Marco Pagni

37 papers B 2Journal 32Unranked 3
YearRankTypeTitle / Venue / Authors
2025 J jnl
MetaboT: AI-based agent for natural language-based interaction with metabolomics knowledge graphs.
CoRR
Madina Bekbergenova, Lucas Pradi, Benjamin Navet, Emma Tysinger, Franck Michel, Matthieu Feraud, Yousouf Taghzouti, Yan Zhou Chen, Olivier Kirchhoffer, Florence Mehl, Martin Legrand, Tao Jiang, Marco Pagni, Soha Hassoun, Jean-Luc Wolfender, Wout Bittremieux, Fabien Gandon, Louis-Félix Nothias
2024 J jnl
A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications.
CoRR
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
2024 — conf
Application of the RDF framework to integrate heterogenous experimental data of a large chemo- and biodiverse collection from a collaborative research project.
SWAT4HCLS
Frédéric Burdet, Luis-Manuel Quiros-Guerrero, Olivier Kirchhoffer, Jahn Nitschke, Pierre-Marie Allard, Louis-Félix Nothias, Arnaud Gaudry, Sébastien Moretti, Robin Engler, Emerson Ferreira Queiroz, Nabil Hanna, Chunyan Wu, Antonio Grondin, Bruno David, Thierry Soldati, Christian Wolfrum, Erick Carreira, Jean-Luc Wolfender, Marco Pagni, Florence Mehl
2024 — conf
CHIST-ERA Triple: improving data interoperability and federation across RDF knowledge graphs and Solid Pods.
SWAT4HCLS
Jerven T. Bolleman, Elias Crum, Iulian Dragan, Jakub Galgonek, Mark Ibberson, Tarcisio Mendes de Farias, Marek Moos, Marco Pagni, Ruben Taelman, Jirí Vondrásek, Ana Claudia Sima
2021 J jnl
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models.
Nucleic Acids Res.
Sébastien Moretti, T. Van Du Tran, Florence Mehl, Mark Ibberson, Marco Pagni
2019 J jnl
Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis.
Bioinform.
T. Van Du Tran, Sébastien Moretti, Alix T. Coste, Sara Amorim-Vaz, Dominique Sanglard, Marco Pagni
2019 J jnl
Inferring gene expression networks with hubs using a degree weighted Lasso approach.
Bioinform.
Nurgazy Sulaimanov, Sunil Kumar, Frédéric Burdet, Mark Ibberson, Marco Pagni, Heinz Koeppl
2017 J jnl
Updates in Rhea - an expert curated resource of biochemical reactions.
Nucleic Acids Res.
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
2016 J jnl
MetaNetX/MNXref - reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks.
Nucleic Acids Res.
Sébastien Moretti, Olivier Martin, T. Van Du Tran, Alan J. Bridge, Anne Morgat, Marco Pagni
2014 J jnl
Reconciliation of metabolites and biochemical reactions for metabolic networks.
Briefings Bioinform.
Thomas Bernard, Alan J. Bridge, Anne Morgat, Sébastien Moretti, Ioannis Xenarios, Marco Pagni
2013 J jnl
Density-based hierarchical clustering of pyro-sequences on a large scale - the case of fungal ITS1.
Bioinform.
Marco Pagni, Hélène Niculita-Hirzel, Loïc Pellissier, Anne Dubuis, Ioannis Xenarios, Antoine Guisan, Ian R. Sanders, Jérôme Goudet, Nicolas Guex
2013 J jnl
MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks.
Bioinform.
Mathias Ganter, Thomas Bernard, Sébastien Moretti, Jörg Stelling, Marco Pagni
2013 J jnl
pfsearchV3: a code acceleration and heuristic to search PROSITE profiles.
Bioinform.
Thierry Schüpbach, Marco Pagni, Alan J. Bridge, Lydie Bougueleret, Ioannis Xenarios, Lorenzo Cerutti
2011 — conf
A Preliminary Study on the Prediction of Human Protein Functions.
IWINAC (1)
Guido Bologna, Anne-Lise Veuthey, Marco Pagni, Lydie Lane, Amos Bairoch
2009 J jnl
The Microbe browser for comparative genomics.
Nucleic Acids Res.
