Dr. Reinhard Schneider
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| Faculté ou Centre | Luxembourg Centre for Systems Biomedicine | ||||||||
| Department | Bioinformatics Core | ||||||||
| Adresse postale |
Université du Luxembourg 2, Avenue de l'Université L-4365 Esch-sur-Alzette |
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| Téléphone | (+352) 46 66 44 6170 | ||||||||
| Réseaux sociaux & blogs | |||||||||
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Dr. Reinhard Schneider (LCSB)
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| Langues parlées | English, German | ||||||||
| Séjours de recherche en | Germany, Luxembourg, USA | ||||||||
Dr. Reinhard Schneider is the Head of the Bioinformatics Core group at the Luxembourg Centre for Systems Biomedicine (LCSB) at the University of Luxembourg. In addition, he heads the Luxembourg Elixir node since 2017.
Between 1994-2010, he worked as a Team Leader at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, where he led the “Data Integration and Knowledge Management”.
Before joining the EMBL he was co-founder of LION bioscience AG, Heidelberg where he served as Chief Information Officer being responsible for the worldwide software development. He was also the CEO of LION bioscience Research Inc., Cambridge, Massachusetts, when he established an IT-based knowledge management system for Bayers gene-based research and development efforts.
Prior to founding LION bioscience, he worked as a scientist in the biocomputing department at the EMBL, Heidelberg, where he studied various aspects of protein structures. He co-developed a large-scale automated sequence analysis system which became the foundation of LION’s software offering and is an expert in the use of massive parallel computers in biology. Dr. Schneider received his Ph.D. in biology at the University of Heidelberg, Germany and has over 90 research papers published.
He is a member of the International Society for Computational Biology where he served as the treasurer and chairs the Governance, Fundraising and Finance Committee. Besides his academic career, he is involved in several start-up projects in Germany and Luxembourg.
Last updated on: mercredi 27 janvier 2021
Download the full version of the CV
Employment
| 2011 |
Head of the Bioinformatics Core facility, Luxembourg Centre for Systems Biomedicine (LCSB), University of |
| 2017 |
Head of the Luxembourg ELIXIR node |
| 2004-2012 |
Team Leader at the EMBL-Heidelberg, Germany |
| 2007-2013 |
Project Leader VIROQUANT: Systems Biology of Virus-Cell Interactions, Bioquant Institute, Heidelberg, Germany |
| 2006 |
Founder and Consultant, OnScale GmbH, Berlin, Germany |
Education
| 1990-1994 |
PhD thesis at the EMBL-Heidelberg, Germany |
| 1988-1989 |
Diploma thesis (master equivalent) at the EMBL-Heidelberg, Germany |
| 1981-1989 |
Biology studies at the RWTH Aachen and University Heidelberg, Germany |
Honors and Achivements
Elsevier Grand Challenge winner, 2009
Last updated on: 19 fév 2018
PhD and Master students supervised
10 PhD students supervised, 10 PhD students co-supervised, >25 Master and Bachelor students
Publicly funded projects
| A Systems medicine approach to chronic inflammatory diseases, 2017 to present |
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| Organising Knowledge about Neurodegenerative Disease Mechanisms for the Improvement of Drug Development and |
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| Biomarker Development for Postoperative Cognitive Impairment in the Elderly, FP7, 2014-2017 |
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| A Proposal for Developing and Deploying a European Translation Information & Knowledge Management Service |
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| Epilepsy Pharmacogenomics: delivering biomarkers for clinical use, 2011-2015 |
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| Complex genetics of idiopathic epilepsies, (EUROEPINOMICS), 2010-2015 |
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| Beta-cell function in juvenile diabetes and obesity, 2011-2016 |
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| eTRIKS: |
A Proposal for Developing and Deploying a European Translation Information & Knowledge Management Service |
| TAMAHUD: |
