The BioPAX community standard for pathway data sharing
Abstract Biological Pathway Exchange (BioPAX) is a standard language to represent
biological pathways at the molecular and cellular level and to facilitate the exchange of …
biological pathways at the molecular and cellular level and to facilitate the exchange of …
Advantages and limitations of current network inference methods
R De Smet, K Marchal - Nature Reviews Microbiology, 2010 - nature.com
Network inference, which is the reconstruction of biological networks from high-throughput
data, can provide valuable information about the regulation of gene expression in cells …
data, can provide valuable information about the regulation of gene expression in cells …
iML1515, a knowledgebase that computes Escherichia coli traits
Figure 1 iML1515 genome-scale reconstruction.(a) The iML1515 model contains 1,515
open reading frames that encode enzymes that catalyze 2,719 reactions involving 1,192 …
open reading frames that encode enzymes that catalyze 2,719 reactions involving 1,192 …
Universal resilience patterns in complex networks
Resilience, a system's ability to adjust its activity to retain its basic functionality when errors,
failures and environmental changes occur, is a defining property of many complex systems …
failures and environmental changes occur, is a defining property of many complex systems …
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond
S Gama-Castro, H Salgado… - Nucleic acids …, 2016 - academic.oup.com
Abstract RegulonDB (http://regulondb. ccg. unam. mx) is one of the most useful and
important resources on bacterial gene regulation, as it integrates the scattered scientific …
important resources on bacterial gene regulation, as it integrates the scattered scientific …
[HTML][HTML] COBRApy: constraints-based reconstruction and analysis for python
Abstract Background COnstraint-Based Reconstruction and Analysis (COBRA) methods are
widely used for genome-scale modeling of metabolic networks in both prokaryotes and …
widely used for genome-scale modeling of metabolic networks in both prokaryotes and …
Antigen receptor repertoire profiling from RNA-seq data
To the Editor: Somatic recombination and accumulation of mutations in VDJ segments result
in vast heterogeneity of T-cell receptor (TCR) and immunoglobulin repertoires1, 2. High …
in vast heterogeneity of T-cell receptor (TCR) and immunoglobulin repertoires1, 2. High …
[HTML][HTML] Inferring regulatory networks from expression data using tree-based methods
One of the pressing open problems of computational systems biology is the elucidation of
the topology of genetic regulatory networks (GRNs) using high throughput genomic data, in …
the topology of genetic regulatory networks (GRNs) using high throughput genomic data, in …
Characterization of 582 natural and synthetic terminators and quantification of their design constraints
Large genetic engineering projects require more cistrons and consequently more strong and
reliable transcriptional terminators. We have measured the strengths of a library of …
reliable transcriptional terminators. We have measured the strengths of a library of …
Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models
After hundreds of generations of adaptive evolution at exponential growth, Escherichia coli
grows as predicted using flux balance analysis (FBA) on genome‐scale metabolic models …
grows as predicted using flux balance analysis (FBA) on genome‐scale metabolic models …