St. Jude Proteomics Facility,
Departments of Structural Biology and Developmental Neurobiology,
Center for Proteomics and Metabolomics
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SOX4 interacts with plakoglobin in a Wnt3a-dependent manner in prostate cancer cells.
BMC cell biology , 2011 | Pubmed ID: 22098624
Analysis of ubiquitinated proteome by quantitative mass spectrometry.
Methods in molecular biology (Clifton, N.J.) , 2012 | Pubmed ID: 22665315
Characterizing ubiquitination sites by peptide-based immunoaffinity enrichment.
Molecular & cellular proteomics : MCP Dec, 2012 | Pubmed ID: 22729469
PHD3-dependent hydroxylation of HCLK2 promotes the DNA damage response.
The Journal of clinical investigation Aug, 2012 | Pubmed ID: 22797300
Quantitative proteomics to decipher ubiquitin signaling.
Amino acids Sep, 2012 | Pubmed ID: 22821265
Synaptic protein ubiquitination in rat brain revealed by antibody-based ubiquitome analysis.
Journal of proteome research Sep, 2012 | Pubmed ID: 22871113
Ubiquitin-specific protease 9x deubiquitinates and stabilizes the spinal muscular atrophy protein-survival motor neuron.
The Journal of biological chemistry Dec, 2012 | Pubmed ID: 23112048
Sjogren syndrome antigen B (SSB)/La promotes global microRNA expression by binding microRNA precursors through stem-loop recognition.
The Journal of biological chemistry Jan, 2013 | Pubmed ID: 23129761
Regulation of behavioral circadian rhythms and clock protein PER1 by the deubiquitinating enzyme USP2.
Biology open Aug, 2012 | Pubmed ID: 23213472
The cotranslational function of ribosome-associated Hsp70 in eukaryotic protein homeostasis.
Cell Jan, 2013 | Pubmed ID: 23332755
Proteomic analysis of postsynaptic density in Alzheimer's disease.
Clinica chimica acta; international journal of clinical chemistry May, 2013 | Pubmed ID: 23537733
Structural Insights into the Functions of TBK1 in Innate Antimicrobial Immunity.
Structure (London, England : 1993) Jul, 2013 | Pubmed ID: 23746807
U1 small nuclear ribonucleoprotein complex and RNA splicing alterations in Alzheimer's disease.
Proceedings of the National Academy of Sciences of the United States of America Oct, 2013 | Pubmed ID: 24023061
A conserved protein with AN1 zinc finger and ubiquitin-like domains modulates Cdc48 (p97) function in the ubiquitin-proteasome pathway.
The Journal of biological chemistry Nov, 2013 | Pubmed ID: 24121501
Identification and characterization of phosphorylation sites within the pregnane X receptor protein.
Biochemical pharmacology Jan, 2014 | Pubmed ID: 24184507
The U4/U6 recycling factor SART3 has histone chaperone activity and associates with USP15 to regulate H2B deubiquitination.
The Journal of biological chemistry Mar, 2014 | Pubmed ID: 24526689
A nano ultra-performance liquid chromatography-high resolution mass spectrometry approach for global metabolomic profiling and case study on drug-resistant multiple myeloma.
Analytical chemistry Apr, 2014 | Pubmed ID: 24611431
Autoregulation of the 26S proteasome by in situ ubiquitination.
Molecular biology of the cell Jun, 2014 | Pubmed ID: 24743594
Cell type-restricted activity of hnRNPM promotes breast cancer metastasis via regulating alternative splicing.
Genes & development Jun, 2014 | Pubmed ID: 24840202
Integrated approaches for analyzing U1-70K cleavage in Alzheimer's disease.
Journal of proteome research Nov, 2014 | Pubmed ID: 24902715
Global ubiquitination analysis by SILAC in mammalian cells.
Methods in molecular biology (Clifton, N.J.) , 2014 | Pubmed ID: 25059610
JUMP: a tag-based database search tool for peptide identification with high sensitivity and accuracy.
Molecular & cellular proteomics : MCP Dec, 2014 | Pubmed ID: 25202125
Refined phosphopeptide enrichment by phosphate additive and the analysis of human brain phosphoproteome.
