Browsing NTNU Open by Author "Bar, Nadav"
Now showing items 1-20 of 27
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A Sensory-Motor Control Model of Animal Flight Explains Why Bats Fly Differently in Light Versus Dark
Bar, Nadav; Skogestad, Sigurd; Marçal, Jose M.; Ulanovsky, Nachum; Yovel, Yossi (Journal article; Peer reviewed, 2015)Animal flight requires fine motor control. However, it is unknown how flying animals rapidly transform noisy sensory information into adequate motor commands. Here we developed a sensorimotor control model that explains ... -
Analysis of temporal gene regulation of Listeria monocytogenes revealed distinct regulatory response modes after exposure to high pressure processing
Nikparvar, Bahareh; Andreevskaya, Margarita; Duru, Ilhan C.; Bucur, Florentina I.; Leontina, Grigore-Gurgu; Borda, Daniela; Nicolau, Anca I.; Riedel, Christian U.; Auvinen, Petri; Bar, Nadav (Peer reviewed; Journal article, 2021)Background The pathogen Listeria (L.) monocytogenes is known to survive heat, cold, high pressure, and other extreme conditions. Although the response of this pathogen to pH, osmotic, temperature, and oxidative stress has ... -
Bayesian Estimators for Bioprocess Monitoring Under Uncertainty
Tuveri, Andrea (Doctoral theses at NTNU;2023:128, Doctoral thesis, 2023)The simultaneous growing interest in the application of digital solutions and the use of biological organisms such as bacteria and yeasts for the production of chemicals, has increased the necessity to apply digital solutions ... -
The complete genome sequence of Listeria monocytogenes strain S2542 and expression of selected genes under high-pressure processing
Duru, Ilhan Cem; Bucur, Florentina Ionela; Andreevskaya, Margarita; Ylinen, Anne; Crauwels, Peter; Grigore-Gurgu, Leontina; Nikparvar, Bahareh; Rode, Tone Mari; Laine, Pia; Paulin, Lars; Løvdal, Trond; Riedel, Christian U.; Bar, Nadav; Borda, Daniela; Nicolau, Anca Ioana; Auvinen, Petri (Peer reviewed; Journal article, 2021)Objectives The study aims to generate the whole genome sequence of L. monocytogenes strain S2542 and to compare it to the genomes of strains RO15 and ScottA. In addition, we aimed to compare gene expression profiles of ... -
Constrained Fourier estimation of short-term time-series gene expression data reduces noise and improves clustering and gene regulatory network predictions
Bar, Nadav; Nikparvar, Bahareh; Doni Jayavelu, Naresh; Roessler, Fabienne Krystin (Peer reviewed; Journal article, 2022)Background Biological data suffers from noise that is inherent in the measurements. This is particularly true for time-series gene expression measurements. Nevertheless, in order to to explore cellular dynamics, scientists ... -
Core Decomposition Analysis of Weighted Biological Networks
Eidsaa, Marius (Doctoral thesis at NTNU;2016:162, Doctoral thesis, 2016)Summary of thesis: English version: In biology, advanced, high-throughput experimental methods are becoming faster, cheaper and more accessible. Effective network analysis tools applicable to a broad range of networks ... -
A Diffusion Model to Quantify Membrane Repair Process in Listeria Monocytogenes Exposed to High Pressure Processing based on Fluorescence Microscopy Data
Nikparvar, Bahareh; Subires, Alicia; Capellas, Marta; Hernandez-Herrero, Manuela; Crauwels, Peter; Riedel, Christian U.; Bar, Nadav (Peer reviewed; Journal article, 2021)The effects of environmental stresses on microorganisms have been well-studied, and cellular responses to stresses such as heat, cold, acids, and salts have been extensively discussed. Although high pressure processing ... -
Dynamic Co-Cultivation Process of Corynebacterium glutamicum Strains for the Fermentative Production of Riboflavin.
