BiGCaT people

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People

Chris Evelo Prof. Dr. Chris Evelo

Chris started the BiGCaT group in 2001.

His main research interest is to use bioinformatics and systems biology approaches to integrate data obtained from different genomics and genetics technologies with existing knowledge 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 data. We more and more combine results from transcriptomics, proteomics and metabolomics studies with epigenomics, ChIP and SNP data using sequence, pathway and network analyses, in this way BiGCaT's hunting field is shifting to "Systems Biology".

ORCID: 0000-0002-5301-3142

Twitter: @Chris_Evelo

LinkedIn: Chris Evelo

Google Scholar: 2dm_Du0AAAAJ

Susan Coort Dr. Susan LM Coort

Susan is as assistant professor active in the biological interpretation of genomics data using systems biology. Her research focuses on methods and tools that are needed to understand regulation of gene expression by both microRNAs and transcription factors. In addition, she has several teaching tasks within the faculty of Health, Medicine and Life Sciences at Maastricht University, the Netherlands.

ORCID: 0000-0003-1224-9690

Google Scholar: XyHJkkMAAAAJ

Lars Eijssen 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.

ORCID: 0000-0002-6473-2839

Google Scholar: 29GWitEAAAAJ

Egon Willighagen Dr. Egon Willighagen

Egon is assistant professor working in the fields of drug discovery, metabolomics, and nanotoxicology. This works applies cheminformatics and chemometrics to these bioinformatics fields. He works on the EU FP7 projects Open PHACTS and eNanoMapper. 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/.

ORCID: 0000-0001-7542-0286

Twitter: @egonwillighagen

LinkedIn: egonw

Google Scholar: u8SjMZ0AAAAJ

Martina Summer-Kutmon Dr. Martina Summer-Kutmon

Martina is a Postdoc at BiGCaT and the Maastricht Centre for Systems Biology. She is working on pathway and network-based approaches.

ORCID: 0000-0002-7699-8191

Friederike Ehrhart Dr. Friederike Ehrhart

Friederike is a Postdoc at BiGCaT. She is expert for biomaterials and cellular biotechnology and currently working on eNanoMapper project.

ORCID: 0000-0002-7770-620X

Elisa Cirillo Elisa Cirillo

Elisa is a PhD student at BiGCaT. Her work is focused on visualization and integration of genetic variants data in pathway-based analysis.

LinkedIn: elisa-cirillo

Nuno.jpg Nuno Nunes

Systems Administrator

Jonathan Melius.jpg Jonathan Mélius, MSc

Scientific programmer

Ryan.png Ryan Miller

Ryan is a PhD student at BiGCaT. He works as a developer for both Open PHACTS and WikiPathways. His main research is using semantic information about pathway diagrams to re-position and traverse the pathway diagram.

ORCID: 0000-0003-3477-7443

Google Scholar: bJYJJVMAAAAJ


Mirella Kalafati Mirella Kalafati

Mirella is a PhD student at the Department of Bioinformatics (BiGCaT) and the Maastricht Centre for Systems Biology (MaCSBio), working on the project of “Personalized risk profiles for cardiovascular disease: sub-typing obesity”. As part of the MUMC+ 2020 portfolio program “Healthy Living”, the Department of Bioinformatics, Epidemiology, Human Biology, Internal Medicine, and Systems Biology are collaborating to better understand the biological heterogeneity of obesity, to improve and personalize cardiometabolic risk classification of obese individuals and provide novel targets for prevention, early diagnosis and treatment of cardiometabolic diseases in those obese who are ‘at risk’.

LinkedIn: Mirella Kalafati

Profile pic MM.png Marvin Martens

Marvin is a PhD student at BiGCaT.

ORCID: 0000-0003-2230-0840

LinkedIn: Marvin Martens

Profile pic Desl.png Denise Slenter

Denise is a PhD student at BiGCaT.

ORCID: 0000-0001-8449-1318

LinkedIn: Denise Slenter

[ex]visitors of the BiGCaT group

Gareth Owen Gareth Owen

Gareth Owen, a researcher from the European Bioinformatics Institute (EBI) in Hinxton, UK, visited BiGCaT for a week in February 2016. He is working with Egon Willighagen on the eNanoMapper project.

Jiakang Chang Jiakang Chang

Jiakang Chang, a researcher from the European Bioinformatics Institute (EBI) in Hinxton, UK, visited BiGCaT for a week in February 2016. He is working with Egon Willighagen on the eNanoMapper project.