Identification of early disease markers, novel pharmacologically tractable targets and small molecule phenotypic |
| FANCI: |
Functional analysis of non-coding RNAs in living cells, 2009-2011 |
| VIROQUANT: |
Systems Biology of Virus-Cell Interactions, 2007-2011 |
| SIMDAT: |
Grids for Industrial Product Development, 2004-2008 |
| TTA: |
Technologies for Target Assessment, ATP-NIST, 2002 |
| EUROPORT: |
ESPRIT European Porting Projects, 1994-1996 |
| ZEUS: |
Massively Parallel Computing, 1992-1993 |
Organizer and Co-Organizer (>30) conferences and lecture series, selected list:
BeNeLux Bioinformatics Conference, Luxembourg 2014
ISMB 2007 – 2014: Vienna, Austria; Toronto, Canada; Stockholm, Sweden; Boston, USA; Vienna, Austria; Long Beach, USA; Berlin, Germany; Boston, USA
ISCB-Asia/SCCG 2012: Shenzen, China
ISCB Latin America 2012:Santiago, Chile
VizBi 2012: Visualizing Biological Data, EMBL-Heidelberg, Germany
BBC 2011: BeNeLux Bioinformatics conference, Luxembourg
ISCB Asia 2011: Kuala Lumpur, Malaysia
VizBi 2010: EMBO workshop, Heidelberg, Germany
ISCB Latin-America 2009: Montevideo, Uruguay
ISCB Africa ASBCB 2009: Bioinformatics of Infectious Diseases, Bamako, Mali,
ISMB 1999: Heidelberg, Germany
Reviewer
Over 200 referee reports for peer-reviewed journals (including JMB, Bioinformatics, PLOS Comp.Bio., Nature Methods)
Last updated on: 19 fév 2018
2020
GigaSOM.jl: High-performance clustering and visualization of huge cytometry datasets; ; ; ; ; ; ; ;
in GigaScience (2020), 9(11),
COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Scientific Data (2020)
BioKC: a platform for quality controlled curation and annotation of systems biology models; ; ; ;
Scientific Conference (2020, September 04)
BioKC: a collaborative platform for systems biology model curation and annotation; ; ; ;
in bioRxiv (2020)
Supporting findability of COVID-19 research with large-scale text mining of scientific publications; ; ; ; ; ;
Poster (2020, November 27)
2019
Optimization ACE inhibition activity in hypertension based on random vector functional link and sine-cosine algorithm; ; ; ;
in Chemometrics and Intelligent Laboratory Systems (2019)
DAISY: A Data Information System for accountability under the General Data Protection Regulation; ; ; ; ; ; ; ; ;
in GigaScience (2019), 8(12),
A genome-wide association study of sodium levels and drug metabolism in an epilepsy cohort treated with carbamazepine and oxcarbazepine; ; ; ; ; ; ; ; ; ; ;
in Epilepsia Open (2019)
Multicenter Alzheimer's and Parkinson's disease immune biomarker verification study;
in Alzheimer's and Dementia: the Journal of the Alzheimer's Association (2019)
Data and knowledge management in translational research: implementation of the eTRIKS platform for the IMI OncoTrack consortium; ; ; ; ; ; ; ; ; ; ; ; ;
in BMC Bioinformatics (2019), 20(1), 164
Closing the gap between formats for storing layout information in systems biology.; ; ; ;
in Briefings in bioinformatics (2019)
MINERVA API and plugins: opening molecular network analysis and visualization to the community.; ; ; ;
in Bioinformatics (Oxford, England) (2019)
2018
Presenting and Sharing Clinical Data using the eTRIKS Standards Master Tree for tranSMART; ; ; ; ; ; ; ; ; ; ; ; ;
in Bioinformatics (2018)
Fractalis: A scalable open-source service for platform-independent interactive visual analysis of biomedical data; ; ; ; ; ;
in GigaScience (2018)
Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms.; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in NPJ systems biology and applications (2018), 4
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Nucleic Acids Research (2018)
Community-driven roadmap for integrated disease maps.; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Briefings in bioinformatics (2018)
Clustering approaches for visual knowledge exploration in molecular interaction networks.; ; ; ;
in BMC bioinformatics (2018), 19(1), 308
Personalized risk prediction of postoperative cognitive impairment - rationale for the EU-funded BioCog project.; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in European psychiatry : the journal of the Association of European Psychiatrists (2018), 50
2017
SmartR: An open-source platform for interactive visual analytics for translational research data.; ; ; ; ; ;
