An interdisciplinary area of study in the life sciences with a focus on complex interactions and large networks of biological molecules and processes.

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88
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5answers
11k views

Does DNA have the equivalent of IF-statements, WHILE loops, or function calls? How about GOTO?

Does DNA have anything like IF-statements, GOTO-jumps, or WHILE loops? In software development, these constructs have the following functions: IF-statements: An IF statement executes the code in a ...
11
votes
2answers
888 views

Are the inverse problems of Systems Biology impossible to solve?

I have heard Sydney Brenner give a talk (see link below) on how the entire program of Systems Biology is suspect because, according to him, a chap named Hadamard showed that inverse problems are ...
9
votes
6answers
492 views

Introductory literature for synthetic / systems biology?

I'm a computer engineer (MsC Computer Engineering) who's looking to switch into the field of synthetic / systems biology. I've got a comprehensive layman's understanding of evolution, genetics, ...
5
votes
2answers
55 views

tools to reconstruct the transcriptional regulatory circuits?

What are commonly used tools to reconstruct the transcriptional regulatory circuits that govern diverse cellular responses and what input data sets do they accept?
4
votes
1answer
58 views

Negative feedback loop and oscillations

According to the textbook Alberts Molecular Biology of the Cell (5th ed., p. 902), negative feedback loops cause oscillations when they are long delayed. I just can't figure out why. Except for ...
4
votes
1answer
46 views

A good software for agent based modelling?

Hello i'm gonna start my master degree in systems biology and i'm thinking of working with agent based modelling, but i really don´t know which platform can be the best to simulate interactions ...
4
votes
1answer
76 views

Statistics on energy consumption breakdown per biological functions across organisms?

Are there any statistics available on how much energy organisms use for each biological functions (i.e. something similar to the line of "Bacteria spend X% of energy on information processing, Y% for ...
3
votes
2answers
65 views

Is “A” inhibiting “B” and vice-versa, a positive feedback loop?

If product A inhibits the expression of product B, and product B inhibits the expression of product A, is this a positive feedback loop? My thinking was to consider the scenario that A starts off ...
3
votes
1answer
1k views

Difference between “transcriptional activity” and “RNA expression”

I am working with a network object where the nodes are different events in molecular biology. Specifically; Catalytic activity of X, RNA expression of X, GTP-bound activity of X, Kinase activity of ...
3
votes
1answer
458 views

Is the activity of enzymes in the human body affected by the outer temperature?

I have to do a research about the enzymes in the human body and the things that affect them. I know that the body temperature affects the activity of enzyemes but I'd like to know if the outer ...
2
votes
1answer
36 views

What network motifs or other mechanisms can make the expression of a gene invariable to the environment?

Next to double positive feedback loops and chromatin modification, which other mechanisms can make a gene susceptible to a certain environment in one cell-type but not in another?
2
votes
1answer
96 views

Does this equation have a typo? (Systems Biology, singular value decomposition) [closed]

I'm reading a systems biology paper, and I'm suspecting there's a typo in an equation, but I want to make sure. The article is "Systemic metabolic reactions are obtained by singular value ...
2
votes
1answer
27 views

how to solve gap reactions in genome scale metabolic reconstruction [closed]

I'm making a project about modeling of nannochloropsis metabolism. My model is in the refinement stage. However, it is not running in the FBA test. Then i found there are 87 reactions that did not ...
2
votes
1answer
97 views

System biology and evolution: Book-recommendations

I have relatively good knowledge in evolutionary biology and in population genetics. I am getting more and more interested in the evolution of ... genetic developmental processes gene interactions ...
2
votes
2answers
80 views

Valid comparison of gene expression between several genes in several cell lines

We have gene expression data (Affimetrix mRNA gene expression results) for several cell lines, over a set of genes. Our goal would be to be able to compare relative gene expression for genes over the ...
2
votes
1answer
110 views

How usable is the Human Metabolic Model to predict biomass?

