook, Justin, additional, Weiser, Joel, additional, Shorser, Solomon, additional, Sidiropoulos, Konstantinos, additional, Fabregat, Antonio, additional, Haw, Robin, additional, Wu, Guanming, additional, Stein, Lincoln, additional, D’Eustachio, Peter, additional, and Hermjakob, Henning, additional

Published
2019
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35. The reactome pathway knowledgebase.

Author

Jassal, Bijay, Matthews, Lisa, Viteri, Guilherme, Gong, Chuqiao, Lorente, Pascual, Fabregat, Antonio, Sidiropoulos, Konstantinos, Cook, Justin, Gillespie, Marc, Haw, Robin, Loney, Fred, May, Bruce, Milacic, Marija, Rothfels, Karen, Sevilla, Cristoffer, Shamovsky, Veronica, Shorser, Solomon, Varusai, Thawfeek, Weiser, Joel, and Wu, Guanming

Published
2020
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36. The Reactome Pathway Knowledgebase

Author

Fabregat, Antonio, primary, Jupe, Steven, additional, Matthews, Lisa, additional, Sidiropoulos, Konstantinos, additional, Gillespie, Marc, additional, Garapati, Phani, additional, Haw, Robin, additional, Jassal, Bijay, additional, Korninger, Florian, additional, May, Bruce, additional, Milacic, Marija, additional, Roca, Corina Duenas, additional, Rothfels, Karen, additional, Sevilla, Cristoffer, additional, Shamovsky, Veronica, additional, Shorser, Solomon, additional, Varusai, Thawfeek, additional, Viteri, Guilherme, additional, Weiser, Joel, additional, Wu, Guanming, additional, Stein, Lincoln, additional, Hermjakob, Henning, additional, and D’Eustachio, Peter, additional

Published
2017
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37. Reactome enhanced pathway visualization

Author

Sidiropoulos, Konstantinos, primary, Viteri, Guilherme, additional, Sevilla, Cristoffer, additional, Jupe, Steve, additional, Webber, Marissa, additional, Orlic-Milacic, Marija, additional, Jassal, Bijay, additional, May, Bruce, additional, Shamovsky, Veronica, additional, Duenas, Corina, additional, Rothfels, Karen, additional, Matthews, Lisa, additional, Song, Heeyeon, additional, Stein, Lincoln, additional, Haw, Robin, additional, D’Eustachio, Peter, additional, Ping, Peipei, additional, Hermjakob, Henning, additional, and Fabregat, Antonio, additional

Published
2017
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38. Reactome from a WikiPathways Perspective

Author

Bohler, Anwesha, primary, Wu, Guanming, additional, Kutmon, Martina, additional, Pradhana, Leontius Adhika, additional, Coort, Susan L., additional, Hanspers, Kristina, additional, Haw, Robin, additional, Pico, Alexander R., additional, and Evelo, Chris T., additional

Published
2016
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39. The Reactome Pathway Knowledgebase.

Author

Fabregat, Antonio, Jupe, Steven, Matthews, Lisa, Sidiropoulos, Konstantinos, Gillespie, Marc, Garapati, Phani, Haw, Robin, Jassal, Bijay, Korninger, Florian, and May, Bruce

Published
2018
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40. The Reactome pathway Knowledgebase

Author

Fabregat, Antonio, primary, Sidiropoulos, Konstantinos, additional, Garapati, Phani, additional, Gillespie, Marc, additional, Hausmann, Kerstin, additional, Haw, Robin, additional, Jassal, Bijay, additional, Jupe, Steven, additional, Korninger, Florian, additional, McKay, Sheldon, additional, Matthews, Lisa, additional, May, Bruce, additional, Milacic, Marija, additional, Rothfels, Karen, additional, Shamovsky, Veronica, additional, Webber, Marissa, additional, Weiser, Joel, additional, Williams, Mark, additional, Wu, Guanming, additional, Stein, Lincoln, additional, Hermjakob, Henning, additional, and D'Eustachio, Peter, additional

Published
2015
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44. The Reactome pathway knowledgebase

Author

Croft, David, primary, Mundo, Antonio Fabregat, additional, Haw, Robin, additional, Milacic, Marija, additional, Weiser, Joel, additional, Wu, Guanming, additional, Caudy, Michael, additional, Garapati, Phani, additional, Gillespie, Marc, additional, Kamdar, Maulik R., additional, Jassal, Bijay, additional, Jupe, Steven, additional, Matthews, Lisa, additional, May, Bruce, additional, Palatnik, Stanislav, additional, Rothfels, Karen, additional, Shamovsky, Veronica, additional, Song, Heeyeon, additional, Williams, Mark, additional, Birney, Ewan, additional, Hermjakob, Henning, additional, Stein, Lincoln, additional, and D'Eustachio, Peter, additional

Published
2013
Full Text
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45. Gramene 2013: comparative plant genomics resources

Author

Monaco, Marcela K., primary, Stein, Joshua, additional, Naithani, Sushma, additional, Wei, Sharon, additional, Dharmawardhana, Palitha, additional, Kumari, Sunita, additional, Amarasinghe, Vindhya, additional, Youens-Clark, Ken, additional, Thomason, James, additional, Preece, Justin, additional, Pasternak, Shiran, additional, Olson, Andrew, additional, Jiao, Yinping, additional, Lu, Zhenyuan, additional, Bolser, Dan, additional, Kerhornou, Arnaud, additional, Staines, Dan, additional, Walts, Brandon, additional, Wu, Guanming, additional, D’Eustachio, Peter, additional, Haw, Robin, additional, Croft, David, additional, Kersey, Paul J., additional, Stein, Lincoln, additional, Jaiswal, Pankaj, additional, and Ware, Doreen, additional

Published
2013
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46. The Reactome pathway Knowledgebase.

