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Publications

48Posavec Marjanović M, Hurtado-Bagès S, Lassi M, Valero V, Malinverni R, Delage H, Navarro M, Corujo D, Guberovic I, Douet J, Gama-Perez P, Garcia-Roves PM, Ahel I, Ladurner AG, Yanes O, Bouvet P, Suelves M, Teperino R, Pospisilik JA, Buschbeck M. “The histone macroH2A1.1 facilitates mitochondrial respiration by limiting nuclear NAD+ consumption in differentiated muscle cells”. Nature Structural & Molecular Biology, 2017 Oct 9. doi: 10.1038/nsmb.3481.

47Soukupova J , Malfettone A, Hyroššová P, Hernández-Alvarez M , Peñuelas-Haro I, Dr. Bertran E, Junza A, Capellades J, Giannelli G, Yanes O, Zorzano A, Perales J, Fabregat I. “Role of the Transforming Growth Factor-β in regulating hepatocellular carcinoma oxidative metabolism”. Scientific Reports, 2017 Oct 2;7(1):12486. doi: 10.1038/s41598-017-12837-y.

46Leal-Witt M, Ramon-Krauel M, Samino S, Llobet M, Cuadras D, Jiménez-Chillarón J, Yanes O, Lerin C. “Untargeted metabolomics identifies a plasma sphingolipid-related signature associated with lifestyle intervention in prepubertal children with obesity”. International Journal of Obesity, 2017 Aug 17. doi: 10.1038/ijo.2017.201. Open data via MetaboLights (MTBLSxxx).

45Ràfols P, Torres S, Ramírez N, del Castillo E, Yanes O, Brezmes J, Correig X. “rMSI: an R package for MS imaging data handling and visualization”. Bioinformatics, 2017 Mar 29. doi: 10.1093/bioinformatics/btx182.

44Vinaixa M, Rodríguez MA, Aivio S, Capellades J, Gómez J, Canyellas N, Stracker TH, Yanes O. “Positional Enrichment by Proton Analysis (PEPA): A One-Dimensional 1H-NMR Approach for 13C Stable Isotope Tracer Studies in Metabolomics“. Angewandte Chemie Int Ed. 2017 Feb 21. doi: 10.1002/anie.201611347. Open data via MetaboLights (MTBLS247).

43Cacciatore S, Zadra G, Bango C, Penney KL, Tyekucheva S, Yanes O, Loda M. “Metabolic Profiling in Formalin-Fixed and Paraffin Embedded Prostate Cancer Tissues“. Molecular Cancer Research. 2017 Jan 10. doi: 10.1158/1541-7786.

42Ràfols P, Vilalta D, Brezmes J, Cañellas N, del Castillo E, Yanes O, Ramírez N, Correig X. “Signal preprocessing, multivariate analysis and software tools for MA(LDI)-TOF mass spectrometry imaging for biological applications“. Mass Spectrometry Reviews, 2016 Nov 9. doi: 10.1002/mas.21527.

41Ratajczak J, Joffraud M, Trammell S, Ras R, Canela N, Boutant M, Kulkarni S, Rodrigues M, Redpath P, Migaud M, Auwerx J, Yanes O, Brenner C, Canto C. “NRK1 controls nicotinamide mononucleotide and nicotinamide riboside metabolism in mammalian cells“. Nature Communications, 2016 Oct 11;7:13103. doi: 10.1038/ncomms13103..

40Aguilar-Mogas A, Sales-Pardo M, Navarro M, Guimerà R, Yanes O. “iMet: a network-based computational tool to assist in the annotation of metabolites from tandem mass spectra“. Analytical Chemistry, 2017 Mar 21;89(6):3474-3482. doi: 10.1021/acs.analchem.6b04512. Alpha-version here.

39, , , , ,, , , , , , . “eRah: A computational tool integrating spectral deconvolution and alignment with quantification and identification of metabolites in GC-MS-based metabolomics“. Analytical Chemistry, 2016. doi: 10.1021/acs.analchem.6b02927. CRAN-Package eRah. Open data via MetaboLights (MTBLS321).

