Members of the lab

Current members

Nicolas Le NovereNicolas Le Novère is group leader at the  Babraham Institute. His research interests revolve around signal transduction, in particular in neurons. He tries to understand them using computational models. Besides his neurobiological-oriented research, Le Novère develops resources for systems biology, for instance standards like  SBML and  SBGN or databases like BioModels Database.

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Stephen ColeStephen Cole is an Amgen Scholar working on the transduction of calcium signals by allosteric proteins.

Piero Dalle PezzePiero Dalle Pezze is a postdoc in the lab. He is interested in data-driven computational models of biological networks, data analysis, and the development of bioinformatics software. His current projects are related to autophagosome formation, mitochondrial turnover, insulin/ amino acids signalling pathways and software pipelines for model design & simulation.

Google ScholarGitHub.

Janna HastingsJanna Hastings  is a PhD student in Olivia Casanueva's group and ours. Her main interests lie in the interplay between metabolism, epigenetics and ageing, using the worm Caenorhabiditis elegans as a biological model, and computational biology approaches.

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Vincent Knight SchrijverVincent Knight Schrijver  is a BBSRC-GSK CASE PhD student. His main research projects relate to systems pharmacology models: retrieval of existing ones, encoding and enriching them, and creating new ones

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Varun Kothamachu is a postdoc in the lab, and a BBSRC funded curator for BioModels and SBO. He obtained his bachelors engineering degree (BE) in biotechnology from Visvesvaraya Technological University, India; MSc in Drug Discovery from University of Edinburgh and completed his PhD on characterizing the dynamic and computational properties of prokaryotic signalling networks (University of Exeter). His current work involves curating models on BioModels and developing standards and tools to share modular multi-scale models. 

Google Scholar.

Lu LiLu Li  is a post-doc in the laboratory. She currently focuses on the understanding of molecular mechanisms involved in the late onset of Alzheimer's disease, using spatial modelling approaches.

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An NguyenAn Nguyen obtained a Bachelor degree (2007) in Computer Science at the Posts and Telecommunications Institute of Technology, Vietnam and spent one year doing a Master degree in Information Technology at the Federation University Australia in 2009. He also completed a PhD degree about gene expression at the University of Southampton. He is now working as a postdoctoral bioinformatician at the Babraham Institute in the groups of Michael Wakelam and Le Novère. His main research project is to analyse lipid signalling and metabolic pathway in human bronchial epithelial cells infected with rhinoviruses.

Juliette PearceJuliette Pearce is a PhD student interested in the links between metabolism and pluripotency. Her project is a collaboration with Wolf Reik's group.

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Nicolas RodriguezNicolas Rodriguez is a senior technical support in the laboratory. His main duties are the maintenance and further development of the group software infrastructure.

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Manusnan SuriyalakshManusnan Suriyalaksh is a PhD student in Olivia Casanueva's group and ours. Her main interests lie in the molecular networks underpinning ageing, using the worm Caenorhabiditis elegans as a biological model, and bioinformatics approaches.

Letizia VestitoLetizia Vestito is a Da Vinci ERASMUS+ intern from the University of Roma. She is working on the reconstruction the regulatory network underlying identity of subpopulations of striatal neurons.

Visitors

Sven_Bergmann-150x150.jpg.jpgSven Bergmann heads the Computational Biology Group at the University of Lausanne. His work includes designing and applying novel algorithms for the analysis of large-scale biological and medical data, as well as modeling genetic networks pertaining to the development of the Drosophila embryo and the response of plants to environmental changes.

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Stuart_Edelstein-150x150-2.jpgAfter a full career as a Professor at Cornell University and then at the University of Geneva, upon reaching Emeritus in 2006 Stuart Edelstein returned to his first love: mathematical modeling of allosteric proteins and related phenomena.