in Bioinformatics (Oxford, England) (2017)
2016
Making sense of big data in health research: Towards an EU action plan.; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Genome medicine (2016), 8(1), 71
MINERVA—a platform for visualization and curation of molecular interaction networks; ; ; ; ; ; ; ; ; ;
in NPJ Systems Biology and Applications (2016)
ReconMap: An interactive visualisation of human metabolism; ; ; ; ; ; ; ; ; ;
in Bioinformatics (2016)
Integration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases.; ; ; ; ; ; ; ;
in Big data (2016), 4(2), 97-108
2015
Biomarkers of postoperative delirium and cognitive dysfunction; ; ;
in Frontiers in Aging Neuroscience (2015), 7(112),
Comparative pathway and network analysis of brain transcriptome changes during adult aging and in Parkinson's disease;
in Neurobiology of Disease (2015), 74
RepExplore: Addressing technical replicate variance in proteomics and metabolomics data analysis;
in Bioinformatics (2015), 31(13), 2235
Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders; ; ; ; ; ; ; ; ; ;
in International Journal of Molecular Sciences (2015), 16(12), 29179-29206
siRNA screen identifies QPCT as a druggable target for Huntington's disease.; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Nature chemical biology (2015), 11(5), 347354
A Novel Multi-objectivisation Approach for Optimising the Protein Inverse Folding Problem; ; ; ; ; ;
in Applications of Evolutionary Computation: 18th European Conference, EvoApplications 2015, Copenhagen, Denmark, April 8-10, 2015, Proceedings (2015)
2014
COMPARTMENTS: unification and visualization of protein subcellular localization evidence.; ; ; ; ; ;
in Database: the Journal of Biological Databases and Curation (2014), 2014
The HIV Mutation Browser: A Resource for Human Immunodeficiency Virus Mutagenesis and Polymorphism Data; ; ; ; ; ;
in PLoS Computational Biology (2014)
Integrating Pathways of Parkinson's Disease in a Molecular Interaction Map; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Molecular Neurobiology (2014)
Systems genomics evaluation of the SH-SY5Y neuroblastoma cell line as a model for Parkinson’s disease; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in BMC Genomics (2014), 15(1154),
Evolutionary Multi-Objective Optimisation with Quantile Constraint for the Protein Structure Similarity Problem; ; ; ; ; ;
Scientific Conference (2014)
Evolutionary multi objective optimisation with diversity as objective for the protein structure similarity problem; ; ; ; ; ;
Scientific Conference (2014)
BioTextQuest+: a knowledge integration platform for literature mining and concept discovery; ; ; ; ; ; ; ; ;
in Bioinformatics (2014)
PredictProtein--an open resource for online prediction of protein structural and functional features; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Nucleic Acid Research (2014), 42(8),
2013
Genome-wide identification and functional analyses of microRNA signatures associated with cancer pain.; ; ; ; ;
in EMBO Molecular Medicine (2013), 5(11), 1740-58
Transcriptional mechanisms underlying sensitization of peripheral sensory neurons by Granulocyte-/Granulocyte-macrophage colony stimulating factors.; ; ; ; ;
in Molecular pain (2013), 9(1), 48
Functional Genomics, Proteomics, Metabolomics and Bioinformatics for Systems Biology; ; ; ; ; ; ; ; ; ; ; ;
in Prokop, Ales; Csukás, Bela (Eds.) Systems Biology: Integrative Biology and Simulation Tools (2013)
Signaling in Insulin-Secreting MIN6 Pseudoislets and Monolayer Cells.; ; ; ; ; ; ;
in Journal of proteome research (2013)
Computational infrastructures for data and knowledge management in systems biology; ; ; ; ; ; ; ; ; ;
in Prokop, Ales; Csukás, Bela (Eds.) Systems Biology: Integrative Biology and Simulation Tools (2013)
IAnn: An event sharing platform for the life sciences; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Bioinformatics (2013)
The Parkinson's Disease Map: A Framework for Integration, Curation and Exploration of Disease-related Pathways; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
Poster (2013, March 09)
OnTheFly 2.0: a tool for automatic annotation of files and biological information extraction.; ; ; ; ; ; ; ;
Poster (2013)
Unraveling genomic variation from next generation sequencing data; ; ; ; ; ; ;
in BioData Mining (2013), 6(1), 13
