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Publications

Last updated: 03 May 2018

Journal Papers

[2018]

ARTENOLIS: Automated Reproducibility and Testing Environment for Licensed Software
Laurent Heirendt, Sylvain Arreckx, Christophe Trefois, Yohan Yarosz, Maharshi Vyas, Venkata P. Satagopam, Reinhard Schneider, Ines Thiele, Ronan M.T. Fleming
Submitted

Fractalis: A scalable open-source service for platform-independent interactive visual analytics of biomedical data
Sascha Herzinger, Valentin Grouès, Wei Gu, Venkata Satagopam, Peter Banda, Christophe Trefois, Reinhard Schneider
GigaScience, giy109, https://doi.org/10.1093/gigascience/giy109

[2016]

Characterization of Differentiated SH-SY5Y as Neuronal Screening Model Reveals Increased Oxidative Vulnerability - [Get PDF]
Julia Forster, Sandra Köglsberger, Christophe Trefois, Olga Boyd, Aidos Baumuratov, Laurent Bück, Rudi Balling, Paul Antony
Journal of Biomedical Screening, ebup ahead of print, pp. 1-14, SAGE journals 2016.

[2015]

Critical transitions in chronic disease: transferring concepts from ecology to systems medicine - [Get PDF]
Christophe Trefois, Paul MA Antony, Jorge Goncalves, Alexander Skupin, Rudi Balling
Current Opinion in Biotechnology, 34, pp. 48-55, Elsevier 2015

[2014]

Systems genomics evaluation of the SH-SY5Y neuroblastoma cell line as a model for Parkinson’s disease - [Get PDF] - Highly Accessed
Krishna A, Biryukov M, Trefois C, Antony PM, Hussong R, Lin J, Heinäniemi M, Glusman G, Koeglsberger S, Boyd O, et al.
BMC Genomics 2014, 15:1154.

Platelet mitochondrial membrane potential in Parkinson's disease - [Get PDF]
Paul MA Antony, Olga Boyd, Christophe Trefois, Wim Ammerlaan, Marek Ostaszewski, Aidos S. Baumuratov, Laura Longhino, Laurent Antunes, Werner Koopman, Rudi Balling and Nico J. Diederich
Annals of Clinical and Translational Neurology, early view pub, Wiley 2014

Integrating Pathways of Parkinson's Disease in a Molecular Interaction Map - [Get PDF]
Kazuhiro A. Fujita, Marek Ostaszewski, Yukiko Matsuoka, Samik Ghosh, Enrico Glaab, Christophe Trefois, Isaac Crespo, Thanneer M. Perumal, Wiktor Jurkowski, Paul M. A. Antony, Nico Diederich, Manuel Buttini, Akihiko Kodama, Venkata P. Satagopam, Serge Eifes, Antonio del Sol, Reinhard Schneider, Hiroaki Kitano, Rudi Balling
Molecular Neurobiology, 49(1), pp. 88-102, SpringerLink 2014

[2013]

Light microscopy applications in systems biology: opportunities and challenges - [Get PDF] - Highly Accessed
Paul MA Antony, Christophe Trefois, Alexandar Stojanovic, Aidos S Baumuratov, Karol Kozak
Cell Communication and Signaling, 11:24, BioMed Central 2013

[2009]

Efficient Access Control for Wireless Sensor Data - [Get PDF] - [Master thesis results were published in this paper]
Alessandro Sorniotti, Refik Molva, Laurent Gomez, Christophe Trefois, Annett Laube, Piervito Scaglioso
International Journal of Wireless Information Networks 6 (3) p. 165-174, SpringerLink 2009

Papers published in a book

[2014]

Evaluation of Cell Line Suitability for Disease Specific Perturbation Experiments
Biryukov. M., Antony, P., Krishna, A., May, P., Trefois, C. 
Studies in Classification, Data Analysis, and Knowledge Organization, Springer Series 2014; 
978-3-662-44982-0

Conference Proceedings / Papers

[2018]

Provenance-enabled stewardship of human data in the GDPR era
Pinar Alper, Regina Becker, Venkata Satagopam, Christophe Trefois, Valentin Groues, Jacek Lebioda, Yohan Jarosz
ProvenanceWeek 2018 IPAW, London, July 9-10 2018.

