Publications

2017

Ewald J, Bartl M, Dandekar T and Kaleta C
Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism.
PLoS Computational Biology., February, 2017. Vol. 13, pp e1005371
Hölzer M, Krähling V, Amman F, Barth E, Bernhart SH, Carmelo VAO, Collatz M, Doose G, Eggenhofer F, Ewald J, Fallmann J, Feldhahn LM, Fricke M, Gebauer J, Gruber AJ, Hufsky F, Indrischek H, Kanton S, Linde J, Mostajo N, Ochsenreiter R, Riege K, Rivarola-Duarte L, Sahyoun AH, Saunders SJ, Seemann SE, Tanzer A, Vogel B, Wehner S, Wolfinger MT, Backofen R, Gorodkin J, Grosse I, Hofacker I, Hoffmann S, Kaleta C, Stadler PF, Becker S and Marz M
Corrigendum: Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells.
Scientific Reports., January, 2017. Vol. 7, pp 39421

2016

Häsler R, Sheibani-Tezerji R, Sinha A, Barann M, Rehman A, Esser D, Aden K, Knecht C, Brandt B, Nikolaus S, Schäuble S, Kaleta C, Franke A, Fretter C, Müller W, Hütt M-T, Krawczak M, Schreiber S and Rosenstiel P
Uncoupling of mucosal gene regulation, mRNA splicing and adherent microbiota signatures in inflammatory bowel disease.
Gut., September, 2016.
Hölzer M, Krähling V, Amman F, Barth E, Bernhart SH, Carmelo VAO, Collatz M, Doose G, Eggenhofer F, Ewald J, Fallmann J, Feldhahn LM, Fricke M, Gebauer J, Gruber AJ, Hufsky F, Indrischek H, Kanton S, Linde J, Mostajo N, Ochsenreiter R, Riege K, Rivarola-Duarte L, Sahyoun AH, Saunders SJ, Seemann SE, Tanzer A, Vogel B, Wehner S, Wolfinger MT, Backofen R, Gorodkin J, Grosse I, Hofacker I, Hoffmann S, Kaleta C, Stadler PF, Becker S and Marz M
Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells.
Scientific Reports., October, 2016. Vol. 6, pp 34589
Gebauer J, Gentsch C, Mansfeld J, Schmeißer K, Waschina S, Brandes S, Klimmasch L, Zamboni N, Zarse K, Schuster S, Ristow M, Schäuble S and Kaleta C
A Genome-Scale Database and Reconstruction of Caenorhabditis elegans Metabolism.
Cell Syst., May, 2016. Vol. 2(5), pp 312-322
Germerodt S, Bohl K, Lück A, Pande S, Schröter A, Kaleta C, Schuster S and Kost C
Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities.
PLoS Comput Biol., Jun, 2016. Vol. 12(6), pp e1004986
Waschina S, D'Souza G, Kost C and Kaleta C
Metabolic network architecture and carbon source determine metabolite production costs.
FEBS J., Jun, 2016. Vol. 283(11), pp 2149-2163

2015

Bartl M, Pfaff M, Ghallab A, Driesch D, Henkel SG, Hengstler JG, Schuster S, Kaleta C, Gebhardt R, Zellmer S and Li P
Optimality in the zonation of ammonia detoxification in rodent liver.
Arch Toxicol., Nov, 2015. Vol. 89(11), pp 2069-2078
D'Souza G, Waschina S, Kaleta C and Kost C
Plasticity and epistasis strongly affect bacterial fitness after losing multiple metabolic genes.
Evolution., May, 2015. Vol. 69(5), pp 1244-1254
de Hijas-Liste GM, Balsa-Canto E, Ewald J, Bartl M, Li P, Banga JR and Kaleta C
Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation.
BMC Bioinformatics. Vol. 16, pp 163
Ewald J, Kötzing M, Bartl M and Kaleta C
Footprints of optimal protein assembly strategies in the operonic structure of prokaryotes.
Metabolites. Vol. 5(2), pp 252-269
Mansfeld J, Urban N, Priebe S, Groth M, Frahm C, Hartmann N, Gebauer J, Ravichandran M, Dommaschk A, Schmeisser S, Kuhlow D, Monajembashi S, Bremer-Streck S, Hemmerich P, Kiehntopf M, Zamboni N, Englert C, Guthke R, Kaleta C, Platzer M, Sühnel Jü, Witte OW, Zarse K and Ristow M
Branched-chain amino acid catabolism is a conserved regulator of physiological ageing.
Nat Commun. Vol. 6, pp 10043
Schmidt R, Waschina S, Boettger-Schmidt D, Kost C and Kaleta C
Computing autocatalytic sets to unravel inconsistencies in metabolic network reconstructions.
Bioinformatics., Feb, 2015. Vol. 31(3), pp 373-381
Schuster S, Boley D, Möller P and Kaleta C
A minimal model for explaining the higher ATP production in the Warburg effect
In Proceedings of German Conference on Bioinformatics.
Schuster S, Boley D, Möller P, Stark H and Kaleta C
Mathematical models for explaining the Warburg effect: a review focussed on ATP and biomass production.
Biochem Soc Trans., Dec, 2015. Vol. 43(6), pp 1187-1194

