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Items: 41

1.

p13CMFA: Parsimonious 13C metabolic flux analysis.

Foguet C, Jayaraman A, Marin S, Selivanov VA, Moreno P, Messeguer R, de Atauri P, Cascante M.

PLoS Comput Biol. 2019 Sep 6;15(9):e1007310. doi: 10.1371/journal.pcbi.1007310. eCollection 2019 Sep.

2.

Interoperable and scalable data analysis with microservices: applications in metabolomics.

Emami Khoonsari P, Moreno P, Bergmann S, Burman J, Capuccini M, Carone M, Cascante M, de Atauri P, Foguet C, Gonzalez-Beltran AN, Hankemeier T, Haug K, He S, Herman S, Johnson D, Kale N, Larsson A, Neumann S, Peters K, Pireddu L, Rocca-Serra P, Roger P, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Schober D, Selivanov V, Thévenot EA, van Vliet M, Zanetti G, Steinbeck C, Kultima K, Spjuth O.

Bioinformatics. 2019 Oct 1;35(19):3752-3760. doi: 10.1093/bioinformatics/btz160.

3.

PhenoMeNal: processing and analysis of metabolomics data in the cloud.

Peters K, Bradbury J, Bergmann S, Capuccini M, Cascante M, de Atauri P, Ebbels TMD, Foguet C, Glen R, Gonzalez-Beltran A, Günther UL, Handakas E, Hankemeier T, Haug K, Herman S, Holub P, Izzo M, Jacob D, Johnson D, Jourdan F, Kale N, Karaman I, Khalili B, Emami Khonsari P, Kultima K, Lampa S, Larsson A, Ludwig C, Moreno P, Neumann S, Novella JA, O'Donovan C, Pearce JTM, Peluso A, Piras ME, Pireddu L, Reed MAC, Rocca-Serra P, Roger P, Rosato A, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Selivanov V, Spjuth O, Schober D, Thévenot EA, Tomasoni M, van Rijswijk M, van Vliet M, Viant MR, Weber RJM, Zanetti G, Steinbeck C.

Gigascience. 2019 Feb 1;8(2). pii: giy149. doi: 10.1093/gigascience/giy149.

4.

Untargeted metabolomics reveals distinct metabolic reprogramming in endothelial cells co-cultured with CSC and non-CSC prostate cancer cell subpopulations.

Jayaraman A, Kumar P, Marin S, de Atauri P, Mateo F, M Thomson T, J Centelles J, F Graham S, Cascante M.

PLoS One. 2018 Feb 21;13(2):e0192175. doi: 10.1371/journal.pone.0192175. eCollection 2018.

5.

Network modules uncover mechanisms of skeletal muscle dysfunction in COPD patients.

Tényi Á, Cano I, Marabita F, Kiani N, Kalko SG, Barreiro E, de Atauri P, Cascante M, Gomez-Cabrero D, Roca J.

J Transl Med. 2018 Feb 20;16(1):34. doi: 10.1186/s12967-018-1405-y.

6.

In-silico gene essentiality analysis of polyamine biosynthesis reveals APRT as a potential target in cancer.

Pey J, San José-Eneriz E, Ochoa MC, Apaolaza I, de Atauri P, Rubio A, Cendoya X, Miranda E, Garate L, Cascante M, Carracedo A, Agirre X, Prosper F, Planes FJ.

Sci Rep. 2017 Oct 30;7(1):14358. doi: 10.1038/s41598-017-14067-8.

7.

De novo MYC addiction as an adaptive response of cancer cells to CDK4/6 inhibition.

Tarrado-Castellarnau M, de Atauri P, Tarragó-Celada J, Perarnau J, Yuneva M, Thomson TM, Cascante M.

Mol Syst Biol. 2017 Oct 4;13(10):940. doi: 10.15252/msb.20167321.

8.

Oncogenic regulation of tumor metabolic reprogramming.

Tarrado-Castellarnau M, de Atauri P, Cascante M.

Oncotarget. 2016 Sep 20;7(38):62726-62753. doi: 10.18632/oncotarget.10911. Review.

9.

Strategies for structuring interdisciplinary education in Systems Biology: an European perspective.

Cvijovic M, Höfer T, Aćimović J, Alberghina L, Almaas E, Besozzi D, Blomberg A, Bretschneider T, Cascante M, Collin O, de Atauri P, Depner C, Dickinson R, Dobrzynski M, Fleck C, Garcia-Ojalvo J, Gonze D, Hahn J, Hess HM, Hollmann S, Krantz M, Kummer U, Lundh T, Martial G, Dos Santos VM, Mauer-Oberthür A, Regierer B, Skene B, Stalidzans E, Stelling J, Teusink B, Workman CT, Hohmann S.

NPJ Syst Biol Appl. 2016 May 26;2:16011. doi: 10.1038/npjsba.2016.11. eCollection 2016.

10.

Metabolic Reprogramming and Dependencies Associated with Epithelial Cancer Stem Cells Independent of the Epithelial-Mesenchymal Transition Program.

