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  1. Employees

Språkvelger

Norsk

Nadav Bar

Nadav Bar

Professor
Department of Chemical Engineering
Faculty of Natural Sciences

nadi.bar@ntnu.no
+4773594124 +4746664743 Kjemi 4, 227, Gløshaugen, Sem Sælands vei 6
CyberGenome laboratory The Biosystems Lab website
About Research Publications Teaching Media

About

 

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. NEW! Coordinator of iCulture, a Horzon Europe project (7.8 mill EUR), will start 2023.
  2. Coordinator of iFermenter, a bio-based EU H2020 BBI-JU project, 5.6 mill Euro, 2018-2022.
  3. Coordinator of SafeFood, an EU project of 6 countries and 8 groups (about 2.5 mill euro, 2016-2019).
    1. 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 were applied in this project.
  4. NEW! BacPress (2023-2025) Innovation project (Norwegian Research Council) - explores and upscales the synargy between antimicrobials and High pressure processing. 
  5. Leader in ERA SysMed-COPD project, 5.1 mill NOK (2018-2022), Here we use machine learning to improve diagnosis and prognosis for COPD.
  6. 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

Competencies

  • Circular bioeconomy
  • Control engineering
  • Machine learning
  • Microbial bioprocesses
  • Modelling and simulations
  • programming

Research

Our laboratory (microbial feedback control, the MFC lab) is expert on modeling, simulations, and real-time feedback control of microbial bioprocesses. We design and program microbial models, from the simple monod-growth model to more complex bacterial processes. 

We use this models to design digital controllers, including design such as Proportional derivative Integral (PID) controllers in cascade and other designs, Optimal control models, such as the Model predictive control (MPC), implemented in CASADI and programmed in Matlab, and recently the Reinforcement Learning controllers, one of the three machine learning schemes.

Control of bioprocess includes adding inducers and inhibitors, antibiotics, different sugar mixtures (glucose, Arabinose, mannose, Xylose, etc.), bases and acids, antifoam, and other nutrients, all these to secure that the bioprocess will operate according to the specification of the designer. 

Every effective control needs a reliable feedback from the bioprocess, so we also design Digital Twins (DT), which is a software sensor that integrates all the sensors, probes and analytics in our laboratory to one supervised entity that can report the state of the bioprocess at any time and can be used by the controller to predict and apply control decisions. Idealy, the DT is far more reliable than the models, because it uses statistics and optimization to balance between the model and the noisy measurement signals.   

Because we use real-time experiments, we need several layers of software to communicate between Matlab, the control designer, the DT and the microbial environment (e.g. bioreactors). Matlab communicates with an OPC server, that sends data to Lucullus (Securecell), the bioprocess software that monitors the reactors and probes. We are therefore using cutting edge prototype equipment, including autosamplers, robots and state of the art probes and instrumentation to report measurement values back to the main software. 

OUR LAB is RECRUITING! we seek good students and PhD candidates from Eng. Cybernetics, process control, analytical chemistry and biotechnology. 

Publications

  • Chronological
  • By category
  • See all publications in Cristin

2023

  • Tuveri, Andrea; Nakama, Caroline Satye Martins; Matias, José O.A.; Eng Holck, Haakon; Jäschke, Johannes; Imsland, Lars Struen; Bar, Nadav S. (2023) A regularized Moving Horizon Estimator for combined state and parameter estimation in a bioprocess experimental application. Computers and Chemical Engineering. volum 172.
    Academic article

2022

  • 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. volum 23 (1).
    Academic article
  • Lira Parada, Pedro Antonio; Sinner, Peter; Kohlstedt, Michael; Kager, Julian; Wittmann, Christoph; Herwig, Christoph; Bar, Nadav S. (2022) Linking process and metabolic modelling for the estimation of carbon flux distribution in Corynebacterium glutamicum growth in spent sulfite liquor. IFAC-PapersOnLine. volum 55 (7).
    Academic article
  • 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. volum 12 (14).
    Academic article
  • Tuveri, Andrea; Eng Holck, Haakon; Nakama, Caroline Satye; Matias, José O.A.; Jäschke, Johannes; Imsland, Lars Struen; Bar, Nadav S. (2022) Bioprocess Monitoring: A Moving Horizon Estimation Experimental Application. IFAC-PapersOnLine.
    Short communication
  • 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. volum 21 (11).
    Academic article
  • 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. volum 21 (1).
    Errata

