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2023
1 Tuveri, Andrea; Martins Nakama, Caroline Satye; Assumpcao Matias, Jose Otavio; Holck, Haakon Eng; Jäschke, Johannes; Imsland, Lars Struen; Bar, Nadav S.
A regularized Moving Horizon Estimator for combined state and parameter estimation in a bioprocess experimental application. Computers and Chemical Engineering 2023 ;Volum 172. s. -
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2022
2 Bar, Nadav; Nikparvar, Bahareh; Doni Jayavelu, Naresh; Roessler, Fabienne Krystin.
Constrained Fourier estimation of short-term time-series gene expression data reduces noise and improves clustering and gene regulatory network predictions. BMC Bioinformatics 2022 ;Volum 23.(1) s. 1-21
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3 Lira Parada, Pedro Antonio; Sinner, Peter; Kohlstedt, Michael; Kager, Julian; Wittmann, Christoph; Herwig, Christoph; Bar, Nadav S.
Linking process and metabolic modelling for the estimation of carbon flux distribution in Corynebacterium glutamicum growth in spent sulfite liquor. IFAC-PapersOnLine 2022 ;Volum 55.(7) s. 228-233
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4 Ovchinnikov, Kirill; Oftedal, Thomas Førland; Reich, Sebastian J.; Bar, Nadav; Holo, Helge; Skaugen, Morten; Riedel, Christian U.; Diep, Dzung B..
Genome-assisted Identification, Purification, and Characterization of Bacteriocins. Bio-protocol 2022 ;Volum 12.(14)
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5 Tuveri, Andrea; Eng Holck, Haakon; Nakama, Caroline Satye; Matias, José O.A.; Jäschke, Johannes; Imsland, Lars Struen; Bar, Nadav S.
Bioprocess Monitoring: A Moving Horizon Estimation Experimental Application. IFAC-PapersOnLine 2022
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6 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..
Recombinant production of the lantibiotic nisin using Corynebacterium glutamicum in a two-step process. Microbial Cell Factories 2022 ;Volum 21.(11)
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7 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..
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 2022 ;Volum 21.(1) s. -
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2021
8 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.
High-pressure processing-induced transcriptome response during recovery of Listeria monocytogenes. BMC Genomics 2021 ;Volum 22.(1) s. 1-20
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9 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.
The complete genome sequence of Listeria monocytogenes strain S2542 and expression of selected genes under high-pressure processing. BMC Research Notes 2021 ;Volum 14.(1) s. 1-6
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10 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..
Establishing recombinant production of pediocin PA-1 in Corynebacterium glutamicum. Metabolic Engineering 2021 ;Volum 68. s. 34-45
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11 Lira Parada, Pedro Antonio; Pettersen, Even; Biegler, Lorenz T.; Bar, Nadav S.
Implications of dimensional analysis in bioreactor models: parameter estimation and identifiability.. Chemical Engineering Journal 2021 ;Volum 417. s. -
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12 Lira Parada, Pedro Antonio; Tuveri, Andrea; Seibold, Gerd M.; Bar, Nadav.
Comparison of noninvasive, in-situ and external monitoring of microbial growth in fed-batch cultivations in Corynebacterium glutamicum. Biochemical engineering journal 2021 ;Volum 170.(107989) s. -
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13 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.
Analysis of temporal gene regulation of Listeria monocytogenes revealed distinct regulatory response modes after exposure to high pressure processing. BMC Genomics 2021 ;Volum 22.(266) s. -
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14 Nikparvar, Bahareh; Subires, Alicia; Capellas, Marta; Hernandez-Herrero, Manuela; Crauwels, Peter; Riedel, Christian U.; Bar, Nadav.
A Diffusion Model to Quantify Membrane Repair Process in Listeria Monocytogenes Exposed to High Pressure Processing based on Fluorescence Microscopy Data. Frontiers in Microbiology 2021 ;Volum 12.
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15 Perez-Garcia, Fernando; Burgardt, Arthur; Kallman, Dina Riis; Wendisch, Volker F.; Bar, Nadav.
