Benjamin A. Garcia

Improvement in the apparent mass resolution of oligonucleotides by using 12C/14N-enriched samples.

Improvement of the MALDI-TOF analysis of DNA with thin-layer matrix preparation.

Characterization of phosphorylation sites on histone H1 isoforms by tandem mass spectrometry.

Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct combinations of post-translational modifications.

Simian virus 40 small t antigen mediates conformation-dependent transfer of protein phosphatase 2A onto the androgen receptor.

Analysis of protein phosphorylation by mass spectrometry.

Serine 31 phosphorylation of histone variant H3.3 is specific to regions bordering centromeres in metaphase chromosomes.

Modifications of human histone H3 variants during mitosis.

The platelet microparticle proteome.

Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation.

Expression patterns and post-translational modifications associated with mammalian histone H3 variants.

Resetting the epigenetic histone code in the MRL-lpr/lpr mouse model of lupus by histone deacetylase inhibition.

Negative regulation of LRP6 function by casein kinase I epsilon phosphorylation.

Comprehensive phosphoprotein analysis of linker histone H1 from Tetrahymena thermophila.

Site-specific casein kinase 1epsilon-dependent phosphorylation of Dishevelled modulates beta-catenin signaling.

Protein profile of osteoarthritic human articular cartilage using tandem mass spectrometry.

A novel histone deacetylase pathway regulates mitosis by modulating Aurora B kinase activity.

Characterization of histones and their post-translational modifications by mass spectrometry.

Identification of histone H3 lysine 36 acetylation as a highly conserved histone modification.

Organismal differences in post-translational modifications in histones H3 and H4.

Protein phosphatase 1 regulates assembly and function of the beta-catenin degradation complex.

Chemical derivatization of histones for facilitated analysis by mass spectrometry.

Pervasive combinatorial modification of histone H3 in human cells.

Mild performic acid oxidation enhances chromatographic and top down mass spectrometric analyses of histones.

Tissue-specific expression and post-translational modification of histone H3 variants.

Cathepsin L proteolytically processes histone H3 during mouse embryonic stem cell differentiation.

Analysis of histones in Xenopus laevis. II. mass spectrometry reveals an index of cell type-specific modifications on H3 and H4.

Tandem mass spectrometry with ultrahigh mass accuracy clarifies peptide identification by database retrieval.

Chromatin-specific remodeling by HMGB1 and linker histone H1 silences proinflammatory genes during endotoxin tolerance.

Histone h3 lysine 56 acetylation is linked to the core transcriptional network in human embryonic stem cells.

Mass spectrometric analysis of histone variants and post-translational modifications.

Heterochromatin protein 1 is extensively decorated with histone code-like post-translational modifications.

High throughput characterization of combinatorial histone codes.

Proteome-wide prediction of acetylation substrates.

A mixed integer linear optimization framework for the identification and quantification of targeted post-translational modifications of highly modified proteins using multiplexed electron transfer dissociation tandem mass spectrometry.

Protein quantification across hundreds of experimental conditions.

One-pot shotgun quantitative mass spectrometry characterization of histones.

Electron transfer dissociation facilitates sequencing of adenosine diphosphate-ribosylated peptides.

In vivo residue-specific histone methylation dynamics.

What does the future hold for Top Down mass spectrometry?

A novel approach for untargeted post-translational modification identification using integer linear optimization and tandem mass spectrometry.

Modern approaches for investigating epigenetic signaling pathways.

Systems-wide proteomic characterization of combinatorial post-translational modification patterns.

Combinatorial profiling of chromatin binding modules reveals multisite discrimination.

Collective mass spectrometry approaches reveal broad and combinatorial modification of high mobility group protein A1a.

Histone H1 variant-specific lysine methylation by G9a/KMT1C and Glp1/KMT1D.

Quantitative proteomics reveals direct and indirect alterations in the histone code following methyltransferase knockdown.

Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development.

The significance, development and progress of high-throughput combinatorial histone code analysis.

Branched tricarboxylic acid metabolism in Plasmodium falciparum.

Trimethylation of histone H3 lysine 4 impairs methylation of histone H3 lysine 9: regulation of lysine methyltransferases by physical interaction with their substrates.

