All Stories

  1. The ability of pentose pathways to form all essential metabolites provides clues to the origins of metabolism

    Article • PLoS Biology, January 2025, PLOS

    Prof. Markus Ralser

  2. Quantitative protein biomarker panels: a path to improved clinical practice through proteomics

    Article • EMBO Molecular Medicine, March 2023, EMBO

    Prof. Markus Ralser

  3. Speedy-PASEF: Analytical flow rate chromatography and trapped ion mobility for deep high-throughput proteomics

    Article • February 2023, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  4. Metabolic heterogeneity and cross-feeding within isogenic yeast populations captured by DILAC

    Article • Nature Microbiology, February 2023, Springer Science + Business Media

    Prof. Markus Ralser

  5. The brain reacting to COVID-19: analysis of the cerebrospinal fluid proteome, RNA and inflammation

    Article • Journal of Neuroinflammation, February 2023, Springer Science + Business Media

    Prof. Markus Ralser

  6. The central nervous system’s proteogenomic and spatial imprint upon systemic viral infections with SARS-CoV-2

    Article • January 2023, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  7. Cell-cell metabolite exchange creates a pro-survival metabolic environment that extends lifespan

    Article • Cell, January 2023, Elsevier

    Prof. Markus Ralser

  8. SARS-CoV-2-specific nasal IgA wanes 9 months after hospitalisation with COVID-19 and is not induced by subsequent vaccination

    Article • EBioMedicine, December 2022, Elsevier

    MD Pilar Rivera Ortega, Mark Philip Cassar, Prof. Markus Ralser, Dr Ahilanandan Dushianthan, Dr Cherie Armour

  9. Inorganic sulfur fixation via a new homocysteine synthase allows yeast cells to cooperatively compensate for methionine auxotrophy

    Article • PLoS Biology, December 2022, PLOS

    Prof. Markus Ralser

  10. Functional proteomic profiling links deficient DNA clearance with increased mortality in individuals with severe COVID-19 pneumonia

    Article • Immunity, December 2022, Elsevier

    Prof. Markus Ralser

  11. Metal ion availability and homeostasis as drivers of metabolic evolution and enzyme function

    Article • Current Opinion in Genetics & Development, December 2022, Elsevier

    Prof. Markus Ralser

  12. High-throughput proteomics of nanogram-scale samples with Zeno SWATH MS

    Article • eLife, November 2022, eLife

    Prof. Markus Ralser

  13. N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast

    Article • eLife, November 2022, eLife

    Prof. Markus Ralser

  14. Mass spectrometry‐based high‐throughput proteomics and its role in biomedical studies and systems biology

    Article • PROTEOMICS, November 2022, Wiley

    Prof. Markus Ralser

  15. Slice-PASEF: fragmenting all ions for maximum sensitivity in proteomics

    Article • October 2022, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  16. Synthetic metabolism without the TCA cycle

    Article • Nature Metabolism, October 2022, Springer Science + Business Media

    Prof. Markus Ralser

  17. Integrated genomic surveillance enables tracing of person-to-person SARS-CoV-2 transmission chains during community transmission and reveals extensive onward transmission of travel-imported infections, Germany, June to July 2021

    Article • Eurosurveillance, October 2022, European Centre for Disease Control and Prevention (ECDC)

    Prof. Markus Ralser

  18. MSBooster: Improving Peptide Identification Rates using Deep Learning-Based Features

    Article • October 2022, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  19. Cystatin C is associated with adverse COVID-19 outcomes in diverse populations

    Article • iScience, October 2022, Elsevier

    Prof. Markus Ralser

  20. The human host response to monkeypox infection: a proteomic case series study

    Article • EMBO Molecular Medicine, September 2022, EMBO

    Prof. Markus Ralser

  21. Intestinal epithelial c-Maf expression determines enterocyte differentiation and nutrient uptake in mice

    Article • Journal of Experimental Medicine, September 2022, Rockefeller University Press

    Prof. Markus Ralser

  22. Editorial overview: The metabolic network

    Article • Current Opinion in Systems Biology, September 2022, Elsevier

    Prof. Markus Ralser

  23. Integration of protein context improves protein-based COVID-19 patient stratification

    Article • Clinical Proteomics, August 2022, Springer Science + Business Media

    Prof. Markus Ralser

  24. Microbe capture by splenic macrophages triggers sepsis via T cell-death-dependent neutrophil lifespan shortening

    Article • Nature Communications, August 2022, Springer Science + Business Media

    Prof. Markus Ralser

  25. Clinical characteristics with inflammation profiling of long COVID and association with 1-year recovery following hospitalisation in the UK: a prospective observational study

    Article • The Lancet Respiratory Medicine, August 2022, Elsevier

    Dr Omer Elneima, MD Pilar Rivera Ortega, Mark Philip Cassar, Prof Nicholas Hart, Prof. Markus Ralser, Trudie Chalder, Dr Cherie Armour

