Nadav Bar

Professor

Department of Chemical Engineering Faculty of Natural Sciences

nadi.bar@ntnu.no +47 73594124 +47 46664743

Kjemi 4, 227, Gløshaugen, Sem Sælands vei 6

nadi.bar@ntnu.no

Our mission is to control the microworld.

Combining biotechnology and control theory, we explore feedback control of microorganisms, particularly of bacteria. Our vision is to gain control over microbiological processes and to harness the power of microorganisms for research and industrial purposes.

Awards:

1. Coordinator of iFermenter, a bio-based EU H2020 BBI-JU project, 5.6 mill Euro, 2018-2022.

2. Coordinator of SafeFood, an EU project of 6 countries and 8 groups (about 2.5 mill euro, 2016-2019).

The main aim of the project is to turn food products (ready-to-eat products based on meat, fish and vegetables) safer and more durable, by reducing or inhibit the ability of Listeria monocytogenes to recover from high pressure processing (HPP). This can extend the shelf-life of food, increasing its resistance to food-related bacteria (by rendering the food “non-hospitable” for this type of bacteria) and decrease the amount of food waste from processing and throughout the food chain. Cutting edge biotechnological methods will be applied in this project.

3. Leader in ERA SysMed-COPD project, 5.1 mill NOK (2018-2021), Here we use machine learning to improve diagnosis and prognosis for COPD.

4. BacPress: :Qualification Project Norwegian research Council 2021.

5. Head of the BioSystems feedback control real-time fermentation laboratory (MFCL).

RESEARCH AREA:

Feedback control of bacteria (e.g. L. monocytogenes, C. glutamicum)
Transcription and translation regulation - modelling, analysis and control
Sensory motor control in animals (neuroscience)
Bioinformatics tools: Gene network discovery (advance analysis tools)
cellular regulation and signaling (modelling)

Current PhD students:

Andrea Tuveri
Fabienne Roessler
Alex Wong

Former and Graduated students: (PhD level)

Naresh D. Jayavelu, PhD
Jørgen Skancke, PhD
Haakon Holck
Pedro Lira
Bahareh Nikvarpar

Graduated Students (M.Sc level)