Lysine methylation of the NF-κB subunit RelA by SETD6 couples activity of the histone methyltransferase GLP at chromatin to tonic repression of NF-κB signaling.

Global turnover of histone post-translational modifications and variants in human cells.

The histone variant macroH2A suppresses melanoma progression through regulation of CDK8.

Isoform-specific phosphorylation of human linker histone H1.4 in mitosis by the kinase Aurora B.

Revealing histone variant induced changes via quantitative proteomics.

Proteomics.

Histone deacetylase 9 deficiency protects against effector T cell-mediated systemic autoimmunity.

The RING finger protein MSL2 in the MOF complex is an E3 ubiquitin ligase for H2B K34 and is involved in crosstalk with H3 K4 and K79 methylation.

A chemical probe selectively inhibits G9a and GLP methyltransferase activity in cells.

Methylation of H2AR29 is a novel repressive PRMT6 target.

Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization.

Proteomic interrogation of human chromatin.

Quantitative proteomic approaches to studying histone modifications.

Breaking the histone code with quantitative mass spectrometry.

Novel protein identification methods for biomarker discovery via a proteomic analysis of periodontally healthy and diseased gingival crevicular fluid samples.

NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming.

Methylation of H4 lysines 5, 8 and 12 by yeast Set5 calibrates chromatin stress responses.

Histone H3 lysine 56 methylation regulates DNA replication through its interaction with PCNA.

ATRX-mediated chromatin association of histone variant macroH2A1 regulates α-globin expression.

Smyd3 regulates cancer cell phenotypes and catalyzes histone H4 lysine 5 methylation.

Origins and formation of histone methylation across the human cell cycle.

H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence.

Melanoma exosomes educate bone marrow progenitor cells toward a pro-metastatic phenotype through MET.

BclAF1 restriction factor is neutralized by proteasomal degradation and microRNA repression during human cytomegalovirus infection.

Global secretome analysis identifies novel mediators of bone metastasis.

Discovery of lysine post-translational modifications through mass spectrometric detection.

SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation.

Poly-acetylated chromatin signatures are preferred epitopes for site-specific histone H4 acetyl antibodies.

PILOT_PROTEIN: identification of unmodified and modified proteins via high-resolution mass spectrometry and mixed-integer linear optimization.

Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins.

Examining histone posttranslational modification patterns by high-resolution mass spectrometry.

Asymmetrically modified nucleosomes.

Novel phosphorylation sites in the S. cerevisiae Cdc13 protein reveal new targets for telomere length regulation.

Discovery of biomarker combinations that predict periodontal health or disease with high accuracy from GCF samples based on high-throughput proteomic analysis and mixed-integer linear optimization.

Chromatin proteins captured by ChIP-mass spectrometry are linked to dosage compensation in Drosophila.

SETD6 monomethylates H2AZ on lysine 7 and is required for the maintenance of embryonic stem cell self-renewal.

Comprehending dynamic protein methylation with mass spectrometry.

Validation of protein acetylation by mass spectrometry.

Heavy methyl-SILAC labeling coupled with liquid chromatography and high-resolution mass spectrometry to study the dynamics of site-specific histone methylation.

Quantitative dynamics of the link between cellular metabolism and histone acetylation.

Inhibition of PRC2 activity by a gain-of-function H3 mutation found in pediatric glioblastoma.

Retraction: Branched tricarboxylic acid metabolism in Plasmodium falciparum.

Large-scale global identification of protein lysine methylation in vivo.

Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency.

Dysregulation of PAD4-mediated citrullination of nuclear GSK3β activates TGF-β signaling and induces epithelial-to-mesenchymal transition in breast cancer cells.

A quantitative atlas of histone modification signatures from human cancer cells.

Combining genomic and proteomic approaches for epigenetics research.

Proteomic characterization of novel histone post-translational modifications.

H4K20 methylation regulates quiescence and chromatin compaction.

Initial characterization of histone H3 serine 10 O-acetylation.

H3R42me2a is a histone modification with positive transcriptional effects.

Proteomic analysis of the SIRT6 interactome: novel links to genome maintenance and cellular stress signaling.

Identification and interrogation of combinatorial histone modifications.

Neutron-encoded mass signatures for quantitative top-down proteomics.

