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Volume 49; Issue 26
Main
IFAC-PapersOnLine
Volume 49; Issue 26
IFAC-PapersOnLine
Volume 49; Issue 26
1
Finding targets for genome reduction in Streptomyces lividans TK24 using flux balance analysis
Daniels, Wouter
,
Bouvin, Jeroen
,
Busche, Tobias
,
Kalinowski, Jörn
,
Bernaerts, Kristel
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 1.26 MB
Your tags:
english, 2016
2
Metabolic modeling of C. sorokiniana diauxic heterotrophic growth
Baroukh, Caroline
,
Bernard, Olivier
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 1.08 MB
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english, 2016
3
Integrating classifiers across datasets improves consistency of biomarker predictions for sepsis
Saraiva, João Pedro
,
Oswald, Marcus
,
Biering, Antje
,
Assmann, Cora
,
Klassert, Tilman
,
Blaess, Markus
,
Czakai, Kristin
,
Claus, Ralf
,
Löffler, Jürgen
,
Slevogt, Hortense
,
König, Rainer
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 623 KB
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english, 2016
4
Mathematical Modelling of Anaerobic Digestion with Hydrogen and Methane Production * *This research has been partially supported by the Bulgarian Science Fund under contract No. DFNI–E02/13. The work of the second author has been partially supported by Sofia University “St Kl. Ohridski” under contract No. 58/06.04.2016.
Borisov, Milen
,
Dimitrova, Neli
,
Simeonov, Ivan
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 1.07 MB
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english, 2016
5
Dynamic metabolic flux analysis of underdetermined and overdetermined metabolic networks
Fernandes, Sofia
,
Robitaille, Julien
,
Bastin, Georges
,
Jolicoeur, Mario
,
Wouwer, Alain Vande
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 770 KB
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english, 2016
6
Optimal Scheduling of Vaccination Campaigns Using a Direct Dynamic Optimization Method
Correa Cordova, Max Leo
,
Geletu, Abebe
,
Li, Pu
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 745 KB
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english, 2016
7
Control of the production of Saccharomyces cerevisiae on the basis of a reduced metabolic model * *This research is funded by the German Ministry of Research an Technology (BMBF) in the context of the YeastSent project (031A301A): “Volatile metabolites as proxy for metabolic network operation of Saccharomyces cerevisiae”
Wegerhoff, Sven
,
Engell, Sebastian
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 629 KB
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english, 2016
8
Structural Identifiability Analysis via Extended Observability and Decomposition
Villaverde, Alejandro F.
,
Barreiro, Antonio
,
Papachristodoulou, Antonis
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 379 KB
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english, 2016
9
Improving Bioprocess Productivity Using Constraint-Based Models in a Dynamic Optimization Scheme
Jabarivelisdeh, Banafsheh
,
Waldherr, Steffen
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 487 KB
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english, 2016
10
A Parallel Modelling Algorithm for Simulating Calcium Release in Cells
Stoddard, Jeremy G.
,
Welsh, James S.
,
Laver, Derek R.
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 506 KB
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english, 2016
11
Invariant based control of induction and maintenance phases for anesthesia
Fiacchini, Mirko
,
Queinnec, Isabelle
,
Tarbouriech, Sophie
,
Mazerolles, Michel
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 391 KB
Your tags:
english, 2016
12
A “Virtual Patient” Cohort and Mathematical Model of Glucose Dynamics in Critical Care
Knab, Timothy D.
,
Clermont, Gilles
,
Parker, Robert S.
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 594 KB
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english, 2016
13
Control of gene expression for the study of neurodegenerative disorders: a proof-of-principle experimental study
Perrino, Giansimone
,
Wilson, Cathal
,
Santorelli, Marco
,
di Bernardo, Diego
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 586 KB
Your tags:
english, 2016
14
From a discrete to continuous actuation for improved real-time control of gene expression in mammalian cells
Postiglione, Lorena
,
Santorelli, Marco
,
Tumaini, Barbara
,
di Bernardo, Diego
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 683 KB
Your tags:
english, 2016
15
Bringing the parts together: Steps towards an in-silico protocell
Schneider, Eugenia
,
Schweizer, Jakob
,
Mangold, Michael
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 928 KB
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english, 2016
16
A Simplified 2D Heart Model of the Wolff-Parkinson-White Syndrome
Zeile, Clemens
,
Scholz, Eberhard
,
Sager, Sebastian
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 1.32 MB
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english, 2016
17
Spatiotemporal Metabolic Modeling of a Chronic Wound Biofilm Consortium * *The authors wish to acknowledge NIH (Award U01EB019416) and NSF (Award 1511346) for funding this research.
