Question: Basics Of Systems Biology...
8
gravatar for pixie@bioinfo
8.5 years ago by
pixie@bioinfo1.3k
pixie@bioinfo1.3k wrote:

I have been entrusted with the job of planning some systems biology work. I have gone through numerous papers related to network biology where networks have been built using PPI or gene expression data.

However, I also want to read some books/online stuffs which will cover the basics of systems biology. I specially want to understand what one does after building the networks. How I should go about the statistical analysis, how to find hubs and modules etc. What kind of data we need for building networks?...Does it have to be expression or PPI data?

Things are a bit hazy for me at this point. Will be grateful for any kind of suggestions...

network • 4.3k views
ADD COMMENTlink written 8.5 years ago by pixie@bioinfo1.3k
9
gravatar for Daniel Swan
8.5 years ago by
Daniel Swan13k
Aberdeen, UK
Daniel Swan13k wrote:

I probably wouldn't be the only person to recommend Uri Alon's "An Introduction to Systems Biology: Design Principles of Biological Circuits" which is something of a classic text.

http://www.amazon.co.uk/Introduction-Systems-Biology-Mathematical-Computational/dp/1584886420

ADD COMMENTlink written 8.5 years ago by Daniel Swan13k
5
gravatar for satsurae
8.5 years ago by
satsurae120
satsurae120 wrote:

Kitano is a pretty good authority on systems biology. And he has a very good writing style. Here is a basic overview which you may have already come across:

http://www.sciencemag.org/cgi/content/full/295/5560/1662

EDIT:

Bernhard Palsson is the principal author on this protocol for network construction covering pretty much all bases:

http://www.nature.com/nprot/journal/v5/n1/full/nprot.2009.203.html

ADD COMMENTlink modified 8.5 years ago • written 8.5 years ago by satsurae120
4
gravatar for Samuel Lampa
7.9 years ago by
Samuel Lampa1.2k
Stockholm
Samuel Lampa1.2k wrote:

I just found out that the "Bioinformatics for Systems Biology" is available freely for an online read (PDFs for each chapter) here.

The book claims to cover the common grounds for systems biology and bioinformatics (and so not be only focused on the Bioinformatics part), and with chapters such as "Genomic Tools for Analyzing Transcriptional Regulatory Networks", "Statistical Tools for Gene Expression Analysis and Systems Biology and Related Web Resources" and "Methods for Structural Inference and Functional Module Identification in Intracellular Networks" (and that is only 3 out of 32 chapters), it seems to be of some relevance.

ADD COMMENTlink modified 7.9 years ago • written 7.9 years ago by Samuel Lampa1.2k

Thanks so much for the information..

ADD REPLYlink written 7.9 years ago by pixie@bioinfo1.3k
2
gravatar for Codemanky
7.9 years ago by
Codemanky50
Codemanky50 wrote:

There are several types of biological networks that include(but not limited to) Gene Regulatory Networks, Protein-Protein Interaction(PPI) Networks, Metabolic Networks and Signal Transduction Networks.

Uri Alon's book focuses on Regulatory and Transcriptional Networks. Network Motif is a powerful concept that was first introduced by Uri Alon to understand the design principles of biological networks. You can find Alon's motif finder software here.

I am not aware of any book on Network Biology but Barbasi's this Nature Review article is a very good introduction to the topic and all the terminology that you might come across in Network Biology papers.

This review paper by Yang and Su not only covers Network Biology concepts but also lists a set of algorithms for module discovery. The paper also has nice a "Application" section which discusses how the framework of networks and modules helps in understanding cellular behavior under different biological contexts.

Biological Networks can be built based on several types of data...:

  1. PPI from -Two Hybrid Assays, Mass Spec(protein complexes)
  2. Regulatory and Transcriptional from - ChIP-on-Chip, ChIP-Seq
  3. Metabolic Networks - eg KEGG PATHWAY database - from manual collection of metabolic reactions
  4. Human Disease Networks - based on known disease-gene associations
ADD COMMENTlink written 7.9 years ago by Codemanky50

Thanks so much for the information...

ADD REPLYlink written 7.9 years ago by pixie@bioinfo1.3k
1
gravatar for Samuel Lampa
7.9 years ago by
Samuel Lampa1.2k
Stockholm
Samuel Lampa1.2k wrote:

Except for Alon's book mentioned above, I can recommend "System Modeling in Cellular Biology" by Szallasi and co-authors. I have only skimmed or read parts of both, but from this, it seems that while Alon's book captures the general ideas of regulation networks, this book is more of a collection of relevant methods and modelling approaches in Systems biology. I found the topics practical and interesting (There's even a list of recommended software tools available online).

ADD COMMENTlink written 7.9 years ago by Samuel Lampa1.2k
1
gravatar for Thaman
7.9 years ago by
Thaman3.2k
Finland
Thaman3.2k wrote:

I have been doing this course now and collected some of the resources

All lectures and practical materials are availables which will facilitate in learning system biology.

ADD COMMENTlink modified 7.9 years ago • written 7.9 years ago by Thaman3.2k

thanks so much for these links..

ADD REPLYlink written 7.9 years ago by pixie@bioinfo1.3k
0
gravatar for Fred Fleche
7.9 years ago by
Fred Fleche4.3k
Paris, France
Fred Fleche4.3k wrote:

In my library I have the book Introduction to Systems Biology which should be a good starting point.

ADD COMMENTlink written 7.9 years ago by Fred Fleche4.3k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2033 users visited in the last hour