Tyr phosphorylation of PDP1 toggles recruitment between ACAT1 and SIRT3 to regulate the pyruvate dehydrogenase complex.

Stable isotope labeling of phosphoproteins for large-scale phosphorylation rate determination.

De novo peptide design and experimental validation of histone methyltransferase inhibitors.

De novo peptide design and experimental validation of histone methyltransferase inhibitors.

SMYD3 links lysine methylation of MAP3K2 to Ras-driven cancer.

ChIP-less analysis of chromatin states.

Mass spectrometric analysis of histone proteoforms.

Quantitative proteomic discovery of dynamic epigenome changes that control human cytomegalovirus (HCMV) infection.

Akt-dependent metabolic reprogramming regulates tumor cell histone acetylation.

Stable-isotope-labeled histone peptide library for histone post-translational modification and variant quantification by mass spectrometry.

Middle-Down and Top-Down Mass Spectrometric Analysis of Co-occurring Histone Modifications.

A proteomic glimpse into the initial global epigenetic changes during HIV infection.

Histone methylation has dynamics distinct from those of histone acetylation in cell cycle reentry from quiescence.

Evaluation of proteomic search engines for the analysis of histone modifications.

SnapShot: histone modifications.

In vivo proximity labeling for the detection of protein-protein and protein-RNA interactions.

High resolution is not a strict requirement for characterization and quantification of histone post-translational modifications.

Analytical tools and current challenges in the modern era of neuroepigenomics.

BRD4 assists elongation of both coding and enhancer RNAs by interacting with acetylated histones.

Selective inhibition of EZH2 and EZH1 enzymatic activity by a small molecule suppresses MLL-rearranged leukemia.

Defining heterochromatin in C. elegans through genome-wide analysis of the heterochromatin protein 1 homolog HPL-2.

Identification of nuclear hormone receptor pathways causing insulin resistance by transcriptional and epigenomic analysis.

The cerebral cavernous malformation pathway controls cardiac development via regulation of endocardial MEKK3 signaling and KLF expression.

Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH) Analysis for Characterization and Quantification of Histone Post-translational Modifications.

Drawbacks in the use of unconventional hydrophobic anhydrides for histone derivatization in bottom-up proteomics PTM analysis.

A specific LSD1/KDM1A isoform regulates neuronal differentiation through H3K9 demethylation.

Quantitative proteomic analysis of histone modifications.

Characterization of BRD4 during mammalian postmeiotic sperm development.

Bottom-up and middle-down proteomics have comparable accuracies in defining histone post-translational modification relative abundance and stoichiometry.

EpiProfile Quantifies Histone Peptides With Modifications by Extracting Retention Time and Intensity in High-resolution Mass Spectra.

LLY-507, a Cell-active, Potent, and Selective Inhibitor of Protein-lysine Methyltransferase SMYD2.

Proteogenomics analysis reveals specific genomic orientations of distal regulatory regions composed by non-canonical histone variants.

Multi-faceted quantitative proteomics analysis of histone H2B isoforms and their modifications.

Memory acquisition and retrieval impact different epigenetic processes that regulate gene expression.

Characterization of histone post-translational modifications during virus infection using mass spectrometry-based proteomics.

Critical Role of Histone Turnover in Neuronal Transcription and Plasticity.

Properly reading the histone code by MS-based proteomics.

Analysis of Histones H3 and H4 Reveals Novel and Conserved Post-Translational Modifications in Sugarcane.

Comprehensive Catalog of Currently Documented Histone Modifications.

The histone lysine methyltransferase KMT2D sustains a gene expression program that represses B cell lymphoma development.

Progress in epigenetic histone modification analysis by mass spectrometry for clinical investigations.

The PZP Domain of AF10 Senses Unmodified H3K27 to Regulate DOT1L-Mediated Methylation of H3K79.

Low Resolution Data-Independent Acquisition in an LTQ-Orbitrap Allows for Simplified and Fully Untargeted Analysis of Histone Modifications.

Tumour exosome integrins determine organotropic metastasis.

Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin.

Nitric Oxide Regulates Gene Expression in Cancers by Controlling Histone Posttranslational Modifications.

Monitoring Cellular Phosphorylation Signaling Pathways into Chromatin and Down to the Gene Level.