Phalak, Poonam
,
Chen, Jin
,
Carlson, Ross P.
,
Henson, Michael A.
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 956 KB
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english, 2016
18
Coupling cellular phenotype and mechanics to understand extracellular matrix formation and homeostasis in osteoarthritis * *financial support through BMBF project OVERLOAD-PrevOp, grant number 01EC1408H is acknowledged.
Sunkara, Vikram
,
von Kleist, Max
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 3.15 MB
Your tags:
english, 2016
19
Parameter estimation for leukocyte dynamics after chemotherapy * *This research was supported by a research grant of the “nternational Max Planck Research School (IMPRS) for Advanced Methods in Process and System Engineering (Magdeburg)” and from the European Research Council via the Consolidator Grant MODEST-647573.
Rinke, Kristine
,
Jost, Felix
,
Findeisen, Rolf
,
Fischer, Thomas
,
Bartsch, Rainer
,
Schalk, Enrico
,
Sager, Sebastian
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 572 KB
Your tags:
english, 2016
20
Normalization of Western blot data affects the statistics of estimators * *This work was supported by the German Federal Ministry of Education and Research (BMBF) within the e:Bio-Innovationswettbewerb Systembiologie project PREDICT (grant number FKZ0316186A) and the German Research Foundation (DFG) within the Cluster of Excellence in Simulation Technology (EXC 310/2) at the University of Stuttgart.
Thomaseth, Caterina
,
Radde, Nicole
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 483 KB
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english, 2016
21
New Concepts for Evaluating the Performance of Computational Methods * *The author acknowledge financial support by the by the German Ministry of Education and Research (BMBF) via e:Bio Grant No. 031L0080.
Kreutz, Clemens
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 1.12 MB
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english, 2016
22
A Constrained NMF Approach to Analyze Quantitative Metagenomic Data * *Sebastien Raguideau is funded by a phD grant of the Meta-omics and Microbial Ecosystems (MME) program of INRA.
Raguideau, Sébastien
,
Laroche, Béatrice
,
Leclerc, Marion
,
Plancade, Sandra
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 558 KB
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english, 2016
23
Parameter identification in synthetic biological circuits using multi-objective optimization * *This work is partially supported by Spanish government and European Union (FEDER-CICYT DPI2011-28112-C04-01, and DPI2014-55276-C5-1). Y.B. thanks grant FPI/2013-3242 of Universitat Politècnica de València and Becas Iberoamérica of Santander Group, Spain 2015. G.R.M. thanks the partial support provided by the postdoctoral fellowship BJT-304804/2014-2 from the National Council of Scientific and Technologic Development of Brazil. A.V. thanks the Max Planck Society, the CSBD and the MPI-CBG. We are grateful to Dr. C.Baüerl and Dr. D. Provencio at the SB2CLab for their help in plasmid construction and getting experimental data. Also to Dr. V. Monedero
Boada, Y.
,
Vignoni, A.
,
Reynoso-Meza, G.
,
Picó, J.
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 960 KB
Your tags:
english, 2016
24
Preconditioned Metropolis sampling as a strategy to improve efficiency in Posterior exploration * *The work was supported by the Swedish Research Council within the UPMARC Linnaeus center of Excellence (S. Engblom) and by BMBF (Germany) project PrevOp-OVERLOAD, grant number 01EC1408H (V. Sunkara).
Engblom, Stefan
,
Sunkara, Vikram
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 422 KB
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english, 2016
25
A curvilinear Model Approach: Actin Cortex Clustering Due to ATP-induced Myosin Pulls
Wölfer, Christian
,
Vogel, Sven K.
,
Mangold, Michael
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 1.51 MB
Your tags:
english, 2016
26
Optimising time-series experimental design for modelling of circadian rhythms: the value of transient data
Mombaerts, Laurent
,
Mauroy, Alexandre
,
Gonçalves, Jorge
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 1.03 MB
Your tags:
english, 2016
27
Validation methods for population models of gene expression dynamics
González-Vargas, Andrés M.
,
Cinquemani, Eugenio
,
Ferrari-Trecate, Giancarlo
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 1.01 MB
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english, 2016
28
Robustness and filtering properties of ubiquitous signaling network motifs * *This work has been funded by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Centre (SFB/Transregio) 141 Biological Design and Integrative Structures/project B05.
