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Machine Learning Predicts the Yeast Metabolome from the Quantitative Proteome of Kinase Knockouts.

Zelezniak A, Vowinckel J, Capuano F, Messner CB, Demichev V, Polowsky N, Mülleder M, Kamrad S, Klaus B, Keller MA, Ralser M.

Cell Syst. 2018 Aug 20. pii: S2405-4712(18)30316-8. doi: 10.1016/j.cels.2018.08.001. [Epub ahead of print]


Freeing Yeast from Alcohol Addiction (Just) to Make (It) Fat Instead.

Patil KR, Ralser M.

Cell. 2018 Sep 6;174(6):1342-1344. doi: 10.1016/j.cell.2018.08.024.


An appeal to magic? The discovery of a non-enzymatic metabolism and its role in the origins of life.

Ralser M.

Biochem J. 2018 Aug 30;475(16):2577-2592. doi: 10.1042/BCJ20160866. Review.


The Nucleosome Remodeling and Deacetylation Complex Modulates Chromatin Structure at Sites of Active Transcription to Fine-Tune Gene Expression.

Bornelöv S, Reynolds N, Xenophontos M, Gharbi S, Johnstone E, Floyd R, Ralser M, Signolet J, Loos R, Dietmann S, Bertone P, Hendrich B.

Mol Cell. 2018 Jul 5;71(1):56-72.e4. doi: 10.1016/j.molcel.2018.06.003. Epub 2018 Jun 28.


Cost-effective generation of precise label-free quantitative proteomes in high-throughput by microLC and data-independent acquisition.

Vowinckel J, Zelezniak A, Bruderer R, Mülleder M, Reiter L, Ralser M.

Sci Rep. 2018 Mar 12;8(1):4346. doi: 10.1038/s41598-018-22610-4.


Partitioning of One-Carbon Units in Folate and Methionine Metabolism Is Essential for Neural Tube Closure.

Leung KY, Pai YJ, Chen Q, Santos C, Calvani E, Sudiwala S, Savery D, Ralser M, Gross SS, Copp AJ, Greene NDE.

Cell Rep. 2017 Nov 14;21(7):1795-1808. doi: 10.1016/j.celrep.2017.10.072.


Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow.

Ponomarova O, Gabrielli N, Sévin DC, Mülleder M, Zirngibl K, Bulyha K, Andrejev S, Kafkia E, Typas A, Sauer U, Ralser M, Patil KR.

Cell Syst. 2017 Oct 25;5(4):345-357.e6. doi: 10.1016/j.cels.2017.09.002. Epub 2017 Sep 27.


Metabolomics in Yeast.

Caudy AA, Mülleder M, Ralser M.

Cold Spring Harb Protoc. 2017 Sep 1;2017(9):pdb.top083576. doi: 10.1101/pdb.top083576.


A High-Throughput Method for the Quantitative Determination of Free Amino Acids in Saccharomyces cerevisiae by Hydrophilic Interaction Chromatography-Tandem Mass Spectrometry.

Mülleder M, Bluemlein K, Ralser M.

Cold Spring Harb Protoc. 2017 Sep 1;2017(9):pdb.prot089094. doi: 10.1101/pdb.prot089094.


Variable repeats in the eukaryotic polyubiquitin gene ubi4 modulate proteostasis and stress survival.

Gemayel R, Yang Y, Dzialo MC, Kominek J, Vowinckel J, Saels V, Van Huffel L, van der Zande E, Ralser M, Steensels J, Voordeckers K, Verstrepen KJ.

Nat Commun. 2017 Aug 30;8(1):397. doi: 10.1038/s41467-017-00533-4.


A lncRNA fine tunes the dynamics of a cell state transition involving Lin28, let-7 and de novo DNA methylation.

Li MA, Amaral PP, Cheung P, Bergmann JH, Kinoshita M, Kalkan T, Ralser M, Robson S, von Meyenn F, Paramor M, Yang F, Chen C, Nichols J, Spector DL, Kouzarides T, He L, Smith A.

Elife. 2017 Aug 18;6. pii: e23468. doi: 10.7554/eLife.23468.


The self-inhibitory nature of metabolic networks and its alleviation through compartmentalization.