Proteomics Jan, 2015 | Pubmed ID: 25307156
Systematic optimization of long gradient chromatography mass spectrometry for deep analysis of brain proteome.
Journal of proteome research Feb, 2015 | Pubmed ID: 25455107
Altered ubiquitin causes perturbed calcium homeostasis, hyperactivation of calpain, dysregulated differentiation, and cataract.
Proceedings of the National Academy of Sciences of the United States of America Jan, 2015 | Pubmed ID: 25583491
Quantitative protein analysis by mass spectrometry.
Methods in molecular biology (Clifton, N.J.) , 2015 | Pubmed ID: 25859956
Sequential Elution Interactome Analysis of the Mind Bomb 1 Ubiquitin Ligase Reveals a Novel Role in Dendritic Spine Outgrowth.
Molecular & cellular proteomics : MCP Jul, 2015 | Pubmed ID: 25931508
PHD2/3-dependent hydroxylation tunes cardiac response to β-adrenergic stress via phospholamban.
The Journal of clinical investigation Jul, 2015 | Pubmed ID: 26075818
Molecular characterization of LC3-associated phagocytosis reveals distinct roles for Rubicon, NOX2 and autophagy proteins.
Nature cell biology Jul, 2015 | Pubmed ID: 26098576
Efficacy of Retinoids in IKZF1-Mutated BCR-ABL1 Acute Lymphoblastic Leukemia.
Cancer cell Sep, 2015 | Pubmed ID: 26321221
A Degenerate Cohort of Yeast Membrane Trafficking DUBs Mediates Cell Polarity and Survival.
Molecular & cellular proteomics : MCP Dec, 2015 | Pubmed ID: 26412298
Multiple Weak Linear Motifs Enhance Recruitment and Processivity in SPOP-Mediated Substrate Ubiquitination.
Journal of molecular biology Mar, 2016 | Pubmed ID: 26475525
Joint mouse-human phenome-wide association to test gene function and disease risk.
Nature communications Feb, 2016 | Pubmed ID: 26833085
SUMO Pathway Modulation of Regulatory Protein Binding at the Ribosomal DNA Locus in Saccharomyces cerevisiae.
Genetics Apr, 2016 | Pubmed ID: 26837752
Enhanced Purification of Ubiquitinated Proteins by Engineered Tandem Hybrid Ubiquitin-binding Domains (ThUBDs).
Molecular & cellular proteomics : MCP Apr, 2016 | Pubmed ID: 27037361
The Noncanonical Role of ULK/ATG1 in ER-to-Golgi Trafficking Is Essential for Cellular Homeostasis.
Molecular cell May, 2016 | Pubmed ID: 27203176
JUMPg: An Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells.
Journal of proteome research Jul, 2016 | Pubmed ID: 27225868
C9orf72 Dipeptide Repeats Impair the Assembly, Dynamics, and Function of Membrane-Less Organelles.
Cell Oct, 2016 | Pubmed ID: 27768896
The C. elegans Taste Receptor Homolog LITE-1 Is a Photoreceptor.
Cell 11, 2016 | Pubmed ID: 27863243
Deep Profiling of Proteome and Phosphoproteome by Isobaric Labeling, Extensive Liquid Chromatography, and Mass Spectrometry.
Methods in enzymology , 2017 | Pubmed ID: 28109439
Extensive Peptide Fractionation and y1 Ion-Based Interference Detection Method for Enabling Accurate Quantification by Isobaric Labeling and Mass Spectrometry.
Analytical chemistry Mar, 2017 | Pubmed ID: 28194965
Targeting human Mas-related G protein-coupled receptor X1 to inhibit persistent pain.
Proceedings of the National Academy of Sciences of the United States of America Mar, 2017 | Pubmed ID: 28223516
Integrative Proteomics and Phosphoproteomics Profiling Reveals Dynamic Signaling Networks and Bioenergetics Pathways Underlying T Cell Activation.
Immunity Mar, 2017 | Pubmed ID: 28285833
Quantitative Phosphoproteomic Analysis of Brain Tissues.
Methods in molecular biology (Clifton, N.J.) , 2017 | Pubmed ID: 28508362
Blocking an N-terminal acetylation-dependent protein interaction inhibits an E3 ligase.