Aoife Curran Aoife Curran

Aoife Curran, a PhD student from the University College Dublin in Ireland, visited BiGCaT for a week in January 2016. She was working with Chris Evelo, Susan Coort and Martina Kutmon on her project: Examining the impact of phenotypic parameters on the proteomic signature.


Ingrid Felicidade Ingrid Felicidade

Ingrid Felicidade is an exchange PhD student from São Paulo State University (Universidade Estadual Paulista-UNESP) in Brazil and she visits BiGCaT from April 2015 till January 2016 to work with Susan Coort and Chris Evelo on her project about "Effect of vitamin D (1,25 (OH) 2D3) on adipogenesis: genes of nuclear receptors as biomarkers in normal adipose tissue model and pathway and network analysis in adipose tissue of obese subjects".

Zahra Roudbari Zahra Roudbari

Zahra Roubari is a PhD student from Ferdowsi University of Mashhad in Iran and she visited BiGCaT from January-July 2015 to work with Chris Evelo and Susan Coort on her project about "Identification of molecular pathways of muscle activity, development and regulation in cattle to support and allow research directed towards improved animal breeding".


Ioana Ferariu Ioana Ferariu

Ioana is a Bachelor student at Princeton University who visited BiGCaT (August 2014) to work with Elisa Cirillo on the visualization of GWAS data in pathway analysis.

Otto Mykkänen Otto Mykkänen MSc

Otto was a visitor on a NuGO exchange grant from the University of Kuopio, Finland in 2009.

Alex Pico 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.

ORCID: 0000-0001-5706-2163

Cristina Luceri Cristina 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 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 FoodResearch.

Cinzia Castagnini 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 Toti

Simona was a visitor on a NuGO exchange grant from Firenze University, Italy she collaborated with Cinzia mentioned above.

Peter Olsson Peter Olsson

Peter was a visitor on a NuGO exchange grant from Lund University, Sweden

Franck Tourniaire Franck Tourniaire

Franck was a visitor on a NuGO exchange grant from the university of Newcastle, United Kingdom

Jill Ann McKay 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.

Rasanpreet kaur Rasanpreet Kaur, MSc

Rasna was a student at BiGCaT. She is coming from Manipal University, India.

Alumni of the BiGCaT group

Linda Rieswijk Dr. Linda Rieswijk

Linda is a Postdoc at BiGCaT. She is working on an EUFP7 project called the eNanoMapper project (http://www.enanomapper.net). Within this project she will mainly be focusing on the development of comprehensive ontologies for the nanosafety domain.

ORCID: 0000-0002-6106-1347

Linkedin: Linda Rieswijk

Anwesha Dutta Anwesha Dutta, MSc

Anwesha is a PhD student at BiGCaT. She is working on PathVisio/Wikipathways to enable visualizing data on interactions of biological pathways. She is also working on enabling the visualization of models in PathVisio and the remote procedure call interface of PathVisio, PathVisioRPC. PathVisioRPC is used in the pathway analysis module of arrayanalysis.org.

ORCID: 0000-0001-7073-5852

Twitter : @AnweshaBohler

LinkedIn : anweshabohler

ResearchGate : Anwesha_Bohler

Blog : datanalyzer

Bart Smeets Bart Smeets, MSc

Bart is a PhD student at BiGCaT. His work is part of an EU FP7 project called eNanoMapper that aims to assess safety of new nanomaterials using computer models. He will mainly be involved with the biological interpretation of obtained data. See also: eNanoMapper

ORCID: 0000-0001-6370-6965

Andra Waagmeester 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

ORCID: 0000-0001-9773-4008

Michiel Adriaens Dr. Michiel Adriaens

Michiel was a PhD student at BiGCaT. His project involves the development of analytical tools and statistical models for ChIP-on-chip and DNA methylation microarray data, and more recently next generation ChIP-seq data. He actively collaborates with the NuGO Nutritional Epigenomics Focus Team and with the Human Nutrition Research Centre (Newcastle University) headed by Prof. John Mathers.

Rachel van Haaften 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.

Martijn van Iersel Dr. Martijn van Iersel


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 was appointed as a postdoc for the NBIC BioAssist program that supports the Netherlands Consortium of Systems Biology.

Thomas Kelder Dr. Thomas Kelder


Thomas was a PhD student for the Biorange Pathways program. His primary project involved the development of tools and infrastructure for a community project on pathway content. Thomas was one of the main developers of WikiPathways and PathVisio. Thomas has now finished his PhD thesis. After his PhD he started as bioinformatics scientist at TNO. He is now co-founder and CSO at Edgeleap.