Gearing up to solve the reproducibility crisis in biomedicine
Laurent Heirendt, Sylvain Arreckx, Christophe Trefois, Yohan Jarosz, Maharshi Vyas, Venkata P. Satagopam, Reinhard Schneider, Ines Thiele and Ronan M. T. Fleming
Network Tools and Applications in Biology, NETTAB, Genoa, October 22-24 2018. - ACCEPTED FOR FLASH TALK

Standardisation in life-science research - Making the Case for Harmonization to Improve Communication and Sharing of Data amongst Researchers? [Get PDF]
Susanne Hollmann, Babette Regierer, Markus Frohme, Juliane Pfeil, Domeica D'Elia, Kristina Gruden, Spela Baebler, Ugur Sezerman, Chris T Evelo, Friederike Ehrhart, Berthold Huppertz, Erik Bongcam-Rudloff, Christophe Trefois, Feng He, Aleksandra Gruca, Deborah A. Duca, Gianni Colotti, Roxana Merino-Martinez, Christos Ouzounis, Oliver Hunewald and Andreas Kremer
10th International Conference ICT Innovations 2018, Web Proceedings, ISSN 1857-7288, pp. 149-159, Ohrid, 17-19 September 2018.

[2016]

Semantic Web technologies for a knowledge base of biomedical facts extracted from scientific literature
Maria Biryukov, Valentin Groues, Christophe Trefois, Venkata Satagopam and Reinhard Schneider
9th International SWAT4LS Conference, Amsterdam, December 6-7 2016.

[2014]

Automated nuclei clump splitting by combining local concavity orientation and graph partitioning - [Get PDF] - Selected for oral presentation
Samsi Siddarth, Trefois Christophe, Antony PMA, Skupin Alexander.
International Conference on Biomedical and Health Informatics, Valencia, IEEE-EMBS BHI 2014


[2008]

Encryption-Based Access Control for Building Management - [Get PDF] 
Laurent Gomez, Annett Laube, Vincent Ribiere, Alessandro Sorniotti, Christophe Trefois, Marco Valente, Patrick Wetterwald 
Proceedings of the Fifth Annual International Conference on Mobile and Ubiquitous Systems: Computing, Networking and Services, MobiQuitous 2008


[2007]

Distributed and Component Oriented Tools for Communication Networks Using Web Services[Get PDF]
Sébastien Rumley, Christian Gaumier, Christophe Trefois
Proceedings of the 6th EUROSIM Congress on Modelling and Simulation, vol. 1, EuroSim 2007
ISBN: 978-3-901608-32-2


Talks

[2018]

ELIXIR Luxembourg - Data hosting service as a sustainability solution
Presented by: Christophe Trefois
IMI Networking Events in Luxembourg, Dudelange, December 14, 2018. 

FAIR human data under the GDPR
Christophe Trefois, Pinar Alper, Venkata Satagopam and Regina Becker
Presented by: Christophe Trefois
4th ELIXIR All Hands meeting, Berlin, June 4-7 2018.

[2016]

IT enabled Innovation: A need for speed !(?) - [See Video]
Presented by: Christophe Trefois
10x6: Dix grands projets IT, Cycle Information management & enterprise 2.0, Paperjam 10x6, Luxembourg, November 16 2016.

Drive change management in the lab: Addressing scientists’ unique workflows and encouraging integration with new systems & platforms
Presented by: Christophe Trefois
"The CHARME of standardisation in life sciences" conference, Warsaw, June 21-22 2016.

Semantic Web technologies for a knowledge base of biomedical facts extracted from scientific literature
Maria Biryukov, Valentin Groues, Christophe Trefois, Venkata Satagopam and Reinhard Schneider
Presented by: Valentin Grouès
9th International SWAT4LS Conference, Amsterdam, December 6-7 2016.