Nature chemical biology Aug, 2017 | Pubmed ID: 28581483
Targeting Histone Demethylases in MYC-Driven Neuroblastomas with Ciclopirox.
Cancer research Sep, 2017 | Pubmed ID: 28684529
The neoepitope landscape in pediatric cancers.
Genome medicine Aug, 2017 | Pubmed ID: 28854978
Binding of PLD2-Generated Phosphatidic Acid to KIF5B Promotes MT1-MMP Surface Trafficking and Lung Metastasis of Mouse Breast Cancer Cells.
Developmental cell Oct, 2017 | Pubmed ID: 29033361
Discrete roles and bifurcation of PTEN signaling and mTORC1-mediated anabolic metabolism underlie IL-7-driven B lymphopoiesis.
Science advances 01, 2018 | Pubmed ID: 29399633
CDK2 inhibitors as candidate therapeutics for cisplatin- and noise-induced hearing loss.
The Journal of experimental medicine 04, 2018 | Pubmed ID: 29514916
Target-Decoy-Based False Discovery Rate Estimation for Large-Scale Metabolite Identification.
Journal of proteome research 07, 2018 | Pubmed ID: 29790753
Mutant LRRK2 mediates peripheral and central immune responses leading to neurodegeneration in vivo.
Brain : a journal of neurology 06, 2018 | Pubmed ID: 29800472
Hippo/Mst signalling couples metabolic state and immune function of CD8α dendritic cells.
Nature 06, 2018 | Pubmed ID: 29849151
Isotope Labeling-Assisted Evaluation of Hydrophilic and Hydrophobic Liquid Chromatograph-Mass Spectrometry for Metabolomics Profiling.
Analytical chemistry 07, 2018 | Pubmed ID: 29883117
Quantitative phosphoproteomic analysis of the molecular substrates of sleep need.
Nature 06, 2018 | Pubmed ID: 29899451
Reducing histone acetylation rescues cognitive deficits in a mouse model of Fragile X syndrome.
Nature communications 06, 2018 | Pubmed ID: 29950602
Spectral Library Search Improves Assignment of TMT Labeled MS/MS Spectra.
Journal of proteome research 09, 2018 | Pubmed ID: 30096983
BDNF inhibits neurodegenerative disease-associated asparaginyl endopeptidase activity via phosphorylation by AKT.
JCI insight 08, 2018 | Pubmed ID: 30135302
Epidithiodiketopiperazines Inhibit Protein Degradation by Targeting Proteasome Deubiquitinase Rpn11.
Cell chemical biology 11, 2018 | Pubmed ID: 30146242
Identification of Therapeutic Targets in Rhabdomyosarcoma through Integrated Genomic, Epigenomic, and Proteomic Analyses.
Cancer cell 09, 2018 | Pubmed ID: 30146332
Partial loss of psychiatric risk gene Mir137 in mice causes repetitive behavior and impairs sociability and learning via increased Pde10a.
Nature neuroscience 12, 2018 | Pubmed ID: 30397325
Hippo Kinases Mst1 and Mst2 Sense and Amplify IL-2R-STAT5 Signaling in Regulatory T Cells to Establish Stable Regulatory Activity.
Immunity 11, 2018 | Pubmed ID: 30413360
Deep Profiling of the Aggregated Proteome in Alzheimer's Disease: From Pathology to Disease Mechanisms.
Proteomes Nov, 2018 | Pubmed ID: 30424485
Deubiquitylase USP9X maintains centriolar satellite integrity by stabilizing pericentriolar material 1 protein.
Journal of cell science 01, 2019 | Pubmed ID: 30584065
TET2 stabilization by 14-3-3 binding to the phosphorylated Serine 99 is deregulated by mutations in cancer.
Cell research 03, 2019 | Pubmed ID: 30607016
Differentiation of human pluripotent stem cells into neurons or cortical organoids requires transcriptional co-regulation by UTX and 53BP1.
Nature neuroscience 03, 2019 | Pubmed ID: 30718900
Phosphatidic acid generated by PLD2 promotes the plasma membrane recruitment of IQGAP1 and neointima formation.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology 06, 2019 | Pubmed ID: 30811216
Mutant and Wild-Type Isocitrate Dehydrogenase 1 Share Enhancing Mechanisms Involving Distinct Tyrosine Kinase Cascades in Cancer.