More. For even more complete details, see his University of Geneva web site: http://www.unige.ch/sciences/biochimie/Edelstein/SJE.html

Pinar PirPınar Pir is a senior post-doc in the laboratory. Her research interests include developing interfaces and algoritms for parallel simulation of modular models of cellular processes and developing models of stem cell differentiation and re-programming

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Alumni

Ishan AjmeraIshan Ajmera, 2011, summer intern. Ishan worked as a curator of BioModels, focusing in particular on models of Diabetes. Now (2017) Postdoctoral fellow at University of Nottingham. UK
https://www.linkedin.com/in/ishan-ajmera-47a40227/
Benedetta Frida BaldiBenedetta Frida Baldi, 2009-2015 PhD student. Worked on single cell simulations of post-synaptic assemblies. Now (2017) Post-doc, Garvan Institute of Medical Research, https://uk.linkedin.com/in/benedetta-frida-baldi-5840898
Duncan BerenguierDuncan Berenguier, 2008, summer intern. Duncan developed the first version of the SBML Qual package. Now (2012) PhD student at the University of Marseille, FR
Alexander BroicherAlexander Broicher, 2004, winter interm. Alexander developed the first version of BioModels. Now (2017) Bioinformatician at the University of Applied Sciences Weihenstephan, DE
https://www.linkedin.com/in/alexanderbroicher/
Denis BrunDenis Brun, 2011, summer intern. Denis developed the first hemi-concerted model of Calmodulin. Now (2017) Software Engineer at  Air France-KLM
https://www.linkedin.com/in/denis-brun-43015528/
Finja BuechelFinja Büchel (Wrzodek), 2011, software developer. Finja worked on Path2Models. Now (2017) Senior IT consultant bei MaibornWolff GmbH, DE
https://www.linkedin.com/in/dr-finja-wrzodek-73b403a6/
Vijayalakshmi ChelliahVijayalakshmi Chelliah, 2008-2014, senior database curator for BioModels. Now (2017) Project leader for BioModels. https://www.linkedin.com/in/vijayalakshmi-chelliah-a803761b/
Mélanie CourtotMélanie Courtot, 2004-2006, software developer. Melanie worked on the European project E-MeP. She also developed the Systems Biology Ontology. Now (2017) GO/GA4GH project leader, EMBL-EBI, UK
http://www.linkedin.com/in/mcourtot
Simon DelagneauSimon Delagneau 2014, summer intern. Simon developed single particle simulations of RNA transcription and diffusion.
https://www.linkedin.com/in/simon-delagneau-831931a8/.

 

Agathe DelauneAgathe Delaune, 2017, MSc intern from the Pierre et Marie Curie University (Paris). Agathe was working on the reconstruction the genetic core regulatory network deciding if an epicardial cell becomes a cardiac fibroblast or a coronary smooth muscle cell. Now (2017), Bioinformatician at EMBL-EBI.