Alexandre Gattiker, Christophe Dessimoz, Adrian Schneider, Ioannis Xenarios, Marco Pagni, Jacques Rougemont
2008 B conf
A Multi-protocol Bioinformatics Web Service: Use SOAP, Take a REST or Go with HTML.
CCGRID
Marco Pagni, Jörg Hau, Heinz Stockinger
2008 J jnl
Experience using web services for biological sequence analysis.
Briefings Bioinform.
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
2007 J jnl
HitKeeper, a generic software package for hit list management.
Source Code Biol. Medicine
Jörg Hau, Michael Muller, Marco Pagni
2007 J jnl
MyHits: improvements to an interactive resource for analyzing protein sequences.
Nucleic Acids Res.
Marco Pagni, Vassilios Ioannidis, Lorenzo Cerutti, Monique Zahn-Zabal, C. Victor Jongeneel, Jörg Hau, Olivier Martin, Dmitri Kuznetsov, Laurent Falquet
2006 B conf
Grid Approach to Embarrassingly Parallel CPU-Intensive Bioinformatics Problems.
e-Science
Heinz Stockinger, Marco Pagni, Lorenzo Cerutti, Laurent Falquet
2006 J jnl
The PROSITE database.
Nucleic Acids Res.
Nicolas Hulo, Amos Bairoch, Virginie Bulliard, Lorenzo Cerutti, Edouard De Castro, Petra S. Langendijk-Genevaux, Marco Pagni, Christian J. A. Sigrist
2005 J jnl
InterPro, progress and status in 2005.
Nucleic Acids Res.
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
2005 J jnl
JACOP: A simple and robust method for the automated classification of protein sequences with modular architecture.
BMC Bioinform.
Peter Sperisen, Marco Pagni
2004 J jnl
MyHits: a new interactive resource for protein annotation and domain identification.
Nucleic Acids Res.
Marco Pagni, Vassilios Ioannidis, Lorenzo Cerutti, Monique Zahn-Zabal, C. Victor Jongeneel, Laurent Falquet
2004 J jnl
trome, trEST and trGEN: databases of predicted protein sequences.
Nucleic Acids Res.
Peter Sperisen, Christian Iseli, Marco Pagni, Brian J. Stevenson, Philipp Bucher, C. Victor Jongeneel
2003 J jnl
Automated annotation of microbial proteomes in SWISS-PROT.
Comput. Biol. Chem.
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
2003 J jnl
Swiss EMBnet node web server.
Nucleic Acids Res.
Laurent Falquet, Lorenza Bordoli, Vassilios Ioannidis, Marco Pagni, C. Victor Jongeneel
2003 J jnl
The InterPro Database, 2003 brings increased coverage and new features.
Nucleic Acids Res.
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
2002 J jnl
InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites
Briefings Bioinform.
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
2002 J jnl
PROSITE: A Documented Database Using Patterns and Profiles as Motif Descriptors.
Briefings Bioinform.
Christian J. A. Sigrist, Lorenzo Cerutti, Nicolas Hulo, Alexandre Gattiker, Laurent Falquet, Marco Pagni, Amos Bairoch, Philipp Bucher
2002 J jnl
The PROSITE database, its status in 2002.
Nucleic Acids Res.
Laurent Falquet, Marco Pagni, Philipp Bucher, Nicolas Hulo, Christian J. A. Sigrist, Kay Hofmann, Amos Bairoch
2001 J jnl
Making Sense of Score Statistics for Sequence Alignments.
Briefings Bioinform.
Marco Pagni, C. Victor Jongeneel
2001 J jnl
The InterPro database, an integrated documentation resource for protein families, domains and functional sites.
Nucleic Acids Res.
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
2001 J jnl
mmsearch: a motif arrangement language and search program.
Bioinform.
Thomas Junier, Marco Pagni, Philipp Bucher
2001 J jnl
trEST, trGEN and Hits: access to databases of predicted protein sequences.
Nucleic Acids Res.
Marco Pagni, Christian Iseli, Thomas Junier, Laurent Falquet, C. Victor Jongeneel, Philipp Bucher
2000 J jnl
Dotlet: diagonal plots in a Web browser.
Bioinform.
Thomas Junier, Marco Pagni
2000 J jnl
InterPro-an integrated documentation resource for protein families, domains and functional sites.
Bioinform.
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