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Journal Articles
- 2021
[j30]Sébastien Moretti
, T. Van Du Tran, Florence Mehl, Mark Ibberson, Marco Pagni:
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models. Nucleic Acids Res. 49(Database-Issue): D570-D574 (2021)- 2019
- [j29]Nurgazy Sulaimanov, Sunil Kumar, Frédéric Burdet, Mark Ibberson, Marco Pagni, Heinz Koeppl:
Inferring gene expression networks with hubs using a degree weighted Lasso approach. Bioinform. 35(6): 987-994 (2019) - [j28]T. Van Du Tran, Sébastien Moretti, Alix T. Coste, Sara Amorim-Vaz, Dominique Sanglard, Marco Pagni:
Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis. Bioinform. 35(13): 2258-2266 (2019) - 2017
- [j27]Anne Morgat, Thierry Lombardot, Kristian B. Axelsen, Lucila Aimo, Anne Niknejad, Nevila Hyka-Nouspikel, Elisabeth Coudert, Monica Pozzato, Marco Pagni, Sébastien Moretti, Steven Rosanoff, Joseph Onwubiko, Lydie Bougueleret, Ioannis Xenarios, Nicole Redaschi, Alan J. Bridge:
Updates in Rhea - an expert curated resource of biochemical reactions. Nucleic Acids Res. 45(Database-Issue): D415-D418 (2017) - 2016
- [j26]Sébastien Moretti, Olivier Martin, T. Van Du Tran, Alan J. Bridge, Anne Morgat, Marco Pagni:
MetaNetX/MNXref - reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. Nucleic Acids Res. 44(Database-Issue): 523-526 (2016) - 2014
- [j25]Thomas Bernard, Alan J. Bridge, Anne Morgat, Sébastien Moretti, Ioannis Xenarios, Marco Pagni:
Reconciliation of metabolites and biochemical reactions for metabolic networks. Briefings Bioinform. 15(1): 123-135 (2014) - 2013
- [j24]Mathias Ganter, Thomas Bernard, Sébastien Moretti, Jörg Stelling, Marco Pagni:
MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks. Bioinform. 29(6): 815-816 (2013) - [j23]Thierry Schüpbach, Marco Pagni, Alan J. Bridge, Lydie Bougueleret, Ioannis Xenarios, Lorenzo Cerutti:
pfsearchV3: a code acceleration and heuristic to search PROSITE profiles. Bioinform. 29(9): 1215-1217 (2013) - [j22]Marco Pagni, Hélène Niculita-Hirzel, Loïc Pellissier, Anne Dubuis, Ioannis Xenarios, Antoine Guisan, Ian R. Sanders, Jérôme Goudet, Nicolas Guex:
Density-based hierarchical clustering of pyro-sequences on a large scale - the case of fungal ITS1. Bioinform. 29(10): 1268-1274 (2013) - 2009
- [j21]Alexandre Gattiker, Christophe Dessimoz, Adrian Schneider, Ioannis Xenarios, Marco Pagni, Jacques Rougemont:
The Microbe browser for comparative genomics. Nucleic Acids Res. 37(Web-Server-Issue): 296-299 (2009) - 2008
- [j20]Heinz Stockinger, Teresa K. Attwood, Shahid Nadeem Chohan, Richard G. Côté, Philippe Cudré-Mauroux, Laurent Falquet, Pedro L. Fernandes, Robert D. Finn, Taavi Hupponen, Eija Korpelainen, Alberto Labarga, Aurélie Laugraud, Tania Lima, Evangelos Pafilis, Marco Pagni, Steve Pettifer, Isabelle Phan, Nazim Rahman:
Experience using web services for biological sequence analysis. Briefings Bioinform. 9(6): 493-505 (2008) - 2007
- [j19]Marco Pagni, Vassilios Ioannidis, Lorenzo Cerutti, Monique Zahn-Zabal, C. Victor Jongeneel, Jörg Hau, Olivier Martin, Dmitri Kuznetsov, Laurent Falquet:
MyHits: improvements to an interactive resource for analyzing protein sequences. Nucleic Acids Res. 35(Web-Server-Issue): 433-437 (2007) - [j18]Jörg Hau, Michael Muller, Marco Pagni:
