Machine learning in marine ecology: an overview of techniques and applications

P Rubbens, S Brodie, T Cordier… - ICES Journal of …, 2023 - academic.oup.com
Abstract Machine learning covers a large set of algorithms that can be trained to identify
patterns in data. Thanks to the increase in the amount of data and computing power …

Population heterogeneity in microbial bioprocesses: origin, analysis, mechanisms, and future perspectives

AL Heins, D Weuster-Botz - Bioprocess and biosystems engineering, 2018 - Springer
Population heterogeneity is omnipresent in all bioprocesses even in homogenous
environments. Its origin, however, is only so well understood that potential strategies like bet …

Direct quantification of ecological drift at the population level in synthetic bacterial communities

S Fodelianakis, A Valenzuela-Cuevas… - The ISME …, 2021 - academic.oup.com
In community ecology, drift refers to random births and deaths in a population. In microbial
ecology, drift is estimated indirectly via community snapshots but in this way, it is almost …

Interactions between the gut microbiome and mucosal immunoglobulins A, M, and G in the developing infant gut

A Janzon, JK Goodrich, O Koren, TEDDY Study Group… - Msystems, 2019 - Am Soc Microbiol
Interactions between the gut microbiome and immunoglobulin A (IgA) in the gut during
infancy are important for future health. IgM and IgG are also present in the gut; however …

From biogas and hydrogen to microbial protein through co-cultivation of methane and hydrogen oxidizing bacteria

FM Kerckhof, M Sakarika, M Van Giel… - … in Bioengineering and …, 2021 - frontiersin.org
Increasing efforts are directed towards the development of sustainable alternative protein
sources among which microbial protein (MP) is one of the most promising. Especially when …

Dispersal homogenizes communities via immigration even at low rates in a simplified synthetic bacterial metacommunity

S Fodelianakis, A Lorz, A Valenzuela-Cuevas… - Nature …, 2019 - nature.com
Selection and dispersal are ecological processes that have contrasting roles in the
assembly of communities. Variable selection diversifies and strong dispersal homogenizes …

Measurement techniques to resolve and control population dynamics of mixed-culture processes

I Schlembach, A Grünberger, MA Rosenbaum… - Trends in …, 2021 - cell.com
Microbial mixed cultures are gaining increasing attention as biotechnological production
systems, since they offer a large but untapped potential for future bioprocesses. Effects of …

Fast pathogen identification using single-cell matrix-assisted laser desorption/ionization-aerosol time-of-flight mass spectrometry data and deep learning methods

C Papagiannopoulou, R Parchen, P Rubbens… - Analytical …, 2020 - ACS Publications
In diagnostics of infectious diseases, matrix-assisted laser desorption/ionization-time-of-
flight mass spectrometry (MALDI-TOF MS) can be applied for the identification of pathogenic …

Heterogeneity in pure microbial systems: experimental measurements and modeling

R González-Cabaleiro, AM Mitchell, W Smith… - Frontiers in …, 2017 - frontiersin.org
Cellular heterogeneity influences bioprocess performance in ways that until date are not
completely elucidated. In order to account for this phenomenon in the design and operation …

Rapid detection of microbiota cell type diversity using machine-learned classification of flow cytometry data

BD Özel Duygan, N Hadadi, AF Babu… - Communications …, 2020 - nature.com
The study of complex microbial communities typically entails high-throughput sequencing
and downstream bioinformatics analyses. Here we expand and accelerate microbiota …