Operation of a TCA cycle subnetwork in the mammalian nucleus

The Evolving Landscape of Noncanonical Functions of Metabolic Enzymes in Cancer and Other Pathologies

(2021) Daqian Xu et al.   Cell Metabolism

The Mystery of Extramitochondrial Proteins Lysine Succinylation

(2021) Christos Chinopoulos   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A crucial RNA-binding lysine residue in the Nab3 RRM domain undergoes SET1 and SET3-responsive methylation

(2020) Kwan Yin Lee et al.   NUCLEIC ACIDS RESEARCH

Oncometabolites suppress DNA repair by disrupting local chromatin signalling

(2020) Parker L. Sulkowski et al.   NATURE

MSnbase, Efficient and Elegant R-Based Processing and Visualization of Raw Mass Spectrometry Data

(2020) Laurent Gatto et al.   JOURNAL OF PROTEOME RESEARCH

The evolving metabolic landscape of chromatin biology and epigenetics

(2020) Ziwei Dai et al.   NATURE REVIEWS GENETICS

Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics

(2019) Aikaterini Geladaki et al.   Nature Communications

Succinylation Links Metabolism to Protein Functions

(2019) Yun Yang et al.   NEUROCHEMICAL RESEARCH

Multi-omic measurements of heterogeneity in HeLa cells across laboratories

(2019) Yansheng Liu et al.   NATURE BIOTECHNOLOGY

Nuclear Glycogenolysis Modulates Histone Acetylation in Human Non-Small Cell Lung Cancers

(2019) Ramon C. Sun et al.   Cell Metabolism

α-Ketoglutarate links p53 to cell fate during tumour suppression

(2019) John P. Morris et al.   NATURE

An analytic approach for interpretable predictive models in high-dimensional data in the presence of interactions with exposures

(2018) Sahir Rai Bhatnagar et al.   GENETIC EPIDEMIOLOGY

Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae

(2018) Tomas Strucko et al.   METABOLIC ENGINEERING

Compartmentalized activities of the pyruvate dehydrogenase complex sustain lipogenesis in prostate cancer

(2018) Jingjing Chen et al.   NATURE GENETICS

Wild-type and mutated IDH1/2 enzymes and therapy responses

(2018) Remco J. Molenaar et al.   ONCOGENE

Single-cell transcriptomics reveals a new dynamical function of transcription factors during embryonic hematopoiesis

(2018) Isabelle Bergiers et al.   eLife

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

NOK mediates glycolysis and nuclear PDC associated histone acetylation

(2017) Li Liu   Frontiers in Bioscience-Landmark

Nuclear Acetyl-CoA Production by ACLY Promotes Homologous Recombination

(2017) Sharanya Sivanand et al.   MOLECULAR CELL

Landscape of nuclear transport receptor cargo specificity

(2017) Marie‐Therese Mackmull et al.   Molecular Systems Biology

KAT2A coupled with the α-KGDH complex acts as a histone H3 succinyltransferase

(2017) Yugang Wang et al.   NATURE

BCAT1 restricts αKG levels in AML stem cells leading to IDHmut-like DNA hypermethylation

(2017) Simon Raffel et al.   NATURE

ProHits-viz: a suite of web tools for visualizing interaction proteomics data

(2017) James D R Knight et al.   NATURE METHODS

Liquid phase condensation in cell physiology and disease

(2017) Yongdae Shin et al.   SCIENCE

A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-κB Signaling

(2017) Ramy H. Malty et al.   Cell Systems

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

α-Ketoglutarate Accelerates the Initial Differentiation of Primed Human Pluripotent Stem Cells

(2016) Tara TeSlaa et al.   Cell Metabolism

An improved smaller biotin ligase for BioID proximity labeling

(2016) Dae In Kim et al.   MOLECULAR BIOLOGY OF THE CELL

Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition

(2016) Marco Sciacovelli et al.   NATURE

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

(2016) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

In Planta Determination of the mRNA-Binding Proteome of Arabidopsis Etiolated Seedlings

