Biology Stack Exchange is a question and answer site for biology researchers, academics, and students. Join them; it only takes a minute:

Sign up
Here's how it works:
  1. Anybody can ask a question
  2. Anybody can answer
  3. The best answers are voted up and rise to the top

I'm a biotechnology student and I have to write a sort of non-experimental thesis (30 pages long) within the end of a three years study.

I'm very interested in the "systems biology" field and I'm searching good (innovative) and recent (max 3-4 years old) articles about this subject, but unfortunately I've found my research more difficult than I expected.

I'd like to focus on not immediate/easy articles and possibly containing new and promising approaches.

Does anybody have suggestions?

PS: it all started from Uri Alon's great lessons on YouTube.

share|improve this question

closed as not a real question by rg255, dd3, MattDMo, relf20, Rory M May 15 '13 at 20:44

It's difficult to tell what is being asked here. This question is ambiguous, vague, incomplete, overly broad, or rhetorical and cannot be reasonably answered in its current form. For help clarifying this question so that it can be reopened, visit the help center.If this question can be reworded to fit the rules in the help center, please edit the question.

Welcome to Biology SE. Unfortunately, your question is very broad - there are many topics (not even getting to papers) that fit your criteria. Are there particular types of techniques (or objectives) that you are interested in? – dd3 May 7 '13 at 22:19
Maybe we could start with asking for a list of the most interesting problems currently being worked on in systems biology... what do you think Mattia? – shigeta May 8 '13 at 3:18
Thank you for your answers. I have been broad because i'm not interested in nothing in particular, moreover I don't want to miss something (I'm ignorant in the field, mainly fascinated) that you may think very interesting. I need however that the subject has already been studied in an article. I'm willing to eventually study hard on it for fill my gaps. – Mattia Rovetta May 8 '13 at 17:25
up vote 1 down vote accepted

I'll have a go at a short list. This is more of a highlight and primer sort of response to a somewhat subjective question so pardon if this isn't what you wanted. I don't have paper references for all this, but I'll try to come back and add some later - I usually only have half an hour or so to write an answer so bear with me.

Synthetic biology as defined as the use of genes and promoters to engineer cells or even multicellular organisms like devices is a major category. I like browsing the projects from the iGem Competitions. A couple of outstanding efforts in this field are the use of photoreceptors to program E coli gene expression and the general effort to create logic and computational circuits in the cell.

A major application in systems biology is engineering cells to produce new chemical compounds or to overproduce compounds. A classic example (sort of old, but still pretty outstanding) is the engineering of E coli to produce the antimalarial drug artemisinin at levels which would enable world wide release of the drug. This has inspired efforts to produce fuel from algae and bacteria as well.

If you define Systems biology as being often concerned with modeling some or even all the biological processes of the cell, there are probably too many major efforts to cite, but this is just a list of some favorites.

There are lots of papers focused on flux balance analysis which models how the metabolic machinery processes and synthesizes all the scores of chemical compounds that make up a cell.

Another category of synbio tries to take the genes found in a genome and model the actions of all the genes. One of the most exciting papers to come out in this sort of systems biology is the whole cell model of Mycobacterium genetalium. Using data from a massive effort to characterize every gene in this very small genome, the model consists of over 20 specific models which have combined to make a very impressive simulation of the entire cell dividing.

Then there is metagenomics, which looks at the different populations of microorganisms and tries to look at how they vary with different environmental conditions. A recent paper that's exciting is the review of how different bacteria dominate in the gut of obese mice and people (several references in the link). A tour de force in metagenomics was the global sea survey.

share|improve this answer
Thank you for your list, the whole cell model is very exciting! And pardon me for the broad question, I'll keep it in mind in the future. – Mattia Rovetta May 21 '13 at 18:44
I personally wish more sorts of questions like this were around more - having a good conversation about ongoing science is kinda hard to find on the internet... – shigeta May 21 '13 at 18:47
I agree with you, but maybe this is not the right place to discuss of it since my answer has been closed. I'm trying to figure out what is my favourite subject, so I will ask again but with more precision. For now I am focusing on flux balance analysis and on the cell simulation article (that has an exhaustive 100 pages long supplemental document). – Mattia Rovetta May 21 '13 at 19:12

This question is extremely vague, and can't have any real answer without you specifying a question or at least focus. Keep in mind, there is no high-road to research, you will have to dig in and start reading papers to gain understanding of your field. If you want help from others, you should at least take time to list the papers that you have already read and why you liked them to give readers a flavor of your interests.

To start you off, consider this Google Scholar query for systems biology since 2009. If you've read specific older papers that you've liked, for example this popular 2002 minu-survey:

Kitano, H. (2002). Systems biology: a brief overview. Science, 295(5560), 1662-1664.

Then you can learn how the field has advanced since by doing a forward search in Scholar (and restricted to 2009+). Hopefully this will provide you will some ideas so that you can ask a more precise question!

share|improve this answer

Not the answer you're looking for? Browse other questions tagged or ask your own question.