  26. The human host response to monkeypox infection: a proteomic case series study

    Article • July 2022, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  27. Global analysis of cytosine and adenine DNA modifications across the tree of life

    Article • eLife, July 2022, eLife

    Prof. Markus Ralser

  28. 90K/LGALS3BP Expression is Upregulated in COVID-19 but Does Not Restrict SARS-CoV-2 Infection

    Article • July 2022, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  29. Increasing the throughput of sensitive proteomics by plexDIA

    Article • Nature Biotechnology, July 2022, Springer Science + Business Media

    Prof. Markus Ralser

  30. dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts

    Article • Nature Communications, July 2022, Springer Science + Business Media

    Prof. Markus Ralser

  31. Spermidine reduces neuroinflammation and soluble amyloid beta in an Alzheimer’s disease mouse model

    Article • Journal of Neuroinflammation, July 2022, Springer Science + Business Media

    Prof. Markus Ralser

  32. A multiplex protein panel assay for severity prediction and outcome prognosis in patients with COVID-19: An observational multi-cohort study

    Article • EClinicalMedicine, July 2022, Elsevier

    Prof. Markus Ralser

  33. Optimization of Microflow LC Coupled with Scanning SWATH and Its Application in Hepatocellular Carcinoma Tissues

    Article • Journal of Proteome Research, June 2022, American Chemical Society (ACS)

    Prof. Markus Ralser

  34. OxoScan-MS: Oxonium ion scanning mass spectrometry facilitates plasma glycoproteomics in large scale

    Article • June 2022, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  35. The Proteomic Landscape of Genome-Wide Genetic Perturbations

    Article • May 2022, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  36. An open invitation to the Understudied Proteins Initiative

    Article • Nature Biotechnology, May 2022, Springer Science + Business Media

    Prof. Markus Ralser

  37. Understudied proteins: opportunities and challenges for functional proteomics

    Article • Nature Chemical Biology, May 2022, Springer Science + Business Media

    Prof. Markus Ralser

  38. High-throughput proteomics of nanogram-scale samples with Zeno SWATH DIA

    Article • April 2022, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  39. The natural diversity of the yeast proteome reveals chromosome-wide dosage compensation in aneuploids

    Article • April 2022, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  40. Occurrence and quantities of DNA modifications across the tree of life

    Article • March 2022, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  41. Microbial communities form rich extracellular metabolomes that foster metabolic interactions and promote drug tolerance

    Article • Nature Microbiology, March 2022, Springer Science + Business Media

    Prof. Markus Ralser

  42. Inorganic sulfur fixation via a new homocysteine synthase allows yeast cells to cooperatively compensate for methionine auxotrophy

    Article • March 2022, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  43. Cell-cell metabolite exchange creates a pro-survival metabolic environment that extends lifespan

    Article • March 2022, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  44. Acute caloric restriction acts on the plasma proteome and reveals Apolipoprotein C1 as a signal of nutritional state and metabolic disease

    Article • March 2022, Research Square

    Prof. Markus Ralser

  45. Age-Related Differences in Structure and Function of Nasal Epithelial Cultures From Healthy Children and Elderly People

    Article • Frontiers in Immunology, February 2022, Frontiers

    Prof. Markus Ralser

  46. Complement activation induces excessive T cell cytotoxicity in severe COVID-19

    Article • Cell, February 2022, Elsevier

    Prof. Markus Ralser

  47. Functional proteomic profiling links deficient DNA clearance to mortality in patients with severe COVID-19 pneumonia

    Article • January 2022, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  48. m6A reader Pho92 is recruited co-transcriptionally and couples translation efficacy to mRNA decay to promote meiotic fitness in yeast

    Article • January 2022, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  49. Functional profiling of long intergenic non-coding RNAs in fission yeast

    Article • eLife, January 2022, eLife

    Prof. Markus Ralser

  50. High-Throughput, High-Precision Colony Phenotyping with Pyphe

    Article • January 2022, Springer Science + Business Media

    Prof. Markus Ralser

  51. A multiplex protein panel assay determines disease severity and is prognostic about outcome in COVID-19 patients

    Article • December 2021, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  52. Cysteine and iron accelerate the formation of ribose-5-phosphate, providing insights into the evolutionary origins of the metabolic network structure

    Article • PLoS Biology, December 2021, PLOS

    Prof. Markus Ralser

  53. Glycolysis: How a 300yr long research journey that started with the desire to improve alcoholic beverages kept revolutionizing biochemistry