Paul, Debdas
,
Radde, Nicole
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 455 KB
Your tags:
english, 2016
29
Zero-Retroactivity Subtraction Module for Embedded Feedback Control of Chemical Reaction Networks
Bilotta, Mariaconcetta
,
Cosentino, Carlo
,
Merola, Alessio
,
Bates, Declan G.
,
Amato, Francesco
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 549 KB
Your tags:
english, 2016
30
Irreversible port-Hamiltonian Approach to Modeling and Analyzing of Non-isothermal Chemical Reaction Networks
Wang, Li
,
Maschke, Bernhard
,
van der Schaft, Arjan
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 440 KB
Your tags:
english, 2016
31
The impact of experimental data quality on computational systems biology and engineering
Carius, L.
,
Findeisen, R.
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 1.23 MB
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english, 2016
32
Gene Regulatory Network Inference Using Time-Stamped Cross-Sectional Single Cell Expression Data
Gao, Nan Papili
,
Minhaz Ud-Dean, S.M.
,
Gunawan, Rudiyanto
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 1.34 MB
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english, 2016
33
In silico Analysis of Clostridium difficile Biofilm Metabolism and Treatment * *The authors also wish to acknowledge NIH (Award U01EB019416) and NSF (Award 1511346) for funding this research.
Henson, Michael A.
,
Phalak, Poonam
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 871 KB
Your tags:
english, 2016
34
Dynamic macroscopic model of dengue viral amplification in vero cell cultures
Abbate, T.
,
Dewasme, L.
,
Wouwer, A. Vande
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 437 KB
Your tags:
english, 2016
35
Protein-Level Control of Metabolism: Design Principles and Prospects from a Representative System
Euler, Christian K.
,
Mahadevan, Radhakrishnan
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 709 KB
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english, 2016
36
Identification of Functional Connections in Biological Neural Networks Using Dynamic Bayesian Networks
Dong, Chaoyi
,
Yue, Hong
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 557 KB
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english, 2016
37
Reconstruction of ensemble of single-cell time trajectories from discrete-time fluorescence data: Oscillatory MAPK dynamics
Kalantre, Girija S.
,
Viswanathan, Ganesh A.
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 1.78 MB
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english, 2016
38
Analysis of Circadian Cellular Bioluminescence Recordings using a Kalman Smoother
Ananthasubramaniam, Bharath
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 456 KB
Your tags:
english, 2016
39
Efficient Computation of All Distinct Realization Structures of Kinetic Systems
Tuza, Zoltan A.
,
Ács, Bernadett
,
Szederkényi, Gábor
,
Allgöwer, Frank
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 399 KB
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english, 2016
40
Contractivity of a genetic circuit with internal feedback and cell-to-cell communication * *This research was partially funded by grant FEDER-CICYT DPI2014-55276-C5-1-R. Yadira Boada thanks grant FPI/2013-3242 of the Universitat Politècnica de Valencia.
Picó-Marco, E.
,
Boada, Y.
,
Picó, J.
,
Vignoni, A.
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 1.09 MB
Your tags:
english, 2016
41
Model reduction of detailed-balanced reaction networks by clustering linkage classes
Rao, Shodhan
,
Jayawardhana, Bayu
,
van der Schaft, Arjan
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 382 KB
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english, 2016
42
Analyzing the Impact of Heterogeneity in Genetically Engineered Cell Lines for Influenza Vaccine Production Using Population Balance Modeling
Dürr, Robert
,
Duvigneau, Stefanie
,
Laske, Tanja
,
Bachmann, Mandy
,
Kienle, Achim
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 733 KB
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english, 2016
43
Fusion detection in time-lapse microscopy images : application to lipid droplets coalescence in plant seeds
Deslandes, François
,
Laroche, Béatrice
,
Trubuil, Alain
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 746 KB
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44
Extraction of Physiological State Functions in Heterogeneous Cell Population Models * *The authors of this paper gratefully acknowledge the financial support provided by the DFG (German Research Foundation) for this research work (grant WA2965/1-1).
Hussain, Mubashir
,
Waldherr, Steffen
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 439 KB
Your tags:
english, 2016
45
Quantitative comparison of competing PDE models for Pomlp dynamics in fission yeast * *The authors acknowledge financial support from the Postdoctoral Fellowship Program (PFP) of the Helmholtz Zentrum Munchen.
Hross, Sabrina
,
Fiedler, Anna
,
Theis, Fabian J.
