Publications

Co-occurrence of memory impairment and fatigue distinguishes post COVID from pandemic-related health effects in the 4-year CON-VINCE cohort study

Martins Conde P, Bulaev D, Rauschenberger A, Ohnmacht J, Fritz JV, O'Sullivan MP, Ancien F, Ghosh S, Tsurkalenko O, Kolodkin A, Satagopam V, Vaillant M, Klucken J, Krüger R; CON-VINCE/ORCHESTRA Study Consortium

Scientific Reports, Volume 15, Issue 1, Article 37381, 2025

Creation of a pandemic memory by tracing COVID-19 infections and immunity in Luxembourg (CON-VINCE)

Tsurkalenko O, Bulaev D, O'Sullivan MP, Snoeck C, Ghosh S, Kolodkin A, Rommes B, Gawron P, Moreno CV, Gomes CPC, Kaysen A, Ohnmacht J, Schröder VE, Pavelka L, Meyers GR, Pauly L, Pauly C, Hanff AM, Meyrath M, Leist A, Sandt E, Aguayo GA, Perquin M, Gantenbein M, Abdelrahman T, Klucken J, Satagopam V, Hilger C, Turner J, Vaillant M, Fritz JV, Ollert M, Krüger R; CON-VINCE consortium and the ORCHESTRA working group

BMC Infectious Diseases, Volume 25, Issue 1, Article 892, 2024

Dopamine Pathway and Parkinson's Risk Variants Are Associated with Levodopa-Induced Dyskinesia

Sosero YL, Bandres-Ciga S, Ferwerda B, Tocino MTP, Belloso DR, Gómez-Garre P, Faouzi J, Taba P, Pavelka L, Marques TM, Gomes CPC, Kolodkin A, May P, Milanowski LM, Wszolek ZK, Uitti RJ, Heutink P, van Hilten JJ, Simon DK, Eberly S, Alvarez I, Krohn L, Yu E, Freeman K, Rudakou U, Ruskey JA, Asayesh F, Menéndez-Gonzàlez M, Pastor P, Ross OA, Krüger R; NCER-PD Consortium; Corvol JC, Koks S, Mir P, De Bie RMA, Iwaki H, Gan-Or Z; International Parkinson's Disease Genomic Consortium

Movement Disorders, Volume 39, Issue 10, Pages 1773-1783, 2024

Cardiovascular history and risk of idiopathic Parkinson's disease: a cross-sectional observational study

Acharya S, Lumley AI, Devaux Y; NCER-PD Consortium

BMC Neuroscience, Volume 25, Issue 1, Article 33, 2024

Converging peripheral blood microRNA profiles in Parkinson's disease and progressive supranuclear palsy

Pavelka L, Rauschenberger A, Hemedan A, Ostaszewski M, Glaab E, Krüger R; NCER-PD Consortium

Brain Communications, Volume 6, Issue 3, Article fcae187, 2024

DS-PACK: Tool assembly for the end-to-end support of controlled access human data sharing

Alper P, Dĕd V, Herzinger S, Grouès V, Peter S, Lebioda J, Ebermann L, Popleteeva M, Barry ND, Welter D, Ghosh S, Becker R, Schneider R, Gu W, Trefois C, Satagopam V

Scientific Data, Volume 11, Issue 1, Article 501, 2024

Comprehensive blood metabolomics profiling of Parkinson's disease reveals coordinated alterations in xanthine metabolism

de Lope EG, Loo RTJ, Rauschenberger A, Ali M, Pavelka L, Marques TM, Gomes CPC, Krüger R, Glaab E; NCER-PD Consortium

NPJ Parkinson's Disease, Volume 10, Issue 1, Article 68, 2024

Accurate long-read sequencing identified GBA1 as major risk factor in the Luxembourgish Parkinson's study

Pachchek S, Landoulsi Z, Pavelka L, Schulte C, Buena-Atienza E, Gross C, Hauser AK, Reddy Bobbili D, Casadei N, May P, Krüger R; NCER-PD Consortium

NPJ Parkinson's Disease, Volume 9, Issue 1, Article 156, 2023

Altered infective competence of the human gut microbiome in COVID-19

de Nies L, Galata V, Martin-Gallausiaux C, Despotovic M, Busi SB, Snoeck CJ, Delacour L, Budagavi DP, Laczny CC, Habier J, Lupu PC, Halder R, Fritz JV, Marques T, Sandt E, O'Sullivan MP, Ghosh S, Satagopam V; CON-VINCE Consortium; Krüger R, Fagherazzi G, Ollert M, Hefeng FQ, May P, Wilmes P

Microbiome, Volume 11, Issue 1, Article 46, 2023

Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based models

St. Elmo Wilken, Mathieu Besançon, Miroslav Kratochvíl, Chilperic Armel, Foko Kuate, Christophe Trefois, Wei Gu, Oliver Ebenhöh

Metabolic Engineering, Volume 74, Pages 72-82, 2022

Age at onset as stratifier in idiopathic Parkinson's disease - effect of ageing and polygenic risk score on clinical phenotypes

Pavelka L, Rauschenberger A, Landoulsi Z, Pachchek S, May P, Glaab E, Krüger R; NCER-PD Consortium

NPJ Parkinson's Disease, Volume 8, Issue 1, Article 102, 2022

COBREXA.jl: constraint-based reconstruction and exascale analysis

Miroslav Kratochvíl, Laurent Heirendt, St Elmo Wilken, Taneli Pusa, Sylvain Arreckx, Alberto Noronha, Marvin van Aalst, Venkata P Satagopam, Oliver Ebenhöh, Reinhard Schneider, Christophe Trefois, Wei Gu

