Matthias Scholz and Martin J. Fraunholz.
A computational model of gene expression reveals early transcriptional events at the subtelomeric
regions of the malaria parasite, Plasmodium falciparum.
Genome Biology 9:R88, 2008.
[
pdf |
Animation of gene regulation ]
Stefanie Wienkoop, Katja Morgenthal, Florian Wolschin,
Matthias Scholz, Joachim Selbig, and Wolfram Weckwerth.
Integration of metabolomic and proteomic phenotypes - Analysis of data-covariance dissects starch and
RFO metabolism from low and high temperature compensation response in Arabidopsis thaliana.
Molecular & Cellular Proteomics, 2008.
[
pdf ]
Matthias Scholz, Martin Fraunholz,
and Joachim Selbig.
Nonlinear principal component analysis: neural network models and applications.
In Principal Manifolds for Data Visualization and
Dimension Reduction,
edited by Alexander N. Gorban, Balázs Kégl,
Donald C. Wunsch, and Andrei Zinovyev.
Volume 58 of LNCSE, pages 44-67.
Springer Berlin Heidelberg, 2007.
[
pdf (all book chapters) |
pdf (Springer) |
entire book (Springer) |
nonlinear PCA toolbox for MATLAB ]
Matthias Scholz.
Analysing periodic phenomena by circular PCA.
In S. Hochreiter and R. Wagner, editors,
Proceedings of the Conference on Bioinformatics
Research and Development BIRD'07,
LNCS/LNBI Vol. 4414, pages 38-47.
Springer-Verlag Berlin Heidelberg, 2007.
[
pdf (final version at Springer) |
pdf (author's pre-version) |
bibtex |
nonlinear PCA toolbox for MATLAB ]
Wolfram Stacklies, Henning Redestig,
Matthias Scholz,
Dirk Walther, and Joachim Selbig.
pcaMethods — a bioconductor package providing PCA methods for incomplete data.
Bioinformatics, 23(9):1164-1167. 2007.
[
pdf |
nonlinear PCA ported to R by Henning Redestig ]
Matthias Steinfath, Dirk Repsilber, Matthias Scholz,
Dirk Walther and Joachim Selbig.
Integrated data analysis for genome-wide research.
In Plant Systems Biology, pages 309-329
edited by Sacha Baginski and Alisdair R. Fernie,
Birkhäuser-Verlag, Basel, Boston, Berlin, 2007.
(distributed by Springer)
[
pdf |
entire book ]
Matthias Scholz and Joachim Selbig.
Visualization and analysis of molecular data.
In Wolfram Weckwerth, editor,
Metabolomics: methods and protocols.
Methods in Molecular Biology Series 358:87-104.
Humana Press, New York, 2006.
[
pdf ]
Matthias Scholz. Approaches to analyse
and interpret biological profile data.
University of Potsdam, Germany. Ph.D. thesis. 2006.
URN: urn:nbn:de:kobv:517-opus-7839
URL: http://opus.kobv.de/ubp/volltexte/2006/783/
[
pdf (library) |
pdf (copy) |
bibtex |
figures ]
Matthias Steinfath, Matthias Scholz,
and Joachim Selbig.
Profile data analysis, dimension reduction, clustering and classification.
In European Training and Networking Activity.
Plant Genomics and Bioinformatics:
Expression Micro Arrays and Beyond - a course book.
Ljubljana Slovenia, 2005.
[
pdf |
www.eu-summer-school.org ]
Matthias Scholz,
Fatma Kaplan, Charles L. Guy,
Joachim Kopka, and Joachim Selbig.
Non-linear PCA: a missing data approach.
Bioinformatics 21(20):3887-3895. 2005.
[
pdf (final version) |
pdf (pre-version in colour) |
bibtex ]
Katja Morgenthal, Stefanie Wienkoop,
Matthias Scholz,
Joachim Selbig, and Wolfram Weckwerth.
Correlative GC-TOF-MS-based metabolite profiling and
LC-MS-based protein profiling reveal time-related systemic regulation of
metabolite-protein networks and improve pattern recognition
for multiple biomarker selection.
Metabolomics 1(2):109-121. 2005.
[
pdf |
bibtex ]
Matthias Scholz, Yves Gibon,
Mark Stitt, and Joachim Selbig.
Independent Component Analysis of Starch Deficient PGM Mutants.
In R. Giegerich and J. Stoye, editors,
Proceedings of the German Conference on
Bioinformatics, pages 95-104. 2004.
[
pdf |
bibtex ]
Matthias Scholz, Stephan Gatzek,
Alistair Sterling, Oliver Fiehn, and Joachim Selbig.
Metabolite fingerprinting: detecting biological features by
independent component analysis.
Bioinformatics 20(15):2447-2454. 2004.
[
pdf
| poster ISMB04
| bibtex
| more about ICA
| matlab code
| web tool
]
Matthias Scholz.
Nonlinear PCA based on neural networks.
Dep. of Computer Science, Humboldt-University
Berlin. Diploma Thesis. 2002. In German.
URN: urn:nbn:de:kobv:11-10086728
[
pdf |
bibtex ]
Matthias Scholz and
Ricardo Vigário.
Nonlinear PCA: a new hierarchical approach.
In M. Verleysen, editor,
Proceedings ESANN. 2002.
[
pdf |
bibtex ]
Sebastian Mika, Bernhard Schölkopf,
Alexander J. Smola,
Klaus-Robert Müller, Matthias Scholz, and
Gunnar Rätsch.
Kernel PCA and de-noising in feature spaces.
In M.S. Kearns, S.A. Solla, and D.A. Cohn, editors,
Advances in Neural Information Processing Systems (NIPS) 11,
pages 536-542. MIT Press, 1999.
[
pdf |
bibtex ]