Me (and some colleagues of mine in Pisa) have selected 3 long term research problems which could become, one day, a good (hopefully) starting point as a phd thesis. All this stuff is realeted to systems biology which is, accordingly to wikipedia,

“SB is a relatively new biological study field that focuses on the systematic study of complex interactions in biological systems, thus using a new perspective (integration instead of reduction) to study them. Particularly from year 2000 onwards, the term is used widely in the biosciences, and in a variety of contexts. Because the scientific method has been used primarily toward reductionism, one of the goals of systems biology is to discover new emergent properties that may arise from the systemic view used by this discipline in order to understand better the entirety of processes that happen in a biological system.”   

Here is the list of topics:

  1. Kohn interaction maps[1999]: Eventually to understand the integrated function of the cell cycle regulatory network, we must organize the known interactions in the form of a diagram, map, and/or database. A diagram convention was designed capable of unambiguous representation of networks containing multiprotein complexes, protein modifications, and enzymes that are substrates of other enzymes. To facilitate linkage to a database, each molecular species is symbolically represented only once in each diagram. Molecular species can be located on the map by means of indexed grid coordinates. Each interaction is referenced to an annotation list where pertinent information and references can be found. Parts of the network are grouped into functional subsystems. The map shows how multiprotein complexes could assemble and function at gene promoter sites and at sites of DNA damage. It also portrays the richness of connections between the p53-Mdm2 subsystem and other parts of the network.  TODO: Formal defintion of their semantics (formal, complete, not ambiguos, ….
  2. P Systems[1998]:  A computational model based upon the architecture of a biological cell, abstracting from the way in which chemicals interact and cross cell membranes. This concept was first introduced in a 1998 report by the computer scientist Gheorghe Paun, whose last name is the origin of the letter P in ‘P Systems’. Variations on the P system model led to the formation of a branch of research known as ‘membrane computing.’ Although inspired by biological processes, the research interest regarding P systems is mainly concerned with their use as a computational model, rather than for biological modelling, although this is also being investigated. TODO: definition of more expressive variants of P Systems (space topology, time, ….)
  3. Tumor immune system[XXX]: Occasionally, though, even though cells are changing from normal to abnormal, they may still appear to be normal. Their outer appearance (proteins and other molecules on their surface) may look unchanged, even though profound changes may be happening on the inside. In this way, these abnormal cells manage to escape attack by the immune system and grow and multiply without triggering an immune response. This is how it’s possible for a tumor to form, even when your immune system is working normally. Eventually, however, the tumor becomes so altered and threatening that it can no longer hide its malignant character. The immune system is no longer fooled into recognizing these cells as normal, and launches its attack. The attack may succeed, or it may come too late: the tumor may be beyond the power of the immune system by itself. The immune system may need help—bold measures such as: immune growth factors(medicines that stimulate the production of new immune cells); antibody medications(special antibodies made in a laboratory, designed to target a specific antigen on a cancer cell); vaccines(agents that stimulate your immune system to fight back, giving it a wake-up call to action). TODO: A quantitative approach based on systems biology to study the problem of interaction between the tumor and the immune system.

These sumup of the 3 topics are taken from the web. The avalaible literature is huge and, as always, someone else already did something… I am going to have, in these short period of time, a quick look at all these topics. I found interesting references and I am going to go into deep with the ones more involving…