Simone Sidoli

Epigenetics Program, University of Pennsylvania

Affiliated withUniversity of Pennsylvania University of Pennsylvania Perelman School of Medicine Albert Einstein College of Medicine

Research Area

Biography

Simone Sidoli is an Assistant Professor at the Albert Einstein College of Medicine, Department of Biochemistry, and Scientific Director of the Einstein Proteomics Core. Dr. Sidoli applies proteomics to identify the composition and dynamics of chromatin. This includes the development of new quantitative methods to identify histone modifications, locus-specific proteomes, and biomarkers in disease. His lab is invested in innovating new 3D cell models to reduce the necessity of animal testing, and in advancing the use of minimally invasive devices to collect biopsies.

JoVE Journal Publications

ArticleTotal : 5	Year
Publication title Cited by 227	2016
Publication title Cited by 1	2017
Publication title Cited by 7	2022
Publication title Cited by 2	2023
Publication title Cited by 1	2025

Other Publications

Article	Year
Roles of H3K27me2 and H3K27me3 Examined during Fate Specification of Embryonic Stem Cells. Cell reports\| PubMed ID: 27783950	2016
Proteomics in chromatin biology and epigenetics: Elucidation of post-translational modifications of histone proteins by mass spectrometry. Journal of proteomics\| PubMed ID: 22234360	2012
The C. elegans H3K27 demethylase UTX-1 is essential for normal development, independent of its enzymatic activity. PLoS genetics\| PubMed ID: 22570628	2012
Precision mapping of coexisting modifications in histone H3 tails from embryonic stem cells by ETD-MS/MS. Analytical chemistry\| PubMed ID: 23889513	2013
KYSS: mass spectrometry data quality assessment for protein analysis and large-scale proteomics. Biochemical and biophysical research communications\| PubMed ID: 24480439	2014
Comparative proteomic analysis of histone post-translational modifications upon ischemia/reperfusion-induced retinal injury. Journal of proteome research\| PubMed ID: 24628298	2014
Large scale analysis of co-existing post-translational modifications in histone tails reveals global fine structure of cross-talk. Molecular & cellular proteomics : MCP\| PubMed ID: 24741113	2014
Transcription factor cooperativity in early adipogenic hotspots and super-enhancers. Cell reports\| PubMed ID: 24857652	2014
Middle-down hybrid chromatography/tandem mass spectrometry workflow for characterization of combinatorial post-translational modifications in histones. Proteomics\| PubMed ID: 25073878	2014
Defining heterochromatin in C. elegans through genome-wide analysis of the heterochromatin protein 1 homolog HPL-2. Genome research\| PubMed ID: 25467431	2015
Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH) Analysis for Characterization and Quantification of Histone Post-translational Modifications. Molecular & cellular proteomics : MCP\| PubMed ID: 25636311	2015
Drawbacks in the use of unconventional hydrophobic anhydrides for histone derivatization in bottom-up proteomics PTM analysis. Proteomics\| PubMed ID: 25641854	2015
Bottom-up and middle-down proteomics have comparable accuracies in defining histone post-translational modification relative abundance and stoichiometry. Analytical chemistry\| PubMed ID: 25719549	2015
Two distinct modes for propagation of histone PTMs across the cell cycle. Genes & development\| PubMed ID: 25792596	2015
EpiProfile Quantifies Histone Peptides With Modifications by Extracting Retention Time and Intensity in High-resolution Mass Spectra. Molecular & cellular proteomics : MCP\| PubMed ID: 25805797	2015
Quantitative proteomics analysis of platelet-derived microparticles reveals distinct protein signatures when stimulated by different physiological agonists. Journal of proteomics\| PubMed ID: 25835965	2015
Proteogenomics analysis reveals specific genomic orientations of distal regulatory regions composed by non-canonical histone variants. Epigenetics & chromatin\| PubMed ID: 25878728	2015