Charly John Charly John, MSc

Charly was appointed as a scientific programmer and database manager to assist the NTC project. He worked in a couple of software development companies for about 3 years as a senior architect/developer. He has expertise in web application server architecture to support distributed platform. His main aim was to facilitate the storage and integrated analysis of transcriptomics, proteomics, metabonomics, and microRNA related data.

Magali Jaillard 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, the other was directed towards the collection of more actual content for Nutrigenomics related pathway maps to be stored in Reactome. Since May 2010 Magali worked for us again and has finalized pipelines for array analysis that will appear on arrayanalysis.org.


Willem Ligtenberg 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. goals.

Cristian R. Munteanu Dr. Cristian R. Munteanu

Cristian was a senior post-doc in 2014 on the application of molecular information, complex networks and artificial intelligence technologies in cheminformatics & bioinformatics. He works on the EU FP7 project eNanoMapper. List of publications. He is now associate professor at the University of A Coruna.

ORCID: ORCID:0000-0002-5628-2268

Scopus: 35230297200

ResearcherID: G-1714-2011

Google Scholar: GBZ2jeAAAAAJ

Jahn-Takeshi Saito Jahn-Takeshi Saito

Jahn is a postdoc in Artificial Intelligence. As a BiGCaT member he was involved in the Nutritional Phenotype Data Base (dbNP) project of the European Nutrigenomics Organisation (NuGO). In particular he was co-developing a tool for querying the dbNP.

Edwin ter Voert 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 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 Joris Korbeeck, BSc


Joris was a TU/e masters student who worked for BiGCaT as a database and system manager, mainly on Windows systems.

Patrick Ahles 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.

[ex]Students working at BiGCaT

Master Internships

Student Time Project
Rika-Reihs.jpg Rika Reihs 4 Jan - 10 June 2016 Project: Studying genetic variations involved in hypertension and their role in biological pathways
University: Master Programme of Biomedical Sciences, Maastricht University, The Netherlands
Supervisor: Martina Summer-Kutmon, Elisa Cirillo
Presentation:
Thesis:
Kim Mulders.jpg Kim Mulders 25 Jan - 10 June 2016 Project: Development of a Systems Biology workflow to understand Gene Expression Data.
University: Master Programme of Biomedical Sciences, Maastricht University, The Netherlands
Supervisor: Susan Steinbusch-Coort, Martina Summer-Kutmon
Presentation:
Thesis:
Person m.png Miguel Correa Marrero 18 May - 31 Aug 2015 Project: Developing NanoQSAR descriptors
University: Master Programme of Bioinformatics, Wageningen University & Research Center
Supervisor: Egon Willighagen, Bart Smeets
Presentation:
Thesis:
Person m.png Chris van der Lans Spring 2015 Project:
University:
Supervisor: Lars Eijssen, Jildau Bouwman
Presentation:
Thesis:
Person f.jpg Chitra Ratnam Venugopal 01 Mar - 31 Jul 2015 Project:
University: Manipal University, India
Supervisor: Lars Eijssen
Presentation:
Thesis:
Claire Lemmens.jpg Claire Lemmens 02 Feb - 12 June 2015 Project: The effect of vitamin D supplementation on gene expression in humans
University: Master Programme of Biomedical Sciences, Maastricht University, The Netherlands
Supervisor: Susan Steinbusch-Coort, Martina Summer-Kutmon
Presentation: JPT_Presentation_CLemmens.pdf
Thesis: JPT_CLemmens.pdf
Manuel Gonzales.png Manuel Alejandro Gonzalez Hernandez 02 Feb - 12 June 2015 Project: Integration of Transcriptomics and GWAS Data to Study the Biological Processes Involved in Type 2 Diabetes Mellitus.
University: Master Programme of Biomedical Sciences, Maastricht University, The Netherlands
Supervisor: Martina Summer-Kutmon, Elisa Cirillo, Lars Eijssen
Presentation: PresentationJPTJune11th2015.pdf
Thesis: JPTManuelGlez.pdf
Christian oertlin.png Christian Oertlin 1 Sept 2014 - 20 Mar 2015 Project: miRNA pathway statictics
University: Wageningen University, The Netherlands
Supervisor: Lars Eijssen, Martina Summer-Kutmon, Susan Coort
Presentation:
Thesis:
Blog: http://plugins.pathvisio.org/mipast/
Jonathan Melius.jpg Jonathan Melius 10 Mar - 31 Aug 2014 Project: Connecting PathVisio and WikiPathways to Expression Atlas
University: University of Bordeaux, France
Supervisor: Lars Eijssen, Martina Summer-Kutmon
Presentation: slides
Thesis:
Blog: http://projects.bigcat.unimaas.nl/atlas2wp/