[2015]

CASE STUDY: Advancing Prompt Data Analytics Through Exploring the Readability & Interactivity of Information
Presented by: Christophe Trefois
Big Data Analytics in Pharma Conference, Brussels, September 29 to October 1 2015.

Drive Change Management in the Laboratory: Addressing Scientists’ Unique Workflows and Encouraging Integration With New Systems & Platforms
Presented by: Christophe Trefois
14th Annual Laboratory Informatics, Brussels, September 29 to October 1 2015.

[2013]

The Parkinson’s Disease Map: a framework for 
integration, curation and exploration of disease related 
pathways
Presented by: Christophe Trefois
Redox on the rise - Redox Biology Symposium, Kaiserslautern, April 11-12, 2013, UGR


Workshops (Animator/Speaker)

[2017]

Big data & medicine workshop
Presented by: Christophe Trefois, Reinhard Schneider, Venkata Satagopam, Wei Gu
Paperjam Workshop, Luxembourg, September 21 2017

Workshop Session: SOP and Quality Management
Organized and presented by: Christophe Trefois, Babette Regierer
With “CHARME” into a transdisciplinary dialogue on STANDARDISATION in life-sciences, Cross Cost Actions–Stakeholder Workshop, Split, October 23-25 2017.

Published Poster Abstracts (with Impact Factor)

[2013]

Differentiated SH-SY5Y Cells as PD Model for Mitochondrial Dysfunction: From Whole Genome Sequencing to an Educated Design of High-Throughput Experiments - [Get PDF]
Antony Paul MA, Krishna Abhimanyu, May Patrick, Trefois Christophe, Boyd Olga, Köglsberger Sandra, Baumuratov Aidos, Galas David, Balling Rudi
11th International Conference AD/PD, Florence, March 6-10, 2013: Abstracts, AD/PD 2013
ISBN: 978-3-318-02391-6

The Parkinson's Disease Map: A Framework for Integration, Curation and Exploration of Disease-related Pathways - [Get PDF]
Kazuhiro A. Fujita, Marek Ostaszewski, Yukiko Matsuoka, Samik Ghosh, Enrico Glaab, Christophe Trefois, Isaac Crespo, Thanneer M. Perumal, Wiktor Jurkowski, Paul M. A. Antony, Nico Diederich, Manuel Buttini, Akihiko Kodama, Venkata P. Satagopam, Serge Eifes, Antonio del Sol, Reinhard Schneider, Hiroaki Kitano, Rudi Balling
11th International Conference AD/PD, Florence, March 6-10, 2013: Abstracts, AD/PD 2013
ISBN: 978-3-318-02391-6

Conference Posters

[2018]

Provenance-enabled Stewardship of Human Data in the GDPR era
Pinar Alper, Regina Becker, Venkata Satagopam, Valentin Groues, Jacek Lebioda, Yohan Jarosz, Christophe Trefois, Roland Krause, Sandrine Munoz and Reinhard Schneider
ProvenanceWeek 2018 IPAW, London, July 9-10 2018.

ELIXIR-LU: Giving life to data
Venkata Satagopam, Christophe Trefois, Wei Gu, Roland Krause, Pinar Alper, Valentin Groues, Yohan Jarosz, Jacek Lebioda, Noua Toukourou, Dietlind Gerloff, Regina Becker and Reinhard Schneider
ECCB 2018, Athens, September 8-12, 2018.

DAISY – a Data Information System for GDPR compliance
Pinar Alper, Regina Becker, Venkata Satagopam, Valentin Groues, Jacek Lebioda, Yohan Jarosz, Christophe Trefois, Roland Krause, Sandrine Munoz and Reinhard Schneider
ECCB 2018, Athens, September 8-12, 2018.

LCSB Service Platforms
Rashi Halder, Djalil Coowar, Maria Lorena Cordero Maldonado, Aymeric Fouqier D'Herouël, Christian Jäger, Nicole Paczia, Christophe Trefois and Nicolas Bonjean
CTLS2018@VIB, Gent, July 1-5, 2018.