Properly reading the histone code by MS-based proteomics. Proteomics\| PubMed ID: 26223514	2015
Progress in epigenetic histone modification analysis by mass spectrometry for clinical investigations. Expert review of proteomics\| PubMed ID: 26400466	2015
Top-down and Middle-down Protein Analysis Reveals that Intact and Clipped Human Histones Differ in Post-translational Modification Patterns. Molecular & cellular proteomics : MCP\| PubMed ID: 26424599	2015
The PZP Domain of AF10 Senses Unmodified H3K27 to Regulate DOT1L-Mediated Methylation of H3K79. Molecular cell\| PubMed ID: 26439302	2015
Tumor suppressor ASXL1 is essential for the activation of INK4B expression in response to oncogene activity and anti-proliferative signals. Cell research\| PubMed ID: 26470845	2015
H3K23me2 is a new heterochromatic mark in Caenorhabditis elegans. Nucleic acids research\| PubMed ID: 26476455	2015
Low Resolution Data-Independent Acquisition in an LTQ-Orbitrap Allows for Simplified and Fully Untargeted Analysis of Histone Modifications. Analytical chemistry\| PubMed ID: 26505526	2015
Dynamic changes of histone H3 marks during Caenorhabditis elegans lifecycle revealed by middle-down proteomics. Proteomics\| PubMed ID: 26508544	2016
Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin. Genome research\| PubMed ID: 26537359	2016
Histone modification profiling reveals differential signatures associated with human embryonic stem cell self-renewal and differentiation. Proteomics\| PubMed ID: 26631989	2016
Analyses of Histone Proteoforms Using Front-end Electron Transfer Dissociation-enabled Orbitrap Instruments. Molecular & cellular proteomics : MCP\| PubMed ID: 26785730	2016
Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells. BMC genomics\| PubMed ID: 26847871	2016
Multiplexed data independent acquisition (MSX-DIA) applied by high resolution mass spectrometry improves quantification quality for the analysis of histone peptides. Proteomics\| PubMed ID: 27193262	2016
Differential quantification of isobaric phosphopeptides using data-independent acquisition mass spectrometry. Molecular bioSystems\| PubMed ID: 27301801	2016
Systems Level Analysis of Histone H3 Post-translational Modifications (PTMs) Reveals Features of PTM Crosstalk in Chromatin Regulation. Molecular & cellular proteomics : MCP\| PubMed ID: 27302890	2016
High performance mass spectrometry based proteomics reveals enzyme and signaling pathway regulation in neutrophils during the early stage of surgical trauma. Proteomics. Clinical applications\| PubMed ID: 27672009	2017
Nuclear phosphoproteome analysis of 3T3-L1 preadipocyte differentiation reveals system-wide phosphorylation of transcriptional regulators. Proteomics\| PubMed ID: 27717184	2017
High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells. Molecular cell\| PubMed ID: 27768875	2016
Characterization of Individual Histone Posttranslational Modifications and Their Combinatorial Patterns by Mass Spectrometry-Based Proteomics Strategies. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 27854019	2017
Why proteomics is not the new genomics and the future of mass spectrometry in cell biology. The Journal of cell biology\| PubMed ID: 27956468	2017
Roles of H3K27me2 and H3K27me3 Examined during Fate Specification of Embryonic Stem Cells. Cell reports\| PubMed ID: 28052258	2017
Time-resolved Global and Chromatin Proteomics during Herpes Simplex Virus Type 1 (HSV-1) Infection. Molecular & cellular proteomics : MCP\| PubMed ID: 28179408	2017
Multicellular Tumor Spheroids Combined with Mass Spectrometric Histone Analysis To Evaluate Epigenetic Drugs. Analytical chemistry\| PubMed ID: 28194967	2017
Abnormal levels of histone methylation in the retinas of diabetic rats are reversed by minocycline treatment. Scientific reports\| PubMed ID: 28338045	2017