    Article • Current Opinion in Systems Biology, December 2021, Elsevier

    Prof. Markus Ralser

  54. The evolution of the metabolic network over long timelines

    Article • Current Opinion in Systems Biology, December 2021, Elsevier

    Prof. Markus Ralser

  55. The metabolic growth limitations of petite cells lacking the mitochondrial genome

    Article • Nature Metabolism, November 2021, Springer Science + Business Media

    Prof. Markus Ralser

  56. Increasing the throughput of sensitive proteomics by plexDIA

    Article • November 2021, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  57. Physical, cognitive, and mental health impacts of COVID-19 after hospitalisation (PHOSP-COVID): a UK multicentre, prospective cohort study

    Article • The Lancet Respiratory Medicine, November 2021, Elsevier

    MD Pilar Rivera Ortega, Dr Omer Elneima, Prof Nicholas Hart, Prof. Markus Ralser, Trudie Chalder

  58. Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19

    Article • Immunity, November 2021, Elsevier

    Prof. Markus Ralser

  59. Time-resolved in vivo ubiquitinome profiling by DIA-MS reveals USP7 targets on a proteome-wide scale

    Article • Nature Communications, September 2021, Springer Science + Business Media

    Prof. Markus Ralser

  60. Virus-induced senescence is a driver and therapeutic target in COVID-19

    Article • Nature, September 2021, Springer Science + Business Media

    Prof. Markus Ralser

  61. Cystatin C is glucocorticoid-responsive, directs recruitment of Trem2+ macrophages and predicts failure of cancer immunotherapy

    Article • August 2021, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  62. Metabolic decisions in development and disease—a Keystone Symposia report

    Article • Annals of the New York Academy of Sciences, August 2021, Wiley

    Prof. Markus Ralser

  63. Pre-activated antiviral innate immunity in the upper airways controls early SARS-CoV-2 infection in children

    Article • Nature Biotechnology, August 2021, Springer Science + Business Media

    Prof. Markus Ralser

  64. Temporal omics analysis in Syrian hamsters unravel cellular effector responses to moderate COVID-19

    Article • Nature Communications, August 2021, Springer Science + Business Media

    Prof. Markus Ralser

  65. SIGNR1 promotes immune dysfunction in systemic candidiasis by modulating neutrophil lifespan via T cell-derived histones and G-CSF

    Article • August 2021, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  66. A time-resolved proteomic and prognostic map of COVID-19

    Article • Cell Systems, August 2021, Elsevier

    Prof. Markus Ralser

  67. A serum proteome signature to predict mortality in severe COVID-19 patients

    Article • Life Science Alliance, July 2021, Life Science Alliance, LLC

    Prof. Markus Ralser

  68. Barcode sequencing and a high-throughput assay for chronological lifespan uncover ageing-associated genes in fission yeast

    Article • Microbial Cell, July 2021, Shared Science Publishers OG

    Prof. Markus Ralser

  69. Functional profiling of long intergenic non-coding RNAs in fission yeast

    Article • July 2021, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  70. Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection Clusters Based on Integrated Genomic Surveillance, Outbreak Analysis and Contact Tracing in an Urban Setting

    Article • Clinical Infectious Diseases, June 2021, Oxford University Press (OUP)

    Prof. Markus Ralser

  71. Pre-activated anti-viral innate immunity in the upper airways controls early SARS-CoV-2 infection in children

    Article • June 2021, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  72. A proteomic survival predictor for COVID-19 patients in intensive care

    Article • June 2021, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  73. Complement activation induces excessive T cell cytotoxicity in severe COVID-19

    Article • June 2021, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  74. Swarm Learning for decentralized and confidential clinical machine learning

    Article • Nature, May 2021, Springer Science + Business Media

    Prof. Markus Ralser

  75. High-throughput, high-precision colony phenotyping with pyphe

    Article • April 2021, Research Square

    Prof. Markus Ralser

  76. Ultra-fast proteomics with Scanning SWATH

    Article • Nature Biotechnology, March 2021, Springer Science + Business Media

    Prof. Markus Ralser

  77. High sensitivity dia-PASEF proteomics with DIA-NN and FragPipe

    Article • March 2021, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  78. Barcode Sequencing and a High-throughput Assay for Chronological Lifespan Uncover Ageing-associated Genes in Fission Yeast

    Article • March 2021, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  79. Characterization of SARS-CoV-2 genetic structure and infection clusters in a large German city based on integrated genomic surveillance, outbreak analysis, and contact tracing

    Article • February 2021, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  80. Author Correction: Genetic architecture of host proteins involved in SARS-CoV-2 infection

    Article • Nature Communications, February 2021, Springer Science + Business Media

    Prof. Markus Ralser

  81. Longitudinal omics in Syrian hamsters integrated with human data unravel cellular effector responses to moderate COVID-19

