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Items: 1 to 50 of 60

1.

Publisher Correction: Transcriptomic alterations during ageing reflect the shift from cancer to degenerative diseases in the elderly.

Irizar PA, Schäuble S, Esser D, Groth M, Frahm C, Priebe S, Baumgart M, Hartmann N, Marthandan S, Menzel U, Müller J, Schmidt S, Ast V, Caliebe A, König R, Krawczak M, Ristow M, Schuster S, Cellerino A, Diekmann S, Englert C, Hemmerich P, Sühnel J, Guthke R, Witte OW, Platzer M, Ruppin E, Kaleta C.

Nat Commun. 2019 May 31;10(1):2459. doi: 10.1038/s41467-019-10559-5.

2.

Metastasis of pancreatic cancer: An uninflamed liver micromilieu controls cell growth and cancer stem cell properties by oxidative phosphorylation in pancreatic ductal epithelial cells.

Fabian A, Stegner S, Miarka L, Zimmermann J, Lenk L, Rahn S, Buttlar J, Viol F, Knaack H, Esser D, Schäuble S, Großmann P, Marinos G, Häsler R, Mikulits W, Saur D, Kaleta C, Schäfer H, Sebens S.

Cancer Lett. 2019 Jul 1;453:95-106. doi: 10.1016/j.canlet.2019.03.039. Epub 2019 Mar 28.

PMID:
30930235
3.

Natural C. elegans Microbiota Protects against Infection via Production of a Cyclic Lipopeptide of the Viscosin Group.

Kissoyan KAB, Drechsler M, Stange EL, Zimmermann J, Kaleta C, Bode HB, Dierking K.

Curr Biol. 2019 Mar 18;29(6):1030-1037.e5. doi: 10.1016/j.cub.2019.01.050. Epub 2019 Feb 28.

4.

Modeling Meets Metabolomics-The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans.

Witting M, Hastings J, Rodriguez N, Joshi CJ, Hattwell JPN, Ebert PR, van Weeghel M, Gao AW, Wakelam MJO, Houtkooper RH, Mains A, Le Novère N, Sadykoff S, Schroeder F, Lewis NE, Schirra HJ, Kaleta C, Casanueva O.

Front Mol Biosci. 2018 Nov 14;5:96. doi: 10.3389/fmolb.2018.00096. eCollection 2018.

5.

Gut dysbiosis with Bacilli dominance and accumulation of fermentation products precedes late-onset sepsis in preterm infants.

Graspeuntner S, Waschina S, Künzel S, Twisselmann N, Rausch TK, Cloppenborg-Schmidt K, Zimmermann J, Viemann D, Herting E, Göpel W, Baines JF, Kaleta C, Rupp J, Härtel C, Pagel J.

Clin Infect Dis. 2018 Oct 16. doi: 10.1093/cid/ciy882. [Epub ahead of print]

PMID:
30329017
6.

Epithelial RNase H2 Maintains Genome Integrity and Prevents Intestinal Tumorigenesis in Mice.

Aden K, Bartsch K, Dahl J, Reijns MAM, Esser D, Sheibani-Tezerji R, Sinha A, Wottawa F, Ito G, Mishra N, Knittler K, Burkholder A, Welz L, van Es J, Tran F, Lipinski S, Kakavand N, Boeger C, Lucius R, von Schoenfels W, Schafmayer C, Lenk L, Chalaris A, Clevers H, Röcken C, Kaleta C, Rose-John S, Schreiber S, Kunkel T, Rabe B, Rosenstiel P.

Gastroenterology. 2019 Jan;156(1):145-159.e19. doi: 10.1053/j.gastro.2018.09.047. Epub 2018 Sep 28.

7.

Impact of Chromosomal Architecture on the Function and Evolution of Bacterial Genomes.

Krogh TJ, Møller-Jensen J, Kaleta C.

Front Microbiol. 2018 Aug 27;9:2019. doi: 10.3389/fmicb.2018.02019. eCollection 2018. Review.

8.

Transcriptomic alterations during ageing reflect the shift from cancer to degenerative diseases in the elderly.

Aramillo Irizar P, Schäuble S, Esser D, Groth M, Frahm C, Priebe S, Baumgart M, Hartmann N, Marthandan S, Menzel U, Müller J, Schmidt S, Ast V, Caliebe A, König R, Krawczak M, Ristow M, Schuster S, Cellerino A, Diekmann S, Englert C, Hemmerich P, Sühnel J, Guthke R, Witte OW, Platzer M, Ruppin E, Kaleta C.