Alam MT, Olin-Sandoval V, Stincone A, Keller MA, Zelezniak A, Luisi BF, Ralser M.

Nat Commun. 2017 Jul 10;8:16018. doi: 10.1038/ncomms16018.


Nonenzymatic gluconeogenesis-like formation of fructose 1,6-bisphosphate in ice.

Messner CB, Driscoll PC, Piedrafita G, De Volder MFL, Ralser M.

Proc Natl Acad Sci U S A. 2017 Jul 11;114(28):7403-7407. doi: 10.1073/pnas.1702274114. Epub 2017 Jun 26.


Sulfate radicals enable a non-enzymatic Krebs cycle precursor.

Keller MA, Kampjut D, Harrison SA, Ralser M.

Nat Ecol Evol. 2017 Mar 13;1(4):83. doi: 10.1038/s41559-017-0083.


THADA Regulates the Organismal Balance between Energy Storage and Heat Production.

Moraru A, Cakan-Akdogan G, Strassburger K, Males M, Mueller S, Jabs M, Muelleder M, Frejno M, Braeckman BP, Ralser M, Teleman AA.

Dev Cell. 2017 May 22;41(4):450. doi: 10.1016/j.devcel.2017.05.001. No abstract available.


THADA Regulates the Organismal Balance between Energy Storage and Heat Production.

Moraru A, Cakan-Akdogan G, Strassburger K, Males M, Mueller S, Jabs M, Muelleder M, Frejno M, Braeckman BP, Ralser M, Teleman AA.

Dev Cell. 2017 Apr 10;41(1):72-81.e6. doi: 10.1016/j.devcel.2017.03.016. Erratum in: Dev Cell. 2017 May 22;41(4):450.


3D structures of individual mammalian genomes studied by single-cell Hi-C.

Stevens TJ, Lando D, Basu S, Atkinson LP, Cao Y, Lee SF, Leeb M, Wohlfahrt KJ, Boucher W, O'Shaughnessy-Kirwan A, Cramard J, Faure AJ, Ralser M, Blanco E, Morey L, Sansó M, Palayret MGS, Lehner B, Di Croce L, Wutz A, Hendrich B, Klenerman D, Laue ED.

Nature. 2017 Apr 6;544(7648):59-64. doi: 10.1038/nature21429. Epub 2017 Mar 13.


Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy.

Weber RJM, Lawson TN, Salek RM, Ebbels TMD, Glen RC, Goodacre R, Griffin JL, Haug K, Koulman A, Moreno P, Ralser M, Steinbeck C, Dunn WB, Viant MR.

Metabolomics. 2017;13(2):12. doi: 10.1007/s11306-016-1147-x. Epub 2016 Dec 27. No abstract available.


Saccharomyces cerevisiae single-copy plasmids for auxotrophy compensation, multiple marker selection, and for designing metabolically cooperating communities.

Mülleder M, Campbell K, Matsarskaia O, Eckerstorfer F, Ralser M.

F1000Res. 2016 Sep 20;5:2351. doi: 10.12688/f1000research.9606.1. eCollection 2016.


Functional Metabolomics Describes the Yeast Biosynthetic Regulome.

Mülleder M, Calvani E, Alam MT, Wang RK, Eckerstorfer F, Zelezniak A, Ralser M.

Cell. 2016 Oct 6;167(2):553-565.e12. doi: 10.1016/j.cell.2016.09.007. Epub 2016 Sep 29.


The metabolic background is a global player in Saccharomyces gene expression epistasis.

Alam MT, Zelezniak A, Mülleder M, Shliaha P, Schwarz R, Capuano F, Vowinckel J, Radmanesfahar E, Krüger A, Calvani E, Michel S, Börno S, Christen S, Patil KR, Timmermann B, Lilley KS, Ralser M.

Nat Microbiol. 2016 Feb 1;1:15030. doi: 10.1038/nmicrobiol.2015.30.


Sall4 controls differentiation of pluripotent cells independently of the Nucleosome Remodelling and Deacetylation (NuRD) complex.

Miller A, Ralser M, Kloet SL, Loos R, Nishinakamura R, Bertone P, Vermeulen M, Hendrich B.

