M. Scott Marshall, Ph.D.
Department of Medical Statistics and Bioinformatics
Leiden University Medical Center
Adaptive Information Disclosure, Project Manager
Informatics Institute, University of Amsterdam
[Updated Curriculum Vitae available on request]
M. Scott Marshall is a member of the Bioinformatics Core of the Bioinformatics Expertise Center, which acts as a bioinformatics hub for the Leiden University Medical Center. As part of a split appointment, he also coordinates work in Adaptive Information Disclosure (AID). AID combines expertise in information retrieval, machine learning, and semantic web in the context of the Virtual Laboratory e-science project to create an e-science infrastructure for computational experiments and knowledge capture. Dr. Marshall co-chairs the W3C Semantic Web for Health Care and Life Sciences Interest Group, where his focus is on coordinating efforts to apply Semantic Web tools such as AIDA to support research in biology and medicine, with a special focus on building applications that are useful to participants in the Bioinformatics Expertise Center of the Leiden University Medical Center. Dr. Marshall was a visiting scholar at the National Center for Biomedical Ontologies at Stanford University Jan - Aug 2010.
E-Science Vision:I envision a future where scientists share and manipulate knowledge using visual and concept-based interfaces that adapt to their own terminologies and interests. Knowledge provenance that links a given assertion to evidence will enable scientists to explore, analyze, and compare data and hypotheses that span multiple disciplines. Many are working toward this future using the Semantic Web.
Andrea Splendiani, Albert Burger, Adrian Paschke, Paolo Romano, M Scott Marshall. Biomedical semantics in the Semantic Web, Journal of Biomedical Semantics 2011, 2(Suppl 1):S1 (7 March 2011)
Marco Roos, Sean Bechhofer, Jun Zhao, Paolo Missier, David Newman, Dave de Roure, M. Scott Marshall. A Linked Data Approach to Sharing Workflows and Workflow Results, Proceedings of Tools in Scientific Workflow Composition Track of ISoLA 2010, Crete, Greece. accepted for publication
Helena Deus, Jun Zhao, Satya Sahoo, Matthias Samwald, Eric Prud’hommeaux, Michael Miller, M.Scott Marshall and Kei-Hoi Cheung. Provenance of Microarray Experiments for a Better Understanding of Experiment Results, Proceedings of Second International Workshop on the role of Semantic Web in Provenance Management (SWPM-2010), Shanghai, China. accepted for publication
Samwald, Matthias, Michel Dumontier, Jun Zhao, Joanne Luciano, M Scott Marshall, and Kei-Hoi Cheung. Integrating findings from traditional medicine into modern pharmaceutical research: the potential role of linked open data, Chinese Medicine. accepted for publication
M. Scott Marshall, Marco Roos, Edgar Meij, Sophia Katrenko, Willem Robert van Hage, Pieter W. Adriaans, Semantic disclosure in an e-Science environment, Book Chapter in Huajun Chen, Yimin Wang and Kei Cheung (eds.) - Semantic e-Science, Springer Annals of Information Systems AoIS, Springer, April 2009.
Marco Roos, M. Scott Marshall, Andrew P. Gibson, Martijn Schuemie, Edgar Meij, Sophia Katrenko, Willem Robert van Hage, Konstantinos Krommydas and Pieter W. Adriaans, Structuring and extracting knowledge for the support of hypothesis generation in molecular biology, BMC Bioinformatics Volume 10 Supplement 10, Oct 2009.
Kei-Hoi Cheung, H. Robert Frost, M. Scott Marshall, Eric Prud'hommeaux, Matthias Samwald, Jun Zhao, Adrian Paschke, A Journey to Semantic Web Query Federation in Life Sciences, BMC Bioinformatics Volume 10 Supplement 10, Oct 2009.