    Article • January 2021, Research Square

    Prof. Markus Ralser

  82. Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients

    Article • Genome Medicine, January 2021, Springer Science + Business Media

    Prof. Markus Ralser

  83. Complement Activation Induces Excessive T Cell Cytotoxicity in Severe COVID-19

    Article • SSRN Electronic Journal, January 2021, Elsevier

    Prof. Markus Ralser

  84. Longitudinal omics in Syrian hamsters integrated with human data unravel complexity of moderate immune responses to SARS-CoV-2

    Article • December 2020, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  85. Genetic architecture of host proteins involved in SARS-CoV-2 infection

    Article • Nature Communications, December 2020, Springer Science + Business Media

    Prof. Markus Ralser

  86. Ribosome profiling reveals ribosome stalling on tryptophan codons and ribosome queuing upon oxidative stress in fission yeast

    Article • Nucleic Acids Research, December 2020, Oxford University Press (OUP)

    Prof. Markus Ralser

  87. Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19

    Article • Immunity, December 2020, Elsevier

    Jun.-Prof. Dr. Andreas Dräger, Prof. Markus Ralser

  88. Slow Growth and Increased Spontaneous Mutation Frequency in Respiratory Deficientafo1- Yeast Suppressed by a Dominant Mutation inATP3

    Article • G3 Genes Genomes Genetics, December 2020, Oxford University Press (OUP)

    Prof. Markus Ralser

  89. A time-resolved proteomic and diagnostic map characterizes COVID-19 disease progression and predicts outcome

    Article • November 2020, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  90. Amino Acids Whose Intracellular Levels Change Most During Aging Alter Chronological Life Span of Fission Yeast

    Article • The Journals of Gerontology Series A, November 2020, Oxford University Press (OUP)

    Prof. Markus Ralser

  91. Extraction and Integration of Genetic Networks from Short-Profile Omic Data Sets

    Article • Metabolites, October 2020, MDPI AG

    Prof. Markus Ralser

  92. Longitudinal multi-omics analysis identifies responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories

    Article • September 2020, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  93. Mitochondrial respiration is required to provide amino acids during fermentative proliferation of fission yeast

    Article • EMBO Reports, September 2020, EMBO

    Prof. Markus Ralser

  94. SARS-CoV-2 infection paralyzes cytotoxic and metabolic functions of the immune cells

    Article • September 2020, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  95. Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment

    Article • Cell, September 2020, Elsevier

    Prof. Markus Ralser

  96. Amino acids whose intracellular levels change most during aging alter chronological lifespan of fission yeast

    Article • August 2020, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  97. Single amino acid-promoted reactions link a non-enzymatic chemical network to the early evolution of enzymatic pentose phosphate pathway

    Article • August 2020, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  98. Genetic architecture of host proteins interacting with SARS-CoV-2

    Article • July 2020, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  99. Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection

    Article • Cell Systems, July 2020, Elsevier

    Prof. Markus Ralser

  100. Pyphe, a python toolbox for assessing microbial growth and cell viability in high-throughput colony screens

    Article • eLife, June 2020, eLife

    Prof. Markus Ralser

  101. Suppressive myeloid cells are a hallmark of severe COVID-19

    Article • June 2020, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  102. Clinical classifiers of COVID-19 infection from novel ultra-high-throughput proteomics

    Article • May 2020, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  103. Marmota marmota

    Article • Trends in Genetics, May 2020, Elsevier

    Prof. Markus Ralser

  104. Ribosome profiling reveals ribosome stalling on tryptophan codons upon oxidative stress in fission yeast

    Article • April 2020, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  105. Pyruvate kinase variant of fission yeast tunes carbon metabolism, cell regulation, growth and stress resistance

    Article • Molecular Systems Biology, April 2020, EMBO

    Prof. Markus Ralser

  106. Cooperative genetic networks drive a mammalian cell state transition

    Article • March 2020, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  107. Mitochondrial respiration is required to provide amino acids during fermentative proliferation of fission yeast

    Article • February 2020, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  108. Pyphe: A python toolbox for assessing microbial growth and cell viability in high-throughput colony screens

    Article • January 2020, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  109. DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput

    Article • Nature Chemical Biology, November 2019, Springer Science + Business Media

    Prof. Markus Ralser

  110. From its origins to the modern metabolic network

    Article • Endocrine Abstracts, November 2019, Bioscientifica

    Prof. Markus Ralser

  111. A natural variant of the sole pyruvate kinase of fission yeast lowers glycolytic flux triggering increased respiration and oxidative-stress resistance but decreased growth

    Article • September 2019, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  112. A mouse model for intellectual disability caused by mutations in the X-linked 2′‑O‑methyltransferase Ftsj1 gene

    Article • Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, September 2019, Elsevier