Cancer discovery 06, 2019 | Pubmed ID: 30862724
LKB1 orchestrates dendritic cell metabolic quiescence and anti-tumor immunity.
Cell research 05, 2019 | Pubmed ID: 30911060
Metabolic switching in pluripotent stem cells reorganizes energy metabolism and subcellular organelles.
Experimental cell research 06, 2019 | Pubmed ID: 30922922
Regulation of gene expression by miR-144/451 during mouse erythropoiesis.
Blood 06, 2019 | Pubmed ID: 30971389
ULK1 and ULK2 Regulate Stress Granule Disassembly Through Phosphorylation and Activation of VCP/p97.
Molecular cell 05, 2019 | Pubmed ID: 30979586
Identification of a Functional Non-coding Variant in the GABA Receptor α2 Subunit of the C57BL/6J Mouse Reference Genome: Major Implications for Neuroscience Research.
Frontiers in genetics , 2019 | Pubmed ID: 30984232
Deep undepleted human serum proteome profiling toward biomarker discovery for Alzheimer's disease.
Clinical proteomics , 2019 | Pubmed ID: 31019427
Corrigendum to "Metabolic switching in pluripotent stem cells reorganizes energy metabolism and subcellular organelles" [379 (2019) 55-64].
Experimental cell research Aug, 2019 | Pubmed ID: 31079852
Kinase network dysregulation in a human induced pluripotent stem cell model of DISC1 schizophrenia.
Molecular omics 06, 2019 | Pubmed ID: 31106784
Circadian gene variants and the skeletal muscle circadian clock contribute to the evolutionary divergence in longevity across populations.
Genome research 08, 2019 | Pubmed ID: 31249065
Regulation of MAGE-A3/6 by the CRL4-DCAF12 ubiquitin ligase and nutrient availability.
EMBO reports 07, 2019 | Pubmed ID: 31267705
Akt Phosphorylates NQO1 and Triggers its Degradation, Abolishing Its Antioxidative Activities in Parkinson's Disease.
The Journal of neuroscience : the official journal of the Society for Neuroscience 09, 2019 | Pubmed ID: 31358653
ALS-FTLD-linked mutations of SQSTM1/p62 disrupt selective autophagy and NFE2L2/NRF2 anti-oxidative stress pathway.
Autophagy 05, 2020 | Pubmed ID: 31362587
A Key Role for the Ubiquitin Ligase UBR4 in Myofiber Hypertrophy in Drosophila and Mice.
Cell reports 07, 2019 | Pubmed ID: 31365869
Deep multiomics profiling of brain tumors identifies signaling networks downstream of cancer driver genes.
Nature communications 08, 2019 | Pubmed ID: 31420543
Multimodal Imaging of Amyloid Plaques: Fusion of the Single-Probe Mass Spectrometry Image and Fluorescence Microscopy Image.
Analytical chemistry 10, 2019 | Pubmed ID: 31536324
Amino Acids License Kinase mTORC1 Activity and Treg Cell Function via Small G Proteins Rag and Rheb.
Immunity 12, 2019 | Pubmed ID: 31668641
Cerebrospinal fluid tau fragment correlates with tau PET: a candidate biomarker for tangle pathology.
Brain : a journal of neurology 02, 2020 | Pubmed ID: 31834365
Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer's Disease Progression.
Neuron 03, 2020 | Pubmed ID: 31926610
An ABC Transporter Drives Medulloblastoma Pathogenesis by Regulating Sonic Hedgehog Signaling.
Cancer research Apr, 2020 | Pubmed ID: 31948942
A Cancer-Specific Ubiquitin Ligase Drives mRNA Alternative Polyadenylation by Ubiquitinating the mRNA 3' End Processing Complex.
Molecular cell 03, 2020 | Pubmed ID: 31980388
Novel specialized cell state and spatial compartments within the germinal center.
Nature immunology Jun, 2020 | Pubmed ID: 32341509
27-Plex Tandem Mass Tag Mass Spectrometry for Profiling Brain Proteome in Alzheimer's Disease.