Ruttenberg A, Rees JA, Samwald M, Marshall MS. Life sciences on the Semantic Web: The Neurocommons and Beyond. Briefings in Bioinformatics, 10(2): 193-204, Mar 2009[online]
M. Roos, M. S. Marshall, A.P. Gibson, P. W. Adriaans, Structuring mined knowledge for the support of hypothesis generation in molecular biology, Benelux Bioinformatics Conference, December 2008. [Poster]
M. S. Marshall, M. Roos, E. Meij, S. Katrenko, W.R. van Hage, P. Adriaans, De AIDA toolbox: een gecombineerde aanpak voor het beheren van kennis, Agro Informatica 21 (4), pp. 5-6.
M. Roos, M. S. Marshall, A.P. Gibson, P. W. Adriaans, Structuring mined knowledge for the support of hypothesis generation in molecular biology, Semantic Web Applications and Tools for Life Sciences 2008, November 18, Edinburgh, UK
M. Scott Marshall, Kasper van den Berg, Kamel Boulebiar, Piter de Boer, Marco Roos, Tristan Glatard, Silvia Olabarriaga, A Metadata Management Approach to fMRI Data, UK e-Science All Hands Meeting (AHM), Edinburgh, UK, September 8- 11, 2008.
S. Koulouzis, E. Meij, M.S. Marshall, and A. Belloum, Enabling Data Transport between Web Services through alternative protocols and Streaming, In: 4th IEEE International Conference on e-Science, 2008.
M. Roos, P.T. de Boer, M.S. Marshall, K. van den Berg, S. Katrenko, E. Meij, W.R. van Hage, P.W. Adriaans, Biological applications of AIDA knowledge management components, In: The 16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008. [Poster]
Marshall MS, Prud'hommeaux E. A Prototype Knowledge Base for the Life Sciences (W3C Interest Group Note). http://www.w3.org/TR/hcls-kb/.
M. Roos, S. Katrenko, W.R. van Hage, E. Meij, F. Verster, M.S. Marshall, P.W. Adriaans, My first BioAID: heuristic support for hypothesis construction from literature, In: The 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 6th European Conference on Computational Biology (ECCB), 2007. [Poster]
Lennart J. G. Post, Marco Roos, M. Scott Marshall, Roel van Driel, and Timo M. Breit, A semantic web approach applied to integrative bioinformatics experimentation: a biological use case with genomics data. Bioinformatics, 23(22):3080-3087, 2007. [online]
M. Roos, M. S. Marshall, E. Meij, S. Katrenko, W. van Hage, P. W. Adriaans, AIDA: combining text mining and e-Science for bioinformatics, UK e-Science All Hands Meeting (AHM), September 10-13, 2007, Nottingham, United Kingdom
Keet, C.M., Roos, M. and Marshall, M.S. A survey of requirements for automated reasoning services for bio-ontologies in OWL. Third international Workshop OWL: Experiences and Directions (OWLED 2007), 6-7 June 2007, Innsbruck, Austria. CEUR-WS Vol xxx. abstract
Advancing translational research with the Semantic Web, Alan Ruttenberg, Tim Clark, William Bug, Matthias Samwald, Olivier Bodenreider, Helen Chen, Donald Doherty, Kerstin Forsberg, Yong Gao, Vipul Kashyap, June Kinoshita, Joanne Luciano, M Scott Marshall, Chimezie Ogbuji, Jonathan Rees, Susie Stephens, Gwendolyn T Wong, Elizabeth Wu, Davide Zaccagnini1, Tonya Hongsermeier, Eric Neumann, Ivan Herman and Kei-Hoi Cheung. BMC Bioinformatics 2007, 8(Suppl 3):S2 http://www.biomedcentral.com/1471-2105/8/S3/S2
Vipul Kashyap, Kei-Hoi Cheung, Don Doherty, Matthias Samwald, M. Scott Marshall, Joanne Luciano, Susie Stephens, Ivan Herman and Ray Hookway, An Ontology-based approach for Data Integration - An Application in Biomedical Research, Book Chapter in Cardoso, J., Hepp, M., Lytras, M. (Eds.) "Real-world Applications of Semantic Web Technology and Ontologies", Springer 2007. Hardcover ISBN-10: 0-387-48530-9, ISBN-13: 978-0-387-48530-0
Marshall, M.S., Post, L., Roos, M., Breit, T.M. Using semantic web tools to integrate
experimental measurement data on our own terms. Workshop on Knowledge
Systems in Bioinformatics (KSinBIT?06), Springer Verlag LNCS 4277, 2006, 679-688.