38Temprano A, Sembongi H, Han GS, Sebastián D, Capellades J, Moreno C, Guardiola J, Wabitsch M, Richart C, Yanes O, Zorzano A, Carman GM, Siniossoglou S, Miranda M. “Redundant roles of the phosphatidate phosphatase family in triacylglycerol synthesis in human adipocytes“. Diabetologia. 2016 Jun 25. doi:10.1007/s00125-016-4018-0.

37Wright RH, Lioutas A, Le Dily F, Soronellas D, Pohl A, Bonet J, Nacht AS, Samino S, Font-Mateu J, Vicent GP, Wierer M, Trabado MA, Schelhorn C, Carolis C, Macias MJ, Yanes O, Oliva B, Beato M. “ADP-ribose-derived nuclear ATP synthesis by NUDIX5 is required for chromatin remodeling“. Science. 2016 Jun 3;352(6290):1221-5. doi: 10.1126/science.aad9335.

36Slebe F, Rojo F, Vinaixa M, García-Rocha M, Testoni G, Guiu M, Planet E, Samino S, Arenas EJ, Beltran A, Rovira A, Lluch A, Salvatella X, Yanes O, Albanell J, Guinovart JJ, Gomis RR. “FoxA and LIPG endothelial lipase control the uptake of extracellular lipids for breast cancer growth“. Nature Communications. 2016 Apr 5;7:11199. doi: 10.1038/ncomms11199.

35Amigó N, Mallol R, Heras M, Martínez-Hervás S, Blanco-Vaca F, Escolà-Gil JC, Plana N, Yanes O, Masana L, Correig X. “Lipoprotein hydrophobic core lipids are partially extruded to surface in smaller HDL: Herniated HDL, a common feature in diabetes“. Scientific Reports, 2016 Jan 18;6:19249. doi: 10.1038/srep19249.

34Capellades J, Navarro M, Samino S, Garcia-Ramirez M, Hernandez C, Simo R, Vinaixa M, Yanes O. “geoRge: a computational tool to detect the presence of stable isotope labeling in LC/MS-based untargeted metabolomics“. Analytical Chemistry, Dec 6 2015; doi: 10.1021/acs.analchem.5b03628. geoRge is available as an R script and open data via MetaboLights (MTBLS213).

33Ceperuelo-Mallafre V, Ejarque M, Duran X, Montori-Grau M, Rodríguez MA, Yanes O, Núñez-Roa C, Roche K, Garrido-Sánchez L, Saez E, Tinahones FJ, Gómez-Foix A, Vendrell J, Fernández-Veledo S. “Adipose tissue glycogen accumulation is associated with obesity-linked inflammation in humans“. Molecular Metabolism, Jan 2016; doi: 10.1016/j.molmet.2015.10.001.

32Vinaixa M, Schymanski EL, Neumann S, Navarro M, Salek RM, Yanes O. “Mass spectral databases for LC/MS and GC/MS-based metabolomics: state of the field and future prospects“. Trends in Analytical Chemistry, 2016; 78, 23-35. doi:10.1016/j.trac.2015.09.005.

31Samino S, Vinaixa M, Diaz M, Beltran A, Rodriguez MA, Mallol R, Heras M, Cabre A, Garcia L, Canela N, de Zegher F, Correig X, Ibañez L, Yanes O. “Metabolomics reveals impaired maturation of HDL particles in adolescents with hyperinsulinaemic androgen excess”. Scientific Reports, 2015; 5, 11496; doi: 10.1038/srep11496. Open data via MetaboLights (MTBLS103)

30Valli A, Rodriguez M, Moutsianas L, Fischer R, Fedele V, Huang HL, Van Stiphout R, Jones D, Mccarthy M, Vinaxia M, Igarashi K, Sato M, Soga T, Buffa F, Mccullagh J, Yanes O, Harris A, Kessler B. “Hypoxia induces a lipogenic cancer cell phenotype via HIF1α-dependent and -independent pathways”. Oncotarget. 2015 Feb 10;6(4):1920-41.

29Mallol R, Amigó N, Rodríguez MA, Heras M, Vinaixa M, Plana N, Rock E, Ribalta J, Yanes O, Masana L, Correig C. “Liposcale: a novel advanced lipoprotein test based on 2D diffusion-ordered 1H NMR spectroscopy”. Journal of Lipid Research, 2015 Jan 7. pii: jlr.D050120. [Epub ahead of print].