Quantitative chromatin proteomics reveals a dynamic histone post-translational modification landscape that defines asexual and sexual Plasmodium falciparum parasites. Scientific reports\| PubMed ID: 28377601	2017
Middle-down proteomics: a still unexploited resource for chromatin biology. Expert review of proteomics\| PubMed ID: 28649883	2017
Metabolic labeling in middle-down proteomics allows for investigation of the dynamics of the histone code. Epigenetics & chromatin\| PubMed ID: 28683815	2017
Identification of Nidogen 1 as a lung metastasis protein through secretome analysis. Genes & development\| PubMed ID: 28827399	2017
Proteome-wide acetylation dynamics in human cells. Scientific reports\| PubMed ID: 28860605	2017
Phosphoproteomics reveals that glycogen synthase kinase-3 phosphorylates multiple splicing factors and is associated with alternative splicing. The Journal of biological chemistry\| PubMed ID: 28916722	2017
An HDAC3-PROX1 corepressor module acts on HNF4α to control hepatic triglycerides. Nature communications\| PubMed ID: 28916805	2017
Quantitation of Single and Combinatorial Histone Modifications by Integrated Chromatography of Bottom-up Peptides and Middle-down Polypeptide Tails. Journal of the American Society for Mass Spectrometry\| PubMed ID: 31512222	2019
A mass spectrometry-based assay using metabolic labeling to rapidly monitor chromatin accessibility of modified histone proteins. Scientific reports\| PubMed ID: 31541121	2019
Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation. Nature communications\| PubMed ID: 31624313	2019
Bullet points to evaluate the performance of the middle-down proteomics workflow for histone modification analysis. Methods (San Diego, Calif.)\| PubMed ID: 32070774	2020
Lysine 4 of histone H3.3 is required for embryonic stem cell differentiation, histone enrichment at regulatory regions and transcription accuracy. Nature genetics\| PubMed ID: 32139906	2020
Comprehensive Map of the Artemisia annua Proteome and Quantification of Differential Protein Expression in Chemotypes Producing High versus Low Content of Artemisinin. Proteomics\| PubMed ID: 32311217	2020
Disruption of ATRX-RNA interactions uncovers roles in ATRX localization and PRC2 function. Nature communications\| PubMed ID: 32376827	2020
Mass Spectrometry to Study Chromatin Compaction. Biology\| PubMed ID: 32604817	2020
Mutant FOXL2 Hijacks SMAD4 and SMAD2/3 to Drive Adult Granulosa Cell Tumors. Cancer research\| PubMed ID: 32641411	2020
PR-DUB maintains the expression of critical genes through FOXK1/2- and ASXL1/2/3-dependent recruitment to chromatin and H2AK119ub1 deubiquitination. Genome research\| PubMed ID: 32747411	2020
nuclear RNAi factor SET-32 deposits the transgenerational histone modification, H3K23me3. eLife\| PubMed ID: 32804637	2020
Phosphoproteomic Analysis of Rat Neutrophils Shows the Effect of Intestinal Ischemia/Reperfusion and Preconditioning on Kinases and Phosphatases. International journal of molecular sciences\| PubMed ID: 32823483	2020
Guide for protein fold change and p-value calculation for non-experts in proteomics. Molecular omics\| PubMed ID: 32968743	2020
An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer's disease. Nature genetics\| PubMed ID: 32989324	2020
Author Correction: An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer's disease. Nature genetics\| PubMed ID: 33033384	2020
White adipose remodeling during browning in mice involves YBX1 to drive thermogenic commitment. Molecular metabolism\| PubMed ID: 33285300	2021
H1 histones control the epigenetic landscape by local chromatin compaction. Nature\| PubMed ID: 33299182	2021
Toxoplasma gondii PPM3C, a secreted protein phosphatase, affects parasitophorous vacuole effector export. PLoS pathogens\| PubMed ID: 33370417	2020
One-shot analysis of translated mammalian lncRNAs with AHARIBO. eLife\| PubMed ID: 33594971	2021
A Workflow for Ultra-rapid Analysis of Histone Post-translational Modifications with Direct-injection Mass Spectrometry. Bio-protocol\| PubMed ID: 33659415	2020