2021

  • 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. volum 22 (1).
    Academic article
  • 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. volum 14 (1).
    Academic article
  • 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. volum 68.
    Academic article
  • 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. volum 417.
    Academic article
  • 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. volum 170 (107989).
    Academic article
  • 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. volum 22 (266).
    Academic article
  • 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. volum 12.
    Academic article
  • 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. volum 7 (1).
    Academic article
  • 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.
    Academic article
  • 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. volum 106.
    Academic article

2020

  • 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. volum 21.
    Academic article

2019

  • 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. volum 14.
    Academic literature review
  • Lira Parada, Pedro Antonio; Pettersen, Even; Bar, Nadav. (2019) Bioreactor Scaling Enhances Feedback Control Of Concentration, Rates, and Yields. IFAC-PapersOnLine. volum 52 (1).
    Academic article
  • Lira Parada, Pedro Antonio; Pettersen, Even; Perez-Garcia, Fernando; Bar, Nadav S. (2019) The development of a fed-batch Corynebacterium glutamicum fermentation model. IFAC-PapersOnLine. volum 52 (26).
    Academic article
  • 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. volum 52 (1).
    Academic article

2018

  • 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. volum 9.
    Academic article

2017

  • Jayavelu, Naresh; Bar, Nadav. (2017) ISNCA: A new iterative approach for constrained matrix factorization methods. Journal of Process Control. volum 60.
    Academic article

2016

  • Bar, Nadav; Jayavelu, Naresh. (2016) New iterative approach (ISNCA) for constrained matrix factorization methods. IFAC-PapersOnLine. volum 49 (7).
    Academic article

2015

  • 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. volum 13 (1).
    Academic article
  • Doni Jayavelu, Naresh; Aasgaard, Lasse Svenkerud; Bar, Nadav. (2015) Iterative sub-network component analysis enables reconstruction of large scale genetic networks. BMC Bioinformatics. volum 16 (1).
    Academic article
  • Doni Jayavelu, Naresh; Bar, Nadav. (2015) Reconstruction of temporal activity of microRNAs from gene expression data in breast cancer cell line. BMC Genomics. volum 16 (1).
    Academic article
  • 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. volum 54 (28).
    Academic article

2014

  • Bar, Nadav. (2014) Physiological and hormonal changes during prolonged starvation in fish. Canadian Journal of Fisheries and Aquatic Sciences. volum 71 (10).
    Academic article
  • Doni, Jayavelu Naresh; Bar, Nadav. (2014) Dynamics of Regulatory Networks in Gastrin-Treated Adenocarcinoma Cells. PLOS ONE. volum 9 (1).
    Academic article
  • Jayavelu, Naresh Doni; Bar, Nadav. (2014) Metabolomic studies of human gastric cancer: Review. World Journal of Gastroenterology (WJG). volum 20 (25).
    Academic literature review

2013

  • Doni Jayavelu, Naresh; Bar, Nadav. (2013) A Noise Removal Algorithm for Time Series Microarray Data. Progress in Artificial Intelligence.
    Academic chapter/article/Conference paper

2012

  • 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.
    Academic chapter/article/Conference paper
  • 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. (2012) Landscape of transcription in human cells. Nature. volum 489 (7414).
    Academic article

2010

  • Radde, Nicole; Bar, Nadav; Banaji, Murad. (2010) Graphical Methods for analysing feedback in biological networks - A survey. International Journal of Systems Science. volum 41 (1).
    Academic article

2009

  • Bar, Nadav. (2009) Analysis of protein synthesis dynamic model in eukaryotic cells: Input control. Mathematical Biosciences. volum 219 (2).
    Academic article
  • Bar, Nadav; Radde, Nicole. (2009) Long-term prediction of fish growth under varying ambient temperature using a multiscale dynamic model. BMC Systems Biology. volum 3.
    Academic article

2008

  • 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.
    Academic article

2007

  • Bar, Nadav; Morris, David R.. (2007) Dynamic model of the process of protein synthesis in eukaryotic cells. Bulletin of Mathematical Biology. volum 69.
    Academic article
  • 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. volum 64 (12).
    Academic article

2005

  • Imsland, Lars Struen; Bar, Nadav; Foss, Bjarne Anton. (2005) More Efficient Predictive Control. Automatica. volum 41 (8).
    Academic article