Aguilar E, Marin de Mas I, Zodda E, Marin S, Morrish F, Selivanov V, Meca-Cortés Ó, Delowar H, Pons M, Izquierdo I, Celià-Terrassa T, de Atauri P, Centelles JJ, Hockenbery D, Thomson TM, Cascante M.

Stem Cells. 2016 May;34(5):1163-76. doi: 10.1002/stem.2286. Epub 2016 Feb 2.

11.

HepatoDyn: A Dynamic Model of Hepatocyte Metabolism That Integrates 13C Isotopomer Data.

Foguet C, Marin S, Selivanov VA, Fanchon E, Lee WN, Guinovart JJ, de Atauri P, Cascante M.

PLoS Comput Biol. 2016 Apr 28;12(4):e1004899. doi: 10.1371/journal.pcbi.1004899. eCollection 2016 Apr.

12.

ChainRank, a chain prioritisation method for contextualisation of biological networks.

Tényi Á, de Atauri P, Gomez-Cabrero D, Cano I, Clarke K, Falciani F, Cascante M, Roca J, Maier D.

BMC Bioinformatics. 2016 Jan 5;17:17. doi: 10.1186/s12859-015-0864-x.

13.

Sampling with poling-based flux balance analysis: optimal versus sub-optimal flux space analysis of Actinobacillus succinogenes.

Binns M, de Atauri P, Vlysidis A, Cascante M, Theodoropoulos C.

BMC Bioinformatics. 2015 Feb 18;16:49. doi: 10.1186/s12859-015-0476-5.

14.

Workforce preparation: the Biohealth computing model for Master and PhD students.

Cascante M, de Atauri P, Gomez-Cabrero D, Wagner P, Centelles JJ, Marin S, Cano I, Velickovski F, Marin de Mas I, Maier D, Roca J, Sabatier P.

J Transl Med. 2014 Nov 28;12 Suppl 2:S11. doi: 10.1186/1479-5876-12-S2-S11. Epub 2014 Nov 28. Review.

15.

Effects of cadmium and mercury on the upper part of skeletal muscle glycolysis in mice.

Ramírez-Bajo MJ, de Atauri P, Ortega F, Westerhoff HV, Gelpí JL, Centelles JJ, Cascante M.

PLoS One. 2014 Jan 28;9(1):e80018. doi: 10.1371/journal.pone.0080018. eCollection 2014.

16.

Relevance of the MEK/ERK signaling pathway in the metabolism of activated macrophages: a metabolomic approach.

Través PG, de Atauri P, Marín S, Pimentel-Santillana M, Rodríguez-Prados JC, Marín de Mas I, Selivanov VA, Martín-Sanz P, Boscá L, Cascante M.

J Immunol. 2012 Feb 1;188(3):1402-10. doi: 10.4049/jimmunol.1101781. Epub 2011 Dec 21.

17.

Enzymatic and metabolic characterization of the phosphoglycerate kinase deficiency associated with chronic hemolytic anemia caused by the PGK-Barcelona mutation.

Ramírez-Bajo MJ, Repiso A, la Ossa PP, Bañón-Maneus E, de Atauri P, Climent F, Corrons JL, Cascante M, Carreras J.

Blood Cells Mol Dis. 2011 Mar 15;46(3):206-11. doi: 10.1016/j.bcmd.2010.12.009. Epub 2011 Jan 26.

PMID:
21269848
18.

Carbon metabolism and the sign of control coefficients in metabolic adaptations underlying K-ras transformation.

de Atauri P, Benito A, Vizán P, Zanuy M, Mangues R, Marín S, Cascante M.

Biochim Biophys Acta. 2011 Jun;1807(6):746-54. doi: 10.1016/j.bbabio.2010.11.015. Epub 2010 Dec 23.

19.

Metabolic network adaptations in cancer as targets for novel therapies.

Cascante M, Benito A, Zanuy M, Vizán P, Marín S, de Atauri P.

Biochem Soc Trans. 2010 Oct;38(5):1302-6. doi: 10.1042/BST0381302.

PMID:
20863303
20.

In silico strategy to rationally engineer metabolite production: A case study for threonine in Escherichia coli.

Rodríguez-Prados JC, de Atauri P, Maury J, Ortega F, Portais JC, Chassagnole C, Acerenza L, Lindley ND, Cascante M.

Biotechnol Bioeng. 2009 Jun 15;103(3):609-20. doi: 10.1002/bit.22271.

PMID:
19219914
21.

The changes in the energy metabolism of human muscle induced by training.

Selivanov VA, de Atauri P, Centelles JJ, Cadefau J, Parra J, Cussó R, Carreras J, Cascante M.

J Theor Biol. 2008 Jun 7;252(3):402-10. Epub 2007 Oct 5.

PMID:
17996255
22.

Evolution of 'design' principles in biochemical networks.

de Atauri P, Orrell D, Ramsey S, Bolouri H.

Syst Biol (Stevenage). 2004 Jun;1(1):28-40.