Marie-Ange DjiteMarie-Ange Djite, 2004, summer interm. Marie-Ange worked on the Ligand-Gated Ion Channel database. Now (2012) unknown position
Koray Dogan KayaKoray Doğan Kaya, 2008, Marie Curie visiting PhD. Koray analyses microarray data. Now (2017) Research fellow at NIH-NEI, USA
https://www.linkedin.com/in/koray-do%C4%9Fan-kaya-7719a233/
Marco DonizelliMarco Donizelli, 2003-2005, Software engineer. Marco developed the first released version of BioModels, among many  other things. Now (2017) CEO Bonk consulting AS, Norway.
https://www.linkedin.com/in/marcodonizelli/
Marine DumousseauMarine Dumousseau, 2009, summer intern and software developer. Marine developed MELTING v5. Now (2017) Software architext at Woonoz, FR  
https://www.linkedin.com/in/marine-sivade-9b09ab1a/
Ranjita Dutta-RoyRanjita Dutta Roy, 2008, summer intern. Ranjita developed an allosteric model of AMPA receptor. Now (2016) PhD student at the Karolinska Institute, SE
https://www.linkedin.com/in/ranjita-dutta-roy-593a5a75/
Lukas EndlerLukas Endler, 2008-2011, curator of BioModels. Now (2017) Bioinformatician, University of Vienna, AT
https://www.linkedin.com/in/lukas-endler-990a6629/
Eric FernandezÉric Fernandez, 2004-2006, postdoctoral fellow. Éric developed models of signalling in striatal neurons. Now (2017) Quantitative Systems Pharmacology Engineer at GSK, UK
https://www.linkedin.com/in/eric-fernandez-1172675/
Martina FroehlichMartina Fröhlich, 2012-2015, postdoctoral fellow. Now (2017) postdoc at the German Cancer Research Center (DKFZ), DE.
https://www.linkedin.com/in/martina-froehlich-a09b6256/
Mihai GlontMihai Glont, 2012-2014, software developer. Mihai developed a new software infrastructure for BioModels and worked for the DDMoRe project. Now (2017) software developer at EMBL-EBI.
https://www.linkedin.com/in/mihaiglont/
John_Gowers-150x150.jpgJohn Gowers. 2013 summer intern. John extended the capabilities of MELTING v5. Now (2013) studying mathematics at the University of Cambridge.
Enuo HeEnuo He, 2006, BioModels database curator. Now (2017) Audit manager, GSK, UK
https://www.linkedin.com/in/heenuo/
Ron HenkelRon Henkel, 2009, visiting PhD. Ron developed a semantic search system for BioModels. Now (2017) Scientific programmer at Heidelberg Institute for Theoretical Studies, DE
https://www.linkedin.com/profile/view?id=325357103
Arnaud HenryArnaud Henry, 2006, summer intern. Arnaud developed the first SBML to BioPAX translator. Now (2017) Consultant at Agfa Healthcare, FR
https://www.linkedin.com/in/arnaud-henry-b9148444/
Noriko HiroiNoriko Hiroi, 2008, postdoctoral fellow. Noriko worked on trkB signalling in synaptic plasticity. Now (2017) Researcher, at the University of Tokyo, JP
https://www.linkedin.com/in/noriko-hiroi-a957ba1/
Gael JalowickiGael Jalowicki, 2011, summer intern. Gael developed an SBML to SBGN-ML converter. Now (2013) PhD student University College Dublin
Marija_Jankovic-150x150.jpgMarija Jankovic, 2013, summer intern. Marija worked on a model of phosphoinositide signalling. Now (2017) Physicist at Imperial College London, UK https://www.linkedin.com/in/marija-jankovic-b1300b25/
Nick JutyNick Juty, 2008-2014, database curator (Identifiers.org registry) and Systems Biology Ontology developer. Now (2016), database curator and ontology developer at EMBL-EBI.
https://www.linkedin.com/in/nick-juty/
Sarah KeatingSarah Keating, 2009-2014, software developer. Sarah was the main developer behind libSBML and several of SBML core tools. Now (2014) software developer at EMBL-EBI.
https://www.linkedin.com/in/sarah-keating-b0644331/
Vladimir KiselevVladimir Kiselev , 2011-2015, postdoctoral fellow. Vladimir analysed the effects of PI3K signalling on the transcriptional landscape of cell lines. Now (2017), postdoctoral fellow at the Sanger Institute, UK
https://www.linkedin.com/in/wikiselev/
Christian KnuepferChristian Knüpfer, 2007, Marie Curie visiting PhD. Christian developed the Terminology for the Description of Dynamics. Now (2012) PhD student at the University of Jena, DE

Massimo LaiMassimo Lai, 2011-2015, post-doc. Massimo developed models to understand how calmodulin interprets calcium signals.  Now (2017) Computational biologist Certara. https://www.linkedin.com/in/massimo-lai-482b871a/