Long-term behavioral and cell-type-specific molecular effects of early life stress are mediated by H3K79me2 dynamics in medium spiny neurons. Nature neuroscience\| PubMed ID: 33723435	2021
QSER1 protects DNA methylation valleys from de novo methylation. Science (New York, N.Y.)\| PubMed ID: 33833093	2021
Author Correction: Long-term behavioral and cell-type-specific molecular effects of early life stress are mediated by H3K79me2 dynamics in medium spiny neurons. Nature neuroscience\| PubMed ID: 33833436	2021
Protective neutralizing antibodies from human survivors of Crimean-Congo hemorrhagic fever. Cell\| PubMed ID: 34077751	2021
VAL genes regulate vegetative phase change via miR156-dependent and independent mechanisms. PLoS genetics\| PubMed ID: 34181637	2021
The Polycomb protein RING1B enables estrogen-mediated gene expression by promoting enhancer-promoter interaction and R-loop formation. Nucleic acids research\| PubMed ID: 34428304	2021
Independent transcriptomic and proteomic regulation by type I and II protein arginine methyltransferases. iScience\| PubMed ID: 34505004	2021
High throughput and low bias DNA methylation and hydroxymethylation analysis by direct injection mass spectrometry. Analytica chimica acta\| PubMed ID: 34538324	2021
A Key Silencing Histone Mark on Chromatin Is Lost When Colorectal Adenocarcinoma Cells Are Depleted of Methionine by Methionine γ-Lyase. Frontiers in molecular biosciences\| PubMed ID: 34660696	2021
Quantitative subcellular acyl-CoA analysis reveals distinct nuclear metabolism and isoleucine-dependent histone propionylation. Molecular cell\| PubMed ID: 34856123	2022
Pipecolic Acid, a Putative Mediator of the Encephalopathy of Cerebral Malaria and the Experimental Model of Cerebral Malaria. The Journal of infectious diseases\| PubMed ID: 34932816	2022
Type I and II PRMTs inversely regulate post-transcriptional intron detention through Sm and CHTOP methylation. eLife\| PubMed ID: 34984976	2022
Genotype-specific features reduce the susceptibility of South American yellow fever virus strains to vaccine-induced antibodies. Cell host & microbe\| PubMed ID: 34998466	2022
DNA methylation and hydroxymethylation analysis using a high throughput and low bias direct injection mass spectrometry platform. MethodsX\| PubMed ID: 35004218	2021
Multi-omic profiling of histone variant H3.3 lysine 27 methylation reveals a distinct role from canonical H3 in stem cell differentiation. Molecular omics\| PubMed ID: 35044400	2022
A Dynamic and Combinatorial Histone Code Drives Malaria Parasite Asexual and Sexual Development. Molecular & cellular proteomics : MCP\| PubMed ID: 35051657	2022
CpG island reconfiguration for the establishment and synchronization of polycomb functions upon exit from naive pluripotency. Molecular cell\| PubMed ID: 35202573	2022
Synthesis and Characterization of Transition-State Analogue Inhibitors against Human DNA Methyltransferase 1. Journal of medicinal chemistry\| PubMed ID: 35324190	2022
Macrophages use apoptotic cell-derived methionine and DNMT3A during efferocytosis to promote tissue resolution. Nature metabolism\| PubMed ID: 35361955	2022
Altered abundances of human immunoglobulin M and immunoglobulin G subclasses in Alzheimer's disease frontal cortex. Scientific reports\| PubMed ID: 35484384	2022
The transcription factor PAX8 promotes angiogenesis in ovarian cancer through interaction with SOX17. Science signaling\| PubMed ID: 35380877	2022
Dense Granule Protein GRA64 Interacts with Host Cell ESCRT Proteins during Infection. mBio\| PubMed ID: 35730903	2022
Methamphetamine Dysregulates Macrophage Functions and Autophagy to Mediate HIV Neuropathogenesis. Biomedicines\| PubMed ID: 35740279	2022
CRISPR screening uncovers a central requirement for HHEX in pancreatic lineage commitment and plasticity restriction. Nature cell biology\| PubMed ID: 35787684	2022