Nat Commun. 2018 Jan 30;9(1):327. doi: 10.1038/s41467-017-02395-2. Erratum in: Nat Commun. 2019 May 31;10(1):2459.

9.
10.

Model-based genome-wide determination of RNA chain elongation rates in Escherichia coli.

Großmann P, Lück A, Kaleta C.

Sci Rep. 2017 Dec 8;7(1):17213. doi: 10.1038/s41598-017-17408-9.

11.

Deciphering the regulation of metabolism with dynamic optimization: an overview of recent advances.

Ewald J, Bartl M, Kaleta C.

Biochem Soc Trans. 2017 Jul 28. pii: BST20170137. doi: 10.1042/BST20170137. [Epub ahead of print] Review.

PMID:
28754658
12.

Microbiomarkers in inflammatory bowel diseases: caveats come with caviar.

Sommer F, Rühlemann MC, Bang C, Höppner M, Rehman A, Kaleta C, Schmitt-Kopplin P, Dempfle A, Weidinger S, Ellinghaus E, Krauss-Etschmann S, Schmidt-Arras D, Aden K, Schulte D, Ellinghaus D, Schreiber S, Tholey A, Rupp J, Laudes M, Baines JF, Rosenstiel P, Franke A.

Gut. 2017 Oct;66(10):1734-1738. doi: 10.1136/gutjnl-2016-313678. Epub 2017 Jul 21. No abstract available.

13.

Modelling the host-pathogen interactions of macrophages and Candida albicans using Game Theory and dynamic optimization.

Dühring S, Ewald J, Germerodt S, Kaleta C, Dandekar T, Schuster S.

J R Soc Interface. 2017 Jul;14(132). pii: 20170095. doi: 10.1098/rsif.2017.0095.

14.

BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities.

Bauer E, Zimmermann J, Baldini F, Thiele I, Kaleta C.

PLoS Comput Biol. 2017 May 22;13(5):e1005544. doi: 10.1371/journal.pcbi.1005544. eCollection 2017 May.

15.

Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism.

Ewald J, Bartl M, Dandekar T, Kaleta C.

PLoS Comput Biol. 2017 Feb 17;13(2):e1005371. doi: 10.1371/journal.pcbi.1005371. eCollection 2017 Feb.

16.

Corrigendum: Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells.

Hölzer M, Krähling V, Amman F, Barth E, Bernhart SH, Carmelo VA, 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, Marz M.

Sci Rep. 2017 Jan 11;7:39421. doi: 10.1038/srep39421. No abstract available.

17.

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells.

Hölzer M, Krähling V, Amman F, Barth E, Bernhart SH, Carmelo VA, 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, Marz M.

Sci Rep. 2016 Oct 7;6:34589. doi: 10.1038/srep34589. Erratum in: Sci Rep. 2017 Jan 11;7:39421.

18.

Uncoupling of mucosal gene regulation, mRNA splicing and adherent microbiota signatures in inflammatory bowel disease.

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 MT, Krawczak M, Schreiber S, Rosenstiel P.

Gut. 2017 Dec;66(12):2087-2097. doi: 10.1136/gutjnl-2016-311651. Epub 2016 Sep 30.

19.

Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities.

Germerodt S, Bohl K, Lück A, Pande S, Schröter A, Kaleta C, Schuster S, Kost C.

PLoS Comput Biol. 2016 Jun 17;12(6):e1004986. doi: 10.1371/journal.pcbi.1004986. eCollection 2016 Jun.

20.

A Genome-Scale Database and Reconstruction of Caenorhabditis elegans Metabolism.

Gebauer J, Gentsch C, Mansfeld J, Schmeißer K, Waschina S, Brandes S, Klimmasch L, Zamboni N, Zarse K, Schuster S, Ristow M, Schäuble S, Kaleta C.

Cell Syst. 2016 May 25;2(5):312-22. doi: 10.1016/j.cels.2016.04.017. Epub 2016 May 19.

21.

Metabolic network architecture and carbon source determine metabolite production costs.

Waschina S, D'Souza G, Kost C, Kaleta C.

FEBS J. 2016 Jun;283(11):2149-63. doi: 10.1111/febs.13727. Epub 2016 May 5.

22.

Branched-chain amino acid catabolism is a conserved regulator of physiological ageing.

