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2020 – today
- 2023
[j18]Adrien Rougny
, Irina Balaur, Augustin Luna, Alexander Mazein:
StonPy: a tool to parse and query collections of SBGN maps in a graph database. Bioinform. 39(3) (2023)- [j17]Alexander Mazein, Marcio Luis Acencio, Irina Balaur, Adrien Rougny, Danielle Welter, Anna Niarakis, Diana Ramirez Ardila, Ugur Dogrusoz, Piotr Gawron, Venkata P. Satagopam, Wei Gu, Andreas Kremer, Reinhard Schneider, Marek Ostaszewski:
A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance. Frontiers Bioinform. 3 (2023) - 2022
- [j16]Irina Balaur, Ludovic Roy, Vasundra Touré, Alexander Mazein, Charles Auffray:
GraphML-SBGN bidirectional converter for metabolic networks. J. Integr. Bioinform. 19(4) (2022) - 2021
- [j15]Alexander Mazein, Adrien Rougny, Jonathan R. Karr, Julio Saez-Rodriguez, Marek Ostaszewski, Reinhard Schneider:
Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling. Briefings Bioinform. 22(5) (2021) - [j14]Adrien Rougny, Vasundra Touré, John Albanese, Dagmar Waltemath, Denis Shirshov, Anatoly A. Sorokin, Gary D. Bader, Michael L. Blinov, Alexander Mazein:
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. Briefings Bioinform. 22(5) (2021) - [j13]Hasan Balci, Metin Can Siper, Nasim Saleh, Ilkin Safarli, Ludovic Roy, Merve Kilicarslan, Rumeysa Ozaydin, Alexander Mazein, Charles Auffray, Özgün Babur, Emek Demir, Ugur Dogrusoz:
Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps. Bioinform. 37(10): 1475-1477 (2021) - 2020
- [j12]Martin Siebenhaller, Sune S. Nielsen, Fintan McGee, Irina Balaur, Charles Auffray, Alexander Mazein:
Human-like layout algorithms for signalling hypergraphs: outlining requirements. Briefings Bioinform. 21(1): 62-72 (2020) - [j11]Vidisha Singh, George D. Kalliolias, Marek Ostaszewski, Maëva Veyssiere, Eleftherios Pilalis, Piotr Gawron, Alexander Mazein, Eric Bonnet, Elisabeth Petit-Teixeira, Anna Niarakis:
RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis. Database J. Biol. Databases Curation 2020 (2020) - [j10]Irina Balaur, Ludovic Roy, Alexander Mazein, S. Gökberk Karaca, Ugur Dogrusoz, Emmanuel Barillot, Andrei Yu. Zinovyev:
cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats. Bioinform. 36(8): 2620-2622 (2020) - [j9]Irina Balaur, Ludovic Roy, Alexander Mazein, S. Gökberk Karaca, Ugur Dogrusoz, Emmanuel Barillot, Andrei Yu. Zinovyev:
cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats. Bioinform. 36(19): 4975 (2020) - [j8]Frank T. Bergmann, Tobias Czauderna, Ugur Dogrusoz, Adrien Rougny, Andreas Dräger, Vasundra Touré, Alexander Mazein, Michael L. Blinov, Augustin Luna:
Systems biology graphical notation markup language (SBGNML) version 0.3. J. Integr. Bioinform. 17(2-3) (2020)
2010 – 2019
- 2019
- [j7]Marek Ostaszewski, Stephan Gebel, Inna Kuperstein, Alexander Mazein, Andrei Yu. Zinovyev, Ugur Dogrusoz, Jan Hasenauer, Ronan M. T. Fleming, Nicolas Le Novère, Piotr Gawron, Thomas S. Ligon, Anna Niarakis, David P. Nickerson, Daniel Weindl, Rudi Balling, Emmanuel Barillot, Charles Auffray, Reinhard Schneider:
Community-driven roadmap for integrated disease maps. Briefings Bioinform. 20(2): 659-670 (2019) - [j6]Adrien Rougny, Vasundra Touré, Stuart L. Moodie, Irina Balaur, Tobias Czauderna, Hanna Borlinghaus, Ugur Dogrusoz, Alexander Mazein, Andreas Dräger, Michael L. Blinov, Alice Villéger, Robin Haw, Emek Demir, Huaiyu Mi, Anatoly A. Sorokin, Falk Schreiber, Augustin Luna:
Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0. J. Integr. Bioinform. 16(2) (2019) - 2018
- [j5]Bertrand De Meulder, Diane Lefaudeux, Aruna T. Bansal, Alexander Mazein, Amphun Chaiboonchoe, Hassan Ahmed, Irina Balaur, Mansoor A. S. Saqi, Johann Pellet, Stéphane Ballereau, Nathanaël Lemonnier, Kai Sun, Ioannis Pandis, Xian Yang, Manohara Batuwitage, Kosmas Kretsos, Jonathan van Eyll, Alun Bedding, Timothy Davison, Paul Dodson, Christopher Larminie, Anthony D. Postle, Julie Corfield, Ratko Djukanovic, Kian Fan Chung, Ian M. Adcock, Yike Guo, Peter J. Sterk, Alexander Manta, Anthony Rowe, Frédéric Baribaud, Charles Auffray:
A computational framework for complex disease stratification from multiple large-scale datasets. BMC Syst. Biol. 12(1): 60:1-60:23 (2018) - 2017
- [j4]Irina Balaur, Alexander Mazein, Mansoor A. S. Saqi, Artem Lysenko, Christopher J. Rawlings:
Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks. Bioinform. 33(7): 1096-1098 (2017) - [j3]Irina Balaur, Mansoor A. S. Saqi, Ana Barat, Artem Lysenko, Alexander Mazein, Christopher J. Rawlings, Heather J. Ruskin, Charles Auffray:
EpiGeNet: A Graph Database of Interdependencies Between Genetic and Epigenetic Events in Colorectal Cancer. J. Comput. Biol. 24(10): 969-980 (2017) - 2016
- [j2]Artem Lysenko, Irina A. Roznovat, Mansoor A. S. Saqi, Alexander Mazein, Christopher J. Rawlings, Charles Auffray:
Representing and querying disease networks using graph databases. BioData Min. 9: 23 (2016) - [j1]Vasundra Touré, Alexander Mazein, Dagmar Waltemath, Irina Balaur, Mansoor A. S. Saqi, Ron Henkel, Johann Pellet, Charles Auffray:
STON: exploring biological pathways using the SBGN standard and graph databases. BMC Bioinform. 17: 494:1-494:9 (2016)
Coauthor Index
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