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MATTHIAS-SCHOLZ.DE

Matthias Scholz - Research

Bioinformatics, Metabolomics, Plasmodium faciparum (Malaria), Nonlinear PCA, ICA, Complex networks

http://www.matthias-scholz.de/

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Matthias Scholz - Research | matthias-scholz.de Reviews
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Bioinformatics, Metabolomics, Plasmodium faciparum (Malaria), Nonlinear PCA, ICA, Complex networks
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1 metagenomics
2 Bioinformatics
3 principal component analysis
4 PCA
5 independent component analysis
6 ICA
7 nonlinear PCA
8 non-linear PCA
9 auto-associative neural networks
10 autoencoder
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research,bioinformatics,computational metagenomics,metabolomics,machine learning,network science,nonlinear pca,dr matthias scholz,publications,nutrition and nutrigenomics,strain level metagenomics,microbial metabolomics,postdoctoral research,metagenomics
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Matthias Scholz - Research | matthias-scholz.de Reviews

https://matthias-scholz.de

Bioinformatics, Metabolomics, Plasmodium faciparum (Malaria), Nonlinear PCA, ICA, Complex networks

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phdthesis-bioinformatics-maxplanckinstitute-molecularplantphys.matthias-scholz.de phdthesis-bioinformatics-maxplanckinstitute-molecularplantphys.matthias-scholz.de

Ph.D. thesis - Matthias Scholz - Max Planck Institute of Molecular Plant Physiology

Max Planck Institute of Molecular Plant Physiology. Approaches to analyse and interpret biological profile data. University of Potsdam, Germany. Advances in biotechnologies rapidly increase the number of molecules of a cell which can be observed simultaneously. This includes expression levels of thousands or ten-thousands of genes as well as concentration levels of metabolites or proteins. The full text PDF version. Is available at: URN: urn:nbn:de:kobv:517-opus-7839. Figures of this thesis. Visualising ...

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1

Matthias Scholz - Publications

http://www.matthias-scholz.de/publications.html

Matthias Scholz, Ph.D. For citation indices, see Google Scholar. Strain-level microbial epidemiology and population genomics from shotgun metagenomics. Doyle V. Ward*, Edoardo Pasolli*, Thomas Tolio, Moreno Zolfo, Francesco Asnicar, Duy Tin Truong, Adrian Tett, Ardythe L. Morrow, and Nicola Segata. 13, 435 438, 2016. (* Equal contribution). Strain-level article by Vivien Marx. Metagenomic sequencing with strain level resolution implicates uropathogenic E. coli. Doyle V. Ward*, Matthias Scholz. Adrian Tet...

2

Scholz and Fraunholz, Plasmodium falciparum, Genome Biology (2008)

http://www.matthias-scholz.de/plasmodium-falciparum-subtelomeric-regions-gene-expression-animation-video.html

And Martin J. Fraunholz. A computational model of gene expression reveals early transcriptional events at the subtelomeric regions of the malaria parasite, Plasmodium falciparum. Free full text version at Genome Biology. Animation of the intraerythrocytic development cycle based on change of expression rates of the P. falciparum genome. Description: This animation of the intraerythrocytic development cycle is based on change of expression rates of genes on the 14 nuclear chromosomes of P. falciparum.

3

Stellar spectral analysis

http://www.matthias-scholz.de/stars.html

An analysis of spectral data. And fundamental parameters of stars. Centro de Investigaciones de Astronomia, Venezuela. JStock and M.J.Stock. Quantitative Stellar Spectral Classification. Revista Mexicana de Astronomia y Astrofisica. 34, 143-156, 1999. Linear analysis of the spectral data space by PCA. The colors illustrate different spectral type groups:. Stars which can not be classified exactly because of the blue and red spectrum. Stars with very low temperature. Artificial neural networks are used fo...

4

Komplexe Netzwerke - Vorlesung - Matthias Scholz - Universität Greifswald

http://www.matthias-scholz.de/komplexe-Netzwerke-Vorlesung-Greifswald.html

Ernst Moritz Arndt Universität Greifswald. Institut für Mathematik und Informatik. Institut für Mikrobiologie. Kompetenzzentrum für funktionelle Genomforschung (ZIK). E-mail: matthias.scholz at network-science.org. Ort: Mehringstr. 48, Raum 4. Zeit: Fr. 14-16 Uhr. Gradverteilung der Knoten, Skalenfreiheit ( scale-free. Erdös–Rényi Zufallsgraph-Modell. Barabási-Albert Attraktivitätsmodell ( preferential attachment model. Kleine-Welt-Phänomen ( small world phenomenon.