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 J, Witte OW, Zarse K, Ristow M.

Nat Commun. 2015 Dec 1;6:10043. doi: 10.1038/ncomms10043.

23.

Mathematical models for explaining the Warburg effect: a review focussed on ATP and biomass production.

Schuster S, Boley D, Möller P, Stark H, Kaleta C.

Biochem Soc Trans. 2015 Dec;43(6):1187-94. doi: 10.1042/BST20150153. Review.

PMID:
26614659
24.

Optimality in the zonation of ammonia detoxification in rodent liver.

Bartl M, Pfaff M, Ghallab A, Driesch D, Henkel SG, Hengstler JG, Schuster S, Kaleta C, Gebhardt R, Zellmer S, Li P.

Arch Toxicol. 2015 Nov;89(11):2069-78. doi: 10.1007/s00204-015-1596-4. Epub 2015 Oct 5.

PMID:
26438405
25.

Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation.

de Hijas-Liste GM, Balsa-Canto E, Ewald J, Bartl M, Li P, Banga JR, Kaleta C.

BMC Bioinformatics. 2015 May 16;16:163. doi: 10.1186/s12859-015-0587-z.

26.

Footprints of optimal protein assembly strategies in the operonic structure of prokaryotes.

Ewald J, Kötzing M, Bartl M, Kaleta C.

Metabolites. 2015 Apr 28;5(2):252-69. doi: 10.3390/metabo5020252.

27.

Plasticity and epistasis strongly affect bacterial fitness after losing multiple metabolic genes.

D'Souza G, Waschina S, Kaleta C, Kost C.

Evolution. 2015 May;69(5):1244-54. doi: 10.1111/evo.12640. Epub 2015 Apr 27.

PMID:
25765095
28.

Computing autocatalytic sets to unravel inconsistencies in metabolic network reconstructions.

Schmidt R, Waschina S, Boettger-Schmidt D, Kost C, Kaleta C.

Bioinformatics. 2015 Feb 1;31(3):373-81. doi: 10.1093/bioinformatics/btu658. Epub 2014 Oct 5.

PMID:
25286919
29.

Less is more: selective advantages can explain the prevalent loss of biosynthetic genes in bacteria.

D'Souza G, Waschina S, Pande S, Bohl K, Kaleta C, Kost C.

Evolution. 2014 Sep;68(9):2559-70. doi: 10.1111/evo.12468. Epub 2014 Jul 9.

PMID:
24910088
30.

Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria.

Pande S, Merker H, Bohl K, Reichelt M, Schuster S, de Figueiredo LF, Kaleta C, Kost C.

ISME J. 2014 May;8(5):953-62. doi: 10.1038/ismej.2013.211. Epub 2013 Nov 28.

31.

In silico approaches and the role of ontologies in aging research.

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, Wuttke D.

Rejuvenation Res. 2013 Dec;16(6):540-6. doi: 10.1089/rej.2013.1517.

32.

Dynamic optimization identifies optimal programmes for pathway regulation in prokaryotes.

Bartl M, Kötzing M, Schuster S, Li P, Kaleta C.

Nat Commun. 2013;4:2243. doi: 10.1038/ncomms3243.

PMID:
23979724
33.

Metabolic costs of amino acid and protein production in Escherichia coli.

Kaleta C, Schäuble S, Rinas U, Schuster S.

Biotechnol J. 2013 Sep;8(9):1105-14. doi: 10.1002/biot.201200267. Epub 2013 Jul 15.

PMID:
23744758
34.

Detecting and investigating substrate cycles in a genome-scale human metabolic network.

Gebauer J, Schuster S, de Figueiredo LF, Kaleta C.

FEBS J. 2012 Sep;279(17):3192-202. doi: 10.1111/j.1742-4658.2012.08700.x. Epub 2012 Aug 17.

35.

Against the stream: relevance of gluconeogenesis from fatty acids for natives of the arctic regions.

Kaleta C, de Figueiredo LF, Schuster S.

Int J Circumpolar Health. 2012 May 3;71(0):1-2. doi: 10.3402/ijch.v71i0.18436.

36.

More than just a metabolic regulator--elucidation and validation of new targets of PdhR in Escherichia coli.

Göhler AK, Kökpinar Ö, Schmidt-Heck W, Geffers R, Guthke R, Rinas U, Schuster S, Jahreis K, Kaleta C.

BMC Syst Biol. 2011 Dec 14;5:197. doi: 10.1186/1752-0509-5-197.