PhenoTimer: Software for the Visual Mapping of Time-Resolved Phenotypic Landscapes;
in PLoS ONE (2013), 8(8), 72361
Nuclear calcium signaling in spinal neurons drives a genomic program required for persistent inflammatory pain; ; ; ; ; ; ; ; ; ;
in Neuron (2013), 77(1), 43-57
2012
Bioinformatics as a driver, not a passenger, of translational biomedical research: Perspectives from the 6th Benelux bioinformatics conference.; ; ; ; ; ;
in Journal of Clinical Bioinformatics (2012), 2(7),
EnrichNet: network-based gene set enrichment analysis; ; ; ;
in Bioinformatics (2012), 28(18), 451-457
PathVar: analysis of gene and protein expression variance in cellular pathways using microarray data;
in Bioinformatics (2012)
ReLiance: a machine learning and literature-based prioritization of receptor—ligand pairings.; ; ; ; ; ;
in Bioinformatics (2012), 28(18), 569-574
Human gene correlation analysis (HGCA): A tool for the identification of transcriptionally co-expressed genes; ; ; ; ; ;
in BMC Research Notes (2012), 5(265), 1-11
Paving the future: finding suitable ISMB venues; ; ; ; ; ; ; ;
in Bioinformatics (2012), 28(19), 2556-9
Arena3D: visualizing time-driven phenotypic differences in biological systems; ; ;
in BMC Bioinformatics (2012), (13), 45
Constructing a comprehensive map of Parkinson’s disease to elucidate underlying mechanisms of its multifaceted molecular pathology; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
Poster (2012, August)
2011
Which clustering algorithm is better for predicting protein complexes?; ; ; ; ; ;
in BMC Research Notes (2011), (4), 549
Medusa: A tool for exploring and clustering biological networks.; ; ; ;
in BMC Research Notes (2011), 4(1), 384
Using graph theory to analyze biological networks; ; ; ; ; ; ;
in BioData Mining (2011), 4(10), 1-27
2010
LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships.; ; ; ; ; ; ;
in BMC Bioinformatics (2010), 11
From experimental setup to bioinformatics: An RNAi screening platform to identify host factors involved in HIV-1 replication; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Biotechnology Journal (2010), 5(1), 39-49
Visualization of omics data for systems biology; ; ; ; ; ; ; ; ; ;
in Nature Methods (2010), 7(3), 56-68
A series of PDB related databases for everyday needs; ; ; ; ; ; ;
in Nucleic Acids Research (2010), 39(1), 411-419
Live Coverage of Intelligent Systems for Molecular Biology; ; ; ; ; ;
in PLoS Computational Biology (2010), 6
Live Coverage of Scientific Conferences Using Web Technologies; ; ; ; ; ;
in PLoS Computational Biology (2010), 6(1), 1-2
Defective Lamin A-Rb Signaling in Hutchinson-Gilford Progeria Syndrome and Reversal by Farnesyltransferase Inhibition; ; ; ; ; ; ; ;
in PLoS ONE (2010), 5(6),
Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Nature (2010), 464(7289), 721-727
Reflect: A practical approach to web semantics; ; ; ; ; ; ;
in Journal of Web Semantics (2010), 8(2-3), 182-189
GPCRs, G-proteins, Effectors and their interactions: Human-gpDB, a database employing advanced visualization tools and data integration techniques; ; ; ; ; ; ;
in Database: the Journal of Biological Databases and Curation (2010)
GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques.; ; ; ; ; ; ;
in Database: the Journal of Biological Databases and Curation (2010), 2010
Martini: using literature keywords to compare gene sets.; ; ; ; ; ;
in Nucleic acids research (2010), 38(1), 26-38
2009
New in protein structure and function annotation: Hotspots, single nucleotide polymorphisms and the 'Deep Web'; ; ; ;
in Current Opinion in Drug Discovery & Development (2009), 12(3), 408-419
Reflect: augmented browsing for the life scientist; ; ; ; ; ;
in Nature Biotechnology (2009), 27(6), 508-510
OnTheFly: a tool for automated document-based text annotation, data linking and network generation; ; ; ;
in Bioinformatics (2009), 25(7), 977-978
2008
Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence.; ; ;
in BMC bioinformatics (2008), 9
SuperTarget and Matador: resources for exploring drug-target relationships; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Nucleic Acids Research (2008), 36(SI), 919-922
2007
Development of SRS.php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases.; ; ;
in Genetics & Molecular Research [=GMR] (2007), 6(4), 1142-1150
