--- title: Systems Biology description: Systems biology models cells and organisms as networks rather than parts lists. You will understand gene regulatory circuits, feedback and robustness, stochastic gene expression, and the quantitative methods used to predict how biological networks behave. category: sciences subcategory: biology difficulty: intermediate, advanced url: /subject/systems-biology --- # Systems Biology Systems biology models cells and organisms as networks rather than parts lists. You will understand gene regulatory circuits, feedback and robustness, stochastic gene expression, and the quantitative methods used to predict how biological networks behave. ## Where to start Start with Systems Biology 2018, Uri Alon's free Weizmann Institute lecture course, with recorded sessions, notes and worked solutions on autoregulation, feed-forward loops and robustness. If you only use one resource, make it Alon's paid textbook An Introduction to Systems Biology, the canonical entry text. Next, Biological Circuit Design (Caltech BE 150 / Bi 250b) by Michael Elowitz and Justin Bois adds stochastic simulation in Python. ## Available Resources 3 Books • 3 Courses • 1 Papers ## Courses ### 1. Systems Biology (MIT 8.591J) **Author:** Jeff Gore Cellular and population-level systems biology: genetic switches and oscillators, network motifs, cellular decision-making, pattern formation, cell-cell communication and evolutionary dynamics, with an emphasis on synthetic biology. Includes 24 lecture videos, problem sets and exams for learning to model genetic networks quantitatively. **Difficulty:** Advanced | **Language:** English | **Price:** Free **Link:** https://ocw.mit.edu/courses/8-591j-systems-biology-fall-2014/ **Tags:** systems-biology, gene-regulatory-networks, synthetic-biology, network-motifs, evolutionary-dynamics ### 2. Biological Circuit Design (Caltech BE 150 / Bi 250b) **Author:** Michael Elowitz, Justin Bois Caltech's open circuit-design textbook, twenty-two chapters with Python notebooks. Covers repression motifs, amplification, oscillators, stochastic gene expression via Gillespie simulation and patterning. Readers finish able to build, simulate and analyse genetic circuit models in code. The one resource that closes Alon's weakest gap — stochasticity — with executable Gillespie/ODE code and 50+ exercises rather than prose. **Difficulty:** Advanced | **Language:** English | **Price:** Free **Link:** https://biocircuits.github.io/ **Tags:** synthetic biology, genetic circuits, gillespie algorithm, stochastic simulation, python ### 3. Systems Biology 2018 — Uri Alon's Full Course **Author:** Uri Alon Alon's complete graduate lecture course, free: twelve recorded sessions covering autoregulation, feed-forward loops, chemotaxis robustness, fold-change detection, oscillators, optimality and modularity, plus downloadable notes, problem sets and worked solutions. **Difficulty:** Intermediate | **Language:** English | **Price:** Free **Link:** https://www.weizmann.ac.il/mcb/alon/courses/systems-biology-2018 **Tags:** network motifs, feed-forward loops, robustness, bacterial chemotaxis, systems biology ## Books ### 1. Cell Biology by the Numbers **Author:** Ron Milo, Rob Phillips Free online book of short vignettes, each answering a quantitative question about cells: sizes, copy numbers, concentrations, energies, forces, rates and error frequencies. Using measured values and back-of-the-envelope estimates, it builds physical intuition and the habit of checking biological claims against numbers. **Difficulty:** Beginner | **Language:** English | **Price:** Free **Link:** https://book.bionumbers.org/ **Tags:** quantitative-biology, cell-biology, order-of-magnitude-estimation, bionumbers, biophysics ### 2. Mathematical Modeling in Systems Biology — Free Preprint and Course Materials **Author:** Brian P. Ingalls Ingalls hosts the full preprint of his MIT Press textbook alongside exercise solutions, errata and MATLAB/Python code. It teaches ODE modelling of metabolic, signalling, gene regulatory and electrophysiological networks from a standing start. **Difficulty:** Intermediate | **Language:** English | **Price:** Free **Link:** https://www.math.uwaterloo.ca/~bingalls/MMSB/ **Tags:** mathematical modeling, ordinary differential equations, gene regulatory networks, signal transduction, metabolic networks ### 3. An Introduction to Systems Biology: Design Principles of Biological Circuits (2nd Edition) **Author:** Uri Alon The canonical systems biology text, universally cited as THE entry text. Builds network motifs, feedback loops, robustness and optimality from simple differential equations, using measured bacterial and developmental circuits. Readers finish able to derive and analyse gene-circuit dynamics themselves. **Difficulty:** Intermediate | **Language:** English | **Price:** Paid **Link:** https://www.amazon.com/dp/1439837171?tag=edmonddante07-20 **Tags:** network motifs, gene circuits, feedback loops, robustness, systems biology ## Papers ### 1. Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences **Author:** Arjun Raj, Alexander van Oudenaarden The standard review of gene expression noise: intrinsic versus extrinsic sources, transcriptional bursting, and how cells exploit or suppress variability in stress response, development and cell fate. Free full text via PubMed Central. **Difficulty:** Advanced | **Language:** English | **Price:** Free **Link:** https://pmc.ncbi.nlm.nih.gov/articles/PMC3118044/ **Tags:** gene expression noise, stochastic gene expression, transcriptional bursting, cell fate, systems biology --- *This content is part of Dantes.io - Your Treasure Map to Knowledge* *Curated by humans at Dantes.io. Personal study use welcome; republishing this curation requires permission (team@dantes.io).* View this page online: https://dantes.io/subject/systems-biology