PMID:
17052113
23.

Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast.

Ramsey SA, Smith JJ, Orrell D, Marelli M, Petersen TW, de Atauri P, Bolouri H, Aitchison JD.

Nat Genet. 2006 Sep;38(9):1082-7. Epub 2006 Aug 27.

PMID:
16936734
24.

Transcriptional noise and cellular heterogeneity in mammalian macrophages.

Ramsey S, Ozinsky A, Clark A, Smith KD, de Atauri P, Thorsson V, Orrell D, Bolouri H.

Philos Trans R Soc Lond B Biol Sci. 2006 Mar 29;361(1467):495-506. Review.

25.

A data integration methodology for systems biology.

Hwang D, Rust AG, Ramsey S, Smith JJ, Leslie DM, Weston AD, de Atauri P, Aitchison JD, Hood L, Siegel AF, Bolouri H.

Proc Natl Acad Sci U S A. 2005 Nov 29;102(48):17296-301. Epub 2005 Nov 21.

26.

A data integration methodology for systems biology: experimental verification.

Hwang D, Smith JJ, Leslie DM, Weston AD, Rust AG, Ramsey S, de Atauri P, Siegel AF, Bolouri H, Aitchison JD, Hood L.

Proc Natl Acad Sci U S A. 2005 Nov 29;102(48):17302-7. Epub 2005 Nov 21.

27.

Metabolic homeostasis in the human erythrocyte: in silico analysis.

de Atauri P, Ramírez MJ, Kuchel PW, Carreras J, Cascante M.

Biosystems. 2006 Feb-Mar;83(2-3):118-24. Epub 2005 Oct 19.

PMID:
16236423
28.

Characterization of the first described mutation of human red blood cell phosphoglycerate mutase.

de Atauri P, Repiso A, Oliva B, Vives-Corrons JL, Climent F, Carreras J.

Biochim Biophys Acta. 2005 Jun 10;1740(3):403-10. Epub 2004 Dec 10.

29.

Is the regulation of galactose 1-phosphate tuned against gene expression noise?

de Atauri P, Orrell D, Ramsey S, Bolouri H.

Biochem J. 2005 Apr 1;387(Pt 1):77-84.

30.

A method for estimating stochastic noise in large genetic regulatory networks.

Orrell D, Ramsey S, de Atauri P, Bolouri H.

Bioinformatics. 2005 Jan 15;21(2):208-17. Epub 2004 Aug 19.

PMID:
15319259
31.

Mathematical modelling of the urea cycle. A numerical investigation into substrate channelling.

Maher AD, Kuchel PW, Ortega F, de Atauri P, Centelles J, Cascante M.

Eur J Biochem. 2003 Oct;270(19):3953-61.

32.

Characterization of the transit and transition times for a pathway unit of Michaelis-Menten mechanism.

Sakamoto N, de Atauri P, Cascante M.

Biochim Biophys Acta. 2003 Sep 8;1623(1):6-12.

PMID:
12957711
33.

Dynamic simulation of pollutant effects on the threonine pathway in Escherichia coli.

Chassagnole C, Quentin E, Fell DA, de Atauri P, Mazat JP.

C R Biol. 2003 May;326(5):501-8.

PMID:
12886877
34.
35.

Metabolic control analysis aimed at the ribose synthesis pathways of tumor cells: a new strategy for antitumor drug development.

Boren J, Montoya AR, de Atauri P, Comin-Anduix B, Cortes A, Centelles JJ, Frederiks WM, Van Noorden CJ, Cascante M.

Mol Biol Rep. 2002;29(1-2):7-12.

PMID:
12241078
36.
37.

Metabolic control analysis in drug discovery and disease.

Cascante M, Boros LG, Comin-Anduix B, de Atauri P, Centelles JJ, Lee PW.

Nat Biotechnol. 2002 Mar;20(3):243-9. Review.

PMID:
11875424
38.

Occurrence of paradoxical or sustained control by an enzyme when overexpressed: necessary conditions and experimental evidence with regard to hepatic glucokinase.

De Atauri P, Acerenza L, Kholodenko BN, De La Iglesia N, Guinovart JJ, Agius L, Cascante M.

Biochem J. 2001 May 1;355(Pt 3):787-93.

39.

Analysis and prediction of the effect of uncertain boundary values in modeling a metabolic pathway.

de Atauri P, Sorribas A, Cascante M.

Biotechnol Bioeng. 2000 Apr 5;68(1):18-30.

PMID:
10699868
40.

Advantages and disadvantages of aggregating fluxes into synthetic and degradative fluxes when modelling metabolic pathways.

De Atauri P, Curto R, Puigjaner J, Cornish-Bowden A, Cascante M.

Eur J Biochem. 1999 Oct;265(2):671-9.

41.

Effects of feedback inhibition on transit time in a linear pathway of Michaelis-Menten-type reactions.

Sakamoto N, de Atauri P, Cascante M.

Biosystems. 1998 Mar;45(3):221-35.

PMID:
9648667

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