The challenges of in silico biology

By Bernhard O. Palsson. Nature Biotechnology, 2000

343 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/cd218b4bccdf6de0d270f7b500309c68a60a4b7e

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In Molecular Biology

Citations in the corpus

The Commodification of Emergence: Systems Biology, Synthetic Biology and Intellectual Property (2008, background): “For some, the reduction of complexity needed to make biology into an engineering discipline is not merely an instrumental aim, but is based on a faith that synthetic biology will ultimately lead to ‘the elucidation of the underlying simplicity’ of nature (Palsson, 2000: 1149).”
Plant metabolomics: large-scale phytochemistry in the functional genomics era. (2003, background): “To accomplish this, metabolomic data sets must be integrated and correlated in a global manner with genetic and enzymatic data, pathways assembled into systems, and literature references incorporated as learning tools to annotate existing data to yield in silico biological information (Palsson, 2000”
Towards multidimensional genome annotation (2006, background): “Network reconstructions iteratively evolve as a result of network evaluatio”
Using Genome-Scale Models to Predict Biological Capabilities (2015, positive): “The scale of such predictions has grown steadily since the ﬁrst genome-scale model of E. coli appeared in 2000 (Edwards and Palsson, 2000).”
Metabolic pathways in the post-genome era. (2003, methodology): “Some of the key properties studied using network-based pathways are schematically described in Fig. 4. For example, minimal medium requirements have been defined for H. influenzae and H. pylori using extreme pathways [15, 16 ] (Fig. 4a).”
Regulation of gene expression in flux balance models of metabolism. (2001, methodology): “FBA has been described in detail and used in a variety of recent applications (Edwards & Palsson, 1999, 2000; Edwards et al., 2001).”
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth (2002, methodology): “Predictive whole-cell metabolic models can be developed using a constraints-based modelling procedur”
Thirteen Years of Building Constraint-Based In Silico Models of Escherichia coli (2003, background): “…b, reference 55; c, reference 32; d, references 59 and 60; e, references 42 and 43; f, reference 16; g, reference 11; h, reference 9; and i, reference 1. ture, and while correct predictions are desirable, the incorrect predictions are the ones that lead to an iterative reﬁnement of the models (37).”
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) (2003, methodology): “As a part of the iterative model building process [2] iJR904 can be used to design informative experiments to systematically address this issue.”
Progress in Neuroengineering for brain repair: New challenges and open issues (2018, background): “At the beginning of the third millennium, we are witnessing the birth of the new biology era in which the issues related to biology and medicine are approached in a totally different and revolutionary way with respect to the past (Palsson, 2000).”
Integrating high-throughput and computational data elucidates bacterial networks (2004, background): “jpg" NDATA ITEM> ]> The flood of high-throughput biological data has led to the expectation that computational (or in silico ) models can be used to direct biological discovery, enabling biologists to reconcile heterogeneous data types, find inconsistencies and systematically generate ”
Cleaning up with genomics: applying molecular biology to bioremediation (2003, background): “Such descriptions are becoming possible owing to important advances in the development of in silico models of cell metabolis”