28Beltran A, Samino S, Yanes O. “Sample Preparation Methods for LC-MS-Based Global Aqueous Metabolite Profiling”. Methods Mol Biol. 2014;1198:75-80. doi:10.1007/978-1-4939-1258-2_5.

27Malpique R, Figueiredo H, Esteban Y, Rebuffat SA, Hanzu FA, Vinaixa M, Yanes O, Correig X, Barceló-Batllori S, Gasa R, Kalko SG, Gomis R. “Integrative analysis reveals novel pathways mediating the interaction between adipose tissue and pancreatic islets in obesity in rats”. Diabetologia, 2014 Jun;57(6):1219-31. doi: 10.1007/s00125-014-3205-0.

26Saez I, Duran J, Sinadinos C, Beltran A, Yanes O, Tevy MF, Martínez-Pons C, Milán M, Guinovart JJ. “Neurons have an active glycogen metabolism that contributes to tolerance to hypoxia”. J Cereb Blood Flow Metab, 2014, Feb 26. doi:10.1038/jcbfm.2014.33.

25Yanes O. “Metabolomics: Playing piñata with single cells”. Nature Chemical Biology, 2013, 9(8):471-3.

24Vinaixa M, Samino S, Saez I, Duran J, Guinovart JJ, Yanes O. “A guideline to univariate statistical analysis for LC/MS-based untargeted metabolomics-derived data”. Metabolites, 2012, 2(4), 775-795; doi:10.3390/metabo2040775.

23Beltran A, Suarez M, Rodríguez MA, Vinaixa M, Samino S, Arola L, Correig X, Yanes O. “Assessment of compatibility between extraction methods for NMR- and LC/MS-based metabolomics”. Analytical Chemistry, 2012 Jul 17;84(14):5838-44.

22Calavia R, Annanouch F, Correig X, Yanes O. “Nanostructure Initiator Mass Spectrometry for Tissue Imaging in Metabolomics: Future Prospects and Perspectives”. Journal of Proteomics, 2012 Aug 30;75(16):5061-8. doi: 10.1016/j.jprot.2012.05.00.

21Patti G.J., Yanes O., Siuzdak G. “Metabolomics: The Apogee of the Omic Trilogy”. Nature Reviews Molecular Cell Biology, 2012, 13; 263-269. doi: 10.1038/nrm3314.

20Vinaixa M, Rodríguez MA,Samino S, Díaz M, Beltran A, Mallol R, Bladé C, Ibañez L, Correig X, Yanes O. “Metabolomics reveals reduction of metabolic oxidation in women with polycystic ovary syndrome after pioglitazone-flutamide-metformin polytherapy”. PLoS ONE2011; 6(12):e29052.

19Panopoulos AD*, Yanes O*, Ruiz S, Kida Y, Diep D, Tautenhahn R, Herrerías A, Batchelder EM, Plongthongkum N, Lutz M, Berggren WT, Zhang K, Evans RM, Siuzdak G, Izpisua-Belmonte JC. “The metabolome of induced pluripotent stem cells reveals metabolic changes required for somatic cell reprogramming”. Cell Research2011 Nov 8. doi: 10.1038/cr.2011.177

18Marchetti V*, Yanes O*, AguilarE, Friedlander D, Wong M, Naccache S, Nemerow G, Siuzdak G, Friedlander M. “Differential Macrophage Polarization promotes Tissue Remodeling and Repair in a Model of Ischemic Retinopathy”. Scientific Reports, 2011; 1 (76), doi:10.1038/srep00076.

17Patti GJ*, Yanes O*, Shriver L, Courade JP, Tautenhahn R, Manchester M, Siuzdak G. “Metabolomics implicates altered sphingolipids in chronic pain of neuropathic origin”. Nature Chemical Biology, 2012 Jan 22. doi: 10.1038/nchembio.767.

16Yanes O, Tautenhahn R, Patti GJ, Siuzdak G. “Expanding Coverage of the Metabolome for Global Metabolite Profiling”. Analytical Chemistry, 2011; 83(6):2152-61

15Yanes O, Clark J, Wong D.M, Patti J.G., Sanchez-Ruiz A, Benton P, Trauger S.A, Desponts C, Ding S, Siuzdak G. “Metabolic oxidation regulates stem cell differentiation”. Nature Chemical Biology, 2010; 6(6): 411-7.

