My views on anything – Page 9

My PhD thesis Understanding the epigenome using system genetics is now online in the repository of the University of Cambridge

By Sander Timmer | February 5, 2015 | Comments 0 Comment

http://www.repository.cam.ac.uk/handle/1810/246693

Understanding the epigenome using system genetics
Genetics has been successful in associating DNA sequence variants to both dichotomous and continuous traits in a variety of organisms, from plant and farm animal studies to human disease. With the advent of high-throughput genotyping, there has been an almost routine gen- eration of genome-wide …

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The future is bright!

By Sander Timmer | February 2, 2015 | Comments 0 Comment

"The lives of people in poor countries will improve faster in the next 15 years than at any other time in history. And their lives will improve more than anyone else's."

2015 Gates Annual Letter
See how the lives of people in poor countries will improve faster in the next 15 years than they have in any other time in history. And join us!

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Quantitative Genetics of CTCF Binding Reveal Local Sequence Effects and Different Modes of X-Chromosome Association

By Sander Timmer | January 11, 2015 | Comments 0 Comment

My first paper came out featuring work done during my PhD. The results regarding the binding of CTCF on the X chromosome is my work.

CTCF binding can be regulated by genetic variations

We have systematically measured the effect of normal genetic variation present in a human population on the binding of a specific chromatin protein (CTCF) to DNA by measuring its binding in 51 human cell lines. We observed a large number of changes in protein binding that we can confidently attribute to genetic effects. The corresponding genetic changes are often clustered around the binding motif for CTCF, but only a minority are actually within the motif.

The X chromosome and CTCF

Unexpectedly, we also find that at most binding sites on the X chromosome, CTCF binding occurs equally on both the X chromosomes in females at the same level as on the single X chromosome in males. This finding suggests that in general, CTCF binding is not subject to global dosage compensation, the process which equalizes gene expression levels from the two female X chromosomes and the single male X.

A. Plot of the metric to distinguish single-active from both active-sites, across the X chromosome for a variety of molecular assays (mRNA, ncRNA, DNase I and CTCF, coloured according to the key). B. A smooth density of the distribution of the dosage compensation fit for the 4 molecular assay types, with CTCF split into the 3 classifications (single active, both active and female specific). C. Allele-specific signal of heterozygote sites on the X chromosome from the 13 clonal female lines in the sample. The both-active sites show balanced allele-specificity, whereas the single-active sites show strong single allele CTCF binding. D. Box plot of the gender-specific behaviour of the DNase I assay at the major classes of X chromosome CTCF sites. DNase I data was collected in a different laboratory on different cell lines [17]. The both-active class shows a strong gender split, consistent with females having around double the signal, whereas the single-active sites show no gender change. doi:10.1371/journal.pgen.1004798.g005 — A. Plot of the metric to distinguish single-active from both active-sites, across the X chromosome for a variety of molecular assays (mRNA, ncRNA, DNase I and CTCF, coloured according to the key). B. A smooth density of the distribution of the dosage compensation fit for the 4 molecular assay types, with CTCF split into the 3 classifications (single active, both active and female specific). C. Allele-specific signal of heterozygote sites on the X chromosome from the 13 clonal female lines in the sample. The both-active sites show balanced allele-specificity, whereas the single-active sites show strong single allele CTCF binding. D. Box plot of the gender-specific behaviour of the DNase I assay at the major classes of X chromosome CTCF sites. DNase I data was collected in a different laboratory on different cell lines [17]. The both-active class shows a strong gender split, consistent with females having around double the signal, whereas the single-active sites show no gender change.
doi:10.1371/journal.pgen.1004798.g005

Full paper

PLOS Genetics

Decoding Deep Neural Network to generate images that can be identified with a high confidence by computers yet not by humans. Fascinating!

By Sander Timmer | January 10, 2015 | Comments 0 Comment

https://www.youtube.com/watch?v=M2IebCN9Ht4

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Machine learning techniques are used to study overlap and influence of paintings.

By Sander Timmer | January 5, 2015 | Comments 0 Comment

This overlap is achieved by comparing concepts that are present on the paintings. These concepts include everything from simple object description such as duck, frisbee, man, wheelbarrow to shades of colour to higher-level descriptions such as dead body, body of water, walking and so on. For each painting a vector of 3,000 concepts is determined. For each vector they searched for similar vectors using natural language techniques and a machine learning algorithm.

"The algorithm is also able to identify individual paintings that have influenced others. It picked out Georges Braque’s Man with a Violin and Pablo Picasso’s Spanish Still Life: Sun and Shadow, both painted in 1912 with a well-known connection as pictures that helped found the Cubist movement."

#Science #Art #MachineLearning

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Saw my first live robot demo: so uber cool! If you are ever in Tokyo, the Science museum is a must go.

By Sander Timmer | January 3, 2015 | Comments 0 Comment

#Japan #Tokyo #Robot

https://plus.google.com/photos/114695574233495700986/albums/6100112306266152081/6100112303835137810

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