Oliver Ebenhöh

Does specific membrane surface area constrain Escherichia coli energy spillage and therefore aerobic and anaerobic growth rates?

This study quantifies how specific membrane surface area (sMSA) constrains Escherichia coli growth rates and energy metabolism across aerobic and anaerobic conditions.

Steady state ratios in bipartite population models emerge through obligate cross-feeding

The paper shows that stable biomass ratios emerge in mutually obligate cross-feeding microbial systems and can be predicted from measurable parameters.

Multi-omic data fusion reveals the in vivo enzyme kinetics of Vibrio natriegens at the genome-scale

This study measures in vivo enzyme turnover numbers in Vibrio natriegens using multi-omic data fusion, revealing enzymes are 14-fold faster than E. coli and showing machine learning underestimates these kinetics.

Helixer--de novo Prediction of Primary Eukaryotic Gene Models Combining Deep Learning and a Hidden Markov Model

Helixer, a hybrid convolutional/bLSTM network with a hidden Markov model post-processor, predicts eukaryotic primary gene models from DNA alone, outscoring GenemarkES and AUGUSTUS on most species.

Integrative Thermodynamics Strategies in Microbial Metabolism

This study extends thermodynamic analysis of microbial metabolism to non-carbon nutrient limitations, showing more negative Gibbs free energy values for the Net Catabolic Reaction under anabolic limitations.

Alternatives to photorespiration: A systems-level analysis reveals mechanisms of enhanced plant productivity

Modelling 12 alternative photorespiratory pathways predicts the largest carbon-export gains for carbon-fixing designs (TaCo); complete decarboxylation bypasses help mainly by releasing CO2 in chloroplasts, raising carboxylation and recapturing lost CO2.

Rule-Based Deconstruction and Reconstruction of Diterpene Libraries: Categorizing Patterns & Unravelling the Structural Landscape

The paper deconstructs and reconstructs diterpene structures to categorize patterns and model synthesis mechanisms, revealing core skeletons and predicting compound diversity.

Beyond blooms: A novel time series analysis framework predicts seasonal keystone species and sheds light on Arctic pelagic ecosystem stability

This paper develops a time series analysis framework to identify seasonal keystone species and assess Arctic pelagic ecosystem stability using microbial community data.

Microbial pathway thermodynamics: structural models unveil anabolic and catabolic processes

The paper presents strategies to split microbial metabolic equations into anabolic and catabolic components and evaluates their thermodynamic efficiency.

dismo: building and analysing discrete spatial ODE models

dismo is a Python package for creating and analyzing discrete spatial ODE models on various grid types.

What controls carbon sequestration in plants under which conditions?

The paper uses a mathematical model to study how external conditions affect control over carbon fixation in photosynthesis.

Network reconstruction and modelling made reproducible with moped

The paper introduces moped, a Python package for reproducible metabolic model construction, curation, and analysis, supporting both genome-based reconstruction and SBML import.

COBREXA.jl: constraint-based reconstruction and exascale analysis

COBREXA.jl is a Julia package for scalable constraint-based metabolic modeling, designed for high-performance computing environments and multi-organism community models.

Constructing and analysing dynamic models withn modelbasev1.0 - a software update

The paper updates modelbase, an open-source Python package for constructing and analysing dynamic models, enhancing its capabilities for model reuse, isotope labelling, and SBML compatibility.

Balancing energy supply during photosynthesis - a theoretical perspective

The paper develops a merged theoretical model to analyze how energy and redox supply in photosynthesis matches carbon fixation demand, showing the necessity of a stand-by mode for efficient carbon fixation.

Building mathematical models of biological systems with modelbase, a Python package for semi-automatic ODE assembly and construction of isotope-specific models

The paper introduces modelbase, a Python package for building and analyzing dynamic mathematical models of biological systems, with features for ODE assembly and isotope-specific modeling.

Emergent sub-population behavior uncovered with a community dynamic metabolic model of Escherichia coli diauxic growth

The paper models E. coli diauxic growth as an emergent result of sub-population dynamics rather than a uniform metabolic shift, using a dynamic metabolic framework.

Dynamical modelling of the heat shock response in Chlamydomonas reinhardtii

The paper develops a dynamical model of the heat shock response in Chlamydomonas reinhardtii to study adaptation to prolonged heat stress and temperature changes.

The intertwined metabolism of Medicago truncatula and its nitrogen fixing symbiont Sinorhizobium meliloti elucidated by genome-scale metabolic models.

The paper develops genome-scale metabolic models for Medicago truncatula and its symbiont Sinorhizobium meliloti to study their interlinked metabolism and the impact of oxygen availability on metabolic exchanges.

Modelling reactions catalysed by carbohydrate-active enzymes

This paper reviews theoretical approaches to modeling biochemical reactions involving carbohydrate-active enzymes and highlights challenges in describing polymer-reactant interactions.