Development. 2016 Sep 1;143(17):3074-84. doi: 10.1242/dev.139113. Epub 2016 Jul 28.


Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans.

Watson E, Olin-Sandoval V, Hoy MJ, Li CH, Louisse T, Yao V, Mori A, Holdorf AD, Troyanskaya OG, Ralser M, Walhout AJ.

Elife. 2016 Jul 6;5. pii: e17670. doi: 10.7554/eLife.17670.


Cell-to-cell heterogeneity emerges as consequence of metabolic cooperation in a synthetic yeast community.

Campbell K, Vowinckel J, Ralser M.

Biotechnol J. 2016 Sep;11(9):1169-78. doi: 10.1002/biot.201500301. Epub 2016 Jul 5.


Analysis of Drosophila melanogaster proteome dynamics during embryonic development by a combination of label-free proteomics approaches.

Fabre B, Korona D, Groen A, Vowinckel J, Gatto L, Deery MJ, Ralser M, Russell S, Lilley KS.

Proteomics. 2016 Aug;16(15-16):2068-80. doi: 10.1002/pmic.201500482. Epub 2016 May 10.


Conditional iron and pH-dependent activity of a non-enzymatic glycolysis and pentose phosphate pathway.

Keller MA, Zylstra A, Castro C, Turchyn AV, Griffin JL, Ralser M.

Sci Adv. 2016 Jan 15;2(1):e1501235. doi: 10.1126/sciadv.1501235. eCollection 2016 Jan.


Unbiased Metabolomic Investigation of Alzheimer's Disease Brain Points to Dysregulation of Mitochondrial Aspartate Metabolism.

Paglia G, Stocchero M, Cacciatore S, Lai S, Angel P, Alam MT, Keller M, Ralser M, Astarita G.

J Proteome Res. 2016 Feb 5;15(2):608-18. doi: 10.1021/acs.jproteome.5b01020. Epub 2016 Jan 12.


Methionine Metabolism Alters Oxidative Stress Resistance via the Pentose Phosphate Pathway.

Campbell K, Vowinckel J, Keller MA, Ralser M.

Antioxid Redox Signal. 2016 Apr 1;24(10):543-7. doi: 10.1089/ars.2015.6516. Epub 2016 Mar 15.


Self-establishing communities enable cooperative metabolite exchange in a eukaryote.

Campbell K, Vowinckel J, Mülleder M, Malmsheimer S, Lawrence N, Calvani E, Miller-Fleming L, Alam MT, Christen S, Keller MA, Ralser M.

Elife. 2015 Oct 26;4. pii: e09943. doi: 10.7554/eLife.09943.


The Impact of Non-Enzymatic Reactions and Enzyme Promiscuity on Cellular Metabolism during (Oxidative) Stress Conditions.

Piedrafita G, Keller MA, Ralser M.

Biomolecules. 2015 Sep 10;5(3):2101-22. doi: 10.3390/biom5032101. Review.


Metabolic Remodeling in Times of Stress: Who Shoots Faster than His Shadow?

Dick TP, Ralser M.

Mol Cell. 2015 Aug 20;59(4):519-21. doi: 10.1016/j.molcel.2015.08.002.


Genomics and drug profiling of fatal TCF3-HLF-positive acute lymphoblastic leukemia identifies recurrent mutation patterns and therapeutic options.

Fischer U, Forster M, Rinaldi A, Risch T, Sungalee S, Warnatz HJ, Bornhauser B, Gombert M, Kratsch C, Stütz AM, Sultan M, Tchinda J, Worth CL, Amstislavskiy V, Badarinarayan N, Baruchel A, Bartram T, Basso G, Canpolat C, Cario G, Cavé H, Dakaj D, Delorenzi M, Dobay MP, Eckert C, Ellinghaus E, Eugster S, Frismantas V, Ginzel S, Haas OA, Heidenreich O, Hemmrich-Stanisak G, Hezaveh K, Höll JI, Hornhardt S, Husemann P, Kachroo P, Kratz CP, Te Kronnie G, Marovca B, Niggli F, McHardy AC, Moorman AV, Panzer-Grümayer R, Petersen BS, Raeder B, Ralser M, Rosenstiel P, Schäfer D, Schrappe M, Schreiber S, Schütte M, Stade B, Thiele R, von der Weid N, Vora A, Zaliova M, Zhang L, Zichner T, Zimmermann M, Lehrach H, Borkhardt A, Bourquin JP, Franke A, Korbel JO, Stanulla M, Yaspo ML.