Journal publications

  • Tuveri, Andrea; Nakama, Caroline Satye Martins; Matias, José O.A.; Eng Holck, Haakon; Jäschke, Johannes; Imsland, Lars Struen; Bar, Nadav S. (2023) A regularized Moving Horizon Estimator for combined state and parameter estimation in a bioprocess experimental application. Computers and Chemical Engineering. volum 172.
    Academic article
  • 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. volum 23 (1).
    Academic article
  • Lira Parada, Pedro Antonio; Sinner, Peter; Kohlstedt, Michael; Kager, Julian; Wittmann, Christoph; Herwig, Christoph; Bar, Nadav S. (2022) Linking process and metabolic modelling for the estimation of carbon flux distribution in Corynebacterium glutamicum growth in spent sulfite liquor. IFAC-PapersOnLine. volum 55 (7).
    Academic article
  • 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. volum 12 (14).
    Academic article
  • Tuveri, Andrea; Eng Holck, Haakon; Nakama, Caroline Satye; Matias, José O.A.; Jäschke, Johannes; Imsland, Lars Struen; Bar, Nadav S. (2022) Bioprocess Monitoring: A Moving Horizon Estimation Experimental Application. IFAC-PapersOnLine.
    Short communication
  • 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. volum 21 (11).
    Academic article
  • 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. volum 21 (1).
    Errata
  • 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. volum 22 (1).
    Academic article
  • 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. volum 14 (1).
    Academic article
  • 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. volum 68.
    Academic article
  • 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. volum 417.
    Academic article
  • 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. volum 170 (107989).
    Academic article
  • 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. volum 22 (266).
    Academic article
  • 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. volum 12.
    Academic article
  • 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. volum 7 (1).
    Academic article
  • 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.
    Academic article
  • 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. volum 106.
    Academic article
  • 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. volum 21.
    Academic article
  • 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. volum 14.
    Academic literature review
  • Lira Parada, Pedro Antonio; Pettersen, Even; Bar, Nadav. (2019) Bioreactor Scaling Enhances Feedback Control Of Concentration, Rates, and Yields. IFAC-PapersOnLine. volum 52 (1).
    Academic article
  • Lira Parada, Pedro Antonio; Pettersen, Even; Perez-Garcia, Fernando; Bar, Nadav S. (2019) The development of a fed-batch Corynebacterium glutamicum fermentation model. IFAC-PapersOnLine. volum 52 (26).
    Academic article
  • 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. volum 52 (1).
    Academic article
  • 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. volum 9.
    Academic article
  • Jayavelu, Naresh; Bar, Nadav. (2017) ISNCA: A new iterative approach for constrained matrix factorization methods. Journal of Process Control. volum 60.
    Academic article
  • Bar, Nadav; Jayavelu, Naresh. (2016) New iterative approach (ISNCA) for constrained matrix factorization methods. IFAC-PapersOnLine. volum 49 (7).
    Academic article
  • 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. volum 13 (1).
    Academic article
  • Doni Jayavelu, Naresh; Aasgaard, Lasse Svenkerud; Bar, Nadav. (2015) Iterative sub-network component analysis enables reconstruction of large scale genetic networks. BMC Bioinformatics. volum 16 (1).
    Academic article
  • Doni Jayavelu, Naresh; Bar, Nadav. (2015) Reconstruction of temporal activity of microRNAs from gene expression data in breast cancer cell line. BMC Genomics. volum 16 (1).
    Academic article
  • 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. volum 54 (28).
    Academic article
  • Bar, Nadav. (2014) Physiological and hormonal changes during prolonged starvation in fish. Canadian Journal of Fisheries and Aquatic Sciences. volum 71 (10).
    Academic article
  • Doni, Jayavelu Naresh; Bar, Nadav. (2014) Dynamics of Regulatory Networks in Gastrin-Treated Adenocarcinoma Cells. PLOS ONE. volum 9 (1).
    Academic article
  • Jayavelu, Naresh Doni; Bar, Nadav. (2014) Metabolomic studies of human gastric cancer: Review. World Journal of Gastroenterology (WJG). volum 20 (25).
    Academic literature review
  • 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. (2012) Landscape of transcription in human cells. Nature. volum 489 (7414).
    Academic article
  • Radde, Nicole; Bar, Nadav; Banaji, Murad. (2010) Graphical Methods for analysing feedback in biological networks - A survey. International Journal of Systems Science. volum 41 (1).
    Academic article
  • Bar, Nadav. (2009) Analysis of protein synthesis dynamic model in eukaryotic cells: Input control. Mathematical Biosciences. volum 219 (2).
    Academic article
  • Bar, Nadav; Radde, Nicole. (2009) Long-term prediction of fish growth under varying ambient temperature using a multiscale dynamic model. BMC Systems Biology. volum 3.
    Academic article
  • 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.
    Academic article
  • Bar, Nadav; Morris, David R.. (2007) Dynamic model of the process of protein synthesis in eukaryotic cells. Bulletin of Mathematical Biology. volum 69.
    Academic article
  • 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. volum 64 (12).
    Academic article
  • Imsland, Lars Struen; Bar, Nadav; Foss, Bjarne Anton. (2005) More Efficient Predictive Control. Automatica. volum 41 (8).
    Academic article