(2016) Marlene Reichel et al.   PLANT CELL

The Cardiomyocyte RNA-Binding Proteome: Links to Intermediary Metabolism and Heart Disease

(2016) Yalin Liao et al.   Cell Reports

Metabolic Regulation by Lysine Malonylation, Succinylation, and Glutarylation

(2015) Matthew D. Hirschey et al.   MOLECULAR & CELLULAR PROTEOMICS

Histone Deacetylase Inhibitors (HDACi) Cause the Selective Depletion of Bromodomain Containing Proteins (BCPs)

(2015) Marie-Therese Mackmull et al.   MOLECULAR & CELLULAR PROTEOMICS

Local generation of fumarate promotes DNA repair through inhibition of histone H3 demethylation

(2015) Yuhui Jiang et al.   NATURE CELL BIOLOGY

New IDH1 mutant inhibitors for treatment of acute myeloid leukemia

(2015) Ujunwa C Okoye-Okafor et al.   Nature Chemical Biology

Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry

(2015) Holger Franken et al.   Nature Protocols

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(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata

(2014) L. Gatto et al.   BIOINFORMATICS

Citrate – new functions for an old metabolite

(2014) Vito Iacobazzi et al.   BIOLOGICAL CHEMISTRY

A Nuclear Pyruvate Dehydrogenase Complex Is Important for the Generation of Acetyl-CoA and Histone Acetylation

(2014) Gopinath Sutendra et al.   CELL

Intracellular α-ketoglutarate maintains the pluripotency of embryonic stem cells

(2014) Bryce W. Carey et al.   NATURE

Glutamine supports pancreatic cancer growth through a KRAS-regulated metabolic pathway

(2013) Jaekyoung Son et al.   NATURE

The CRAPome: a contaminant repository for affinity purification–mass spectrometry data

(2013) Dattatreya Mellacheruvu et al.   NATURE METHODS

Comparative study of IDH1 mutations in gliomas by immunohistochemistry and DNA sequencing

(2013) S. Agarwal et al.   NEURO-ONCOLOGY

Lysine Succinylation Is a Frequently Occurring Modification in Prokaryotes and Eukaryotes and Extensively Overlaps with Acetylation

(2013) Brian T. Weinert et al.   Cell Reports

Gene Expression, Molecular Class Changes, and Pathway Analysis after Neoadjuvant Systemic Therapy for Breast Cancer

(2012) A. M. Gonzalez-Angulo et al.   CLINICAL CANCER RESEARCH

Inhibition of  -KG-dependent histone and DNA demethylases by fumarate and succinate that are accumulated in mutations of FH and SDH tumor suppressors

(2012) M. Xiao et al.   GENES & DEVELOPMENT

A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells

(2012) Kyle J. Roux et al.   JOURNAL OF CELL BIOLOGY

Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins

(2012) Tamar Geiger et al.   MOLECULAR & CELLULAR PROTEOMICS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation

(2011) Laurent Gatto et al.   BIOINFORMATICS

Oncometabolite 2-Hydroxyglutarate Is a Competitive Inhibitor of α-Ketoglutarate-Dependent Dioxygenases

(2011) Wei Xu et al.   CANCER CELL

The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases

(2011) Rasheduzzaman Chowdhury et al.   EMBO REPORTS

Acetyl-CoA Induces Cell Growth and Proliferation by Promoting the Acetylation of Histones at Growth Genes

(2011) Ling Cai et al.   MOLECULAR CELL

Fumarase: A Mitochondrial Metabolic Enzyme and a Cytosolic/Nuclear Component of the DNA Damage Response

(2010) Ohad Yogev et al.   PLOS BIOLOGY

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Distinct cytoplasmic maturation steps of 40S ribosomal subunit precursors require hRio2

(2009) Ivo Zemp et al.   JOURNAL OF CELL BIOLOGY

Inhibition of succinate dehydrogenase dysregulates histone modification in mammalian cells

(2009) Ana M Cervera et al.   Molecular Cancer

ATP-Citrate Lyase Links Cellular Metabolism to Histone Acetylation

(2009) K. E. Wellen et al.   SCIENCE