Nat Genet. 2015 Sep;47(9):1020-1029. doi: 10.1038/ng.3362. Epub 2015 Jul 27.


Regulation of ribosomal DNA amplification by the TOR pathway.

Jack CV, Cruz C, Hull RM, Keller MA, Ralser M, Houseley J.

Proc Natl Acad Sci U S A. 2015 Aug 4;112(31):9674-9. doi: 10.1073/pnas.1505015112. Epub 2015 Jul 20.


MitoLoc: A method for the simultaneous quantification of mitochondrial network morphology and membrane potential in single cells.

Vowinckel J, Hartl J, Butler R, Ralser M.

Mitochondrion. 2015 Sep;24:77-86. doi: 10.1016/j.mito.2015.07.001. Epub 2015 Jul 13.


Remaining Mysteries of Molecular Biology: The Role of Polyamines in the Cell.

Miller-Fleming L, Olin-Sandoval V, Campbell K, Ralser M.

J Mol Biol. 2015 Oct 23;427(21):3389-406. doi: 10.1016/j.jmb.2015.06.020. Epub 2015 Jul 5. Review.


A roadmap for interpreting (13)C metabolite labeling patterns from cells.

Buescher JM, Antoniewicz MR, Boros LG, Burgess SC, Brunengraber H, Clish CB, DeBerardinis RJ, Feron O, Frezza C, Ghesquiere B, Gottlieb E, Hiller K, Jones RG, Kamphorst JJ, Kibbey RG, Kimmelman AC, Locasale JW, Lunt SY, Maddocks OD, Malloy C, Metallo CM, Meuillet EJ, Munger J, Nöh K, Rabinowitz JD, Ralser M, Sauer U, Stephanopoulos G, St-Pierre J, Tennant DA, Wittmann C, Vander Heiden MG, Vazquez A, Vousden K, Young JD, Zamboni N, Fendt SM.

Curr Opin Biotechnol. 2015 Aug;34:189-201. doi: 10.1016/j.copbio.2015.02.003. Epub 2015 Feb 28. Review.


Tetrahydrobiopterin and alkylglycerol monooxygenase substantially alter the murine macrophage lipidome.

Watschinger K, Keller MA, McNeill E, Alam MT, Lai S, Sailer S, Rauch V, Patel J, Hermetter A, Golderer G, Geley S, Werner-Felmayer G, Plumb RS, Astarita G, Ralser M, Channon KM, Werner ER.

Proc Natl Acad Sci U S A. 2015 Feb 24;112(8):2431-6. doi: 10.1073/pnas.1414887112. Epub 2015 Feb 9.


The genomic and phenotypic diversity of Schizosaccharomyces pombe.

Jeffares DC, Rallis C, Rieux A, Speed D, Převorovský M, Mourier T, Marsellach FX, Iqbal Z, Lau W, Cheng TM, Pracana R, Mülleder M, Lawson JL, Chessel A, Bala S, Hellenthal G, O'Fallon B, Keane T, Simpson JT, Bischof L, Tomiczek B, Bitton DA, Sideri T, Codlin S, Hellberg JE, van Trigt L, Jeffery L, Li JJ, Atkinson S, Thodberg M, Febrer M, McLay K, Drou N, Brown W, Hayles J, Carazo Salas RE, Ralser M, Maniatis N, Balding DJ, Balloux F, Durbin R, Bähler J.

Nat Genet. 2015 Mar;47(3):235-41. doi: 10.1038/ng.3215. Epub 2015 Feb 9.


Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds.

Frankl-Vilches C, Kuhl H, Werber M, Klages S, Kerick M, Bakker A, de Oliveira EH, Reusch C, Capuano F, Vowinckel J, Leitner S, Ralser M, Timmermann B, Gahr M.

Genome Biol. 2015 Jan 29;16:19. doi: 10.1186/s13059-014-0578-9.


The widespread role of non-enzymatic reactions in cellular metabolism.