Analytical chemistry 05, 2020 | Pubmed ID: 32343560
Ligand-induced monoubiquitination of BIK1 regulates plant immunity.
Nature 05, 2020 | Pubmed ID: 32404997
JUMPm: A Tool for Large-Scale Identification of Metabolites in Untargeted Metabolomics.
Metabolites May, 2020 | Pubmed ID: 32408578
Control of Early B Cell Development by the RNA N-Methyladenosine Methylation.
Cell reports Jun, 2020 | Pubmed ID: 32610122
Toxicoproteomic Profiling of Transgenic Mice Treated with Rifampicin and Isoniazid.
Cells Jul, 2020 | Pubmed ID: 32660103
Integrated analysis of ultra-deep proteomes in cortex, cerebrospinal fluid and serum reveals a mitochondrial signature in Alzheimer's disease.
Molecular neurodegeneration 07, 2020 | Pubmed ID: 32711556
Systems immunology: Integrating multi-omics data to infer regulatory networks and hidden drivers of immunity.
Current opinion in systems biology Jun, 2019 | Pubmed ID: 32789283
Combinatorial expression of GPCR isoforms affects signalling and drug responses.
Nature 11, 2020 | Pubmed ID: 33149304
FBXO11-mediated proteolysis of BAHD1 relieves PRC2-dependent transcriptional repression in erythropoiesis.
Blood 01, 2021 | Pubmed ID: 33156908
Deep Profiling of Microgram-Scale Proteome by Tandem Mass Tag Mass Spectrometry.
Journal of proteome research 01, 2021 | Pubmed ID: 33175545
Author Correction: Combinatorial expression of GPCR isoforms affects signalling and drug responses.
Nature Dec, 2020 | Pubmed ID: 33244189
Antagonistic control of myofiber size and muscle protein quality control by the ubiquitin ligase UBR4 during aging.
Nature communications 03, 2021 | Pubmed ID: 33658508
Integrative network analysis reveals USP7 haploinsufficiency inhibits E-protein activity in pediatric T-lineage acute lymphoblastic leukemia (T-ALL).
Scientific reports Mar, 2021 | Pubmed ID: 33664368
Global Profiling of Lysine Accessibility to Evaluate Protein Structure Changes in Alzheimer's Disease.
Journal of the American Society for Mass Spectrometry Apr, 2021 | Pubmed ID: 33683887
Quantifying Proteome and Protein Modifications in Activated T Cells by Multiplexed Isobaric Labeling Mass Spectrometry.
Methods in molecular biology (Clifton, N.J.) , 2021 | Pubmed ID: 33928561
High-Throughput Profiling of Proteome and Posttranslational Modifications by 16-Plex TMT Labeling and Mass Spectrometry.
Methods in molecular biology (Clifton, N.J.) , 2021 | Pubmed ID: 33950493
An age-downregulated ribosomal RpS28 protein variant regulates the muscle proteome.
G3 (Bethesda, Md.) May, 2021 | Pubmed ID: 33974070
Identification of Potent, Selective, and Orally Bioavailable Small-Molecule GSPT1/2 Degraders from a Focused Library of Cereblon Modulators.
Journal of medicinal chemistry 06, 2021 | Pubmed ID: 34042448
Structural analysis of the full-length human LRRK2.
Cell Jun, 2021 | Pubmed ID: 34107286
Network-based systems pharmacology reveals heterogeneity in LCK and BCL2 signaling and therapeutic sensitivity of T-cell acute lymphoblastic leukemia.
Nature cancer Mar, 2021 | Pubmed ID: 34151288
Global Proteomic Profiling of Pediatric AML: A Pilot Study.
Cancers Jun, 2021 | Pubmed ID: 34202615
Proteomic landscape of Alzheimer's Disease: novel insights into pathogenesis and biomarker discovery.
Molecular neurodegeneration 08, 2021 | Pubmed ID: 34384464
Acute depletion of CTCF rewires genome-wide chromatin accessibility.
Genome biology 08, 2021 | Pubmed ID: 34429148
JUMPt: Comprehensive Protein Turnover Modeling of In Vivo Pulse SILAC Data by Ordinary Differential Equations.
Analytical chemistry 10, 2021 | Pubmed ID: 34587451
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