Dynamic Co-Cultivation Process of Corynebacterium glutamicum Strains for the Fermentative Production of Riboflavin.. Fermentation 2021 ;Volum 7.(1) s. -
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16 Roessler, Fabienne K.; Benedikter, Birke J.; Schmeck, Bernd; Bar, Nadav.
Novel computational analysis of large transcriptome datasets identifies sets of genes distinguishing chronic obstructive pulmonary disease from healthy lung samples. Scientific Reports 2021
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17 Tuveri, Andrea; Pérez-García, Fernando; Lira Parada, Pedro Antonio; Imsland, Lars; Bar, Nadav.
Sensor fusion based on Extended and Unscented Kalman Filter for bioprocess monitoring. Journal of Process Control 2021 ;Volum 106. s. 195-207
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2020
18 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.
Genomic characterization of the most barotolerant Listeria monocytogenes RO15 strain compared to reference strains used to evaluate food high pressure processing. BMC Genomics 2020 ;Volum 21. s. 1-14
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2019
19 Bar, Nadav.
Automatic control of bioreactor fermentation with Corynebacterium glutamicum using residual sugar streams. 9th International BIelefeld-CeBiTech research conference; 2019-09-23 - 2019-09-25
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20 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.
Personalized medicine for patients with COPD: where are we?. The International Journal of Chronic Obstructive Pulmonary Disease 2019 ;Volum 14. s. 1465-1484
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21 Lira Parada, Pedro Antonio; Pettersen, Even; Bar, Nadav.
Bioreactor Scaling Enhances Feedback Control Of Concentration, Rates, and Yields. IFAC-PapersOnLine 2019 ;Volum 52.(1) s. 237-242
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22 Lira Parada, Pedro Antonio; Pettersen, Even; Perez-Garcia, Fernando; Bar, Nadav S.
The development of a fed-batch Corynebacterium glutamicum fermentation model. IFAC-PapersOnLine 2019 ;Volum 52.(26) s. 231-237
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23 Nikparvar, Bahareh; Subires, Alicia; Capellas, Marta; Fernandez, Manuella; Bar, Nadav.
A Dynamic Model of Membrane Recovery Mechanisms in Bacteria following High Pressure Processing. Dynamics and Control of Process Systems, including Biosystems - 12th DYCOPS 2019; 2019-04-23 - 2019-04-26
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24 Nikparvar, Bahareh; Subires, Alicia; Capellas, Marta; Hernandez, Manuela; Bar, Nadav.
A Dynamic Model of Membrane Recovery Mechanisms in Bacteria following High Pressure Processing. IFAC-PapersOnLine 2019 ;Volum 52.(1) s. 243-250
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2018
25 Crauwels, Peter; Schäfer, Leonie; Weixler, Dominik; Bar, Nadav; Diep, Dzung B.; Riedel, Christian U.; Seibold, Gerd M..
Intracellular pHluorin as Sensor for Easy Assessment of Bacteriocin-Induced Membrane-Damage in Listeria monocytogenes. Frontiers in Microbiology 2018 ;Volum 9. s. -
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2017
26 Bar, Nadav.
The Iterative sub-network component analysis (ISNCA) relaxes network restrictions. Workshop on Data Analysis for Model Identification using Time Series; 2017-01-07 - 2017-01-07
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27 Jayavelu, Naresh; Bar, Nadav.
ISNCA: A new iterative approach for constrained matrix factorization methods. Journal of Process Control 2017 ;Volum 60. s. 24-33
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2016
28 Bar, Nadav; Jayavelu, Naresh.
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; 2016-10-09 - 2016-10-12
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29 Bar, Nadav; Jayavelu, Naresh.
New iterative approach (ISNCA) for constrained matrix factorization methods. IFAC-PapersOnLine 2016 ;Volum 49.(7) s. 472-477
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2015
30 Bar, Nadav.
Den mystiske flaggermusen. Researchers Night; 2015-12-08
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31 Bar, Nadav.