Bioinformatics, Volume 38, Issue 4, 15 February 2022, Pages 1171–1172, 2022

Model-based assessment of mammalian cell metabolic functionalities using omics data

Anne Richelle, Benjamin P. Kellman, Alexander T. Wenzel, Austin W.T. Chiang, Tyler Reagan, Jahir M. Gutierrez, Chintan Joshi, Shangzhong Li, Joanne K. Liu, Helen Masson, Jooyong Lee, Zerong Li, Laurent Heirendt, Christophe Trefois, Edwin F. Juarez, Tyler Bath, David Borland, Jill P. Mesirov, Kimberly Robasky, Nathan E. Lewis

Cell Reports Methods, 3, vol:1, 2021

PredictProtein - Predicting Protein Structure and Function for 29 Years

Michael Bernhofer, Christian Dallago, Tim Karl, Venkata Satagopam, Michael Heinzinger, Maria Littmann, Tobias Olenyi, Jiajun Qiu, Konstantin Schütze, Guy Yachdav, Haim Ashkenazy, Nir Ben-Tal, Yana Bromberg, Tatyana Goldberg, Laszlo Kajan, Sean O'Donoghue, Chris Sander, Andrea Schafferhans, Avner Schlessinger, Gerrit Vriend, Milot Mirdita, Piotr Gawron, Wei Gu, Yohan Jarosz, Christophe Trefois, Martin Steinegger, Reinhard Schneider, Burkhard Rost

Nucleic Acids Research, 2021, Vol. 49, 2021

Clustering and visualizing huge-scale cytometry datasets with GigaSOM.jl

Miroslav Kratochvil, Oliver Hunewald, Laurent Heirendt, Vasco Verissimo, Jiří Vondrášek, Venkata P. Satagopam, Reinhard Schneider, Christophe Trefois, Markus Ollert

GigaScience, giaa127, 2020

The need for standardisation in life science research - an approach to excellence and trust

Susanne Hollmann, Andreas Kremer, Špela Baebler, Christophe Trefois, Kristina Gruden, Witold R. Rudnicki, Weida Tong, Aleksandra Gruca, Erik Bongcam-Rudloff, Chris T. Evelo, Alina Nechyporenko, Marcus Frohme, David Šafránek, Babette Regierer, Domenica D'Elia

F1000 Research, 9:1398, 2020

Parkinson's disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions

Baldini, F., Hertel, J., Sandt, E. et al.

BMC Biol 18, 62, 2020

DAISY: A Data Information System for accountability under the General Data Protection Regulation

Regina Becker, Pinar Alper, Valentin Grouès, Sandrine Munoz, Yohan Jarosz, Jacek Lebioda, Kavita Rege, Christophe Trefois, Venkata Satagopam, Reinhard Schneider

GigaScience, giz140, 2019

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

arXiv preprint arXiv:1712.05236, 2018

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, 2018

Characterization of Differentiated SH-SY5Y as Neuronal Screening Model Reveals Increased Oxidative Vulnerability

Julia Forster, Sandra Köglsberger, Christophe Trefois, Olga Boyd, Aidos Baumuratov, Laurent Bück, Rudi Balling, Paul Antony

Journal of Biomedical Screening, pp. 1-14, SAGE journals, 2016

Critical transitions in chronic disease: transferring concepts from ecology to systems medicine

Christophe Trefois, Paul MA Antony, Jorge Goncalves, Alexander Skupin, Rudi Balling

Current Opinion in Biotechnology, 34, pp. 48-55, Elsevier, 2015

Evaluation of Cell Line Suitability for Disease Specific Perturbation Experiments

Maria Biryukov, Paul Antony, Abhimanyu Krishna, Patrick May, and Christophe Trefois

Data Science, Learning by Latent Structures, and Knowledge Discovery pp 297-307, Springer, 2015

Systems genomics evaluation of the SH-SY5Y neuroblastoma cell line as a model for Parkinson's disease

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, 2014

Platelet mitochondrial membrane potential in Parkinson's disease

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, Wiley, 2014

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

Molecular Neurobiology, 49(1), pp. 88-102, SpringerLink, 2014

Light microscopy applications in systems biology: opportunities and challenges

Paul MA Antony, Christophe Trefois, Alexandar Stojanovic, Aidos S Baumuratov, Karol Kozak

Cell Communication and Signaling, 11:24, BioMed Central, 2013

Efficient Access Control for Wireless Sensor Data

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

Master thesis results published

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

Standardisation in life-science research - Making the Case for Harmonization to Improve Communication and Sharing of Data amongst Researchers?

Susanne Hollmann, Babette Regierer, Markus Frohme, et al.

10th International Conference ICT Innovations 2018, Web Proceedings, Ohrid, September 17-19, 2018

Automated nuclei clump splitting by combining local concavity orientation and graph partitioning

Samsi Siddarth, Trefois Christophe, Antony PMA, Skupin Alexander

International Conference on Biomedical and Health Informatics, Valencia, IEEE-EMBS BHI 2014

Encryption-Based Access Control for Building Management

Laurent Gomez, Annett Laube, Vincent Ribiere, Alessandro Sorniotti, Christophe Trefois, Marco Valente, Patrick Wetterwald

Fifth Annual International Conference on Mobile and Ubiquitous Systems: Computing, Networking and Services, MobiQuitous 2008

Distributed and Component Oriented Tools for Communication Networks Using Web Services

Sébastien Rumley, Christian Gaumier, Christophe Trefois

6th EUROSIM Congress on Modelling and Simulation, vol. 1, EuroSim 2007, ISBN: 978-3-901608-32-2