Update paper.bib

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paper.bib

@@ -125,5 +125,104 @@ @article{kindschuh2023preterm
   publisher={Nature Publishing Group}
 }
 
+@article{heinken2019systematic,
+  title={Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease},
+  author={Heinken, Almut and Ravcheev, Dmitry A and Baldini, Federico and Heirendt, Laurent and Fleming, Ronan MT and Thiele, Ines},
+  journal={Microbiome},
+  volume={7},
+  pages={1--18},
+  year={2019},
+  publisher={Springer}
+}
+
+@article{hertel2021integration,
+  title={Integration of constraint-based modeling with fecal metabolomics reveals large deleterious effects of Fusobacterium spp. on community butyrate production},
+  author={Hertel, Johannes and Heinken, Almut and Martinelli, Filippo and Thiele, Ines},
+  journal={Gut Microbes},
+  volume={13},
+  number={1},
+  pages={1915673},
+  year={2021},
+  publisher={Taylor \& Francis}
+}
 
+@article{hertel2019integrated,
+  title={Integrated analyses of microbiome and longitudinal metabolome data reveal microbial-host interactions on sulfur metabolism in Parkinson’s disease},
+  author={Hertel, Johannes and Harms, Amy C and Heinken, Almut and Baldini, Federico and Thinnes, Cyrille C and Glaab, Enrico and Vasco, Daniel A and Pietzner, Maik and Stewart, Isobel D and Wareham, Nicholas J and others},
+  journal={Cell reports},
+  volume={29},
+  number={7},
+  pages={1767--1777},
+  year={2019},
+  publisher={Elsevier}
+}
+
+@article{baldini2020parkinson,
+  title={Parkinson’s disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions},
+  author={Baldini, Federico and Hertel, Johannes and Sandt, Estelle and Thinnes, Cyrille C and Neuberger-Castillo, Lorieza and Pavelka, Lukas and Betsou, Fay and Kr{\"u}ger, Rejko and Thiele, Ines},
+  journal={BMC biology},
+  volume={18},
+  pages={1--21},
+  year={2020},
+  publisher={Springer}
+}
+
+@article{ebrahim2013cobrapy,
+  title={COBRApy: constraints-based reconstruction and analysis for python},
+  author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R},
+  journal={BMC systems biology},
+  volume={7},
+  pages={1--6},
+  year={2013},
+  publisher={Springer}
+}
 
+@article{jensen2017optlang,
+  title={Optlang: An algebraic modeling language for mathematical optimization.},
+  author={Jensen, Kristian and Cardoso, Joao GR and Sonnenschein, Nikolaus},
+  journal={J. Open Source Softw.},
+  volume={2},
+  number={9},
+  pages={139},
+  year={2017}
+}
+
+@article{guebila2020vffva,
+  title={VFFVA: dynamic load balancing enables large-scale flux variability analysis},
+  author={Guebila, Marouen Ben},
+  journal={BMC bioinformatics},
+  volume={21},
+  pages={1--13},
+  year={2020},
+  publisher={Springer}
+}
+
+@article{mahadevan2003effects,
+  title={The effects of alternate optimal solutions in constraint-based genome-scale metabolic models},
+  author={Mahadevan, Radhakrishnan and Schilling, Chrisophe H},
+  journal={Metabolic engineering},
+  volume={5},
+  number={4},
+  pages={264--276},
+  year={2003},
+  publisher={Elsevier}
+}
+
+
+@article{heinken2013systems,
+  title={Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut},
+  author={Heinken, Almut and Sahoo, Swagatika and Fleming, Ronan MT and Thiele, Ines},
+  journal={Gut microbes},
+  volume={4},
+  number={1},
+  pages={28--40},
+  year={2013},
+  publisher={Taylor \& Francis}
+}
+
+@misc{gurobi,
+  author = {{Gurobi Optimization, LLC}},
+  title = {{Gurobi Optimizer Reference Manual}},
+  year = 2023,
+  url = "https://www.gurobi.com"
+}