    Prof. Markus Ralser, Professor Sabine Müller

  113. Lysine harvesting is an antioxidant strategy and triggers underground polyamine metabolism

    Article • Nature, July 2019, Springer Science + Business Media

    Prof. Markus Ralser

  114. Low catalytic activity is insufficient to induce disease pathology in triosephosphate isomerase deficiency

    Article • Journal of Inherited Metabolic Disease, June 2019, Wiley

    Prof. Markus Ralser

  115. Scanning SWATH acquisition enables high-throughput proteomics with chromatographic gradients as fast as 30 seconds

    Article • May 2019, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  116. Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity

    Article • Current Biology, May 2019, Elsevier

    Prof. Markus Ralser

  117. Complementary Activity of ETV5, RBPJ, and TCF3 Drives Formative Transition from Naive Pluripotency

    Article • Cell Stem Cell, May 2019, Elsevier

    Prof. Markus Ralser

  118. The Nucleosome Remodelling and Deacetylation complex suppresses transcriptional noise during lineage commitment

    Article • The EMBO Journal, April 2019, EMBO

    Prof. Markus Ralser

  119. A multi-omic analysis of optineurin proteinopathy in a yeast model suggests the involvement of lipid metabolism in Amyotrophic Lateral Sclerosis

    Article • April 2019, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  120. Evolthon: A community endeavor to evolve lab evolution

    Article • PLoS Biology, March 2019, PLOS

    Dr Aaron N Brooks, Prof. Markus Ralser

  121. Reply to ‘Do sulfate radicals really enable a non-enzymatic Krebs cycle precursor?’

    Article • Nature Ecology & Evolution, January 2019, Springer Science + Business Media

    Prof. Markus Ralser

  122. The next decade of metabolism

    Article • Nature Metabolism, January 2019, Springer Science + Business Media

    Prof. Markus Ralser

  123. Self-Establishing Communities: A Yeast Model to Study the Physiological Impact of Metabolic Cooperation in Eukaryotic Cells

    Article • January 2019, Springer Science + Business Media

    Prof. Markus Ralser

  124. Changes of Cell Biochemical States Are Revealed in Protein Homomeric Complex Dynamics

    Article • Cell, November 2018, Elsevier

    Prof. Markus Ralser

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

    Article • Cell, September 2018, Elsevier

    Prof. Markus Ralser

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

    Article • Cell Systems, September 2018, Elsevier

    Prof. Markus Ralser

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

    Article • Biochemical Journal, August 2018, Portland Press Ltd.

    Prof. Markus Ralser

  128. 1H-NMR as implemented in several origin of life studies artificially implies the absence of metabolism-like non-enzymatic reactions by being signal-suppressed

    Article • Wellcome Open Research, May 2018, Faculty of 1000, Ltd.

    Prof. Markus Ralser

  129. Biochemical principles enabling metabolic cooperativity and phenotypic heterogeneity at the single cell level

    Article • Current Opinion in Systems Biology, April 2018, Elsevier

    Prof. Markus Ralser

  130. DIA-NN: Deep neural networks substantially improve the identification performance of Data-independent acquisition (DIA) in proteomics

    Article • March 2018, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

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

    Article • Scientific Reports, March 2018, Springer Science + Business Media

    Prof. Markus Ralser

  132. A Novel Yeast Global Genetic Screen Reveals That Metformin Induces an Iron Deficiency-Like State

    Article • SSRN Electronic Journal, January 2018, Elsevier

    Prof. Markus Ralser

  133. The Response to Past Climate Perturbations Explains Extremely Low Genetic Diversity in the Genome of an Abundant Ice-Age Remnant, the Alpine Marmot

    Article • SSRN Electronic Journal, January 2018, Elsevier

    Prof. Markus Ralser

  134. Designing and interpreting ‘multi-omic’ experiments that may change our understanding of biology

    Article • Current Opinion in Systems Biology, December 2017, Elsevier

    Prof. Markus Ralser

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

    Article • Cell Reports, November 2017, Elsevier

    Prof. Markus Ralser

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

    Article • Cell Systems, October 2017, Elsevier

    Prof. Markus Ralser

  137. A Yeast Global Genetic Screen Reveals that Metformin Induces an Iron Deficiency-Like State

    Article • September 2017, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

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

    Article • Cold Spring Harbor Protocols, September 2017, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  139. Metabolomics in Yeast

    Article • Cold Spring Harbor Protocols, September 2017, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

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

    Article • Nature Communications, August 2017, Springer Science + Business Media

    Prof. Markus Ralser

  141. Primordial Krebs-cycle-like non-enzymatic reactions detected by mass spectrometry and nuclear magnetic resonance

    Article • Wellcome Open Research, July 2017, Faculty of 1000, Ltd.