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Camille LaibeCamille Laibe, 2007-2014. Camille developed the MIRIAM registry, further developed BioModels, the webservices behing BioModels, SBO and MIRIAM registry.  Now (2017) Project manager at ARM, UK. https://www.linkedin.com/in/camillelaibe/
Hoa LeHoa Le, 2014, summer intern. https://www.linkedin.com/profile/view?id=204570704
Chen LiChen Li, 2005-2008, software Engineer. Chen developed BioModels and the related webservices. Now (2017), Computer Scientist at the University of Cambridge, UK and Xi'an Jiaotong University, CN
https://www.linkedin.com/in/chnli/
Catherine LloydCatherine Lloyd, 2010, visiting scientist. Catherine worked as a curator the Physiome Model Repository. Now (2017), HR Project Manager at CeMM, AT
David P. MarshallDavid P. Marshall, 2007, summer intern. David worked on molecular modelling and dynamics simulations of CamKII-calmodulin complexes. Now (2017) senior data scientist at Bloom and Wild, UK.
https://www.linkedin.com/in/david-marshall-5105701a/
Lucas_Marmiesse-150x150.pngLucas Marmiesse, 2015, visiting PhD student. Lucas developped hybrid models of embryonic stem cells, including logic rules and FBA. Now (2016) PhD student at the University of Toulouse.
https://www.linkedin.com/in/lucasmarmiesse/

 

Michele MattioniMichele Mattioni, 2007-2012, PhD student and post-doc. Michele developed a whole cell model of a striatal neuron, including electrophysiological and biochemical activity. Now (2017) Scientific Project Manager, Seven Bridges, UK
https://www.linkedin.com/in/michele-mattioni-47818a6/
Antonia MayerAntonia Mayer, 2007, curator of the Ligand-Gated Ion Channel database. Now (2013) sequence bioinformatics Research Associate at the University of Cambridge, UK
Daniel McGrealDaniel McGreal, 2006-2008, database engineer. Now (2017) Systems architect at RedBite Solutions, UK. https://www.linkedin.com/in/daniel-mcgreal-511654b3/
Florian MittagFlorian Mittag, 2011, software developer. Florian worked on the Path2Models project. Now (2012) PhD student at the University of Tuebingen, DE
http://www.ra.cs.uni-tuebingen.de/mitarb/mittag/
Stuart MoodieStuart Moodie, 2011-2013, developer. Stuart worked on the DDMoRe project. Now (2017) freelance developer https://www.linkedin.com/in/stuart-moodie-1b0427/
Kedar Nath NatarajanKedar Nath Natarajan, 2008, summer intern. Kedar worked on the Systems Biology Format converter. Now (2017) Postdoctoral fellow at Sanger Institute and EMBL-EBI, UK
https://www.linkedin.com/in/kedar-natarajan-aa133316/

Katrina NeiburgaKatrina Neiburga, 2016, summer intern. Katrina worked on gene network inference from translated mRNA data.

Anika OellrichAnika Oellrich, 2007, summer intern. Anika worked on the SBML Multi package. Now (2017) Team manager and data scientist, University of Stralsund, DE https://www.linkedin.com/in/anika-oellrich-11350b66/
Ioana OlanIoana Olan, 2014, summer intern. Ioana worked on DNA methylation regulating the differentiation into ES and TS cells. Now (2017) PhD student at the University of Cambridge https://www.linkedin.com/in/ioana-olan-32994a35/

Krutik PatelKrutik Patel, 2016, summer intern. Krutik worked on single cell RNA-seq. Now (2017) PhD student at Newcastle University.

Jean-Baptiste PettitJean-Baptiste Pettit, 2010, summer intern. Jean-Baptiste developed the core infrastructure of the Systems Biology Format Converter. Now (2017) Data Scientist at Teads.tv
http://www.linkedin.com/profile/view?id=100115767
Renaud SchiappaRenaud Schiappa, 2006, summer intern. Renaud worked on models of signalling in striatal neurons. Now (2017) Data Manager chez Centre Antoine Lacassagne, FR https://www.linkedin.com/in/renaud-schiappa-b450aa20/
Michael SchubertMichael Schubert, 2011, summer intern. Michael was a curator of BioModels database, focussing on Blood clotting. He also worked on the Path2Models project. Now (2017) PhD student at EMBL, DE

Derya SebukhanDerya Sebukhan, 2017, MSc intern. Derya worked on single cell RNA-seq of cardiac stem cells, in particular on differentiation lineages. Now (2017) Bioinformatician at the Institute du Cerveau et de la Moelle, FR.

