People at BiGCaT Bioinformatics
 
Dr. Chris Evelo
Chris started the BiGCaT group in 2001.
His main research interest is to integrate different bioinformatics approaches to allow real understanding of large scale gene expression results. A critical evaluation of data and database quality together with powerful analytical methods and creative ways to look at data can allow us to see the biology behind the omics. While we more and more combine results from transcriptomics, proteomics and metabolomics studies with epigenomics, ChIP and SNP data and sequence and network analysis, BiGCaT's hunting field is shifting to "Systems Biology". Also see: list of publications.
Dr. Susan Coort
Susan is a postdoc active in the biological interpretation of genomics data. For this puprpose she currently develops new biological pathway maps that can be used with GenMAPP and PathVisio. Development is done on the pathway wiki. See: http://www.wikipathways.org. Together with Lars she does the bioinformatics support for the NuGO focus teams and she one of the co-organizers of the Maastricht advanced microarray course.
Dr. Lars Eijssen
Lars is a postdoc whose primary task is the bioinformatics support for NuGO focus teams. He currently develops new QC, normalisation and analytical pipelines in R/Bioconductor and is a co-organizer of the Maastricht advanced microarray course.
Dr. Egon Willighagen
Egon is a postdoc working on the EU FP7 Open PHACTS project. His blog can be found at http://chem-bla-ics.blogspot.com/ and his publication is linked from his homepage at http://egonw.github.com/.
Jos Bien
Jos Bien has been working as a secretary at Maastricht University since 1992. She has worked at several departments, including College of Dean$
Andra Waagmeester, MSc
Andra is a PhD student and database expert. As a BiGCaT member he visited the Pasteur Institute in Paris on a Marie Curie fellowship using a bioinformatics approach to detect sigma factor in myobacteria. He was appointed by IKAT to work on the Biorange PHASAR program on textmining of metabolite related literature. For BiGCaT he will apply this expertise to for improvement of analysis of metabolism related omics studies,
Martina Kutmon
Martina joined the group as a new PhD student. She will try to make pathway analysis more useful. A description of her project is available here.
 

Previous visitors of the BiGCaT group.

 
Otto Mykkänen MSc
Otto was a visitor on a NuGO exchange grant from the University of Kuopio, Finland in 2009.
Alex Pico
Alex was a visitor whose stay was enabled by NuGO and an NWO visitors grant from the Gladstone Institutes of the Universtity of Californa at San Francisco, USA. Alex is a co-author for many of our publications on pathway analysis.
Crisina Luceri
Cristina was a visitor on a NuGO exchange grant from the Department of Pharmacology, Firenze University, Italy. As part of this exchange we re-analysed a dataset on red wine polyphenols. The results of this exchanged were published in Genes and Nutrition.
 
Anna Kipp
Anna was a visitor on a NuGO exchange grant German Institute of Human Nutrition, Potsdam, Germany.  The purpose of this exchange was to analyze the transcriptomics result from the NuGO focus team on selenium. The results of this exchange were published in Mol Nutr. and FoordResearch.
Cinzia Castagnini
Cinzia was a visitor on a NuGO exchange grant from Firenze University, Italy. Cinzia and Simona worked on the analysis of transcriptomics data after feeding different types of apples deomonstrating that differences in polyphenol content lead too differences in biological effect. The result of this exchange were published in Br J Nutr.
Simona Toti
Simona was a visitor on a NuGO exchange grant from Firenze University, Italy she collaborated with Cinzia mentioned above.
Peter Olsson
Peter was a visitor on a NuGO exchange grant from Lund University, Sweden
Franck Tourniaire
Franck was a visitor on a NuGO exchange grant from the university of Newcastle, United Kingdom
Jill Ann McKay
Jill was a visitor on a NuGO exchange grant from the university of Newcastle, United Kingdom. This exchange was part of the NuGO nutritional epigenomics focus team. An initial colllaborative publication appeared in Genes and Nutrition.
 

Alumni of the BiGCaT group.

 
Magali Jaillard, MSc
Magali is a young scientist who worked on two short term NuGO projects. One was directed towards adapted normalization methods for dedicated arrays and should lead to a review paper, the other is directed towards the collection of more actual content for Nutrigenomics related pathway maps to be stored in Reactome. Since May 2010 Magali works for us again and is finalizing pipelines for array analysis that will appear on arrayanalysis.org.
Charly John, MSc
Charly is appointed as a scientific programmer and database manager to assist the NTC project. He worked in a couple of software development co$
Thomas Kelder, MSc
Thomas is a PhD student for the Biorange Pathways program. His primary project involves the development of tools and infrastructure for a community project on pathway content. See: http://www.wikipathways.org. Thomas is also one the main developers of PathVisio.
Michiel Adriaens, MSc
Michiel is a PhD student at BiGCaT. His project involves the development of analytical tools and statistical models for DNA methylation and ChIP-on-chip microarray data. He actively collaborates with the NuGO Nutritional Epigenomics Focus Team.
Martijn van Iersel, MSc
Martijn initially worked as a PhD student appointed by the School of Life Sciences (a collaboration between the Universities of Maastricht and Hasselt) on a project directed towards the integrated analysis of transcriptomics, proteomics and metabolomics data. To allow this kind of analysis Martijn developed PathVisio. Martijn has now finished his PhD thesis and is appointed as a (soon to be) postdoc for the NBIC BioAssist program that supports the Netherlands Consortium of Systems Biology.
Jahn-Takeshi Saito, MSc
Jahn is a PhD student in Artificial Intelligence. As a BiGCaT member he is involved in the Nutritional Phenotype Data Base (dbNP) project of th$
Dr. Rachel van Haaften
Rachel was a postdoc in the Dutch IOP genomics program on gut health. She left the BiGCaT group beginning 2007 to pursue a career in teaching biology. She is experienced in the treatment and quality control of microarray results on different platforms (Affymetrix, Agilent, Incyte and custom arrays). Further analyses of  such data at the pathway level using tools like GenMapp and improvement of such analyses using critical expert and text-mining driven evaluation of pathway content are among her research goals.
Willem Ligtenberg, MSc
Willem worked at BiGCaT during his TUe masters to develop and maintain the BiGCaT tools library, an initiative that is funded by IOP. During that time he is visited the bioinformatics group at the University of Glasgow where he is worked on the development of Vista tools.
ing. Edwin ter Voert, BSc
Edwin was also a TU/e masters student who worked for BiGCaT on database and system management, mainly on Linux based systems.
Gontran Zepeda, BSc
Gontran is a scientific assistant who worked on two short term NuGO projects. The first aiming at export of pathway information from Reactome in to GenMAPP format, the other directed towards an overview and review article about new sensitive transcriptomics measurement technology (large scale measurement of lowly expressed mRNA).
Joris Korbeeck, BSc
Joris was a TU/e masters student who worked for BiGCaT as a database and system manager, mainly on Windows systems.
Ir. Patrick Ahles, MSc
Patrick was our Systems and Database Manager. As such he was involved in the development of services on the NuGO Blackbox (NBX) hardware en software platform for scientific communties.