Computational Biology Web Portal
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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
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