    Prof. Markus Ralser

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

    Article • Nature Communications, July 2017, Springer Science + Business Media

    Prof. Markus Ralser

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

    Article • Proceedings of the National Academy of Sciences, June 2017, Proceedings of the National Academy of Sciences

    Prof. Markus Ralser

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

    Article • Developmental Cell, May 2017, Elsevier

    Prof. Markus Ralser

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

    Article • Developmental Cell, April 2017, Elsevier

    Prof. Markus Ralser

  146. Sulfate radicals enable a non-enzymatic Krebs cycle precursor

    Article • Nature Ecology & Evolution, March 2017, Springer Science + Business Media

    Prof. Markus Ralser

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

    Article • Metabolomics, December 2016, Springer Science + Business Media

    Dr Albert Koulman, Prof. Markus Ralser

  148. Functional Metabolomics Describes the Yeast Biosynthetic Regulome

    Article • Cell, October 2016, Elsevier

    Prof. Markus Ralser

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

    Article • F1000Research, September 2016, Faculty of 1000, Ltd.

    Dr Kate AV Campbell, Prof. Markus Ralser

  150. Precise label-free quantitative proteomes in high-throughput by microLC and data-independent SWATH acquisition

    Article • September 2016, Cold Spring Harbor Laboratory Press

    Prof. Markus Ralser

  151. Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency inC. elegans

    Article • eLife, July 2016, eLife

    Prof. Markus Ralser

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

    Article • Biotechnology Journal, July 2016, Wiley

    Prof. Markus Ralser

  153. Analysis ofDrosophila melanogasterproteome dynamics during embryonic development by a combination of label-free proteomics approaches

    Article • PROTEOMICS, May 2016, Wiley

    Prof. Markus Ralser, Bertrand Fabre

  154. Methionine Metabolism Alters Oxidative Stress Resistanceviathe Pentose Phosphate Pathway

    Article • Antioxidants & Redox Signaling, April 2016, Mary Ann Liebert Inc

    Prof. Markus Ralser

  155. Challenges in microbial ecology: building predictive understanding of community function and dynamics

    Article • The ISME Journal, March 2016, Nature

    Dr Jan-Ulrich Kreft, Dr Ottavio A Croze, Prof. Markus Ralser, Babak Momeni

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

    Article • Nature Microbiology, February 2016, Nature

    Prof. Markus Ralser

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

    Article • Journal of Proteome Research, January 2016, American Chemical Society (ACS)

    Prof. Markus Ralser

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

    Article • Science Advances, January 2016, American Association for the Advancement of Science

    Prof. Markus Ralser

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

    Article • eLife, October 2015, eLife

    Prof. Markus Ralser

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

    Article • Journal of Molecular Biology, October 2015, Elsevier

    Prof. Markus Ralser

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

    Article • Biomolecules, September 2015, MDPI AG

    Prof. Markus Ralser

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

    Article • Mitochondrion, September 2015, Elsevier

    Prof. Markus Ralser

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

    Article • Current Opinion in Biotechnology, August 2015, Elsevier

    Dr Emmanuelle J Meuillet, Dr Daniel A Tennant, Prof. Markus Ralser

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

    Article • Molecular Cell, August 2015, Elsevier

    Prof. Markus Ralser

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

    Article • Current Opinion in Biotechnology, August 2015, Elsevier

    Prof. Markus Ralser

  166. Regulation of ribosomal DNA amplification by the TOR pathway

    Article • Proceedings of the National Academy of Sciences, July 2015, Proceedings of the National Academy of Sciences

    Prof. Markus Ralser

  167. The genomic and phenotypic diversity of Schizosaccharomyces pombe

    Article • Nature Genetics, February 2015, Nature

    Dr Daniel C Jeffares, Professor Jurg Bahler, Dr. Malte Thodberg, Prof. Markus Ralser

  168. Tetrahydrobiopterin and alkylglycerol monooxygenase substantially alter the murine macrophage lipidome

    Article • Proceedings of the National Academy of Sciences, February 2015, Proceedings of the National Academy of Sciences

    Prof. Markus Ralser

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

    Article • Genome Biology, January 2015, Springer Science + Business Media

    Prof. Markus Ralser, Dr Edivaldo HC de Oliveira

  170. A haploproficient interaction of the transaldolase paralogue NQM1 with the transcription factor VHR1 affects stationary phase survival and oxidative stress resistance

    Article • BMC Genetics, January 2015, Springer Science + Business Media

    Prof. Markus Ralser

  171. 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

    Article • Magnetic Resonance in Medicine, December 2014, Wiley

    Prof. Markus Ralser

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

    Article • Biological Reviews, September 2014, Wiley

    Prof. Markus Ralser

  173. The RNA world and the origin of metabolic enzymes: Figure 1

    Article • Biochemical Society Transactions, August 2014, Portland Press Ltd.