Part of book/report

  • Doni Jayavelu, Naresh; Bar, Nadav. (2013) A Noise Removal Algorithm for Time Series Microarray Data. Progress in Artificial Intelligence.
    Academic chapter/article/Conference paper
  • 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.
    Academic chapter/article/Conference paper

Teaching

Courses

  • TKP4195 - Bio-Systems Engineering
  • TKP4580 - Chemical Engineering, Specialization Project
  • TKP4581 - Chemical Engineering, Specialization Project
  • KP8130 - Systembiology, Modelling and Analysis
  • TKP4555 - Process Systems Engineering, Specialization Course

Media

2019

  • Academic lecture
    Bar, Nadav. (2019) Automatic control of bioreactor fermentation with Corynebacterium glutamicum using residual sugar streams. 9th International BIelefeld-CeBiTech research conference . Center for Interdisciplinary Research (ZiF), Bielefeld Unive; Center for Interdisciplinary Research (ZiF), Bielefeld. 2019-09-23 - 2019-09-25.
  • Academic lecture
    Nikparvar, Bahareh; Subires, Alicia; Capellas, Marta; Fernandez, Manuella; Bar, Nadav. (2019) A Dynamic Model of Membrane Recovery Mechanisms in Bacteria following High Pressure Processing. Dynamics and Control of Process Systems, including Biosystems - 12th DYCOPS 2019 . IFAC; Florianópolis. 2019-04-23 - 2019-04-26.

2017

  • Academic lecture
    Bar, Nadav. (2017) The Iterative sub-network component analysis (ISNCA) relaxes network restrictions. Workshop on Data Analysis for Model Identification using Time Series . Dept. of Chemical Engineering, IIT Madras,; Chennai. 2017-01-07 - 2017-01-07.

2016

  • Lecture
    Bar, Nadav; Jayavelu, Naresh. (2016) Dynamic Network Analysis Combined with Protein-Protein Interaction Knowledge Identified Short Feedback and Feed-Forward Circuits in Genetic Networks. 6th IFAC Conference on Foundations of Systems Biology in Engineering . IFAC; Magdeburg. 2016-10-09 - 2016-10-12.

2015

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

2012

  • Academic lecture
    Doni Jayavelu, Naresh; Bar, Nadav. (2012) Comparative study of EGF and HRG induced dynamic transcriptional networks in human subjects. ICSB 2012 - International Conference on Systems Biology ; Paris. 2012-11-28.

2010

  • Academic lecture
    Bar, Nadav. (2010) Aquaculture Nutrition research. Hebrew University, Rehovot ; Rehovot. 2010-05-22 - 2010-05-23.
  • Academic lecture
    Bar, Nadav. (2010) Dynamic Modelling of Fish Growth. HAKI ; 2010-06-24 - 2010-06-25.
  • Academic lecture
    Bar, Nadav. (2010) Introduction to System Biology. CSIC ; Vigo. 2010-01-21.
  • Academic lecture
    Bar, Nadav. (2010) Modelling approach to aquaculture research. Guelph University ; Guelph, Ontario. 2010-09-06 - 2010-09-12.
  • Academic lecture
    Bar, Nadav. (2010) Multiscale dynamic model of fish growth. SIAMB ; Erlat. 2010-05-24 - 2010-05-25.
  • Academic lecture
    Bar, Nadav. (2010) Prediction of body composition in Aquaculture. Seminar University of Beograd ; Beograd. 2010-07-06.
  • Academic lecture
    Skancke, Jørgen; Lale, Rahmi; Bar, Nadav. (2010) Free Energy Caculations Give Insight Into The Process of Promoter Escape. 11th International Conference on Systems Biology ; Edinburgh, Scotland. 2010-10-11 - 2010-10-14.
  • Poster
    Tripathi, Sushil; Thommesen, Liv; Skjøndal-Bar, Nadav; Almaas, Eivind; Kuiper, Martin; Lægreid, Astrid. (2010) Modelling the gastrin signalling pathways. 11th International Conference on Systems Biology ; Edinburgh. 2010-10-10 - 2010-10-16.
  • Poster
    Tripathi, Sushil; Thommesen, Liv; Skjøndal-Bar, Nadav; Almaas, Eivind; Kuiper, Martin; Lægreid, Astrid. (2010) Modelling the gastrin signalling pathways. 22nd International Conference of the Society for Medical Innovation and Technology ; Trondheim. 2010-09-02 - 2010-09-04.