Keller MA, Piedrafita G, Ralser M.

Curr Opin Biotechnol. 2015 Aug;34:153-61. doi: 10.1016/j.copbio.2014.12.020. Epub 2015 Jan 22. Review.


Hyperpolarized [U-(2) H, U-(13) C]Glucose reports on glycolytic and pentose phosphate pathway activity in EL4 tumors and glycolytic activity in yeast cells.

Timm KN, Hartl J, Keller MA, Hu DE, Kettunen MI, Rodrigues TB, Ralser M, Brindle KM.

Magn Reson Med. 2015 Dec;74(6):1543-7. doi: 10.1002/mrm.25561. Epub 2014 Dec 17.


Comparative analysis and modeling of the severity of steatohepatitis in DDC-treated mouse strains.

Pandey V, Sultan M, Kashofer K, Ralser M, Amstislavskiy V, Starmann J, Osprian I, Grimm C, Hache H, Yaspo ML, Sültmann H, Trauner M, Denk H, Zatloukal K, Lehrach H, Wierling C.

PLoS One. 2014 Oct 27;9(10):e111006. doi: 10.1371/journal.pone.0111006. eCollection 2014.


The return of metabolism: biochemistry and physiology of the pentose phosphate pathway.

Stincone A, Prigione A, Cramer T, Wamelink MM, Campbell K, Cheung E, Olin-Sandoval V, Grüning NM, Krüger A, Tauqeer Alam M, Keller MA, Breitenbach M, Brindle KM, Rabinowitz JD, Ralser M.

Biol Rev Camb Philos Soc. 2015 Aug;90(3):927-63. doi: 10.1111/brv.12140. Epub 2014 Sep 22. Review.


Influence of RNA extraction methods and library selection schemes on RNA-seq data.

Sultan M, Amstislavskiy V, Risch T, Schuette M, Dökel S, Ralser M, Balzereit D, Lehrach H, Yaspo ML.

BMC Genomics. 2014 Aug 11;15:675. doi: 10.1186/1471-2164-15-675.


The RNA world and the origin of metabolic enzymes.

Ralser M.

Biochem Soc Trans. 2014 Aug;42(4):985-8. doi: 10.1042/BST20140132. Review.


A gatekeeper helix determines the substrate specificity of Sjögren-Larsson Syndrome enzyme fatty aldehyde dehydrogenase.

Keller MA, Zander U, Fuchs JE, Kreutz C, Watschinger K, Mueller T, Golderer G, Liedl KR, Ralser M, Kräutler B, Werner ER, Marquez JA.

Nat Commun. 2014 Jul 22;5:4439. doi: 10.1038/ncomms5439.


Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing.

Hovestadt V, Jones DT, Picelli S, Wang W, Kool M, Northcott PA, Sultan M, Stachurski K, Ryzhova M, Warnatz HJ, Ralser M, Brun S, Bunt J, Jäger N, Kleinheinz K, Erkek S, Weber UD, Bartholomae CC, von Kalle C, Lawerenz C, Eils J, Koster J, Versteeg R, Milde T, Witt O, Schmidt S, Wolf S, Pietsch T, Rutkowski S, Scheurlen W, Taylor MD, Brors B, Felsberg J, Reifenberger G, Borkhardt A, Lehrach H, Wechsler-Reya RJ, Eils R, Yaspo ML, Landgraf P, Korshunov A, Zapatka M, Radlwimmer B, Pfister SM, Lichter P.

Nature. 2014 Jun 26;510(7506):537-41. doi: 10.1038/nature13268. Epub 2014 May 18.


Non-enzymatic glycolysis and pentose phosphate pathway-like reactions in a plausible Archean ocean.

Keller MA, Turchyn AV, Ralser M.

Mol Syst Biol. 2014 Apr 25;10:725. doi: 10.1002/msb.20145228.


Cytosine DNA methylation is found in Drosophila melanogaster but absent in Saccharomyces cerevisiae, Schizosaccharomyces pombe, and other yeast species.

Capuano F, Mülleder M, Kok R, Blom HJ, Ralser M.

Anal Chem. 2014 Apr 15;86(8):3697-702. doi: 10.1021/ac500447w. Epub 2014 Mar 25.

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