14 students

Courses

Scientific, academic and artistic work

Displaying a selection of activities. See all publications in the database

Journal publications

Bar, Nadav; Nikparvar, Bahareh; Doni Jayavelu, Naresh; Roessler, Fabienne Krystin. (2022) Constrained Fourier estimation of short-term time-series gene expression data reduces noise and improves clustering and gene regulatory network predictions. BMC Bioinformatics. vol. 23 (1).
Ovchinnikov, Kirill; Oftedal, Thomas Førland; Reich, Sebastian J.; Bar, Nadav; Holo, Helge; Skaugen, Morten; Riedel, Christian U.; Diep, Dzung B.. (2022) Genome-assisted Identification, Purification, and Characterization of Bacteriocins. Bio-protocol.
Weixler, D.; Berghoff, M; Ovchinnikov, Kirill; Reich, Sebastian; Goldbeck, Oliver; Seibold, Gerd M.; Wittmann, Christoph; Bar, Nadav S; Eikmanns, Bernhard J; Diep, Dzung B.; Riedel, Christian U.. (2022) Recombinant production of the lantibiotic nisin using Corynebacterium glutamicum in a two-step process. Microbial Cell Factories. vol. 21 (11).
Weixler, Dominik; Berghoff, Max; Ovchinnikov, Kirill; Reich, Sebastian; Goldbeck, Oliver; Seibold, Gerd M.; Wittmann, Christoph; Bar, Nadav S; Eikmanns, Bernhard J.; Diep, Dzung B.; Riedel, Christian U.. (2022) Correction to: Recombinant production of the lantibiotic nisin using Corynebacterium glutamicum in a two‑step process (Microbial Cell Factories, (2022), 21, 1, (11), 10.1186/s12934-022-01739-y). Microbial Cell Factories. vol. 21 (1).
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; Riedel, Christian U.; Bar, Nadav; Borda, Daniela; Nicolau, Anca Ioana; Auvinen, Petri. (2021) High-pressure processing-induced transcriptome response during recovery of Listeria monocytogenes. BMC Genomics. vol. 22 (1).
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. (2021) The complete genome sequence of Listeria monocytogenes strain S2542 and expression of selected genes under high-pressure processing. BMC Research Notes. vol. 14 (1).
Goldbeck, Oliver; Desef, Dominique N; Ovchinnikov, Kirill; Perez-Garcia, Fernando; Christmann, Jens; Sinner, Peter; Crauwels, Peter; Weixler, Dominik; Cao, Peng; Becker, Judith; Kohlstedt, Michael; Kager, Julian; Eikmanns, Bernhard J; Seibold, Gerd M.; Herwig, Christoph; Wittmann, Christoph; Bar, Nadav; Diep, Dzung B.; Riedel, Christian U.. (2021) Establishing recombinant production of pediocin PA-1 in Corynebacterium glutamicum. Metabolic Engineering. vol. 68.
Lira Parada, Pedro Antonio; Pettersen, Even; Biegler, Lorenz T.; Bar, Nadav S. (2021) Implications of dimensional analysis in bioreactor models: parameter estimation and identifiability. Chemical Engineering Journal. vol. 417.
Lira Parada, Pedro Antonio; Tuveri, Andrea; Seibold, Gerd M.; Bar, Nadav. (2021) Comparison of noninvasive, in-situ and external monitoring of microbial growth in fed-batch cultivations in Corynebacterium glutamicum. Biochemical engineering journal. vol. 170 (107989).
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. (2021) Analysis of temporal gene regulation of Listeria monocytogenes revealed distinct regulatory response modes after exposure to high pressure processing. BMC Genomics. vol. 22 (266).
Nikparvar, Bahareh; Subires, Alicia; Capellas, Marta; Hernandez-Herrero, Manuela; Crauwels, Peter; Riedel, Christian U.; Bar, Nadav. (2021) A Diffusion Model to Quantify Membrane Repair Process in Listeria Monocytogenes Exposed to High Pressure Processing based on Fluorescence Microscopy Data. Frontiers in Microbiology. vol. 12.
Perez-Garcia, Fernando; Burgardt, Arthur; Kallman, Dina Riis; Wendisch, Volker F.; Bar, Nadav. (2021) Dynamic Co-Cultivation Process of Corynebacterium glutamicum Strains for the Fermentative Production of Riboflavin. Fermentation. vol. 7 (1).
Roessler, Fabienne K.; Benedikter, Birke J.; Schmeck, Bernd; Bar, Nadav. (2021) Novel computational analysis of large transcriptome datasets identifies sets of genes distinguishing chronic obstructive pulmonary disease from healthy lung samples. Scientific Reports.
Tuveri, Andrea; Pérez-García, Fernando; Lira Parada, Pedro Antonio; Imsland, Lars; Bar, Nadav. (2021) Sensor fusion based on Extended and Unscented Kalman Filter for bioprocess monitoring. Journal of Process Control. vol. 106.
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. (2020) Genomic characterization of the most barotolerant Listeria monocytogenes RO15 strain compared to reference strains used to evaluate food high pressure processing. BMC Genomics. vol. 21.
Franssen, Frits M. E.; Alter, Peter; Bar, Nadav; Benedikter, Birke J.; Iurato, Stella; Maier, Dieter; Maxheim, Michael; Rössler, Fabienne; Spruit, Martijn A.; Vogelmeier, Claus F.; Wouters, Emiel F.M.; Schmeck, Bernd. (2019) Personalized medicine for patients with COPD: where are we?. The International Journal of Chronic Obstructive Pulmonary Disease. vol. 14.
Lira Parada, Pedro Antonio; Pettersen, Even; Bar, Nadav. (2019) Bioreactor Scaling Enhances Feedback Control Of Concentration, Rates, and Yields. IFAC-PapersOnLine. vol. 52 (1).
