Biology Stack Exchange
Biology Stack Exchange

Questions tagged [systems-biology]

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

A system is defined as an assembly of mutually interacting components which, based on the dynamics of the interactions, performs specific functions. Therefore one of the main features of systems biology is to understand the input-output characteristics of a biological system by integrating the fields of experimental biology and applied mathematics.

For a basic yet thorough introduction please read Introduction to Systems Biology -by Uri Alon

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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 subsequent code block if some specific condition is…
user12939
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Are the inverse problems of Systems Biology impossible to solve?

I have heard Sydney Brenner give a talk [0] on how the entire program of Systems Biology is suspect because, according to him, a chap named Hadamard showed that inverse problems are impossible to solve, or something to that effect. I find it…
Joebevo
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Introductory literature for synthetic / systems biology

I am a computer engineer (MSc in Computer Engineering) who's looking to switch into the field of synthetic / systems biology. I have a comprehensive layman's understanding of evolution, genetics, transcription, etc, but my academic studies have been…
uvesten
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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 that, in case of short delayed feedback, the…
user159527
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What does it mean to quantitatively describe a cell?

To begin this question, I will quote Molecular Biology of the Cell (page 38): ... Biological systems are, ..., full of feedback loops, and the behavior of even the simplest of systems with feedback is remarkably difficult to predict by…
seamos
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Which genetic oscillator should I use to generate oscillations in range of 2-20 mins?

I'm looking to phase-separate the expression of two enzymes and hence am looking for a multi-component genetic oscillator. However, repressilators and metabolators have a large period of around 45 mins. Smolen oscillators as described in Stricker et…
Siddharth Fitwe
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How to derive rate of product formation for an allosterically inhibited enzyme?

I'm working through Mathematical Modelling in Systems Biology: An Introduction by Brian Ingalls, and in Chapter 3 there's an example of a simple allosterically inhibited enzyme with reaction scheme shown here: $$\ce{S + E<=>[k_1][k_{-1}] ES->[k_2] E…
Bobbybobbobbo
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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?
719016
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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 temperature of the air affects them, too? When the…
Rehab Tarek
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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 tissue maintenance and Z% for locomotion. Mammals…
Enno Shioji
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How does species diversity vs Earth total biomass relate?

Are there any laws/theoretical foundations about how diversity of species relate with total biomass on Earth? While there is a lot of esoteric sort of talk "humanity dis-balances the live on the Earth", I thought, there are formally seen the…
J. Doe
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What physiological processes give rise to a linear cell survival curve?

If we plot the number of surviving cells in a structure over time (assuming no replacement), the shape of that curve should imply something about the underlying process responsible for cell death. For example, if surrounding conditions mean that…
Michael MacAskill
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Can a protein falling below a threshold trigger another response?

Is it possible that the falling of the concentration of a protein below a threshold triggers the release or production of another protein?
Peter123
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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 gene expression plasticity intrinsic or cellular…
Remi.b
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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 X, Oxidoreductase activity of X, Phosphatase…
Count Zero
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