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2020 – today
- 2024
[c2]Jorge Lázaro
, Jorge Júlvez, Jürgen Zanghellini:
Flexible Nets to Improve GEM Cell Factories by Combining Kinetic and Proteomics Data. CMSB 2024: 137-154- 2023
- [j18]Bianca A. Buchner, Tom J. Clement, Daan H. de Groot, Jürgen Zanghellini:
ecmtool: fast and memory-efficient enumeration of elementary conversion modes. Bioinform. 39(3) (2023) - 2022
- [j17]Christoph Bueschl, Maria Doppler, Elisabeth Varga, Bernhard Seidl, Mira Flasch, Benedikt Warth, Jürgen Zanghellini:
PeakBot: machine-learning-based chromatographic peak picking. Bioinform. 38(13): 3422-3428 (2022) - [j16]Kevin Mildau, Justin J. J. van der Hooft, Mira Flasch, Benedikt Warth, Yasin El Abiead, Gunda Koellensperger, Jürgen Zanghellini, Christoph Bueschl:
Homologue series detection and management in LC-MS data with homologueDiscoverer. Bioinform. 38(22): 5139-5140 (2022) - [j15]Mathias Gotsmy, Julia Brunmair, Christoph Bueschl, Christopher Gerner, Jürgen Zanghellini:
Probabilistic quotient's work and pharmacokinetics' contribution: countering size effect in metabolic time series measurements. BMC Bioinform. 23(1): 379 (2022) - [j14]Stefan Müller, Diana Széliová, Jürgen Zanghellini:
Elementary vectors and autocatalytic sets for resource allocation in next-generation models of cellular growth. PLoS Comput. Biol. 18(2) (2022) - 2021
- [j13]Bianca A. Buchner, Jürgen Zanghellini:
EFMlrs: a Python package for elementary flux mode enumeration via lexicographic reverse search. BMC Bioinform. 22(1): 547 (2021) - [j12]Diana Széliová, Jerneja Stor, Isabella Thiel, Marcus Weinguny, Michael Hanscho, Gabriele Lhota, Nicole Borth, Jürgen Zanghellini, David E. Ruckerbauer, Isabel Rocha:
Inclusion of maintenance energy improves the intracellular flux predictions of CHO. PLoS Comput. Biol. 17(6) (2021)
2010 – 2019
- 2019
- [j11]Matthias P. Gerstl, Stefan Müller, Georg Regensburger, Jürgen Zanghellini:
Flux tope analysis: studying the coordination of reaction directions in metabolic networks. Bioinform. 35(2): 266-273 (2019) - 2017
- [j10]Matthias P. Gerstl, Michael Hanscho, David E. Ruckerbauer, Jürgen Zanghellini, Nicole Borth:
CHOmine: an integrated data warehouse for CHO systems biology and modeling. Database J. Biol. Databases Curation 2017: bax034 (2017) - [j9]Govind Nair, Christian Jungreuthmayer, Jürgen Zanghellini:
Optimal knockout strategies in genome-scale metabolic networks using particle swarm optimization. BMC Bioinform. 18(1): 78:1-78:9 (2017) - [j8]Steffen Klamt, Georg Regensburger, Matthias P. Gerstl, Christian Jungreuthmayer, Stefan Schuster, Radhakrishnan Mahadevan, Jürgen Zanghellini, Stefan Müller:
From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints. PLoS Comput. Biol. 13(4) (2017) - 2016
- [j7]Christian Jungreuthmayer, Stefan Neubauer, Teresa Mairinger, Jürgen Zanghellini, Stephan Hann:
ICT: isotope correction toolbox. Bioinform. 32(1): 154-156 (2016) - [j6]Matthias P. Gerstl, Steffen Klamt, Christian Jungreuthmayer, Jürgen Zanghellini:
Exact quantification of cellular robustness in genome-scale metabolic networks. Bioinform. 32(5): 730-737 (2016) - 2015
- [j5]Govind Nair, Christian Jungreuthmayer, Michael Hanscho, Jürgen Zanghellini:
Designing minimal microbial strains of desired functionality using a genetic algorithm. Algorithms Mol. Biol. 10: 29 (2015) - [j4]Matthias P. Gerstl, Christian Jungreuthmayer, Jürgen Zanghellini:
tEFMA: computing thermodynamically feasible elementary flux modes in metabolic networks. Bioinform. 31(13): 2232-2234 (2015) - 2013
- [j3]Christian Jungreuthmayer, David E. Ruckerbauer, Jürgen Zanghellini:
regEfmtool: Speeding up elementary flux mode calculation using transcriptional regulatory rules in the form of three-state logic. Biosyst. 113(1): 37-39 (2013) - [j2]Christian Jungreuthmayer, Govind Nair, Steffen Klamt, Jürgen Zanghellini:
Comparison and improvement of algorithms for computing minimal cut sets. BMC Bioinform. 14: 318 (2013) - [c1]Christian Jungreuthmayer, Margot Sonnleitner, Gerald Striedner, Jürgen Mairhofer, Jürgen Zanghellini:
Designing an optimally ethanol producing E. coli strain using constrained minimal cut sets. EUSIPCO 2013: 1-5 - 2012
- [j1]Christian Jungreuthmayer, Jürgen Zanghellini:
Designing optimal cell factories: integer programming couples elementary mode analysis with regulation. BMC Syst. Biol. 6: 103 (2012)
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