37.

Detecting structural invariants in biological reaction networks.

Behre J, de Figueiredo LF, Schuster S, Kaleta C.

Methods Mol Biol. 2012;804:377-407. doi: 10.1007/978-1-61779-361-5_20. Review.

PMID:
22144164
38.

Hands-on metabolism analysis of complex biochemical networks using elementary flux modes.

Schäuble S, Schuster S, Kaleta C.

Methods Enzymol. 2011;500:437-56. doi: 10.1016/B978-0-12-385118-5.00022-0.

PMID:
21943910
39.

In silico evidence for gluconeogenesis from fatty acids in humans.

Kaleta C, de Figueiredo LF, Werner S, Guthke R, Ristow M, Schuster S.

PLoS Comput Biol. 2011 Jul;7(7):e1002116. doi: 10.1371/journal.pcbi.1002116. Epub 2011 Jul 21.

40.

Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs.

Wessely F, Bartl M, Guthke R, Li P, Schuster S, Kaleta C.

Mol Syst Biol. 2011 Jul 19;7:515. doi: 10.1038/msb.2011.46.

41.

Combining metabolic pathway analysis with Evolutionary Game Theory: explaining the occurrence of low-yield pathways by an analytic optimization approach.

Schuster S, de Figueiredo LF, Schroeter A, Kaleta C.

Biosystems. 2011 Aug;105(2):147-53. doi: 10.1016/j.biosystems.2011.05.007. Epub 2011 May 19.

PMID:
21620931
42.

Special issue: integration of OMICs datasets into metabolic pathway analysis.

Kaleta C, de Figueiredo LF, Heiland I, Klamt S, Schuster S.

Biosystems. 2011 Aug;105(2):107-8. doi: 10.1016/j.biosystems.2011.05.008. Epub 2011 May 18. No abstract available.

PMID:
21619911
43.

Inhibition of alanine aminotransferase in silico and in vivo promotes mitochondrial metabolism to impair malignant growth.

Beuster G, Zarse K, Kaleta C, Thierbach R, Kiehntopf M, Steinberg P, Schuster S, Ristow M.

J Biol Chem. 2011 Jun 24;286(25):22323-30. doi: 10.1074/jbc.M110.205229. Epub 2011 May 3.

44.

Predicting novel pathways in genome-scale metabolic networks.

Schuster S, de Figueiredo LF, Kaleta C.

Biochem Soc Trans. 2010 Oct;38(5):1202-5. doi: 10.1042/BST0381202.

PMID:
20863284
45.

Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis.

Kaleta C, Göhler A, Schuster S, Jahreis K, Guthke R, Nikolajewa S.

BMC Syst Biol. 2010 Aug 18;4:116. doi: 10.1186/1752-0509-4-116.

46.

A parallel algorithm to compute chemical organizations in biological networks.

Centler F, Kaleta C, Speroni di Fenizio P, Dittrich P.

Bioinformatics. 2010 Jul 15;26(14):1788-9. doi: 10.1093/bioinformatics/btq263. Epub 2010 May 25.

PMID:
20501552
47.

Theoretical study of lipid biosynthesis in wild-type Escherichia coli and in a protoplast-type L-form using elementary flux mode analysis.

Kenanov D, Kaleta C, Petzold A, Hoischen C, Diekmann S, Siddiqui RA, Schuster S.

FEBS J. 2010 Feb;277(4):1023-34. doi: 10.1111/j.1742-4658.2009.07546.x. Epub 2010 Jan 20.

48.

Response to comment on 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'.

de Figueiredo LF, Schuster S, Kaleta C, Fell DA.

Bioinformatics. 2009 Dec 15;25(24):3330-1. doi: 10.1093/bioinformatics/btp591. Epub 2009 Oct 13. No abstract available.

PMID:
19825797
49.

Computing the shortest elementary flux modes in genome-scale metabolic networks.

de Figueiredo LF, Podhorski A, Rubio A, Kaleta C, Beasley JE, Schuster S, Planes FJ.

Bioinformatics. 2009 Dec 1;25(23):3158-65. doi: 10.1093/bioinformatics/btp564. Epub 2009 Sep 30.

PMID:
19793869
50.

Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns.

Kaleta C, de Figueiredo LF, Schuster S.

Genome Res. 2009 Oct;19(10):1872-83. doi: 10.1101/gr.090639.108. Epub 2009 Jun 18.

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