    Prof. Markus Ralser

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

    Article • Nature Communications, July 2014, Nature

    Prof. Markus Ralser

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

    Article • Molecular Systems Biology, April 2014, EMBO

    Prof. Markus Ralser

  176. Cytosine DNA Methylation Is Found in Drosophila melanogaster but Absent in Saccharomyces cerevisiae, Schizosaccharomyces pombe , and Other Yeast Species

    Article • Analytical Chemistry, April 2014, American Chemical Society (ACS)

    Prof. Markus Ralser

  177. The beauty of being (label)-free: sample preparation methods for SWATH-MS and next-generation targeted proteomics

    Article • F1000Research, April 2014, Faculty of 1000, Ltd.

    Prof. Markus Ralser

  178. Inhibition of triosephosphate isomerase by phosphoenolpyruvate in the feedback-regulation of glycolysis

    Article • Open Biology, March 2014, Royal Society Publishing

    Prof. Markus Ralser

  179. Mitochondria in ageing: there is metabolism beyond the ROS

    Article • FEMS Yeast Research, January 2014, Oxford University Press (OUP)

    Prof. Markus Ralser

  180. HIF1α Modulates Cell Fate Reprogramming Through Early Glycolytic Shift and Upregulation of PDK1-3 and PKM2

    Article • Stem Cells, January 2014, Wiley

    Prof. Markus Ralser

  181. The beauty of being (label)-free: sample preparation methods for SWATH-MS and next-generation targeted proteomics

    Article • F1000Research, December 2013, Faculty of 1000, Ltd.

    Prof. Markus Ralser, Dr Kate AV Campbell

  182. Tpo1‐mediated spermine and spermidine export controls cell cycle delay and times antioxidant protein expression during the oxidative stress response

    Article • EMBO Reports, October 2013, EMBO

    Prof. Markus Ralser

  183. Warburg effect and translocation-induced genomic instability: two yeast models for cancer cells

    Article • Frontiers in Oncology, January 2013, Frontiers

    Prof. Markus Ralser

  184. Oxidative stress and neurodegeneration: the yeast model system

    Article • Frontiers in Bioscience, January 2013, IMR Press

    Prof. Markus Ralser

  185. A prototrophic deletion mutant collection for yeast metabolomics and systems biology

    Article • Nature Biotechnology, December 2012, Nature

    Prof. Markus Ralser

  186. Pyruvate kinase is a dosage-dependent regulator of cellular amino acid homeostasis

    Article • Oncotarget, November 2012, Impact Journals, LLC

    Prof. Markus Ralser

  187. Histaminylation of glutamine residues is a novel posttranslational modification implicated in G-protein signaling

    Article • FEBS Letters, September 2012, Wiley

    Prof. Markus Ralser

  188. Genomanalyse von Modellorganismen: Saccharomyces cerevisiae

    Article • BIOspektrum, August 2012, Springer Science + Business Media

    Prof. Markus Ralser

  189. The Saccharomyces cerevisiae W303-K6001 cross-platform genome sequence: insights into ancestry and physiology of a laboratory mutt

    Article • Open Biology, August 2012, Royal Society Publishing

    Prof. Markus Ralser

  190. Functional Analysis of Centrosomal Kinase Substrates in Drosophila melanogaster Reveals a New Function of the Nuclear Envelope Component Otefin in Cell Cycle Progression

    Article • Molecular and Cellular Biology, July 2012, ASM Journals

    Prof. Markus Ralser

  191. Faculty Opinions recommendation of Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism.

    Article • March 2012, F1000Research

    Prof. Markus Ralser

  192. Sirtuins as Regulators of the Yeast Metabolic Network

    Article • Frontiers in Pharmacology, January 2012, Frontiers

    Prof. Markus Ralser

  193. Cancer: Sacrifice for survival

    Article • Nature, December 2011, Nature

    Prof. Markus Ralser

  194. Pyruvate Kinase Triggers a Metabolic Feedback Loop that Controls Redox Metabolism in Respiring Cells

    Article • Cell Metabolism, September 2011, Elsevier

    Prof. Markus Ralser

  195. The Pentose Phosphate Pathway Is a Metabolic Redox Sensor and Regulates Transcription During the Antioxidant Response

    Article • Antioxidants & Redox Signaling, July 2011, Mary Ann Liebert Inc

    Prof. Markus Ralser

  196. No evidence for a shift in pyruvate kinase PKM1 to PKM2 expression during tumorigenesis

    Article • Oncotarget, May 2011, Impact Journals, LLC

    Prof. Markus Ralser

  197. Monitoring protein expression in whole-cell extracts by targeted label- and standard-free LC-MS/MS

    Article • Nature Protocols, May 2011, Nature

    Prof. Markus Ralser

  198. ATM Is a Redox Sensor Linking Genome Stability and Carbon Metabolism

    Article • Science Signaling, April 2011, American Association for the Advancement of Science