Perez-Garcia, Fernando; Burgardt, Arthur; Kallman, Dina; Wendisch, Volker F.; Bar, Nadav (Journal article, 2021)Residual streams from lignocellulosic processes contain sugar mixtures of glucose, xylose, and mannose. Here, the industrial workhorse Corynebacterium glutamicum was explored as a research platform for the rational utilization ... -
Dynamics of Regulatory Networks in Gastrin-Treated Adenocarcinoma Cells
Doni, Jayavelu Naresh; Bar, Nadav (Journal article; Peer reviewed, 2014)Understanding gene transcription regulatory networks is critical to deciphering the molecular mechanisms of different cellular states. Most studies focus on static transcriptional networks. In the current study, we used ... -
Genomic characterization of the most barotolerant Listeria monocytogenes RO15 strain compared to reference strains used to evaluate food high pressure processing
Duru, Ilhan Cem; Andreevskaya, Margarita; Laine, Pia; Rode, Tone Mari; Ylinen, Anne; Løvdal, Trond Karsten; Bar, Nadav; Crauwels, Peter; Riedel, Christian U.; Bucur, Florentina Ionela; Nicolau, Anca Ioana; Auvinen, Petri (Peer reviewed; Journal article, 2020)Background: High pressure processing (HPP; i.e. 100–600 MPa pressure depending on product) is a non-thermal preservation technique adopted by the food industry to decrease significantly foodborne pathogens, including ... -
High-pressure processing-induced transcriptome response during recovery of Listeria monocytogenes
Duru, IC; Bucur, FI; Andreevskaya, Margarita; Nikparvar, Bahareh; Ylinen, Anne; Grigore-Gurgu, L; Rode, Tone Mari; Crauwels, Peter; Laine, P; Paulin, L; Løvdal, Trond; Riedel, Christian U.; Bar, Nadav; Borda, Daniella; Nicolau, Anca Ioana; Auvinen, Petri (Peer reviewed; Journal article, 2021)Background High-pressure processing (HPP) is a commonly used technique in the food industry to inactivate pathogens, including L. monocytogenes. It has been shown that L. monocytogenes is able to recover from HPP injuries ... -
High-pressure processing-induced transcriptome response during recovery of Listeria monocytogenes
Duru, Ilhan Cem; Bucur, Florentina Ionela; Andreevskaya, Margarita; Nikparvar, Bahareh; Ylinen, Anne; Grigore-Gurgu, Leontina; Rode, Tone Mari; Crauwels, Peter; Laine, Pia; Paulin, Lars; Løvdal, Trond Karsten; Riedel, Christian U.; Bar, Nadav; Borda, Daniela; Nicolau, Anca Loana; Auvinen, Petri (Peer reviewed; Journal article, 2021)Background: High-pressure processing (HPP) is a commonly used technique in the food industry to inactivate pathogens, including L. monocytogenes. It has been shown that L. monocytogenes is able to recover from HPP injuries ... -
Integrative approach of modeling, optimization, control and experimental design in microbial biocatalytic processes: Applications to Corynebacterium glutamicum cell factory
Parada, Pedro Antonio Lira (Doctoral theses at NTNU;2021:289, Doctoral thesis, 2021)Global demand for food, pharmaceuticals and energy is constantly increasing, and the transition from a historically hydrocarbon-based economy to a green and renewable energy based-economy is accelerating due to the demands ... -
Intracellular pHluorin as Sensor for Easy Assessment of Bacteriocin-Induced Membrane-Damage in Listeria monocytogenes
Crauwels, Peter; Schäfer, Leonie; Weixler, Dominik; Bar, Nadav; Diep, Dzung B.; Riedel, Christian U.; Seibold, Gerd M. (Journal article; Peer reviewed, 2018)Bacteriocins are antimicrobial peptides naturally produced by many bacteria and were shown to be effective against various pathogens including Listeria monocytogenes. L. monocytogenes is a food-borne pathogen that frequently ... -
Iterative sub-network component analysis enables reconstruction of large scale genetic networks
Jayavelu, Naresh Doni; Aasgaard, Lasse Svenkerud; Bar, Nadav (Journal article; Peer reviewed, 2015)Background: Network component analysis (NCA) became a popular tool to understand complex regulatory networks. The method uses high-throughput gene expression data and a priori topology to reconstruct transcription factor ... -
Iterative sub-network component analysis enables reconstruction of large scale genetic networks
Doni Jayavelu, Naresh; Aasgaard, Lasse Svenkerud; Bar, Nadav (Peer reviewed; Journal article, 2015)Background:Network component analysis (NCA) became a popular tool to understand complex regulatorynetworks. The method uses high-throughput gene expression data and a priori topology to reconstruct transcriptionfactor ... -
Long-term prediction of fish growth under varying ambient temperature using a multiscale dynamic model
Bar, Nadav; Radde, Nicole (Journal article; Peer reviewed, 2009)Background: Feed composition has a large impact on the growth of animals, particularly marine fish. We have developed a quantitative dynamic model that can predict the growth and body composition of marine fish for a ... -
Metaheuristic Parameter Estimation - Using Parallel Computing and MPI
Jenssen, Erlend (Master thesis, 2018)Arguably, bats have the most sophisticated powered flight mechanism among animals. By mimicking their low-frequency dynamics, significant improvements can be made in energy efficiency, reliability and flexibility of ... -
Modelling and analysis of the response of Listeria monocytogenes to high pressure processing
Nikparvar, Bahareh (Doctoral theses at NTNU;2022:58, Doctoral thesis, 2022)The effects of environmental stresses on microorganisms have been well-studied, and cellular responses to stresses such as heat, cold, acids, and salts have been extensively discussed. Some previous works studied the membrane, ... -
Monitoring Techniques for C. glutamicum GABA Producers in Fed-Batch Fermentations
Golden, Kevin (Master thesis, 2020)Fermenteringsindustrien i dag produserer et bredt utvalg av produkter. Typiske produkter inkluderer brensel, industrielle kjemikalier, tilsetningsstoffer til mat og drikke, helseprodukter og mikrobielle enzymer for å nevne ...