14Cedano J*, Yanes O*, Ferrer-Navarro M, Bronsoms S, Querol E, Aviles FX. “MAPI: a Server for Improving Protein Identification from a Four Matrices Mass Spectrometry Approach”. Current Proteomics, 2010; 7.

13Patti G.J, Woo, H.K. Yanes O, Leah S, Diane T, Uritboonthai W, Apon J, Manchester M, Siuzdak G. “Detection of Carbohydrates and Steroids by Cation-enhanced Nanostructure-Initiator Mass Spectrometry (NIMS) for Biofluid Analysis and Tissue Imaging”. Analytical Chemistry, 2010; 82 (1): 121-8.

12Yanes O, Woo H.K, Northen T.R, Oppenheimer S, Shriver L, Apon J, Estrada M.N, Potchoiba MJ, Steenwyk R, Manchester M, Siuzdak G. “Nanostructure Initiator Mass Spectrometry (NIMS): Tissue Imaging and Direct Biofluid Analysis”. Analytical Chemistry, 2009 (20).

11Dorrell MI, Aguilar E, Jacobson R, Yanes O, Gariano R, Heckenlively J, Banin E, Ramirez G.A, Gasmi M, Bird A, Siuzdak G, Friedlander M. “Antioxidant or neurotrophic factor treatment preserves function in a mouse model of neovascularization-associated oxidative stress”. Journal of Clinical Investigation, 2009 (2).

10Woo H.K, Northen T.R, Yanes O, Siuzdak G. “Nanostructure-Initiator Mass Spectrometry (NIMS): a protocol for preparing and applying NIMS surfaces for high sensitivity mass analysis”. Nature Protocols, 2008, 3(8):1341-9.

09Northen TR*, Yanes O*, Northen MT, Marrinucci D, Uritboonthai W, Apon J, Golledge SL, Nordström A, Siuzdak G. “Clathrate nanostructures for mass spectrometry”. Nature, 2007, Oct 25; 449 (7165):1033-6.

08Yanes O, Villanueva J, Querol E, Aviles F.X. “Detection of non-covalent protein interactions by ‘intensity fading’ MALDI-TOF mass spectrometry: applications to proteases and protease inhibitors”. Nature Protocols, 2007, 2(1):119-30.

07Yanes O, Wenzel R, Calvete J.J, Nazabal A, Aviles F.X., Zenobi R. “Proteomic profiling of a snake venom using cryodetection MALDI-TOF mass spectrometry”. J. Am. Soc. Mass Spectrom., 2007, Apr;18(4):600-6.

06Yanes O, Aviles F.X., Roepstorff P, and Jørgensen T.J.D. “Exploring the ‘intensity fading’ phenomenon in the study of noncovalent interactions by MALDI-TOF mass spectrometry”. J. Am. Soc. Mass Spectrom., 2007, Feb;18(2):359-67.

05Yanes O, Nazabal A, Wenzel R, Zenobi R, Aviles F.X. “Detection of Noncovalent Complexes in Biological Samples by Intensity Fading and High-Mass Detection MALDI-TOF mass spectrometry”. Journal of Proteome Research, 2006, 5(10), 2711-2719.

04Ferrer-Navarro M, Gómez A, Yanes O, Planell R, Avilés F.X., Piñol J, Pérez Pons J.A., Querol E. “Proteome of the Bacterium Mycoplasma penetrans”Journal of Proteome Research, 2006; 5(3) 688 – 694.

03Yanes O, Villanueva J, Querol E, Avilés F.X. “Functional screening of serine protease inhibitors in the medical leech Hirudo medicinalis”Molecullar & Cellular Proteomics 2005, 4, 1602-1613.

02Yanes O, Villanueva J, Querol E, Avilés F.X. “Intensity-fading MALDI-TOF MS: novel screening for ligand binding and drug discovery”. Drug Discovery Today: TARGETS 2004, 3, S23.

01Villanueva J*, Yanes O*, Querol E, Serrano L, Avilés F.X. “Identification of protein ligands in complex biological samples using Intensity-Fading MALDI-TOF Mass Spectrometry”. Analytical Chemistry 2003, 75, 3385-3395.

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