2006
Status of text-mining techniques applied to biomedical text; ;
in Drug Discovery Today (2006), 11(7-8), 315-325
2005
A bioinformatics perspective on proteomics: Data storage, analysis, and integration; ;
in Bioscience Reports (2005), 25(1-2), 95-106
Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery; ; ;
in Drug Discovery Today (2005), 10(21), 1475-1482
2002
Improving Research Productivity at a Pharmaceutical Company; ;
in LION bioscience AG White Paper (2002)
2000
Bioinformatik: Verloren im Datendschungel ?in Nachrichten aus der Chemie : Zeitschrift der Gesellschaft Deutscher Chemiker (2000), 48(5), 622-625
1998
The HSSP database of protein structure sequence alignments and family profiles; ;
in Nucleic Acids Research (1998), 26(1), 313-315
Functional Genome Analysisin Proceedings zur Tagung Hoechstleistungsrechnen in der Chemie. Tagung fuer industrielle Anwender (1998)
1997
Characterization of new proteins found by analysis of short open reading frames from the full yeast genome; ; ; ; ;
in Journal of Yeast and Fungal Research (1997), 13(14), 1363-1374
Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function; ; ; ; ; ; ;
in Computer Applications in the Biosciences [=CABIOS] (1997), 13(4), 481-483
Protein fold recognition by prediction-based threading; ;
in Journal of Molecular Biology (1997), 270(3), 471-480
The HSSP database of protein structure-sequence alignments; ;
in Nucleic Acids Research (1997), 25(1), 226-230
1996
Bioinformatics and the discovery of gene function; ; ;
in Trends in Genetics (1996), 128(7), 244-245
GeneCrunch: Experiences on the SGI POWER CHALLENGEarray with Bioinformatics applications; ; ; ; ; ; ;
in Supercomputer 96 : Anwendungen, Architekturen, Trends (1996)
The HSSP database of protein structure sequence alignments;
in Nucleic Acids Research (1996), 24(1), 201-205
GeneCrunch and Europort, examples for Hierarchical Supercomputing at Silicon Graphics;
in WWW-publication (1996)
1995
EXPLORING THE MYCOPLASMA-CAPRICOLUM GENOME - A MINIMAL CELL REVEALS ITS PHYSIOLOGY; ; ; ; ; ; ;
in Molecular Microbiology (1995), 16(5), 955-967
Fast and sensitive search of information databases for biological relationships; ;
in Statustagung des BMBF, HPSC 95, Stand und Perspektiven des Parallelen Höchstleistungsrechnens und seiner Anwendungen (1995)
1994
REDEFINING THE GOALS OF PROTEIN SECONDARY STRUCTURE PREDICTION; ;
in Journal of Molecular Biology (1994), 235(1), 13-26
PHD - AN AUTOMATIC MAIL SERVER FOR PROTEIN SECONDARY STRUCTURE PREDICTION; ;
in Computer Applications in the Biosciences [=CABIOS] (1994), 10(1), 53-60
Evolution and Neural Networks – Protein Secondary Structure Prediction Above 71% Accuracy; ;
in Proceedings of the 27th Hawaii International Conference on System Sciences, Vol. V, Biotechnology Computing (1994)
THE HSSP DATABASE OF PROTEIN-STRUCTURE SEQUENCE ALIGNMENTS;
in Nucleic Acids Research (1994), 22(17), 3597-3599
GeneQuiz: a workbench for sequence analysis; ; ; ; ; ;
in Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, ISMB-94 (1994)
1993
PREDICTION OF PROTEIN-STRUCTURE BY EVALUATION OF SEQUENCE-STRUCTURE FITNESS - ALIGNING SEQUENCES TO CONTACT PROFILES DERIVED FROM 3-DIMENSIONAL STRUCTURES; ; ;
in Journal of Molecular Biology (1993), 232(3), 805-825
PROGRESS IN PROTEIN-STRUCTURE PREDICTION; ;
in Trends in Biochemical Sciences - Regular Edition (1993), 18(4), 120-123
From Sequence Similarity to Structural Homology of Proteins;
in Computation of Biomolecular Structures, Achievements, Problems and Perspectives (1993)
MaxHom;
in The ZEUS Consortium Massively Parallel Computing, Technical Report PC2 / TR-006-94 (1993)
THE HSSP DATA-BASE OF PROTEIN STRUCTURE-SEQUENCE ALIGNMENTS;
in Nucleic Acids Research (1993), 21(13), 3105-3109
1992
COMPREHENSIVE SEQUENCE-ANALYSIS OF THE 182 PREDICTED OPEN READING FRAMES OF YEAST CHROMOSOME-III; ; ; ; ;
in Protein Science : A Publication of the Protein Society (1992), 1(12), 1677-1690
SELECTION OF REPRESENTATIVE PROTEIN DATA SETS; ; ;
in Protein Science : A Publication of the Protein Society (1992), 1(3), 409-417
1991
DATABASE OF HOMOLOGY-DERIVED PROTEIN STRUCTURES AND THE STRUCTURAL MEANING OF SEQUENCE ALIGNMENT;
in Proteins (1991), 9(1), 56-68
| URL: https://wwwfr.uni.lu/lcsb/people/reinhard_schneider | Date: lundi 26 avril 2021 06:56:35 |