220 citations · 223 across the 10 of their papers we have counts for
12 papers
BioSimulators: a central registry of simulation engines and services for recommending specific tools
Bilal Shaikh, Lucian P. Smith, Dan Vasilescu +68
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, becau…
ObjTables: structured spreadsheets that promote data quality, reuse, and integration
Jonathan R. Karr, Wolfram Liebermeister, Arthur P. Goldberg +2
A central challenge in science is to understand how systems behaviors emerge from complex networks. This often requires aggregating, reusing, and integrating heterogeneous informat…
Automated generation of bacterial resource allocation models
Ana Bulović, Stephan Fischer, Marc Dinh +7
Resource Balance Analysis (RBA) is a computational method based on resource allocation, which performs accurate quantitative predictions of whole-cell states (i.e. growth rate, met…
Flux cost functions and optimal metabolic states
Wolfram Liebermeister
The metabolic fluxes in cells follow physical, biochemical, and economic principles. Some flux balance analysis (FBA) methods trade flux benefit against flux cost. However, if flux…
The protein cost of metabolic fluxes: prediction from enzymatic rate laws and cost minimization
Elad Noor, Avi Flamholz, Arren Bar-Even +3
Bacterial growth depends crucially on metabolic fluxes, which are limited by the cell's capacity to maintain metabolic enzymes. The necessary enzyme amount per unit flux is a major…
Optimal enzyme rhythms in cells
Wolfram Liebermeister
Cells can use periodic enzyme activities to adapt to periodic environments or existing internal rhythms and to establish metabolic cycles that schedule biochemical processes in tim…
SBtab - Conventions for structured data tables in Systems Biology
Wolfram Liebermeister, Timo Lubitz, Jens Hahn
Data tables in the form of spreadsheets or delimited text files are the most utilised data format in Systems Biology. However, they are often not sufficiently structured and lack c…
The enzyme cost of given metabolic flux distributions, as a function of logarithmic metabolite levels, is convex
Wolfram Liebermeister, Elad Noor
Enzyme costs play a major role in the choice of metabolic routes, both in evolution and bioengineering. Given desired fluxes, necessary enzyme levels can be estimated based on know…
Enzyme economy and metabolic control
Wolfram Liebermeister
The metabolic state of a cell, comprising fluxes, metabolite concentrations and enzyme levels, is shaped by a compromise between metabolic benefit and enzyme cost. This hypothesis…
Metabolic fluxes and value production
Wolfram Liebermeister
Metabolic fluxes in cells are governed by physical, physiological, and economic principles. Here I assume an optimal allocation of enzyme resources and postulate a general principl…
Structural thermokinetic modelling
Wolfram Liebermeister
Translating metabolic networks into dynamic models is difficult if kinetic constants are unknown. Structural Kinetic Modelling (SKM) replaces reaction elasticities by independent r…
semanticSBML 2.0 - A Collection of Online Services for SBML Models
Falko Krause, Marvin Schulz, Timo Lubitz +1
semanticSBML 2.0 is an online collection of services for the work with biochemical network models in SBML format.