HitKeeper, a generic software package for hit list management. Source Code Biol. Medicine 2 (2007) - 2006
- [j17]Nicolas Hulo, Amos Bairoch, Virginie Bulliard, Lorenzo Cerutti, Edouard De Castro, Petra S. Langendijk-Genevaux, Marco Pagni, Christian J. A. Sigrist:
The PROSITE database. Nucleic Acids Res. 34(Database-Issue): 227-230 (2006) - 2005
- [j16]Peter Sperisen, Marco Pagni:
JACOP: A simple and robust method for the automated classification of protein sequences with modular architecture. BMC Bioinform. 6: 216 (2005) - [j15]Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Paul Bradley, Peer Bork, Phillip Bucher, Lorenzo Cerutti, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Wolfgang Fleischmann, Julian Gough, Daniel H. Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Jennifer McDowall, Alex L. Mitchell, Anastasia N. Nikolskaya, Sandra E. Orchard, Marco Pagni, Chris P. Ponting, Emmanuel Quevillon, Jeremy D. Selengut, Christian J. A. Sigrist, Ville Silventoinen, David J. Studholme, Robert Vaughan, Cathy H. Wu:
InterPro, progress and status in 2005. Nucleic Acids Res. 33(Database-Issue): 201-205 (2005) - 2004
- [j14]Peter Sperisen, Christian Iseli, Marco Pagni, Brian J. Stevenson, Philipp Bucher, C. Victor Jongeneel:
trome, trEST and trGEN: databases of predicted protein sequences. Nucleic Acids Res. 32(Database-Issue): 509-511 (2004) - [j13]Marco Pagni, Vassilios Ioannidis, Lorenzo Cerutti, Monique Zahn-Zabal, C. Victor Jongeneel, Laurent Falquet:
MyHits: a new interactive resource for protein annotation and domain identification. Nucleic Acids Res. 32(Web-Server-Issue): 332-335 (2004) - 2003
- [j12]Alexandre Gattiker, Karine Michoud, Catherine Rivoire, Andrea H. Auchincloss, Elisabeth Coudert, Tania Lima, Paul J. Kersey, Marco Pagni, Christian J. A. Sigrist, Corinne Lachaize, Anne-Lise Veuthey, Elisabeth Gasteiger, Amos Bairoch:
Automated annotation of microbial proteomes in SWISS-PROT. Comput. Biol. Chem. 27(1): 49-58 (2003) - [j11]Nicola J. Mulder, Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Daniel Barrell, Alex Bateman, David Binns, Margaret Biswas, Paul Bradley, Peer Bork, Philipp Bucher, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Sam Griffiths-Jones, Daniel H. Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, Rodrigo Lopez, Ivica Letunic, David Lonsdale, Ville Silventoinen, Sandra E. Orchard, Marco Pagni, David Peyruc, Chris P. Ponting, Jeremy D. Selengut, Florence Servant, Christian J. A. Sigrist, Robert Vaughan, Evgeni M. Zdobnov:
The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res. 31(1): 315-318 (2003) - [j10]Laurent Falquet, Lorenza Bordoli, Vassilios Ioannidis, Marco Pagni, C. Victor Jongeneel:
Swiss EMBnet node web server. Nucleic Acids Res. 31(13): 3782-3783 (2003) - 2002
- [j9]Nicola J. Mulder, Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Margaret Biswas, Paul Bradley, Peer Bork, Philipp Bucher, Richard R. Copley, Emmanuel Courcelle, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Jérôme Gouzy, Sam Griffiths-Jones, Daniel H. Haft, Henning Hermjakob, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, Rodrigo Lopez, Ivica Letunic, Sue Orchard, Marco Pagni, David Peyruc, Chris P. Ponting, Florence Servant, Christian J. A. Sigrist:
InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites. Briefings Bioinform. 3(3): 225-235 (2002) - [j8]Christian J. A. Sigrist, Lorenzo Cerutti, Nicolas Hulo, Alexandre Gattiker, Laurent Falquet, Marco Pagni, Amos Bairoch, Philipp Bucher:
PROSITE: A Documented Database Using Patterns and Profiles as Motif Descriptors. Briefings Bioinform. 3(3): 265-274 (2002) - [j7]Laurent Falquet, Marco Pagni, Philipp Bucher, Nicolas Hulo, Christian J. A. Sigrist, Kay Hofmann, Amos Bairoch:
The PROSITE database, its status in 2002. Nucleic Acids Res. 30(1): 235-238 (2002) - 2001
- [j6]Marco Pagni, C. Victor Jongeneel:
Making Sense of Score Statistics for Sequence Alignments. Briefings Bioinform. 2(1): 51-67 (2001) - [j5]Thomas Junier, Marco Pagni, Philipp Bucher:
mmsearch: a motif arrangement language and search program. Bioinform. 17(12): 1234-1235 (2001) - [j4]Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Alex Bateman, Ewan Birney, Margaret Biswas, Philipp Bucher, Lorenzo Cerutti, Florence Corpet, Michael D. R. Croning, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Jérôme Gouzy, Henning Hermjakob, Nicolas Hulo, Inge Jonassen, Daniel Kahn, Alexander Kanapin, Youla Karavidopoulou, Rodrigo Lopez, Beate Marx, Nicola J. Mulder, Thomas M. Oinn, Marco Pagni, Florence Servant, Christian J. A. Sigrist, Evgeni M. Zdobnov:
The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 29(1): 37-40 (2001) - [j3]Marco Pagni, Christian Iseli, Thomas Junier, Laurent Falquet, C. Victor Jongeneel, Philipp Bucher:
trEST, trGEN and Hits: access to databases of predicted protein sequences. Nucleic Acids Res. 29(1): 148-151 (2001) - 2000
- [j2]Thomas Junier, Marco Pagni:
Dotlet: diagonal plots in a Web browser. Bioinform. 16(2): 178-179 (2000) - [j1]Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Alex Bateman, Ewan Birney, Margaret Biswas, Philipp Bucher, Lorenzo Cerutti, Florence Corpet, Michael D. R. Croning, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Jérôme Gouzy, Henning Hermjakob, Nicolas Hulo, Inge Jonassen, Daniel Kahn, Alexander Kanapin, Youla Karavidopoulou, Rodrigo Lopez, Beate Marx, Nicola J. Mulder, Thomas M. Oinn, Marco Pagni, Florence Servant, Christian J. A. Sigrist, Evgeni M. Zdobnov:
InterPro-an integrated documentation resource for protein families, domains and functional sites. Bioinform. 16(12): 1145-1150 (2000)
Conference and Workshop Papers
- 2011
- [c3]Guido Bologna, Anne-Lise Veuthey, Marco Pagni, Lydie Lane, Amos Bairoch:
A Preliminary Study on the Prediction of Human Protein Functions. IWINAC (1) 2011: 334-343 - 2008
- [c2]Marco Pagni, Jörg Hau, Heinz Stockinger:
A Multi-protocol Bioinformatics Web Service: Use SOAP, Take a REST or Go with HTML. CCGRID 2008: 728-734 - 2006
- [c1]Heinz Stockinger, Marco Pagni, Lorenzo Cerutti, Laurent Falquet:
Grid Approach to Embarrassingly Parallel CPU-Intensive Bioinformatics Problems. e-Science 2006: 58
Informal and Other Publications
- 2024
- [i1]Jerven T. Bolleman, Vincent Emonet, Adrian M. Altenhoff, Amos Bairoch, Marie-Claude Blatter, Alan J. Bridge, Severine Duvaud, Elisabeth Gasteiger, Dmitry Kuznetsov, Sébastien Moretti, Pierre-André Michel, Anne Morgat, Marco Pagni, Nicole Redaschi, Monique Zahn-Zabal, Tarcisio Mendes de Farias, Ana Claudia Sima:
A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications. CoRR abs/2410.06010 (2024)
Coauthor Index
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