Reduced endosomal microautophagy activity in aging associates with enhanced exocyst-mediated protein secretion. Aging cell\| PubMed ID: 36116133	2022
Autophagic state prospectively identifies facultative stem cells in the intestinal epithelium. EMBO reports\| PubMed ID: 36120829	2022
Morphine disrupts macrophage functions even during HIV infection. Journal of leukocyte biology\| PubMed ID: 36205434	2022
Endocrine resistance and breast cancer plasticity are controlled by CoREST. Nature structural & molecular biology\| PubMed ID: 36344844	2022
Investigation of reversible histone acetylation and dynamics in gene expression regulation using 3D liver spheroid model. Epigenetics & chromatin\| PubMed ID: 36411440	2022
Post-Translational Modifications of Histone Variants in the Absence and Presence of a Methionine-Depleting Enzyme in Normal and Cancer Cells. Cancers\| PubMed ID: 36672476	2023
Proximity labeling reveals a new in vivo network of interactors for the histone demethylase KDM5. Epigenetics & chromatin\| PubMed ID: 36803422	2023
Expanding the Epitranscriptomic RNA Sequencing and Modification Mapping Mass Spectrometry Toolbox with Field Asymmetric Waveform Ion Mobility and Electrochemical Elution Liquid Chromatograph... Analytical chemistry\| PubMed ID: 36916610	2023
MAT Gain of Activity Mutation in Is Associated with Resistance to MTAN Transition State Analogues. ACS infectious diseases\| PubMed ID: 36920074	2023
PROTAC-Mediated Selective Degradation of Cytosolic Soluble Epoxide Hydrolase Enhances ER Stress Reduction. ACS chemical biology\| PubMed ID: 36947831	2023
HSV-2 triggers upregulation of MALAT1 in CD4+ T cells and promotes HIV latency reversal. The Journal of clinical investigation\| PubMed ID: 37079384	2023
DPP4 inhibition impairs senohemostasis to improve plaque stability in atherosclerotic mice. The Journal of clinical investigation\| PubMed ID: 37097759	2023
Orally administered sodium nitrite prevents the increased α-1 adrenergic vasoconstriction induced by hypertension and promotes the S-nitrosylation of calcium/calmodulin-dependent protein kin... Biochemical pharmacology\| PubMed ID: 37127250	2023
Epigenetic dysregulation from chromosomal transit in micronuclei. Nature\| PubMed ID: 37286593	2023
The role of histone H3 lysine demethylases in glioblastoma. Cancer metastasis reviews\| PubMed ID: 37286866	2023
Structural and mechanistic basis of neutralization by a pan-hantavirus protective antibody. Science translational medicine\| PubMed ID: 37315110	2023
mTORC2-NDRG1-CDC42 axis couples fasting to mitochondrial fission. Nature cell biology\| PubMed ID: 37386153	2023
Dynamic de novo heterochromatin assembly and disassembly at replication forks ensures fork stability. Nature cell biology\| PubMed ID: 37414849	2023
TMEM106B Puncta Is Increased in Multiple Sclerosis Plaques, and Reduced Protein in Mice Results in Delayed Lipid Clearance Following CNS Injury. Cells\| PubMed ID: 37443768	2023
Tet2 regulates Sin3a recruitment at active enhancers in embryonic stem cells. iScience\| PubMed ID: 37456851	2023
Proteomics and phosphoproteomics profiling in glutamatergic neurons and microglia in an iPSC model of Jansen de Vries Syndrome. bioRxiv : the preprint server for biology\| PubMed ID: 37461463	2023
Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions. Nature genetics\| PubMed ID: 37488417	2023
Prophylactic effect of chronic immunosuppression in a mouse model of CSF-1 receptor-related leukoencephalopathy. Glia\| PubMed ID: 37519044	2023
Antibody attributes, Fc receptor expression, gestation and maternal SARS-CoV-2 infection modulate HSV IgG placental transfer. iScience\| PubMed ID: 37670782	2023
Activity Guided Azide-methyllysine Photo-trapping for Substrate Profiling of Lysine Demethylases. Journal of the American Chemical Society\| PubMed ID: 37703462	2023
paralogs prevent dsRNA accumulation and interferon signaling to maintain intestinal stem cells. bioRxiv : the preprint server for biology\| PubMed ID: 37732252	2023