 

2014

D'Souza G, Waschina S, Pande S, Bohl K, Kaleta C and Kost C
Less is more: selective advantages can explain the prevalent loss of biosynthetic genes in bacteria.
Evolution., Sep, 2014. Vol. 68(9), pp 2559-2570
Pande S, Merker H, Bohl K, Reichelt M, Schuster S, de Figueiredo LF, Kaleta C and Kost C
Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria.
ISME J., May, 2014. Vol. 8(5), pp 953-962
Schmidt R, Waschina S, Boettger-Schmidt D, Kost C and Kaleta C
Computing Autocatalytic Sets to Unravel Inconsistencies in Metabolic Network Reconstructions.
Bioinformatics., Oct, 2014.
 

2013

Bartl M, Kötzing M, Schuster S, Li P and Kaleta C
Dynamic optimization identifies optimal programs for pathway regulation in prokaryotes
Nature Communications. Vol. 4, pp 2243
Fuellen G, Boerries M, Busch H, de Grey A, Hahn U, Hiller T, Hoeflich A, Jansen L, Janssens GE, Kaleta C, Meinema AC, Schäuble S, Simm A, Schofield PN, Smith B, Sühnel J, Vera J, Wagner W, Wönne EC and Wuttke D
In silico approaches and the role of ontologies in aging research.
Rejuvenation Res., Dec, 2013. Vol. 16(6), pp 540-546
de Hijas-Liste G, Balsa-Canto E, Banga J and Kaleta C
Optimal regulatory programs for the control of metabolic pathways: The case of feedback inhibition
In Proceedings of the 21st Mediterranean Conference on Control and Automation.
Kaleta C, Schäuble S, Rinas U and Schuster S
Metabolic costs of amino acid and protein production in Escherichia coli
Biotechnology Journal. Vol. 8(9), pp 1105-14
 

2012

Behre J, de Figueiredo LF, Schuster S and Kaleta C
Detecting structural invariants in biological reaction networks.
Methods Mol Biol. Vol. 804, pp 377-407
Gebauer J, Schuster S, de Figueiredo LF and Kaleta C
Detecting and investigating substrate cycles in a genome-scale human metabolic network.
FEBS J., Jul, 2012.
Göhler A, Kökpinar Ö, Schmidt-Heck W, Geffers R, Guthke R, Rinas U, Schuster S, Jahreis K and Kaleta C
More than just a metabolic regulator – elucidation and validation of new targets of PdhR in Escherichia coli
BMC Syst Biol. Vol. 5, pp 197
Kaleta C, de Figueiredo LF and Schuster S
Against the stream: relevance of gluconeogenesis from fatty acids for natives of the arctic regions.
Int J Circumpolar Health. Vol. 71(0), pp 1-2
Kaleta C and Heiland I
Stoffwechselanalyse: neue Wege im Labyrinth entdecken
Laborwelt. Vol. 4, pp 30-32
Wessely F, Bartl M, Guthke R, Li P and Kaleta C
Out of (transcriptional) control? Design principles of the regulatory network controlling metabolic pathways in Escherichia coli.
In Proceedings of the German Conference on Bioinformatics. , pp 31-34
 

2011

Beuster G, Zarse K, Kaleta C, Thierbach R, Kiehntopf M, Steinberg P, Schuster S and Ristow M
Inhibition of alanine aminotransferase in silico and in vivo promotes mitochondrial metabolism to impair malignant growth.
J Biol Chem., Jun, 2011. Vol. 286(25), pp 22323-22330
Kaleta C, de Figueiredo LF, Werner S, Guthke R, Ristow M and Schuster S
In silico evidence for gluconeogenesis from fatty acids in humans.
PLoS Comput Biol., Jul, 2011. Vol. 7(7), pp e1002116
Kaleta C, de Figueiredo LF, Heiland I, Klamt S and Schuster S
Special issue: integration of OMICs datasets into metabolic pathway analysis.
Biosystems., Aug, 2011. Vol. 105(2), pp 107-108
Rezola A, de Figueiredo LF, Brock M, Pey J, Podhorski A, Wittmann C, Schuster S, Bockmayr A and Planes FJ
Exploring metabolic pathways in genome-scale networks via generating flux modes.
Bioinformatics., Feb, 2011. Vol. 27(4), pp 534-540
Schäuble S, Schuster S and Kaleta C
Hands-on metabolism analysis of complex biochemical networks using elementary flux modes.
Methods Enzymol. Vol. 500, pp 437-456
Schuster S, de Figueiredo LF, Schroeter A and Kaleta C
Combining metabolic pathway analysis with Evolutionary Game Theory: explaining the occurrence of low-yield pathways by an analytic optimization approach.
Biosystems., Aug, 2011. Vol. 105(2), pp 147-153
Wessely F, Bartl M, Guthke R, Li P, Schuster S and Kaleta C
Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs.
Mol Syst Biol. Vol. 7, pp 515
 