Christine SeeligerChristine Seeliger, 2009-2014, PhD student. Christine developed spatial models of PIP3 signalling. Now (2017) Computational biologist, Garvan institute of medical research, AU https://www.linkedin.com/in/christine-seeliger-ba79a671/
Nathan SkeneNathan Skene, 2011, visiting PhD. Nathan worked on the inference of signalling networks from phenotypic screen. Now (2017) Postdoc at the Karolinska Institute, SE
https://www.linkedin.com/in/nathan-skene-506a311b/

Melanie_Stefan-150x150.jpgMelanie I Stefan, 2005-2010, PhD student and postdoc. Melanie developed computational models to understand the impact of calmodulin-mediated calcium signalling on synaptic plasticity. Now (2017) Lecturer at the University of Edinburgh, UK

https://www.linkedin.com/in/melanie-stefan-88890b53/

Maciej SwatMaciej Swat, 2011-2014, software developer. Maciej worked on the DDMoRe project. Now (2017) Principal Scientist at Simcyp, UK
https://www.linkedin.com/in/maciej-swat-532a901/
Grigalius_Taujanska-150x150.jpgGrigalius Taujanska, 2013, Summer intern. Grigalius developed computational models of canonical autophagy. Now (2014) mathematics undergraduate at Cambridge University.
Karim TazibtKarim Tazibt, 2010, summer intern. Karim worked on the SBO browser. Now (2012) unknown position
Dominic TolleDominic Tölle, 2005-2008, PhD student. Dominic developed a single particle simulator to understand the role of AMPA receptor diffusion in synaptic plasticity. Now (2017) IT specialist bei mgm technology partners GmbH https://www.linkedin.com/in/dominic-t%C3%B6lle-795298b2/

Bhupinder VirkBhupinder Virk, 2015-2016, developed training material for epigenetics and systems biology. Now (2017) postdoctoral fellow at The Babraham Institute.

Dagmar WaltemathDagmar Waltemath(Koehn), 2007, Marie Curie visiting PhD. Dagmar developed the MIASE guidelines, the SED-ML format and the Kinetic Simulation Algorithm Ontology. Now (2015) Junior group leader at the University of Rostock, DE
https://www.linkedin.com/in/dagmarwaltemath/
Sarala WimalaratneSarala Wimalaratne, 2011-2014, software developer. Sarala developed the Identifiers.org URI resolver. Now (2017) software developer at EMBL-EBI, UK
http://www.linkedin.com/pub/sarala-wimalaratne/20/229/546
Youwei ZhengYouwei Zheng, 2011, visiting student. Now (2013) visitor Northwestern University, USA
https://www.linkedin.com/in/youwei-zheng-004a893b/
Junmei ZhuJunmei Zhu, 2010-2011, post-doc. Junmei was building maps of synaptic signalling pathways. She tragically passed away in 2011.
Anna ZhukovaAnna Zhukova, 2011, summer intern. Anna further developed KiSAO, TEDDy and latter the Mathematical Modelling Ontology. Now (2015) Post-doc fellow at the University of Bordeaux, FR
https://www.linkedin.com/profile/view?id=55193808

Yangyang ZhaoYangyang Zhao, 2012, summer intern. Yangyang worked on BioModels. Now (2017) PhD student at McGill University, CA

https://www.linkedin.com/in/zhao-yangyang-98126114/

Simone_Zorzan-150x150.jpgSimone Zorzan, 2013, visiting scientist. Simone worked on gene and protein networks involved in Alzheimer's Disease. Now (2017) Research Associate at the Luxembourg Institute of Science and Technology.

https://www.linkedin.com/in/simone-zorzan-a788b02a/