DAISY – a Data Information System for GDPR compliance
Pinar Alper, Christophe Trefois, Venkata Satagopam, Regina Becker
4th ELIXIR All Hands meeting, Berlin, June 4-7 2018.

ELIXIR-LU : Current Node Activities
Venkata Satagopam, Pinar Alper, Regina Becker, Dietlind Gerloff, Wei Gu, Roland Krause, Jacek Lebioda, Noua Toukourou, Christophe Trefois, Reinhard Schneider
4th ELIXIR All Hands meeting, Berlin, June 4-7 2018.

ELIXIR-Luxembourg: providing sustainability to clinical and translational medicine data for research
Venkata Satagopam, Pinar Alper, Regina Becker, Dietlind Gerloff, Wei Gu, Roland Krause, Jacek Lebioda, Noua Toukourou, Christophe Trefois, Reinhard Schneider
Intelligent Systems for Molecular Biology 2018, ISMB, Chicago, July 6-10 2018.

ARTENOLIS: Automated Reproducibility and Testing Environment for Licensed Software
Laurent Heirendt & Sylvain Arreckx, Christophe Trefois, Yohan Jarosz, Maharshi Vyas, Venkata P. Satagopam, Reinhard Schneider, Ines Thiele, Ronan M. T. Fleming, 2018 Genomic Sciences Program Annual Principal Investigator (PI) MeetingWashington DC, February 25-28, 2018.

[2017]

ELIXIR-LU : New Luxembourgish ELIXIR Node Focussed on Translational / Systems Medicine
Venkata Satagopam, Regina Becker, Dietlind Gerloff, Marek Ostaszewski, Stephan Gebel, Wei Gu, Roland Krause, Patrick May, Christophe Trefois and Reinhard Schneider
13th [BC]2 Basel Computational Biology Conference, Basel, September 12-15, 2017.

[2016]

Reproducible Research Results - R3
Yohan Jarosz, Christophe Trefois, Sarah Diehl, Wei Gu, Venkata Satagopam, Sergio Coronado, Reinhard Schneider
EMBNet and NETTAB 2016: Reproducibility, standards and SOP in bioinformatics, Rome, October 25-26 2016.

[2015]

Reproducible Research Results - R3
Christophe Trefois, Yohan Jarosz, Sarah Diehl, Wei Gu, Venkata Satagopam, Sergio Coronado, Reinhard Schneider
3rd International Systems Biomedicine Consortium, Luxembourg, October 28-29, 2015.

Analysis of mitochondrial membrane potential in thrombocytes from Parkinson's disease patients
Paul Antony, Olga Boyd, Christophe Trefois, Wim Ammerlaan, Marek Ostaszewski, Aidos Baumuratov, Laura Longhino, Laurent Antunes, Werner Koopman, Rudi Balling and Nico Diederich
6th World Congress on Targeting Mitochondria, Berlin, October 28-30, 2015. 

[2014]

Reproducible Research Results - R3
Christophe Trefois, Yohan Jarosz, Wei Gu, Venkata Satagopam, Sergio Coronado, Reinhard Schneider
9th Benelux Bioinformatics Conference, Luxembourg, December 8-9 2014.

Curation of complex molecular pathways of Parkinson's disease as a collaborative scientific community effort - [Get PDF]Selected for "Guided Poster Tour"
Gebel S., Ostaszewski M., Gawron P., Antony PMA., Trefois C., Fujita KA., Mosch S., Balling, R.
18th International Congress of Parkinson's Disease and Movement Disorder, Stockholm, June 8-12, 2014: MDS 2014. DOI: 
10.1002/mds.25914

Analysis of mitochondrial membrane potential in idiopathic Parkinson's disease: A case-control study - [Get PDF]
PMA Antony, Olga Boyd, Christophe Trefois, Marek Ostaszewski, Aidos S. Baumuratov, Rudi Balling, Nico J. Diederich.
18th International Congress of Parkinson's Disease and Movement Disorder, Stockholm, June 8-12, 2014: MDS 2014. DOI: 10.1002/mds.25914

[2013]

Integrating Pathways of Parkinson's Disease in a Molecular Interaction Map
Kazuhiro A. Fujita, Marek Ostaszewski, Yukiko Matsuoka, Samik Ghosh, Enrico Glaab, Christophe Trefois, Isaac Crespo, Thanneer M. Perumal, Wiktor Jurkowski, Paul M. A. Antony, Nico Diederich, Manuel Buttini, Akihiko Kodama, Venkata P. Satagopam, Serge Eifes, Antonio del Sol, Reinhard Schneider, Hiroaki Kitano, Rudi Balling
The 36th Annual Meeting of the Molecular Biology Society of Japan, Kobe (Japan), December 3-6, 2013, MBSJ

Critical Transitions in Biological Systems
Christophe Trefois, Paul MA Antony, Laurent Bück, Bob Pepin, Sandra Köglsberger, Rudi Balling
2nd International Systems Biomedicine Symposium, Luxembourg, October 21-22, 2013

Evaluation of Cell Line Suitability for Disease Specific Perturbation Experiments
Maria Biryukov, Paul Antony, Abhimanyu Krishna, Patrick May, Christophe Trefois
2nd International Systems Biomedicine Symposium, Luxembourg, October 21-22, 2013

Differentiated SH-SY5Y Cells as PD Model for Mitochondrial Dysfunction: From Whole Genome Sequencing to an Educated Design of High-Throughput Experiments
Paul MA Antony, Abhimanyu Krishna, Patrick May, Rene Hussong, Maria Biryukov, Julia Ilona Dersidan, Christophe Trefois, Olga Boyd, Sandra Koeglsberger, Bob Pepin, Aidos S Baumuratov, David Galas, and Rudi Balling
2nd International Systems Biomedicine Symposium, Luxembourg, October 21-22, 2013

Integrating Pathways of Parkinson's Disease in a Molecular Interaction Map
Kazuhiro A. Fujita, Marek Ostaszewski, Yukiko Matsuoka, Samik Ghosh, Enrico Glaab, Christophe Trefois, Isaac Crespo, Thanneer M. Perumal, Wiktor Jurkowski, Paul M. A. Antony, Nico Diederich, Manuel Buttini, Akihiko Kodama, Venkata P. Satagopam, Serge Eifes, Antonio del Sol, Reinhard Schneider, Hiroaki Kitano, Rudi Balling
7th Congress of Parkinson's Disease and Movement Disorders, Tokyo, October 10-12, 2013, 7th MDSJ Congress

[2012]

Constructing a comprehensive map of Parkinson’s disease to elucidate underlying mechanisms of its multifaceted molecular pathology
Kazuhiro A. Fujita, Marek Ostaszewski, Yukiko Matsuoka, Samik Ghosh, Enrico Glaab, Christophe Trefois, Isaac Crespo, Thanneer M. Perumal, Wiktor Jurkowski, Paul M. A. Antony, Nico Diederich, Manuel Buttini, Akihiko Kodama, Venkata P. Satagopam, Serge Eifes, Antonio del Sol, Reinhard Schneider, Hiroaki Kitano, Rudi Balling
The 13th International Conference on Systems Biology, Toronto, August 19-23, 2012, ICSB

[2011]

Analysis of critical transitions in Parkinson's disease
Christophe Trefois, Paul Antony, Aidos Baumuratov, Olga Boyd, Sandra Koeglsberger and Rudi Balling
The BeNeLux Bioinformatics Conference 2011, Luxembourg, BBC

Theses

PhD, XXX

Secure Integration of Wireless Sensor Networks into Applications - [Get PDF]
Christophe Trefois
SAP Labs France, Security and Trust Research Unit, Sophia Antipolis 2008
Supervisors: Laurent Gomez (SAP), Jean-Pierre Hubaux, (EPFL)