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Journal Articles
- 2023
[j30]Ronan M. T. Fleming
, Hulda S. Haraldsdóttir, Le Hoai Minh, Phan Tu Vuong, Thomas Hankemeier, Ines Thiele:
Cardinality optimization in constraint-based modelling: application to human metabolism. Bioinform. 39(9) (2023)- 2022
- [j29]Almut Heinken, Ines Thiele:
Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities. Bioinform. 38(8): 2367-2368 (2022) - [j28]Ines Thiele, German A. Preciat Gonzalez, Ronan M. T. Fleming:
MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions. Bioinform. 38(20): 4831-4832 (2022) - 2021
- [j27]Almut Heinken, Stefanía Magnúsdóttir, Ronan M. T. Fleming, Ines Thiele:
DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations. Bioinform. 37(21): 3974-3975 (2021) - [j26]Marouen Ben Guebila, Ines Thiele:
Dynamic flux balance analysis of whole-body metabolism for type 1 diabetes. Nat. Comput. Sci. 1(5): 348-361 (2021) - [j25]Leo Zhu, William Pei, Ines Thiele, Radhakrishnan Mahadevan:
Integration of a physiologically-based pharmacokinetic model with a whole-body, organ-resolved genome-scale model for characterization of ethanol and acetaldehyde metabolism. PLoS Comput. Biol. 17(8) (2021) - 2019
- [j24]Federico Baldini, Almut Heinken, Laurent Heirendt, Stefanía Magnúsdóttir, Ronan M. T. Fleming, Ines Thiele:
The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities. Bioinform. 35(13): 2332-2334 (2019) - [j23]Beatriz Peñalver Bernabé, Ines Thiele, Eugene Galdones, Anaar Siletz, Sriram Chandrasekaran, Teresa K. Woodruff, Linda J. Broadbelt, Lonnie D. Shea:
Dynamic genome-scale cell-specific metabolic models reveal novel inter-cellular and intra-cellular metabolic communications during ovarian follicle development. BMC Bioinform. 20(1): 307:1-307:16 (2019) - [j22]Alberto Noronha, Jennifer Modamio, Yohan Jarosz, Elisabeth Guerard, Nicolas Sompairac, German A. Preciat Gonzalez, Anna Dröfn Daníelsdóttir, Max Krecke, Diane Merten, Hulda S. Haraldsdóttir, Almut Heinken, Laurent Heirendt, Stefanía Magnúsdóttir, Dmitry A. Ravcheev, Swagatika Sahoo, Piotr Gawron, Lucia Friscioni, Beatriz Garcia Santa Cruz, Mabel Prendergast, Alberto Puente, Mariana Rodrigues, Akansha Roy, Mouss Rouquaya, Luca Wiltgen, Alise Zagare, Elisabeth John, Maren Krueger, Inna Kuperstein, Andrei Yu. Zinovyev, Reinhard Schneider, Ronan M. T. Fleming, Ines Thiele:
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 47(Database-Issue): D614-D624 (2019) - [j21]Marouen Ben Guebila, Ines Thiele:
Predicting gastrointestinal drug effects using contextualized metabolic models. PLoS Comput. Biol. 15(6) (2019) - 2017
- [j20]Alberto Noronha, Anna Dröfn Daníelsdóttir, Piotr Gawron, Freyr Jóhannsson, Soffía Jónsdóttir, Sindri Jarlsson, Jón Pétur Gunnarsson, Sigurður Brynjólfsson, Reinhard Schneider, Ines Thiele, Ronan M. T. Fleming:
ReconMap: an interactive visualization of human metabolism. Bioinform. 33(4): 605-607 (2017) - [j19]Laurent Heirendt, Ines Thiele, Ronan M. T. Fleming:
DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia. Bioinform. 33(9): 1421-1423 (2017) - [j18]Hulda S. Haraldsdóttir, Ben Cousins, Ines Thiele, Ronan M. T. Fleming, Santosh S. Vempala:
CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models. Bioinform. 33(11): 1741-1743 (2017) - [j17]German A. Preciat Gonzalez, Lemmer R. P. El Assal, Alberto Noronha, Ines Thiele, Hulda S. Haraldsdóttir, Ronan M. T. Fleming:
Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D. J. Cheminformatics 9(1): 39:1-39:15 (2017) - [j16]Eugen Bauer, Johannes Zimmermann, Federico Baldini, Ines Thiele, Christoph Kaleta:
BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities. PLoS Comput. Biol. 13(5) (2017) - [j15]Maike K. Aurich, Ronan M. T. Fleming, Ines Thiele:
A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines. PLoS Comput. Biol. 13(8) (2017) - 2014
- [j14]Ines Thiele, Nikos Vlassis, Ronan M. T. Fleming:
fastGapFill: efficient gap filling in metabolic networks. Bioinform. 30(17): 2529-2531 (2014) - [j13]Hulda S. Haraldsdóttir, Ines Thiele, Ronan M. T. Fleming:
Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2. J. Cheminformatics 6(1): 2 (2014) - 2013
- [j12]Yuekai Sun, Ronan M. T. Fleming, Ines Thiele, Michael A. Saunders:
Robust flux balance analysis of multiscale biochemical reaction networks. BMC Bioinform. 14: 240 (2013) - [j11]Miranda D. Stobbe, Morris A. Swertz, Ines Thiele, Trebor Rengaw, Antoine H. C. van Kampen, Perry D. Moerland:
Consensus and conflict cards for metabolic pathway databases. BMC Syst. Biol. 7: 50 (2013) - 2011
- [j10]Ronan M. T. Fleming, Ines Thiele:
von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models. Bioinform. 27(1): 142-143 (2011) - [j9]Stefan Gretar Thorleifsson, Ines Thiele:
rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks. Bioinform. 27(14): 2009-2010 (2011) - [j8]Ines Thiele, Daniel R. Hyduke, Benjamin Steeb, Guy Fankam, Douglas K. Allen, Susanna Bazzani, Pep Charusanti, Feng-Chi Chen, Ronan M. T. Fleming, Chao A. Hsiung, Sigrid C. J. De Keersmaecker, Yu-Chieh Liao, Kathleen Marchal, Monica L. Mo, Emre Özdemir, Anu Raghunathan, Jennifer L. Reed, Sook-Il Shin, Sara Sigurbjörnsdóttir, Jonas Steinmann, Suresh Sudarsan, Neil Swainston, Inge M. Thijs, Karsten Zengler, Bernhard O. Palsson, Joshua N. Adkins, Dirk Bumann:
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Syst. Biol. 5: 8 (2011) - [j7]Ottar Rolfsson, Bernhard Ø. Palsson, Ines Thiele:
The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions. BMC Syst. Biol. 5: 155 (2011) - 2010
- [j6]Steinn Gudmundsson, Ines Thiele:
Computationally efficient flux variability analysis. BMC Bioinform. 11: 489 (2010) - [j5]Martin I. Sigurdsson, Neema Jamshidi, Eiríkur Steingrímsson, Ines Thiele, Bernhard Ø. Palsson:
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. BMC Syst. Biol. 4: 140 (2010) - 2009
- [j4]Fan Li, Ines Thiele, Neema Jamshidi, Bernhard O. Palsson:
Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling. PLoS Comput. Biol. 5(2) (2009) - [j3]Ines Thiele, Neema Jamshidi, Ronan M. T. Fleming, Bernhard O. Palsson:
Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization. PLoS Comput. Biol. 5(3) (2009) - 2008
- [j2]Juan Nogales, Bernhard Ø. Palsson, Ines Thiele:
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst. Biol. 2: 79 (2008) - 2007
- [j1]Matthew Yeung, Ines Thiele, Bernhard O. Palsson:
Estimation of the number of extreme pathways for metabolic networks. BMC Bioinform. 8 (2007)
Reference Works
- 2009
- [r1]Nathan E. Lewis, Neema Jamshidi, Ines Thiele, Bernhard O. Palsson:
Metabolic Systems Biology. Encyclopedia of Complexity and Systems Science 2009: 5535-5552
Informal and Other Publications
- 2017
- [i1]Laurent Heirendt, Sylvain Arreckx, Christophe Trefois, Yohan Yarosz, Maharshi Vyas, Venkata P. Satagopam, Reinhard Schneider, Ines Thiele, Ronan M. T. Fleming:
ARTENOLIS: Automated Reproducibility and Testing Environment for Licensed Software. CoRR abs/1712.05236 (2017)
Coauthor Index
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