,
Hasenauer, Jan
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 490 KB
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english, 2016
46
A Comparative Analysis of Dynamic Models of the Central Carbon Metabolism of Escherichia coli
Lima, Ana Patrícia
,
Baixinho, Vítor
,
Machado, Daniel
,
Rocha, Isabel
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 885 KB
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english, 2016
47
A supplemental treatment for chemotherapy: Control simulation using a mathematical model with estimated parameters based on in vivo experiment
Paryad-zanjani, S.
,
Mahjoob, M.J.
,
Amanpour, Saeid
,
Kheirbakhsh, Raheleh
,
Akhoundzadeh, M. Haji
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 1.03 MB
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english, 2016
48
Metabolomics and Network Biology: sex comparative analysis of mouse brain regional metabolic physiology
Vasilopoulou, Catherine G.
,
Margarity, Marigoula
,
Klapa, Maria I.
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 567 KB
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english, 2016
49
Streamlining GC-MS metabolomic analysis using the M-IOLITE software suite
Maga-Nteve, Christoniki
,
Klapa, Maria I.
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 552 KB
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english, 2016
50
Thermodynamically constrained averaging theory for cancer growth modelling * *Horizon 2020 MSCA grant agreement No 642295 www.melplex.eu
Albrecht, Marco
,
Sciumè, Giuseppe
,
Lucarelli, Philippe
,
Sauter, Thomas
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 442 KB
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english, 2016
51
Set-based Experiment Design for Model Discrimination Using Bilevel Optimization
Rudolph, Nadine
,
Streif, Stefan
,
Findeisen, Rolf
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 742 KB
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english, 2016
52
Control of a Class of Large-Scale Boolean Networks for Biological Systems Using Constant Inputs * *This research was supported in part by the National Research Foundation of Korea (NRF) grants funded by the Korea Government, the Ministry of Science, ICT & Future Planning (No. 2015M3A9A7067220, 2014R1A2A1A10052404, and 2013M3A9A7046303), and in part by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT and Future Planning (No. 2015R1A2A1A15054026).
Yang, Jung–Min
,
Cho, Kwang–Hyun
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 390 KB
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english, 2016
53
Monotonicity of Kinetic Proofreading
Kallies, Christian
,
Schliemann-Bullinger, Monica
,
Findeisen, Rolf
,
Lucia, Sergio
,
Bullinger, Eric
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 631 KB
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english, 2016
54
On the personalised modelling of cancer signalling * *Supported by EU FP7 grant “SynSignal” (No. 613879).
Fey, Dirk
,
Kuehn, Axel
,
Kholodenko, Boris N.
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 415 KB
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english, 2016
55
Multi-Physics Modeling of Light-Limited Microalgae Growth in Raceway Ponds
Nikolaou, Andreas
,
Booth, Peter
,
Gordon, Fraser
,
Yang, Junfeng
,
Matar, Omar
,
Chachuat, Benoît
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 778 KB
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english, 2016
56
Metabolic fluxes in recombinant Streptomyces lividans analyzed with 13 C-based metabolic flux analysis
Bouvin, Jeroen
,
Daniels, Wouter
,
Anné, Jozef
,
Nicolaï, Bart
,
Bernaerts, Kristel
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 699 KB
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english, 2016
57
Optimum Experimental Design for Patient Specific Mathematical Leukopenia Models * *This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No 647573), which is gratefully acknowledged.
Jost, Felix
,
Rinke, Kristine
,
Fischer, Thomas
,
Schalk, Enrico
,
Sager, Sebastian
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 608 KB
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english, 2016
58
Inferring Causal Gene Targets from Time Course Expression Data
Noh, Heeju
,
Ziyi, Hua
,
Gunawan, Rudiyanto
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 1.01 MB
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english, 2016
59
Contents
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 364 KB
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english, 2016
60
Maps for when the living gets tough: Maneuvering through a hostile energy landscape
Mondeel, Thierry D.G.A.
,
Rehman, Samrina
,
Zhang, Yanfei
,
Verma, Malkhey
,
Dürre, Peter
,
Barberis, Matteo
,
Westerhoff, Hans V.
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 965 KB
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english, 2016
61
The Regulation of Cell Motility Through an Excitable Network
Bhattacharya, Sayak
,
Iglesias, Pablo A.
Journal:
IFAC-PapersOnLine
Year:
2016
Language:
english
File:
PDF, 703 KB
Your tags:
english, 2016
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