2010

Bartl M, Kötzing M, Kaleta C, Schuster S and Li P
Just-in-time activation of a glycolysis inspired metabolic network - solution with a dynamic optimization approach
In Proceedings of the 55th International Scientific Colloquium. Ilmenau, Germany , pp 217-222
Bohl K, de Figueiredo LF, Hädicke O, Klamt S, Kost C, Schuster S and Kaleta C
CASOP GS: Computing intervention strategies targeted at production improvement in genome-scale metabolic networks
In Proceedings of the 25th German Conference on Bioinformatics. Bonn , pp 71-80 Gesellschaft für Informatik
Centler F, Kaleta C, di Fenizio PS and Dittrich P
A parallel algorithm to compute chemical organizations in biological networks.
Bioinformatics., Jul, 2010. Vol. 26(14), pp 1788-1789
Kaleta C, Göhler A, Schuster S, Jahreis K, Guthke R and Nikolajewa S
Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis.
BMC Syst Biol. Vol. 4, pp 116
Kenanov D, Kaleta C, Petzold A, Hoischen C, Diekmann S, Siddiqui RA and Schuster S
Theoretical study of lipid biosynthesis in wild-type Escherichia coli and in a protoplast-type L-form using elementary flux mode analysis.
FEBS J., Feb, 2010. Vol. 277(4), pp 1023-1034
Ruppin E, Papin JA, de Figueiredo LF and Schuster S
Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks.
Curr Opin Biotechnol., Aug, 2010. Vol. 21(4), pp 502-510
Schuster S, de Figueiredo LF and Kaleta C
Predicting novel pathways in genome-scale metabolic networks.
Biochem Soc Trans., Oct, 2010. Vol. 38(5), pp 1202-1205
 

2009

de Figueiredo LF, Schuster S, Kaleta C and Fell DA
Response to comment on 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'.
Bioinformatics., Dec, 2009. Vol. 25(24), pp 3330-3331
de Figueiredo LF, Podhorski A, Rubio A, Kaleta C, Beasley JE, Schuster S and Planes FJ
Computing the shortest elementary flux modes in genome-scale metabolic networks.
Bioinformatics., Dec, 2009. Vol. 25(23), pp 3158-3165
de Figueiredo LF, Schuster S, Kaleta C and Fell DA
Can sugars be produced from fatty acids? A test case for pathway analysis tools.
Bioinformatics., Jan, 2009. Vol. 25(1), pp 152-158
Kaleta C, de Figueiredo LF and Schuster S
Detecting Metabolic Conversions in Genome-Scale Metabolic Networks on the Basis of Elementary Flux Patterns in Subnetworks
In Proceedings of the Vienna Conference on Mathematical Modelling. Vol. 2, pp 748 - 759
Kaleta C, Richter S and Dittrich P
Using chemical organization theory for model checking.
Bioinformatics., Aug, 2009. Vol. 25(15), pp 1915-1922
Kaleta C, de Figueiredo LF, Behre J and Schuster S
EFMEvolver: Computing elementary flux modes in genome-scale metabolic networks.
In Lecture Notes in Informatics - Proceedings. Bonn Vol. P-157, pp 179-189 Gesellschaft für Informatik
Kaleta C
Artificial Life Models in Software - Vol. I
London , pp 319-342 Springer
Kaleta C, de Figueiredo LF and Schuster S
Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns.
Genome Res., Oct, 2009. Vol. 19(10), pp 1872-1883
 

2008

Centler F, Kaleta C, di Fenizio PS and Dittrich P
Computing chemical organizations in biological networks.
Bioinformatics., Jul, 2008. Vol. 24(14), pp 1611-1618
de Figueiredo LF, Schuster S, Kaleta C and Fell DA
Can sugars be produced from fatty acids? A test case for pathway analysis tools.
Bioinformatics., Nov, 2008. Vol. 24(22), pp 2615-2621
Kaleta C, Centler F, di Fenizio PS and Dittrich P
Phenotype prediction in regulated metabolic networks.
BMC Syst Biol. Vol. 2, pp 37
 

2007

Schwarz R, Liang C, Kaleta C, Kühnel M, Hoffmann E, Kuznetsov S, Hecker M, Griffiths G, Schuster S and Dandekar T
Integrated network reconstruction, visualization and analysis using YANAsquare.
BMC Bioinformatics. Vol. 8, pp 313
 

2006

Kaleta C, Centler F and Dittrich P
Analyzing molecular reaction networks: from pathways to chemical organizations.
Mol Biotechnol., Oct, 2006. Vol. 34(2), pp 117-123

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