Ketone Bodies Rescue Mitochondrial Dysfunction Via Epigenetic Remodeling. JACC. Basic to translational science\| PubMed ID: 37791311	2023
Urine Proteomics Link Complement Activation with Interstitial Fibrosis/Tubular Atrophy in Lupus Nephritis Patients. Seminars in arthritis and rheumatism\| PubMed ID: 37802003	2023
Human cord plasma proteomic analysis reveals sexually dimorphic proteins associated with intrauterine growth restriction. Proteomics\| PubMed ID: 38059784	2024
Functional Contribution and Clinical Implication of Cancer-Associated Fibroblasts in Glioblastoma. Clinical cancer research : an official journal of the American Association for Cancer Research\| PubMed ID: 38060213	2024
Ten questions to AI regarding the present and future of proteomics. Frontiers in molecular biosciences\| PubMed ID: 38074090	2023
Methylation of histone H3 lysine 36 is a barrier for therapeutic interventions of head and neck squamous cell carcinoma. bioRxiv : the preprint server for biology\| PubMed ID: 38076924	2023
Advances in proteomics methods for the analysis of exhaled breath condensate. Mass spectrometry reviews\| PubMed ID: 38149478	2024
FLT3 tyrosine kinase inhibition modulates PRC2 and promotes differentiation in acute myeloid leukemia. Leukemia\| PubMed ID: 38182819	2024
Characterization of the intracellular neurexin interactome by in vivo proximity ligation suggests its involvement in presynaptic actin assembly. PLoS biology\| PubMed ID: 38252619	2024
Methylation of histone H3 lysine 36 is a barrier for therapeutic interventions of head and neck squamous cell carcinoma. Genes & development\| PubMed ID: 38286657	2024
RNA polymerase II promotes the organization of chromatin following DNA replication. EMBO reports\| PubMed ID: 38347224	2024
αKG-mediated carnitine synthesis promotes homologous recombination via histone acetylation. bioRxiv : the preprint server for biology\| PubMed ID: 38370789	2024
An iron rheostat controls hematopoietic stem cell fate. Cell stem cell\| PubMed ID: 38402617	2024
Involution of brown adipose tissue through a Syntaxin 4 dependent pyroptosis pathway. Nature communications\| PubMed ID: 38565851	2024
KDM5-mediated transcriptional activation of ribosomal protein genes alters translation efficiency to regulate mitochondrial metabolism in neurons. Nucleic acids research\| PubMed ID: 38597673	2024
Decoding cocaine-induced proteomic adaptations in the mouse nucleus accumbens. Science signaling\| PubMed ID: 38626009	2024
Linking Aging to Cancer: The Role of Chromatin Biology. The journals of gerontology. Series A, Biological sciences and medical sciences\| PubMed ID: 38761362	2024
Fibroblast Smad7 Induction Protects the Remodeling Pressure-Overloaded Heart. Circulation research\| PubMed ID: 38899461	2024
Mono-methylation of lysine 27 at histone 3 confers lifelong susceptibility to stress. Neuron\| PubMed ID: 38959894	2024
Effect of dynamic exclusion and the use of FAIMS, DIA and MALDI-mass spectrometry imaging with ion mobility on amyloid protein identification. Clinical proteomics\| PubMed ID: 38961380	2024
Patient-specific mutation of Dync1h1 in mice causes brain and behavioral deficits. Neurobiology of disease\| PubMed ID: 39025270	2024
KAT2A and KAT2B prevent double-stranded RNA accumulation and interferon signaling to maintain intestinal stem cell renewal. Science advances\| PubMed ID: 39110797	2024
Enrichment of histone tail methylated lysine residues cavitand-decorated magnetic nanoparticles for ultra-sensitive proteomics. Chemical science\| PubMed ID: 39148787	2024
Productive mRNA Chromatin Escape is Promoted by PRMT5 Methylation of SNRPB. bioRxiv : the preprint server for biology\| PubMed ID: 39149374	2024
Micronuclear collapse from oxidative damage. Science (New York, N.Y.)\| PubMed ID: 39208110	2024