S. Katrenko, M. S. Marshall, M. Roos and P. Adriaans., Learning Biological Interactions from Medline Abstracts, Learning Language in Logic (LLL05) Workshop, ICML05, Bonn, Germany, 2005.
M. Roos, M. G. Jansen, M. S. Marshall, and T. Breit., Future application of ontologies in e-Bioscience, Position paper W3C Workshop on Semantic Web for Life Sciences, 2004.
U. Brandes, M. Eiglsperger, I. Herman, M. Himsolt, and
M. S. Marshall., Graphml progress report: Structural layer
proposal, Proceedings of Symposium on Graph Drawing (GD
2001), pp. 501-512, 2001.
M. S. Marshall, Methods
and Tools for the Visualization and Navigation of Graphs
("Méthodes et outils pour la visualisation et la navigation de
données relationnelles"), Ph.D. Thesis, Dept. of
Mathematics and Computer Science, University of Bordeaux,
France, June 2001.
M. S. Marshall, I. Herman, and G. Melançon, An object-oriented design for
graph visualization, Software: Practice &
I. Herman, M. S. Marshall, G. Melançon, Density Functions for
Visual Attributes and Effective Partitioning in Graph
Visualization, IEEE Information Visualization
Symposium 2000, eds. S.F. Roth and D.A. Keim, IEEE CS Press,
pp. 49-56, 2000.
I. Herman and M. S. Marshall, GraphXML - a graph
description language, Proceedings of the Symposium on
Graph Drawing (GD 2000), Springer Verlag, LNCS 1984,
pp. 52-62, 2000. Available
on-line. A more detailed version of the specification is
in: Reports of the Centre for Mathematics and Computer
Sciences, Amsterdam INS-R0009, 2000.
M. S. Marshall, I. Herman, G. Melançon, Automatic Generation
of Interactive Overview Diagrams for the Navigation of Large
Graphs, Centre for Mathematics and Computer Sciences,
Amsterdam INS-R0014, 2000.
I. Herman, G. Melançon, M. S. Marshall. Graph
Visualization and Navigation in Information
Visualisation: a Survey. In: IEEE Transactions on
Visualization and Computer Graphics, 6(1), pp.
I. Herman, M. S. Marshall, G. Melançon, D.J. Duke,
M. Delest, J.-P. Domenger. Skeletal Images as Visual
Cues in Graph Visualisation. In: Data Visualisation
'99, Proceedings of the joint Eurographics and IEEE TCVG
Symposium on Visualization, eds. E. Gröller, H.
Löffelmann and W. Ribarsky, Springer-Verlag, pp.
D. Duke, I. Herman, M. S. Marshall, PREMO: A Framework for Multimedia Middleware -- Specification, Rationale, and Java Binding, LNCS Volume 1591, Springer-Verlag, 1999.
Dr M. Scott Marshall is an Assistant Professor of Bioinformatics at the Leiden University Medical Center. As part of a split appointment, he is responsible for activities in the Adaptive Information Disclosure subprogramme of the Virtual Laboratory for e-Science project, where semantic e-Science applications for health care and life sciences are being developed. Previously, Dr. Marshall has worked at CWI, Glaucus Proteomics, Kiadis Pharma, and the microarray department at the University of Amsterdam in The Netherlands. He is a co-chair of the W3C Semantic Web Health Care and Life Sciences Interest Group. Dr. Marshall received a PhD for his work in graph visualization.