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network-science.org network-science.org

Cytoscape Installation Ubuntu

http://www.network-science.org/cytoscape-download-install-ubuntu-linux-unix.html

Network Analysis and Visualization. How to install Cytoscape on Ubuntu? Download the Cytoscape installation file for Linux from. Open a terminal and change the execution file property. Chmod a x Cytoscape 3 0 2 unix.sh. Start installation by double-click on the icon. Or by running cytoscape.sh from the command line:. Sh Cytoscape 3 0 2 unix.sh # local installation. Sudo sh Cytoscape 3 0 2 unix.sh # system-wide installation, administrator rights required. Application - Other - Cytoscape.

network-science.org network-science.org

From sparsely to densely connected networks

http://www.network-science.org/highly-connected-society-dense-social-complex-networks.html

Getting connected - The highly connected society. Is a network in which the number of links of each node is close to the maximal number of nodes. Each node is linked to almost all other nodes. The total connected case in which exactly each node is linked to each other node is called a completely connected network. Examples of higher link density are epidemic spreading, the neural network of the brain and telecommunication networks. To measure the link density. The (maximal) link density D. The neurons of...

metagenomicsformicrobiology.com metagenomicsformicrobiology.com

Authors - Metagenomics for Microbiology

http://www.metagenomicsformicrobiology.com/authors.html

Nadim J. Ajami. Baylor College of Medicine, Houston, TX, USA. Metanome Inc., Houston, TX, USA [ Company web site. University of Maryland, College Park, MD, USA. Pacific Biosciences, Menlo Park, CA, USA [ Company web site. The Forsyth Institute, Cambridge, MA, USA. Harvard School of Dental Medicine, Boston, MA, USA. Seoul National University, Seoul, Korea. Georg K. Gerber. Brigham and Women’s Hospital, Boston, MA, USA. Harvard Medical School, Boston, MA, USA [ Laboratory web site. Patricio S. La Rosa.

nlpca.org nlpca.org

Nonlinear PCA toolbox for Matlab - auto-associative neural networks - autoencoder bottleneck neural networks - Matthias Scholz

http://www.nlpca.org/matlab.html

Nonlinear PCA toolbox for MATLAB. Nonlinear principal component analysis (NLPCA). Pc, net] = nlpca(data, k) pc = nlpca get components(net, data) data reconstruction = nlpca get data(net, pc). The nonlinear PCA is based on an auto-associative neural network (autoencoder). See also: www.nlpca.org. Pc = nlpca(data,k). Nonlinear components from the data set. pc. Represents the estimated component values (scores). Can be used in nlpca get components. And nlpca get data. See also the demos of the toolbox.

nlpca.org nlpca.org

PCA - Principal Component Analysis

http://www.nlpca.org/pca_principal_component_analysis.html

PCA - Principal Component Analysis. PCA is a standard technique for visualizing high dimensional data and for data pre-processing. PCA reduces the dimensionality (the number of variables) of a data set by maintaining as much variance as possible. Matthias Scholz, Ph.D. thesis. Such two-dimensional visualization of the samples allow us to draw qualitative conclusions about the separability of experimental conditions (marked by different colors). Independent Component Analysis (ICA). Nonlinear PCA (NLPCA) ...

network-science.org network-science.org

Network science: node degree distribution

http://www.network-science.org/powerlaw_scalefree_node_degree_distribution.html

Random networks versus scale-free power-law networks. The degree of a node in a network is the number of links to other nodes, or simply the number of contacts in a social network. Left: In traditional random networks most nodes have a medium node degree. The degrees of all nodes are distributed around the average. Rarr; The highly connected society. Rarr; A similarity model for dense networks. Rarr; Network-science.org (main page).

faq.nlpca.org faq.nlpca.org

Recent site activity - Nonlinear PCA

http://www.faq.nlpca.org/system/app/pages/recentChanges

Complexity (hidden-units, weight-decay). Nov 5, 2016, 10:07 AM. Matthias Scholz edited Variance of components. Nov 5, 2016, 10:05 AM. Matthias Scholz edited Variance of components. Nov 5, 2016, 9:56 AM. Matthias Scholz edited Variance of components. Nov 5, 2016, 9:56 AM. Matthias Scholz edited Variance of components. Nov 5, 2016, 9:54 AM. Matthias Scholz edited Variance of components. Nov 5, 2016, 9:52 AM. Matthias Scholz edited Variance of components. Nov 5, 2016, 9:47 AM. Nov 5, 2016, 9:41 AM. Matthias...

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