    Prof. Markus Ralser

  199. The Role of Mitochondria in the Aging Processes of Yeast

    Article • January 2011, Springer Science + Business Media

    Prof. Markus Ralser

  200. Human iPSCs Harbor Homoplasmic and Heteroplasmic Mitochondrial DNA Mutations While Maintaining hESC-Like Metabolic Reprogramming

    Article • Stem Cells, January 2011, Wiley

    Prof. Markus Ralser

  201. The KRAB-containing zinc-finger transcriptional regulator ZBRK1 activates SCA2 gene transcription through direct interaction with its gene product, ataxin-2

    Article • Human Molecular Genetics, October 2010, Oxford University Press (OUP)

    Prof. Markus Ralser

  202. A new dominant peroxiredoxin allele identified by whole-genome re-sequencing of random mutagenized yeast causes oxidant-resistance and premature aging

    Article • Aging, August 2010, Impact Journals, LLC

    Prof. Markus Ralser

  203. Faculty Opinions recommendation of Metabolomic and transcriptomic stress response of Escherichia coli.

    Article • August 2010, F1000Research

    Prof. Markus Ralser

  204. The difference between rare and exceptionally rare: molecular characterization of ribose 5-phosphate isomerase deficiency

    Article • Journal of Molecular Medicine, May 2010, Springer Science + Business Media

    Prof. Markus Ralser

  205. Regulatory crosstalk of the metabolic network

    Article • Trends in Biochemical Sciences, April 2010, Elsevier

    Prof. Markus Ralser

  206. Surviving in the cold: yeast mutants with extended hibernating lifespan are oxidant sensitive

    Article • Aging, December 2009, Impact Journals, LLC

    Prof. Markus Ralser

  207. Building a new bridge between metabolism, free radicals and longevity

    Article • Aging, September 2009, Impact Journals, LLC

    Prof. Markus Ralser

  208. Quantification of Saccharomyces cerevisiae pentose-phosphate pathway intermediates by LC-MS/MS

    Article • Protocol Exchange, July 2009, Nature

    Prof. Markus Ralser

  209. Faculty Opinions recommendation of Bleach activates a redox-regulated chaperone by oxidative protein unfolding.

    Article • July 2009, F1000Research

    Prof. Markus Ralser

  210. Metabolic reconfiguration precedes transcriptional regulation in the antioxidant response

    Article • Nature Biotechnology, July 2009, Nature

    Prof. Markus Ralser

  211. Interfering with Glycolysis Causes Sir2-Dependent Hyper-Recombination of Saccharomyces cerevisiae Plasmids

    Article • PLOS One, April 2009, PLOS

    Prof. Markus Ralser

  212. A catabolic block does not sufficiently explain how 2-deoxy-d-glucose inhibits cell growth

    Article • Proceedings of the National Academy of Sciences, November 2008, Proceedings of the National Academy of Sciences

    Prof. Markus Ralser

  213. Reductive stress on life span extension in C. elegans

    Article • BMC Research Notes, January 2008, Springer Science + Business Media

    Prof. Markus Ralser

  214. Sequencing and genotypic analysis of the triosephosphate isomerase (TPI1) locus in a large sample of long-lived Germans

    Article • BMC Genetics, January 2008, Springer Science + Business Media

    Prof. Markus Ralser

  215. Ataxin-2 Interacts with the DEAD/H-Box RNA Helicase DDX6 and Interferes with P-Bodies and Stress Granules

    Article • Molecular Biology of the Cell, April 2007, American Society for Cell Biology (ASCB)

    Prof. Markus Ralser

  216. Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress

    Article • Journal of Biology, January 2007, Springer Science + Business Media

    Prof. Markus Ralser

  217. Triose Phosphate Isomerase Deficiency Is Caused by Altered Dimerization–Not Catalytic Inactivity–of the Mutant Enzymes

    Article • PLOS One, December 2006, PLOS

    Prof. Markus Ralser

  218. An efficient and economic enhancer mix for PCR

    Article • Biochemical and Biophysical Research Communications, September 2006, Elsevier

    Prof. Markus Ralser

  219. Combining SELEX and reverse yeast-2-hybrid system

    Article • September 2005, Elsevier

    Prof. Markus Ralser

  220. Functional association of the polyglutamine proteins ataxin-2 and huntingtin

    Article • September 2005, Elsevier

    Prof. Markus Ralser

  221. Ataxin-2 and huntingtin interact with endophilin-A complexes to function in plastin-associated pathways

    Article • Human Molecular Genetics, August 2005, Oxford University Press (OUP)

    Prof. Markus Ralser

  222. Generation of a yeast two-hybrid strain suitable for competitive protein binding analysis

    Article • BioTechniques, August 2005, Future Science

    Prof. Markus Ralser

  223. An Integrative Approach to Gain Insights into the Cellular Function of Human Ataxin-2

    Article • Journal of Molecular Biology, February 2005, Elsevier

    Prof. Markus Ralser