Computational Biology Web Portal
Note: Articles considered especially worth reading are highlighted using this color .
The last update of this website was in 2026. I probably won't update this website anymore as my interests have changed.
General Topics
Computational Systems Biology
Basics
List of systems biology modeling software (Wikipedia)
Volko (2017): Computational Concepts in Biology
Volko (2018): Computational Concepts in Biology II
Gross et al. (2017): The Sum of the Parts: Large-Scale Modeling in Systems Biology
Wilke (2025): We still can't predict much of anything in biology
Bunne et al. (2024): How to build the virtual cell with artificial intelligence: Priorities and opportunities
Pyrkov et al. (2024): Complexity of life sciences in quantum and AI era
Swat et al. (2011): What it takes to understand and cure a living system: computational systems biology and a systems biology-driven pharmacokinetics-pharmacodynamics platform
Tegnér et al. (2009): Computational disease modeling - fact or fiction?
Slepchenko et al. (2002): Computational Cell Biology: Spatiotemporal Simulation of Cellular Events
Hunter et al. (2005): A Strategy for Integrative Computational Physiology
Oberhardt et al. (2009): Applications of genome-scale metabolic reconstructions
Eils et al. (2003): Computational imaging in cell biology
Dror et al. (2010): Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations
Segata et al. (2013): Computational meta'omics for microbial community studies
Weston et al. (2004): Systems Biology, Proteomics, and the Future of Health Care: Toward Predictive, Preventative, and Personalized Medicine
Kell et al. (2003): Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era
Raes et al. (2008): Molecular eco-systems biology: towards an understanding of community function
Kumar et al. (2006): Applying computational modeling to drug discovery and development
Valencia et al. (2002): Computational methods for the prediction of protein interactions
Alon (2003): Biological Networks: The Tinkerer as an Engineer
Goldbeter (2002): Computational approaches to cellular rhythms
Nowak et al. (2002): Computational and evolutionary aspects of language
Aho (2012): Computation and Computational Thinking
Covert et al. (2003): Identifying Constraints that Govern Cell Behavior: A Key to Converting Conceptual to Computational Models in Biology?
Cronin et al. (2006): The imitation game - A computational chemical approach to recognizing life
Dobson (2004): Chemical space and biology
Syed et al. (2009): Enzyme function prediction with interpretable models
Fernie et al. (2004): Metabolite profiling: from diagnostics to systems biology
Ge et al. (2003): Integrating 'omic' information: a bridge between genomics and systems biology
Draghici et al. (2007): A systems biology approach for pathway level analysis
Hartwell et al. (1999): From Molecular to Modular Cell Biology
Hood et al. (2004): Systems biology and new technologies enable predictive and preventative medicine
Semple et al. (2005): Review: In Vitro, in Vivo, in Silico: Computational Systems in Tissue Engineering and Regenerative Medicine
De Graaf et al. (2009): Nutritional Systems Biology Modeling: From Molecular Mechanisms to Physiology
Laubenbacher (2005): A Discrete Approach to Top-Down Modeling of Biochemical Networks
Mallick et al. (2006): Computational Prediction of Proteotypic Peptides for Quantitative Proteomics
Kell et al. (2005): Metabolic footprinting and Systems Biology: The medium is the message
Le Novère et al. (2009): The Systems Biology Graphical Notation
Fisher et al. (2007): Executable cell biology
Barabási et al. (2004): Network Biology: Understanding the Cell's Functional Organization
Ideker et al. (2001): A New Aproach to Decoding Life: Systems Biology
Chen et al. (2009): Connecting protein interaction data, mutations and disease using bioinformatics
Li et al. (2009): Exploring pathways from gene coexpression to network dynamics
Oprea et al. (2011): Computational Systems Chemical Biology
Walpole et al. (2013): Multiscale Computational Models of Complex Biological Systems
Butcher (2005): Can cell systems biology rescue drug discovery?
Dror et al. (2012): Biomolecular Simulation: A Computational Microscope for Molecular Biology
Keith et al. (2005): Multicomponent therapeutics for networked systems
De Jong (2000): Modeling and Simulation of Genetic Regulatory Systems: A Literature Review
Schmidt et al. (2009): Distilling Free-Form Natural Laws from Experimental Data
Friedman (2004): Inferring Cellular Networks Using Probabilistic Graphical Models
Di Ventura et al. (2006): From in vivo to in silico biology and back
Stiles et al. (unknown year): Spatially Realistic Computational Physiology: Past, Present and Future
Purnick et al. (2009): The second wave of synthetic biology: from modules to systems
Wilensky et al. (2006): Thinking Like a Wolf, a Sheep, or a Firefly: Learning Biology Through Constructing and Testing Computational Theories - An Embodied Modeling Approach
Tyson et al. (2001): Network Dynamics and Cell Physiology
Stephan et al. (2009): The Brain Connectivity Workshops: Moving the frontiers of computational systems neuroscience
Cusick et al. (2005): Interactome: gateway into systems biology
Weckwerth (2003): Metabolomics in systems biology
Wilkinson (2009): Stochastic modelling for quantitative description of heterogeneous biological systems
DeepMind
Proteins
Immune Digital Twins
Artificial Life
Basics
Videos
Challenges
Open Worm
PolyWorld
Synthetic Biology
Basics
Expanded Genetic Alphabet
Biological Computation
Contact: cdvolko (at) gmail (dot) com
Imprint: This website is owned by Claus Volko, Vienna, Austria. No liability is taken for the contents of any of the linked websites. http://www.cdvolko.net/