In order to use the Human Metabolic Model for Flux Balance Analysis of specific cancer cell lines, we would like to know what sort of flux values have been determined for the Human Metabolic Model. ...
2
votes
2answers
107 views

Databases for metabolic pathways of human disease

Which databases contain the metabolic pathway of human diseases? I have searched Metacyc and KEGG but didn't find the appropriate metabolic pathway.
2
votes
0answers
26 views

Metabolic control theory: proof of the summation theorem?

I'm looking for a rigorous proof of the summation theorem of metabolic control theory. The only sources I find are the original papers by Kacser and Burns 1973 and Heinrich and Rapoport 1974, both of ...
1
vote
1answer
124 views

Where can I find the metabolic network for the human erythrocyte?

Where can I find the metabolic network of the human erythrocyte (red blood cell), in SBML format? The red blood cell metabolic network is a model that's usually employed in the literature [see refs ...
1
vote
1answer
35 views

does life make or break?

Ok, this question seems like it may be impossible to answer, but would be interesting to see if anyone has an idea. Throughout the course of a human life, do we make more molecular bonds than we ...
1
vote
5answers
117 views

Can your immune system's cells destroy you? (Critical thinking and Fictional sense)

In an imaginary sense, If you alone were replicated into 2 so that there should now be 2 of "you" (meaning you both have the same DNA). Then let's say one of you shrunk to the size of a bacteria, and ...
1
vote
1answer
48 views

What are good data on the Human Metabolic Model and where can I get them?

Trying to get a good SBML representation of the Human Metabolic Model for use in Flux Balance Analysis and drug targetting (i.e. gene knockout) simulations. What are good sources for these data? ...
1
vote
2answers
218 views

Recent and good quality articles on systems biology [closed]

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 ...
1
vote
1answer
25 views

Difference between pulse coupling and diffusive coupling In biological oscillators

What are the differences between pulse coupling found among neuron cells and diffusive coupling found in cells that exhibit calcium waves? Moreover, in both methods, is it a strict requirement that ...
1
vote
1answer
202 views

How to relate human metabolic model reactions and cancer drug targets / reactome items?

Trying to find a way to take a cancer drug (from CancerDR, for instance) and infer the metabolic reactions that are affected by it in the Human Metabolic Model. Essentially, I would like to know ...
1
vote
0answers
20 views

Barcode exchange between neighbouring cells

I am currently interested in equipping animal cells in a tissue with individual barcodes. These barcodes should get amplified in the cells (not to a cell degrading extent, of course), and also ...
1
vote
0answers
38 views

Why does death exist? [duplicate]

The biological purpose of an organism is to reproduce and as soon as reproductive age is passed, aging kicks in and eventually leads to death. (This is what I learned from a gerontologist.) But then, ...
0
votes
1answer
100 views

Systems Biology of triacylglycerol (TAG) synthesis in Jatropha

I need the genetic regulatory network of TAG synthesis (Kennedy pathway) of Jatropha plant?? Or is there any way to convert metabolic pathway into genetic regulatory network?
0
votes
0answers
17 views

How many Stress Response Transcription Factors are there in yeast (and what are they)

I've Read that there are ~209 TFs in Yeast, but I'd like to know how many (and which) of these TFs are associated with Stress Responses? Is there a paper someone can link me to?
0
votes
1answer
68 views

How does cancer of the larynx (laryngeal cancer) affect the respiratory system?

The larynx is part of the respiratory system and is responsible for producing sound (our voices). My question is how cancer in the larynx (voice box) affect the respiratory system overall? I ...
0
votes
1answer
55 views

Critical discussion: Gene expression and systems biology allows us to understand the control of complex traits

I'm having a bit of trouble tackling this question. Any help on what I should write about or the points I should mention would be much appreciated. I keep seeing articles about eQTL and QTL are these ...
-1
votes
1answer
61 views

Why the name coined for MARKUP LANGUAGE for SBML? [closed]

I'm get the confusion about SYSTEM BIOLOGY filed. SBML is refer to as SYSTEM BIOLOGY MARKUP LANGUAGE why we should called as ...