Research Topics
| C HooglandSummaryAffiliation: Swiss Institute of Bioinformatics Country: Switzerland Publications
| Collaborators
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Detail Information
Publications
A suite of tools to analyse and publish 2-DE dataChristine Hoogland
Proteome Informatics Group, Swiss Institute of Bioinformatics, Geneva, Switzerland
Proteomics 8:4907-9. 2008..This short communication highlights in a single and summarised view, this workflow and the current bioinformatics solutions developed by the Proteome Informatics Group at the Swiss Institute of Bioinformatics...
SWISS-2DPAGE, ten years laterChristine Hoogland
Swiss Institute of Bioinformatics, Geneva, Switzerland
Proteomics 4:2352-6. 2004..With a high level of annotation and integration with other relevant databases, SWISS-2DPAGE is a reference source in the proteomics world. Queries to SWISS-2DPAGE database currently reach 1000 hits per day...- Two-dimensional electrophoresis resources available from ExPASyC Hoogland
Swiss Institute of Bioinformatics, Geneva
Electrophoresis 20:3568-71. 1999..These resources include the SWISS-2DPAGE database, 2-DE software packages, 2-DE technical and educational services, as well as indexes and search engines for 2-DE related sites over the Internet... - SPS' Digest: the Swiss Proteomics Society selection of proteomics articlesChristine Hoogland
Swiss Institute of Bioinformatics, CMU, I Michel Servet, CH 1211 Geneva, Switzerland
Proteomics 5:3045-7. 2005..The purpose of SPS' Digest is to gather a selection of proteomics articles, to categorize them, and to make the list available on a periodic basis through a web page and email alerts... 
The 1999 SWISS-2DPAGE database updateC Hoogland
Swiss Institute of Bioinformatics, 1 rue Michel Servet, CH 1211 Geneve 4, Switzerland
Nucleic Acids Res 28:286-8. 2000....- The SWISS-2DPAGE database: what has changed during the last yearC Hoogland
Swiss Institute of Bioinformatics, c o Medical Informatics Division, Geneva University Hospital, 24 Rue Micheli du Crest, 1211 Geneva 14, Switzerland
Nucleic Acids Res 27:289-91. 1999..Six new maps have been added, and new functions to access the data have been provided through the ExPASy server. Finally, an important change concerns the database funding source... - The World-2DPAGE Constellation to promote and publish gel-based proteomics data through the ExPASy serverChristine Hoogland
Proteome Informatics Group, Swiss Institute of Bioinformatics, CMU, 1 Michel Servet, CH 1211 Geneva 4, Switzerland
J Proteomics 71:245-8. 2008..The lack of necessary informatics infrastructure to build and run a dedicated website is no longer an obstacle to make proteomics data publicly accessible on the Internet... - A molecular scanner to automate proteomic research and to display proteome imagesP A Binz
Swiss Institute of Bioinformatics, University Medical Center, Geneva, Switzerland
Anal Chem 71:4981-8. 1999..This "MS-imaging" method represents a major step toward the development of a clinical molecular scanner... - New perspectives in the Escherichia coli proteome investigationL Tonella
Central Clinical Chemistry Laboratory, Geneva University Hospital, 24 Rue Michell du Crest, 1211 Geneva 14, Switzerland
Proteomics 1:409-23. 2001..coli cell. Moreover, the six new E. coli SWISS-2D PAGE maps (pH 4-5, 4.5-5.5, 5-6, 5.5-6.7, 6-9 and 6-11) presented here displayed altogether more than 70% of the entire E. coli proteome... - The mouse SWISS-2D PAGE database: a tool for proteomics study of diabetes and obesityJ C Sanchez
Clinical Chemistry Laboratory, University Hospital, Geneva, Switzerland
Proteomics 1:136-63. 2001..SWISS-2D PAGE can be accessed through the World Wide Web (WWW) network on the ExPASy molecular biology server (http://www.expasy.ch/ ch2d/)... - Make2ddb: a simple package to set up a two-dimensional electrophoresis database for the World Wide WebC Hoogland
Medical Informatics Division, Geneva University Hospital, Switzerland
Electrophoresis 18:2755-8. 1997..By preparing the data and programs that are required to create a federated 2-DE database, the Make2ddb package, described here, helps to build such a database on the user own World Wide Web site... - Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detectionR Gras
Swiss Institute of Bioinformatics, University Medical Center, Geneva, Switzerland