Bachelor Internships

Student Duration Project
Tessa.jpg Tessa Lebbink 20 Apr - 03 Jul 2015 Project: Development of a Systems Biology Workflow to understand Gene Expression Data
University: Maastricht University, Bachelor Biomedical Sciences
Supervisor: Susan Coort, Bart Smeets
Presentation:
Thesis:
Person f.jpg Kim de Nooijer 07 Apr - 03 Jul 2015 Project: The effect of Vitamin D3 on the (epi)genome at pathway level.
University: Bachelor Health Science, Biology & Health, Maastricht University
Supervisor: Susan Coort, Martina Summer-Kutmon
Presentation:
Thesis:
Marloes.jpg Marloes Poort 20 Apr - 03 Jul 2015 Project: The effect of multi-walled carbon nanotubes (MWCNTs) on the gene expression in bronchial epithelial 2B cells.
University: Bachelor Biomedical Sciences, Maastricht University
Supervisor: Lars Eijssen, Bart Smeets
Presentation:
Thesis:
Person m.png Tom Hooijmeier 20 Apr - 03 Jul 2015 Project: Visualization of Type 1 Diabetes mellitus GWAS data in biological pathways
University: Maastricht University, Bachelor Biomedical Sciences
Supervisor: Martina Summer-Kutmon, Elisa Cirillo
Presentation: presentation.pdf
Thesis:
Person m.png Bram van Steen 20 Apr - 03 Jul 2015 Project: How are drugs regulating biological pathways?
University: Maastricht University, Bachelor Biomedical Sciences
Supervisor: Martina Summer-Kutmon
Presentation: presentation.pdf
Thesis:
Stan-van-Roij-2015.png Stan van Roij 20 Apr - 03 Jul 2015 Project: Effect of TiO2 nanotubes on the gene expression of aortic endothelial cells and vascular smooth muscle cells.
University: Maastricht University, Bachelor Biomedical Sciences
Supervisor: Lars Eijssen, Egon Willighagen, Bart Smeets
Presentation:
Thesis:
Celine.jpg Celine Adriaans 10 Feb - 13 Aug 2014 Project: Functionality of the advanced statistical module: from the workflow to case studies
University: Molecular Life Sciences, Maastricht University, The Netherlands
Supervisor: Lars Eijssen, Anwesha Bohler
Presentation: slides
Thesis:
Person f.jpg Esmee Eeltink Spring 2014 Project: Cytotoxicity of titanium oxides
University: University of Amsterdam
Supervisor: Egon Willighagen
Presentation:
Thesis:
Person m.png Jon Grote Spring 2014 Project:
University: Molecular Life Sciences, Maastricht University, The Netherlands
Supervisor: Lars Eijssen
Presentation:
Thesis:
Rico.jpg Rico Hermanns Spring 2014 Project: A gene expression analysis to study underlying mechanisms in cervical cancer
University: Biological Health (BGK), Maastricht University, The Netherlands
Supervisor: Susan Coort, Martina Summer-Kutmon
Presentation:
Thesis:
Kelly Offermans.jpg Kelly Offermans Spring 2014 Project: Identifying significantly changed biological processes involved in human colorectal cancer and tumour-associated colon mucosa
University: Molecular Life Sciences, Maastricht University, The Netherlands
Supervisor: Lars Eijssen
Presentation: slides
Thesis:
Person m.png Dominik Stankewitz Spring 2014 Project: Analysis of muscle exercise transcriptomics data using bioinformatics tools
University: Molecular Life Sciences, Maastricht University, The Netherlands
Supervisor: Lars Eijssen
Presentation: slides
Thesis:
Vera winthagen.jpg Vera Winthagen Spring 2014 Project: Gene expression differences in lung cancer cell lines after treatment with a Notch inhibitor
University: Molecular Life Sciences, Maastricht University, The Netherlands
Supervisor: Lars Eijssen
Presentation: slides
Thesis:
Patricia zaandam.jpg Patricia Zaandam Spring 2014 Project: Finding human targets for treating Malaria with Systems Biology
University: Molecular Life Sciences, Maastricht University, The Netherlands
Supervisor: Egon Willighagen
Presentation: slides
Thesis:
Blog: http://intership-malaria-solutions.blogspot.nl/
FigShare http://figshare.com/authors/Patricia_Zaandam/595589
Photo-erik-van-zetten.jpg Erik van Zetten Spring 2014 Project: Identifying similar molecular mechanisms between depression and alcoholism
University: Molecular Life Sciences, Maastricht University, The Netherlands
Supervisor: Susan Coort, Martina Summer-Kutmon
Presentation:
Thesis: