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4
votes
1answer
40 views

Best methodology to compare computed phylogeny tree with taxonomy?

I have computed a phylogenetic tree using an alignement of sequences, and I would like to : Compare it to the "known" taxonomy (uniprot/ncbi which I know is not the most up to date one) and extract ...
5
votes
1answer
89 views

What are some examples of undirected weighted networks in ecology?

I'm a math major with a current interest towards network theory. A network can be considered as a collection of nodes, and edges between these nodes signifying some relation between them. The most ...
0
votes
2answers
45 views

Does a gene that regulates itself necessarily be a transcription factor?

I am not a biologist, so please pardon the overly noob question. Some genes are transcription factors (TF) and regulate other genes. My question is: if a gene is NOT a TF gene, can it regulate itself? ...
12
votes
3answers
2k views

Databases for gene regulatory network graphs?

What databases are available for gene regulatory network graphs starting from a given gene? For example, starting from p53 gene, where can I find a gene regulatory network image that can be exported ...
0
votes
1answer
59 views

What pattern can be learned from the data of RNA seq counts and HiC matrix? [closed]

I now have some data on the RNA seq counts and related Hi-C matrix of gene segment on a chromosome. My concern is, basically, what can we do with these data so as to establish the connection between ...
2
votes
2answers
118 views

Converting fmri data to association matrix

I am currently working on a new tool for the analysis of (large) weighted networks. Association matrices (correlation matrices) as obtained from fMRI data are perfect examples of the kind of data I am ...
5
votes
5answers
229 views

What are some examples of evolving networks in biology?

I'm a master student working on networks analysis in general. A network is something that has nodes and there are links between the nodes. Nodes and links could have attributes. An evolving network is ...
3
votes
1answer
225 views

Biological meaning/interpretation of clustering coefficience

I have been looking for some time to find an answer to the following question. I would be grateful for any help/advice or directions. I work very frequently with large number of proteins and assess ...
5
votes
1answer
105 views

Could murder be modeled as an infectious disease?

Background "When swine flu hit the population it spiked in certain areas and tapered off in neighboring regions, it hits hardest where people have least protection and this pattern is more ...
2
votes
0answers
105 views

Predicting host-pathogen gene interaction networks

Background What we have are: ~20 genome sequences for a host species that come with gene annotations Several sequenced genomes for parasite/pathogens of these hosts Question What are the ...
3
votes
2answers
51 views

Have novel interactions or pathways been predicted by GRN or PPI data and later confirmed by experiment?

I've been learning about the gene regulatory network (GRN) and protein-protein interaction network (PPI) recently. I've found a huge amount of extremely interesting papers about how biological network ...
5
votes
2answers
193 views

How to typeset gene regulatory networks

I have a relatively simply gene regulatory network I would like to visualize, complete with the common arrow and bar symbols used to show, respectively, which genes enhance or repress with other ...