Electrophoresis 20:3535-50. 1999..We tested the resulting scoring calculation on a test set of ten proteins and compared the identification results with those of other peptide mass fingerprinting programs... - '98 Escherichia coli SWISS-2DPAGE database updateL Tonella
Clinical Chemistry Laboratory, Geneva University Hospital, Switzerland
Electrophoresis 19:1960-71. 1998..Many proteins have been identified using more than one technique. Faster progress in the E. coli proteome project will now be possible with advances in biochemical methodology and with the completion of the entire E. coli genome... - The establishment of a human liver nuclei two-dimensional electrophoresis reference mapE Jung
Central Clinical Chemistry Laboratory, Geneva University Hospital, Switzerland
Electrophoresis 21:3483-7. 2000..The human liver nuclei 2-DE reference map is now included in the SWISS-2DPAGE database, which can be accessed through the ExPASy server (http://www.expasy.ch/ch2d/)... - MIAPEGelDB, a web-based submission tool and public repository for MIAPE gel electrophoresis documentsXavier Robin
Proteome Informatics Group, Swiss Institute of Bioinformatics, Geneva, Switzerland
J Proteomics 71:249-51. 2008..After publication by their author, documents in MIAPEGelDB can be viewed in HTML or plain text formats, and further used through stable URL links from remote resources. MIAPEGelDB is accessible at: http://miapegeldb.expasy.org/... - ExPASy: The proteomics server for in-depth protein knowledge and analysisElisabeth Gasteiger
Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
Nucleic Acids Res 31:3784-8. 2003..ExPASy started to operate in 1993, as the first WWW server in the field of life sciences. In addition to the main site in Switzerland, seven mirror sites in different continents currently serve the user community... - The molecular scanner: concept and developmentsPierre Alain Binz
Swiss Institute of Bioinformatics, Proteome Informatics Group, CMU, Michel Servet 1, 1211 Geneva, Switzerland
Curr Opin Biotechnol 15:17-23. 2004..Clinical applications of the molecular scanner have also started to be developed for disease diagnosis in biological material... - The Make 2D-DB II package: conversion of federated two-dimensional gel electrophoresis databases into a relational format and interconnection of distributed databasesKhaled Mostaguir
Swiss Institute of Bioinformatics, Centre Medical Universitaire CMU, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
Proteomics 3:1441-4. 2003..Such an environment should be able to fulfill the different needs and requirements arising from both the growing use of 2-DE techniques and the increasing amount of distributed experimental data... - Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004Sandra Orchard
EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Proteomics 5:337-9. 2005..Parallel sessions allowed the three work groups to present their progress to interested parties and to collect feedback from groups already implementing the available formats... - Correlation of proteomic and transcriptomic profiles of Staphylococcus aureus during the post-exponential phase of growthAlexander Scherl
Biomedical Proteomics Research Group, Geneva University Hospitals, Geneva, Switzerland
J Microbiol Methods 60:247-57. 2005..The simultaneous large-scale analysis of transcriptomes and proteomes enables a global and holistic view of the S. aureus biology, allowing the parallel study of multiple active events in an organism... - Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005Sandra Orchard
EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Proteomics 6:738-41. 2006..Common to all these efforts is the field of protein modifications, and work has been initiated to establish an ontology in this field that can be used by both workers in the field of proteomics and the wider scientific community... - Guidelines for reporting the use of gel electrophoresis in proteomicsFrank Gibson
Nat Biotechnol 26:863-4. 2008 - Hydrogen/deuterium exchange for higher specificity of protein identification by peptide mass fingerprintingWilly V Bienvenut
Central Clinical Chemistry Laboratory, Geneva University Hospital, Rue Micheli du Crest 24, CH 1211 Geneva 14, Switzerland
Rapid Commun Mass Spectrom 16:616-26. 2002..Then, information related to primary sequence obtained with this technique could help to identify proteins with high confidence without any expensive tandem mass spectrometry instruments...