Marco Pagni

According to our database, Marco Pagni authored at least 34 papers between 2000 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications.

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

CoRR, 2024

2021

MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models.

Sébastien Moretti, T. Van Du Tran, Florence Mehl, Mark Ibberson, Marco Pagni

Nucleic Acids Res., 2021

2019

Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis.

T. Van Du Tran, Sébastien Moretti, Alix T. Coste, Sara Amorim-Vaz, Dominique Sanglard, Marco Pagni

Bioinform., 2019

Inferring gene expression networks with hubs using a degree weighted Lasso approach.

Nurgazy Sulaimanov, Sunil Kumar, Frédéric Burdet, Mark Ibberson, Marco Pagni, Heinz Koeppl

Bioinform., 2019

2017

Updates in Rhea - an expert curated resource of biochemical reactions.

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

Nucleic Acids Res., 2017

2016

MetaNetX/MNXref - reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks.

Sébastien Moretti, Olivier Martin, T. Van Du Tran, Alan J. Bridge, Anne Morgat, Marco Pagni

Nucleic Acids Res., 2016

2014

Reconciliation of metabolites and biochemical reactions for metabolic networks.

Thomas Bernard, Alan J. Bridge, Anne Morgat, Sébastien Moretti, Ioannis Xenarios, Marco Pagni

Briefings Bioinform., 2014

2013

pfsearchV3: a code acceleration and heuristic to search PROSITE profiles.

Thierry Schüpbach, Marco Pagni, Alan J. Bridge, Lydie Bougueleret, Ioannis Xenarios, Lorenzo Cerutti

Bioinform., 2013

Density-based hierarchical clustering of pyro-sequences on a large scale - the case of fungal ITS1.

Marco Pagni, Hélène Niculita-Hirzel, Loïc Pellissier, Anne Dubuis, Ioannis Xenarios, Antoine Guisan, Ian R. Sanders, Jérôme Goudet, Nicolas Guex

Bioinform., 2013

MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks.

Mathias Ganter, Thomas Bernard, Sébastien Moretti, Jörg Stelling, Marco Pagni

Bioinform., 2013

2011

A Preliminary Study on the Prediction of Human Protein Functions.

Guido Bologna, Anne-Lise Veuthey, Marco Pagni, Lydie Lane, Amos Bairoch

Proceedings of the Foundations on Natural and Artificial Computation, 2011

2009

The Microbe browser for comparative genomics.

Alexandre Gattiker, Christophe Dessimoz, Adrian Schneider, Ioannis Xenarios, Marco Pagni, Jacques Rougemont

Nucleic Acids Res., 2009

2008

Experience using web services for biological sequence analysis.

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

Briefings Bioinform., 2008

A Multi-protocol Bioinformatics Web Service: Use SOAP, Take a REST or Go with HTML.

Marco Pagni, Jörg Hau, Heinz Stockinger

Proceedings of the 8th IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2008), 2008

2007

HitKeeper, a generic software package for hit list management.

Jörg Hau, Michael Muller, Marco Pagni

Source Code Biol. Medicine, 2007

MyHits: improvements to an interactive resource for analyzing protein sequences.

Marco Pagni, Vassilios Ioannidis, Lorenzo Cerutti, Monique Zahn-Zabal, C. Victor Jongeneel, Jörg Hau, Olivier Martin, Dmitri Kuznetsov, Laurent Falquet

Nucleic Acids Res., 2007

2006

The PROSITE database.

Nicolas Hulo, Amos Bairoch, Virginie Bulliard, Lorenzo Cerutti, Edouard De Castro, Petra S. Langendijk-Genevaux, Marco Pagni, Christian J. A. Sigrist

Nucleic Acids Res., 2006

Grid Approach to Embarrassingly Parallel CPU-Intensive Bioinformatics Problems.

Heinz Stockinger, Marco Pagni, Lorenzo Cerutti, Laurent Falquet

Proceedings of the Second International Conference on e-Science and Grid Technologies (e-Science 2006), 2006

2005

InterPro, progress and status in 2005.

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

Nucleic Acids Res., 2005

JACOP: A simple and robust method for the automated classification of protein sequences with modular architecture.

Peter Sperisen, Marco Pagni

BMC Bioinform., 2005

2004

trome, trEST and trGEN: databases of predicted protein sequences.

Peter Sperisen, Christian Iseli, Marco Pagni, Brian J. Stevenson, Philipp Bucher, C. Victor Jongeneel

Nucleic Acids Res., 2004

MyHits: a new interactive resource for protein annotation and domain identification.

Marco Pagni, Vassilios Ioannidis, Lorenzo Cerutti, Monique Zahn-Zabal, C. Victor Jongeneel, Laurent Falquet

Nucleic Acids Res., 2004

2003

The InterPro Database, 2003 brings increased coverage and new features.

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

Nucleic Acids Res., 2003

Swiss EMBnet node web server.

Laurent Falquet, Lorenza Bordoli, Vassilios Ioannidis, Marco Pagni, C. Victor Jongeneel

Nucleic Acids Res., 2003

Automated annotation of microbial proteomes in SWISS-PROT.

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

Comput. Biol. Chem., 2003

2002

The PROSITE database, its status in 2002.

Laurent Falquet, Marco Pagni, Philipp Bucher, Nicolas Hulo, Christian J. A. Sigrist, Kay Hofmann, Amos Bairoch

Nucleic Acids Res., 2002

PROSITE: A Documented Database Using Patterns and Profiles as Motif Descriptors.

Christian J. A. Sigrist, Lorenzo Cerutti, Nicolas Hulo, Alexandre Gattiker, Laurent Falquet, Marco Pagni, Amos Bairoch, Philipp Bucher

Briefings Bioinform., 2002

InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites

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

Briefings Bioinform., 2002

2001

trEST, trGEN and Hits: access to databases of predicted protein sequences.

Marco Pagni, Christian Iseli, Thomas Junier, Laurent Falquet, C. Victor Jongeneel, Philipp Bucher

Nucleic Acids Res., 2001

The InterPro database, an integrated documentation resource for protein families, domains and functional sites.

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

Nucleic Acids Res., 2001

mmsearch: a motif arrangement language and search program.

Thomas Junier, Marco Pagni, Philipp Bucher

Bioinform., 2001

Making Sense of Score Statistics for Sequence Alignments.

Marco Pagni, C. Victor Jongeneel

Briefings Bioinform., 2001

2000

Dotlet: diagonal plots in a Web browser.

Thomas Junier, Marco Pagni

Bioinform., 2000

InterPro-an integrated documentation resource for protein families, domains and functional sites.

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

Bioinform., 2000