Author

Fabregat, Antonio, Sidiropoulos, Konstantinos, Garapati, Phani, Gillespie, Marc, Hausmann, Kerstin, Haw, Robin, Jassal, Bijay, Jupe, Steven, Korninger, Florian, McKay, Sheldon, Matthews, Lisa, May, Bruce, Milacic, Marija, Rothfels, Karen, Shamovsky, Veronica, Webber, Marissa, Weiser, Joel, Williams, Mark, Guanming Wu, and Stein, Lincoln

Published
2016
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47. Kruppel-Like Factor, Klf9, Promotes Proliferation of Notch-Independent Precursor T-Cell Lymphoblastic Lymphomas

Author

Wong, Peggy P. C., primary, Merico, Daniele, additional, Matei, Irina, additional, Ling, Vicki, additional, Bashir, Shaheena, additional, Chang, Stephen G., additional, Cheung, Queenie C. K., additional, Haw, Robin A., additional, Stueker, Oliver, additional, Montpellier, Bertrand, additional, Bader, Gary D., additional, Beyene, Joseph, additional, Danska, Jayne S., additional, and Guidos, Cynthia J., additional

Published
2012
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50. Erratum: Corrigendum: The BioPAX community standard for pathway data sharing

Author

Demir, Emek, primary, Cary, Michael P, additional, Paley, Suzanne, additional, Fukuda, Ken, additional, Lemer, Christian, additional, Vastrik, Imre, additional, Wu, Guanming, additional, D'Eustachio, Peter, additional, Schaefer, Carl, additional, Luciano, Joanne, additional, Schacherer, Frank, additional, Martinez-Flores, Irma, additional, Hu, Zhenjun, additional, Jimenez-Jacinto, Veronica, additional, Joshi-Tope, Geeta, additional, Kandasamy, Kumaran, additional, Lopez-Fuentes, Alejandra C, additional, Mi, Huaiyu, additional, Pichler, Elgar, additional, Rodchenkov, Igor, additional, Splendiani, Andrea, additional, Tkachev, Sasha, additional, Zucker, Jeremy, additional, Gopinath, Gopal, additional, Rajasimha, Harsha, additional, Ramakrishnan, Ranjani, additional, Shah, Imran, additional, Syed, Mustafa, additional, Anwar, Nadia, additional, Babur, Özgün, additional, Blinov, Michael, additional, Brauner, Erik, additional, Corwin, Dan, additional, Donaldson, Sylva, additional, Gibbons, Frank, additional, Goldberg, Robert, additional, Hornbeck, Peter, additional, Luna, Augustin, additional, Murray-Rust, Peter, additional, Neumann, Eric, additional, Reubenacker, Oliver, additional, Samwald, Matthias, additional, van Iersel, Martijn, additional, Wimalaratne, Sarala, additional, Allen, Keith, additional, Braun, Burk, additional, Whirl-Carrillo, Michelle, additional, Cheung, Kei-Hoi, additional, Dahlquist, Kam, additional, Finney, Andrew, additional, Gillespie, Marc, additional, Glass, Elizabeth, additional, Gong, Li, additional, Haw, Robin, additional, Honig, Michael, additional, Hubaut, Olivier, additional, Kane, David, additional, Krupa, Shiva, additional, Kutmon, Martina, additional, Leonard, Julie, additional, Marks, Debbie, additional, Merberg, David, additional, Petri, Victoria, additional, Pico, Alex, additional, Ravenscroft, Dean, additional, Ren, Liya, additional, Shah, Nigam, additional, Sunshine, Margot, additional, Tang, Rebecca, additional, Whaley, Ryan, additional, Letovksy, Stan, additional, Buetow, Kenneth H, additional, Rzhetsky, Andrey, additional, Schachter, Vincent, additional, Sobral, Bruno S, additional, Dogrusoz, Ugur, additional, McWeeney, Shannon, additional, Aladjem, Mirit, additional, Birney, Ewan, additional, Collado-Vides, Julio, additional, Goto, Susumu, additional, Hucka, Michael, additional, Le Novère, Nicolas, additional, Maltsev, Natalia, additional, Pandey, Akhilesh, additional, Thomas, Paul, additional, Wingender, Edgar, additional, Karp, Peter D, additional, Sander, Chris, additional, and Bader, Gary D, additional

Published
2012
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