En dynamisk systembiologimodell forklarer forskjellen på flaggermusens flyvning i dagslys og mørket. Schrødingers katt, NRK [TV] 2015-05-19
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32 Bar, Nadav.
Slik flyr en flaggermus. Gemini [Fagblad] 2015-05-28
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33 Bar, Nadav; Skogestad, Sigurd; Marçal, Jose M.; Ulanovsky, Nachum; Yovel, Yossi.
A Sensory-Motor Control Model of Animal Flight Explains Why Bats Fly Differently in Light Versus Dark. PLoS Biology 2015 ;Volum 13.(1)
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34 Doni Jayavelu, Naresh; Aasgaard, Lasse Svenkerud; Bar, Nadav.
Iterative sub-network component analysis enables reconstruction of large scale genetic networks. BMC Bioinformatics 2015 ;Volum 16.(1)
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35 Doni Jayavelu, Naresh; Bar, Nadav.
Reconstruction of temporal activity of microRNAs from gene expression data in breast cancer cell line. BMC Genomics 2015 ;Volum 16.(1) s. 1077-
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36 Skancke, Jørgen; Bar, Nadav; Kuiper, Martin; Hsu, Lilian M.
Sequence-Dependent Promoter Escape Efficiency Is Strongly Influenced by Bias for the Pretranslocated State during Initial Transcription. Biochemistry 2015 ;Volum 54.(28) s. 4267-4275
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2014
37 Bar, Nadav.
Physiological and hormonal changes during prolonged starvation in fish. Canadian Journal of Fisheries and Aquatic Sciences 2014 ;Volum 71.(10) s. 1447-1458
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38 Doni, Jayavelu Naresh; Bar, Nadav.
Dynamics of Regulatory Networks in Gastrin-Treated Adenocarcinoma Cells. PLOS ONE 2014 ;Volum 9.(1) s. -
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39 Jayavelu, Naresh Doni; Bar, Nadav.
Metabolomic studies of human gastric cancer: Review. World Journal of Gastroenterology (WJG) 2014 ;Volum 20.(25) s. 8092-8101
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2013
40 Doni Jayavelu, Naresh; Bar, Nadav.
A Noise Removal Algorithm for Time Series Microarray Data. I: Progress in Artificial Intelligence. Springer 2013 ISBN 978-3-642-40668-3. s. 152-162
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2012
41 Doni Jayavelu, Naresh; Bar, Nadav.
Comparative study of EGF and HRG induced dynamic transcriptional networks in human subjects. ICSB 2012 - International Conference on Systems Biology; 2012-11-28
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42 Bar, Nadav; Volkoff, Helene.
Adaptation of the Physiological, Endocrine, and Digestive System Functions to Prolonged Food Deprivation in Fish. I: Comparative Physiology of Fasting, Starvation, and Food Limitation. Springer Publishing Company 2012 ISBN 978-3-642-29055-8. s. 69-90
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43 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.
Landscape of transcription in human cells. Nature 2012 ;Volum 489.(7414) s. 101-108
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2010
44 Bar, Nadav.
Aquaculture Nutrition research. Hebrew University, Rehovot; 2010-05-22 - 2010-05-23
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45 Bar, Nadav.
Dynamic Modelling of Fish Growth. HAKI; 2010-06-24 - 2010-06-25
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46 Bar, Nadav.
Introduction to System Biology. CSIC; 2010-01-21
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47 Bar, Nadav.
Modelling approach to aquaculture research. Guelph University; 2010-09-06 - 2010-09-12
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48 Bar, Nadav.
Multiscale dynamic model of fish growth. SIAMB; 2010-05-24 - 2010-05-25
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49 Bar, Nadav.
Prediction of body composition in Aquaculture. Seminar University of Beograd; 2010-07-06
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50 Radde, Nicole; Bar, Nadav; Banaji, Murad.
Graphical Methods for analysing feedback in biological networks - A survey. International Journal of Systems Science 2010 ;Volum 41.(1) s. 35-46
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