analysis.yellowcouch.org

Bioinformatics

We provide consultancy on the mathematical and computational aspects of biology. This includes consultancy on data storage, data modeling, statistical/signal analysis. Deep Sequencing/Sequencing by Synthesis. Highly Detailed Cross Correlation Analysis of Genomic Signal Tracks. 2DE Gel Correlation Analysis. When working with 2D electrophoretic gels, the photographed images often have all kinds of artifacts in them. Such gels are often regarded as 'bad' and while it may be true that they can be better,...

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Bioinformatics | analysis.yellowcouch.org Reviews

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We provide consultancy on the mathematical and computational aspects of biology. This includes consultancy on data storage, data modeling, statistical/signal analysis. Deep Sequencing/Sequencing by Synthesis. Highly Detailed Cross Correlation Analysis of Genomic Signal Tracks. 2DE Gel Correlation Analysis. When working with 2D electrophoretic gels, the photographed images often have all kinds of artifacts in them. Such gels are often regarded as 'bad' and while it may be true that they can be better,...

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2 bioinformatics

3 mass spectrometry denoising

4 2de gel denoising

5 micro array analysis

6 screening normalization

7 scientific reviews

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Bioinformatics | analysis.yellowcouch.org Reviews

https://analysis.yellowcouch.org

We provide consultancy on the mathematical and computational aspects of biology. This includes consultancy on data storage, data modeling, statistical/signal analysis. Deep Sequencing/Sequencing by Synthesis. Highly Detailed Cross Correlation Analysis of Genomic Signal Tracks. 2DE Gel Correlation Analysis. When working with 2D electrophoretic gels, the photographed images often have all kinds of artifacts in them. Such gels are often regarded as 'bad' and while it may be true that they can be better,...

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analysis.yellowcouch.org

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2D Correlation Analysis

http://analysis.yellowcouch.org/2dcor.html

In 2005, I developed the 2D gel correlation technique. Because it was the only viable method to analyze the data we received at that time. The company I worked for tried to patent this method (which was a silly thing to do anyway, its soft. The method correlates the content of multiple 2D gels with some external parameter (survival rate for instance) and will report the correlation using a hue color scheme. There is a. Available that summarizes the following steps. First one starts with a large collectio...

2

Deep Sequencing Notes

http://analysis.yellowcouch.org/dsf

These pages document notes I collected on various aspects of deep sequencing, aka sequencing by synthesis or short fragment sequencing. The machine on which my experience is based is a Illumina/Solexa technologies Genome Analyzer II. The work I performed was related to the deep sequencing facility in Basel (at ETH Zurich) and these are some extra-curricular notes that remain otherwise unused. We collected some notes on compiling the pipeline v0.3 and v1.0. Another important bias is temperature dependence.

3

Screening Normalization

http://analysis.yellowcouch.org/screen/index.html

To normalize a screen we rely on a number of normalisations. The first normalization step involves the inter-plate variance. Here we normalize the different biological replicas for each plate. The second step normalizes the differences between the different plates. This is called the inter-plate variance normalization. The variance between the renila and firefly colors is shown below. The 41 lines are the different plates. Each plate is represented as the average histogram on that plate.

4

Methylation/Acetylation Patterns

http://analysis.yellowcouch.org/dsf/methacet

In short, the right image shows the correlation between the signal around the TSS of a paritcular histone modification (horizontal) against the signal around the TSS of a paritcular other histone modification (vertical). The color reflects the correlation strength. A detailed description of the maps shown below can be found at http:/ werner.yellowcouch.org/Papers/dsapaper/index.html. Http:/ analysis.yellowcouch.org/.

5

Scientific Reviews

http://analysis.yellowcouch.org/reviews.html

Some papers we enjoyed reading and have comments/remarks on:. GOToolBox: functional analysis of gene datasets based on Gene Ontology. Analysis of cell-based RNAi screens. We review scientific papers regarding the mathematical/signal processing aspects of the provided research. If you are interested in buying such a review, then send an email to review@yellowcouch.org. Http:/ analysis.yellowcouch.org/.

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analysis.yellowcouch.org

Bioinformatics

We provide consultancy on the mathematical and computational aspects of biology. This includes consultancy on data storage, data modeling, statistical/signal analysis. Deep Sequencing/Sequencing by Synthesis. Highly Detailed Cross Correlation Analysis of Genomic Signal Tracks. 2DE Gel Correlation Analysis. When working with 2D electrophoretic gels, the photographed images often have all kinds of artifacts in them. Such gels are often regarded as 'bad' and while it may be true that they can be better,...

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