Nikparvar, Bahareh; Subires, Alicia; Capellas, Marta; Hernandez, Manuela; Bar, Nadav. (2019) A Dynamic Model of Membrane Recovery Mechanisms in Bacteria following High Pressure Processing. IFAC-PapersOnLine. vol. 52 (1).
Crauwels, Peter; Schäfer, Leonie; Weixler, Dominik; Bar, Nadav; Diep, Dzung B.; Riedel, Christian U.; Seibold, Gerd M.. (2018) Intracellular pHluorin as Sensor for Easy Assessment of Bacteriocin-Induced Membrane-Damage in Listeria monocytogenes. Frontiers in Microbiology. vol. 9.
Jayavelu, Naresh; Bar, Nadav. (2017) ISNCA: A new iterative approach for constrained matrix factorization methods. Journal of Process Control. vol. 60.
Bar, Nadav; Jayavelu, Naresh. (2016) New iterative approach (ISNCA) for constrained matrix factorization methods. IFAC-PapersOnLine. vol. 49 (7).
Bar, Nadav; Skogestad, Sigurd; Marçal, Jose M.; Ulanovsky, Nachum; Yovel, Yossi. (2015) A Sensory-Motor Control Model of Animal Flight Explains Why Bats Fly Differently in Light Versus Dark. PLoS Biology. vol. 13 (1).
Doni Jayavelu, Naresh; Aasgaard, Lasse Svenkerud; Bar, Nadav. (2015) Iterative sub-network component analysis enables reconstruction of large scale genetic networks. BMC Bioinformatics. vol. 16 (1).
Doni Jayavelu, Naresh; Bar, Nadav. (2015) Reconstruction of temporal activity of microRNAs from gene expression data in breast cancer cell line. BMC Genomics. vol. 16 (1).
Skancke, Jørgen; Bar, Nadav; Kuiper, Martin; Hsu, Lilian M. (2015) Sequence-Dependent Promoter Escape Efficiency Is Strongly Influenced by Bias for the Pretranslocated State during Initial Transcription. Biochemistry. vol. 54 (28).
Bar, Nadav. (2014) Physiological and hormonal changes during prolonged starvation in fish. Canadian Journal of Fisheries and Aquatic Sciences. vol. 71 (10).
Doni, Jayavelu Naresh; Bar, Nadav. (2014) Dynamics of Regulatory Networks in Gastrin-Treated Adenocarcinoma Cells. PLOS ONE. vol. 9 (1).
Jayavelu, Naresh Doni; Bar, Nadav. (2014) Metabolomic studies of human gastric cancer: Review. World Journal of Gastroenterology (WJG). vol. 20 (25).
Djebali, S; Davis, CA; Merkel, Angelika; Dobin, A; Lassmann, T; Mortazavi, A; Tanzer, A; Lagarde, J; Lin, Wei; Schlesinger, F; Xue, CH; Marinov, GK; Khatun, Jainab; Williams, Brian A; Zaleski, C; Rozowsky, J; Röder, M; Kokocinski, F; Abdelhamid, RF; Alioto, T; Antoshechkin, I; Baer, M.; Bar, Nadav; Batut, P; Bell, K; Bell, I; Chakrabortty, S; Chen, X; Chrast, J; Curado, J; Derrien, T; Drenkow, J; Dumais, E; Dumais, J; Duttagupta, R; Falconnet, E; Fastuca, M; Fejes-Toth, K; Ferreira, P.; Foissac, S; Fullwood, MJ; Gao, H; Gonzalez, D; Gordon, A; Gunawardena, H; Howald, C; Jha, Sonali; Johnson, R.; Kapranov, P; King, B; Kingswood, C; Luo, OJ; Park, Eddie; Persaud, K; Preall, JB; Ribeca, P; Risk, B; Robyr, D; Sammeth, M; Schaffer, L; See, LH; Shahab, A; Skancke, Jørgen; Suzuki, AM; Takahashi, H; Tilgner, H; Trout, D; Walters, N; Wang, Huaien; Wrobel, J; Yu, YB; Ruan, XA; Hayashizaki, Yoshihide; Harrow, J; Gerstein, M; Hubbard, Tim; Reymond, A; Antonarakis, SE; Hannon, Gregory; Giddings, MC; Ruan, YJ; Wold, B; Carninci, Piero; Guigo, R; Gingeras, TR. (2012) Landscape of transcription in human cells. Nature. vol. 489 (7414).
Radde, Nicole; Bar, Nadav; Banaji, Murad. (2010) Graphical Methods for analysing feedback in biological networks - A survey. International Journal of Systems Science. vol. 41 (1).
Bar, Nadav. (2009) Analysis of protein synthesis dynamic model in eukaryotic cells: Input control. Mathematical Biosciences. vol. 219 (2).
Bar, Nadav; Radde, Nicole. (2009) Long-term prediction of fish growth under varying ambient temperature using a multiscale dynamic model. BMC Systems Biology. vol. 3.
Bar, Nadav; Lale, Rahmi. (2008) Modeling and Control of the Protein Synthesis process in Eukaryotic cells. Proceedings of the IEEE Conference on Decision & Control, including the Symposium on Adaptive Processes.
Bar, Nadav; Morris, David R.. (2007) Dynamic model of the process of protein synthesis in eukaryotic cells. Bulletin of Mathematical Biology. vol. 69.
Bar, Nadav; Sigholt, Trygve; Shearer, Karl; Krogdahl, Åshild. (2007) A dynamic model of nutrient Pathways, growth and body composition in fish. Canadian Journal of Fisheries and Aquatic Sciences. vol. 64 (12).
Imsland, Lars Struen; Bar, Nadav; Foss, Bjarne Anton. (2005) More Efficient Predictive Control. Automatica. vol. 41 (8).

Part of book/report

Doni Jayavelu, Naresh; Bar, Nadav. (2013) A Noise Removal Algorithm for Time Series Microarray Data. Progress in Artificial Intelligence.
Bar, Nadav; Volkoff, Helene. (2012) Adaptation of the Physiological, Endocrine, and Digestive System Functions to Prolonged Food Deprivation in Fish. Comparative Physiology of Fasting, Starvation, and Food Limitation.

Others

Bar, Nadav. (2015) Den mystiske flaggermusen. Researchers Night . Samarbeidsforum; NTNU. 2015-12-08.
Bar, Nadav. (2015) En dynamisk systembiologimodell forklarer forskjellen på flaggermusens flyvning i dagslys og mørket. Schrødingers katt, NRK [TV]. 2015-05-19.
Bar, Nadav. (2015) Slik flyr en flaggermus. Gemini [Fagblad]. 2015-05-28.

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