H4K44 Acetylation Facilitates Chromatin Accessibility during Meiosis.

Histone modification profiling reveals differential signatures associated with human embryonic stem cell self-renewal and differentiation.

Permuting the PGF Signature Motif Blocks both Archaeosortase-Dependent C-Terminal Cleavage and Prenyl Lipid Attachment for the Haloferax volcanii S-Layer Glycoprotein.

Tet2 Catalyzes Stepwise 5-Methylcytosine Oxidation by an Iterative and de novo Mechanism.

Quantitative Profiling of the Activity of Protein Lysine Methyltransferase SMYD2 Using SILAC-Based Proteomics.

Analyses of Histone Proteoforms Using Front-end Electron Transfer Dissociation-enabled Orbitrap Instruments.

Bioorthogonal Chemistry for the Isolation and Study of Newly Synthesized Histones and Their Modifications.

Reshaping the Chromatin and Epigenetic Landscapes with Quantitative Mass Spectrometry.

Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells.

Folate deficiency affects histone methylation.

A novel quantitative mass spectrometry platform for determining protein O-GlcNAcylation dynamics.

PRDM16 Suppresses MLL1r Leukemia via Intrinsic Histone Methyltransferase Activity.

Inhibition of DHHC20-Mediated EGFR Palmitoylation Creates a Dependence on EGFR Signaling.

Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape.

Protein Kinase C Epsilon Is a Key Regulator of Mitochondrial Redox Homeostasis in Acute Myeloid Leukemia.

Human chimeric antigen receptor macrophages for cancer immunotherapy.

Interaction with the CCT chaperonin complex limits APOBEC3A cytidine deaminase cytotoxicity.

Multi-omic profiling of histone variant H3.3 lysine 27 methylation reveals a distinct role from canonical H3 in stem cell differentiation.

Data-Independent Acquisition for the Detection of Mononucleoside RNA Modifications by Mass Spectrometry.

H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells.

Permethylation of Ribonucleosides Provides Enhanced Mass Spectrometry Quantification of Post-Transcriptional RNA Modifications.

Kabuki syndrome stem cell models reveal locus specificity of histone methyltransferase 2D (KMT2D/MLL4).

Nucleome programming is required for the foundation of totipotency in mammalian germline development.

Top-"Double-Down" Mass Spectrometry of Histone H4 Proteoforms: Tandem Ultraviolet-Photon and Mobility/Mass-Selected Electron Capture Dissociations.

Combination of common mtDNA variants results in mitochondrial dysfunction and a connective tissue dysregulation.

K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas.

Stable isotope tracing in vivo reveals a metabolic bridge linking the microbiota to host histone acetylation.

Arginine Methylation of the PGC-1α C-Terminus Is Temperature-Dependent.

Characterizing crosstalk in epigenetic signaling to understand disease physiology.

Expanding the Epitranscriptomic RNA Sequencing and Modification Mapping Mass Spectrometry Toolbox with Field Asymmetric Waveform Ion Mobility and Electrochemical Elution Liquid Chromatography.

Single substitution in H3.3G34 alters DNMT3A recruitment to cause progressive neurodegeneration.

Alternative splicing of HDAC7 regulates its interaction with 14-3-3 proteins to alter histone marks and target gene expression.

Comparative analysis of drug-like EP300/CREBBP acetyltransferase inhibitors.

A Novel Brain PET Radiotracer for Imaging Alpha Synuclein Fibrils in Multiple System Atrophy.

Acetyl-methyllysine marks chromatin at active transcription start sites.

Comparative Analysis of Drug-like EP300/CREBBP Acetyltransferase Inhibitors.

SWAMNA: a comprehensive platform for analysis of nucleic acid modifications.

Altered chromatin occupancy of patient-associated H4 mutants misregulate neuronal differentiation.

An Optimized and High-Throughput Method for Histone Propionylation and Data-Independent Acquisition Analysis for the Identification and Quantification of Histone Post-translational Modifications.

The antiproliferative effect of FGF2 in K-Ras-driven tumor cells involves modulation of rRNA and the nucleolus.

Electrostatic encoding of genome organization principles within single native nucleosomes.

Phosphorylation regulates viral biomolecular condensates to promote infectious progeny production.