Question: graph theory with applications to biology/bioinformatics
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15 months ago by
stefanweiss020719870 wrote:

Hi,

I am ver new to this forum so please leave me notes if I did something wrong.

I am currently preparing for an exam in graph theory, but I find it rather boring, because I am already quite advanced in my studies and the course was intended for beginners (basically first chapters of this book: https://www.amazon.de/Graphentheorie-Springer-Lehrbuch-Masterclass-Reinhard-Diestel/dp/3642149111/ref=sr_1_1?ie=UTF8&qid=1484152081&sr=8-1&keywords=graphentheorie )

So I am wondering if there is a more useful book or review or reference to prepare for this oral exam with applications to biology or/and bioinformatics.

It should still cover the basics in graph theory but with applications to biology on modern level.

I have a background as mathematician and biolgist, so I hav ein-depth knowledge of mathematics and biology.

modified 15 months ago by Steven Lakin1.3k • written 15 months ago by stefanweiss020719870
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15 months ago by
Steven Lakin1.3k
Fort Collins, CO, USA
Steven Lakin1.3k wrote:

We have a bioinformatician in our group, Christina Boucher, who works on succinct data structures based on de Bruijn graphs and FM-indexing/BWT. You can read the blog of one of her PhD students here; it's an interesting topic. BioRxiv pdf to the advance publication here.

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15 months ago by
romain.lannes80 wrote:

Graph theorie is begin to be use to infer homology relation. But also to study gene and genome relation ship https://www.ncbi.nlm.nih.gov/pubmed/26774999 is a review (made by lab) about this subject.

Is also worth mentioning that hogenom ( a homology database host in LYON france) is done with SILIX ( which use graph theorie ).

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15 months ago by
jrj.healey3.8k
United Kingdom
jrj.healey3.8k wrote:

Sequence assemblers use de Brujin graph traversal to assemble reads.

You should be able to find papers on that. I'm not at my PC at the mo so can't easily find you a reference but it's a well documented concept.

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15 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche15k wrote:

Example of use of kernels on graph nodes. Although not graph theory per se, you may be interested in how dynamic graphs can be analyzed using tensor factorization methods, see some of my notes here.