2009

  • Academic lecture
    Radde, Nicole; Bar, Nadav; Tresch, Achim. (2009) A COMPARISON OF LIKELIHOODS FOR DYNAMIC STOCHASTIC MODELS OF BIOLOGICAL NETWORKS. Sixth International Workshop on Computational Systems Biology, WCSB 2009 ; Århus. 2009-06-10 - 2009-06-12.

2008

  • Academic lecture
    Bar, Nadav. (2008) Dynamic model of Fish Growth. Systems biology meeting Stuttgart . Center systems Biology Stuttgart; Stuttgart. 2008-11-07 - 2008-11-09.
  • Academic lecture
    Bar, Nadav. (2008) Feedback Control in the Translational Process in Eukaryotic cells. Systems biology meeting KTH . KTH; Stockholm. 2008-10-16 - 2008-10-17.
  • Academic lecture
    Bar, Nadav. (2008) Modeling, Analysis and Control of the Translational Initiation Regulation Process. 1. International Workshop on Systems Biology . Center systems Biology Stuttgart; Stuttgart. 2008-06-23 - 2008-06-24.
  • Academic lecture
    Bar, Nadav. (2008) Modeling, Analysis and Control of the Translational Initiation Regulation Process. Kolloquium Technische Kybernetik . Institute for Systems Theory and Automatic Control; Stuttgart. 2008-06-16 - 2008-06-17.
  • Academic lecture
    Bar, Nadav. (2008) Modeling, Analysis and Control of the Translational Initiation Regulation Process in Eukaryota. International Conference on Systems Biology ; Gothenborg. 2008-08-22 - 2008-08-29.
  • Academic lecture
    Bar, Nadav. (2008) Modeling, Analysis and Control of the Translational Initiation Regulation Process in Eukaryotic Cells. Winter 2008 Systems Biology Seminar Series . The Center for Control, Dynamical Systems, and Computation; University of California at Santa Barbara. 2008-02-29 - 2008-03-01.
  • Academic lecture
    Bar, Nadav. (2008) Modeling, Analysis and Control of the Translational Initiation Regulation Process in Eukaryotic Cells. International Workshop on Systems Biology . Hamilton Institutte; Maynooth. 2008-08-18 - 2008-08-21.

2007

  • Academic lecture
    Bar, Nadav. (2007) Modeling of nutrient partitioning in fish production – A tool for identification of bottle necks. Standardizing Research Approaches in the Evaluation of Plant Feedstuffs in Carnivorous Fish Diets . Plant Products in Aquafeed (PPA); San Antonio, TX. 2007-02-26 - 2007-03-03.

2006

  • Academic lecture
    Bar, Nadav Skjøndal; Sigholt, Trygve; Krogdahl, Åshild. (2006) A Dynamic model of Nutrient pathways, Growth and Body Composition in Fish. XII International Symposium on Fish Nutrition & Feeding ; Biarritz. 2006-05-28 - 2006-06-01.
  • Academic lecture
    Bar, Nadav Skjøndal; Morris, David R.. (2006) Dynamic model of the process of Protein synthesis and Initiation control. Translation control . Cold Spring Harbour Laboratory; NY. 2006-09-06 - 2006-09-10.
  • Academic lecture
    Bar, Nadav Skjøndal; Sigholt, Trygve. (2006) Dynamic model for fish growth. Norwegian conference for fish nutrition ; 2006-03-28 - 2006-03-29.

2004

  • Academic lecture
    Imsland, Lars Struen; Bar, Nadav; Foss, Bjarne Anton. (2004) A new algorithm for efficient MPC and a comparison with other schemes. ACC 2004 ; Boston. 2004-06-30 - 2004-07-02.
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