The scaffolding function of LSD1 controls DNA methylation in mouse ESCs. Nature communications\| PubMed ID: 39237615	2024
Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model. Neuron\| PubMed ID: 39353433	2024
Fibroblast-specific TGF-β signaling mediates cardiac dysfunction, fibrosis, and hypertrophy in obese diabetic mice. Cardiovascular research\| PubMed ID: 39373248	2024
Multi-omics identification of extracellular components of the fetal monkey and human neocortex. bioRxiv : the preprint server for biology\| PubMed ID: 39386730	2024
Parallel genome-scale CRISPR-Cas9 screens uncouple human pluripotent stem cell identity versus fitness. Nature communications\| PubMed ID: 39419994	2024
A proteogenomic surfaceome study identifies DLK1 as an immunotherapeutic target in neuroblastoma. Cancer cell\| PubMed ID: 39454577	2024
PROSER1 modulates DNA demethylation through dual mechanisms to prevent syndromic developmental malformations. Genes & development\| PubMed ID: 39562138	2024
-Active Soluble Epoxide Hydrolase-Targeting PROTACs with Improved Potency and Stability. ACS medicinal chemistry letters\| PubMed ID: 39563815	2024
Two H3K23 histone methyltransferases, SET-32 and SET-21, function synergistically to promote nuclear RNAi-mediated transgenerational epigenetic inheritance in . bioRxiv : the preprint server for biology\| PubMed ID: 39574755	2024
Unique structural configuration of EV-DNA primes Kupffer cell-mediated antitumor immunity to prevent metastatic progression. Nature cancer\| PubMed ID: 39627554	2024
DNA hypomethylation promotes UHRF1-and SUV39H1/H2-dependent crosstalk between H3K18ub and H3K9me3 to reinforce heterochromatin states. Molecular cell\| PubMed ID: 39631394	2025
Two H3K23 histone methyltransferases, SET-32 and SET-21, function synergistically to promote nuclear RNAi-mediated transgenerational epigenetic inheritance in Caenorhabditis elegans. Genetics\| PubMed ID: 39661453	2025
Smoking-Associated Carcinogen-Induced Inflammation Promotes Lung Carcinogenesis via IRAK4 Activation. Clinical cancer research : an official journal of the American Association for Cancer Research\| PubMed ID: 39704655	2025
PX-12 modulates vorinostat-induced acetylation and methylation marks in CAL 27 cells. Epigenomics\| PubMed ID: 39716806	2025
Bidirectional histone monoaminylation dynamics regulate neural rhythmicity. Nature\| PubMed ID: 39779849	2025
Analogue-Sensitive Inhibition of Histone Demethylases Uncovers Member-Specific Function in Ribosomal Protein Synthesis. Journal of the American Chemical Society\| PubMed ID: 39808475	2025
Hydrogen/Deuterium Exchange and Protein Oxidative Footprinting with Mass Spectrometry Collectively Discriminate the Binding of Small-Molecule Therapeutics to Bcl-2. Analytical chemistry\| PubMed ID: 39969248	2025
Extracellular Histones as Exosome Membrane Proteins Regulated by Cell Stress. Journal of extracellular vesicles\| PubMed ID: 39976275	2025
Myocardial Proteome in Human Heart Failure With Preserved Ejection Fraction. Journal of the American Heart Association\| PubMed ID: 40079330	2025
Automated Sample Preparation for the Unbiased Analysis of Histone Posttranslational Modifications Via Mass Spectrometry. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 40257557	2025
Identification of Chromatin Readers Using a Peptide Pull-Down and Mass Spectrometry Integrated Approach. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 40257567	2025
Spatial hepatocyte plasticity of gluconeogenesis during the metabolic transitions between fed, fasted and starvation states. Nature metabolism\| PubMed ID: 40281362	2025
Loss of CARM1 alters the developmental programming of Glioma stem-like cells and creates a druggable NGFR/NTRK dependency. bioRxiv : the preprint server for biology\| PubMed ID: 40321217	2025
Widespread discordance between mRNA expression, protein abundance and lipogenesis activity in hepatocytes during the fed-starvation transition. bioRxiv : the preprint server for biology\| PubMed ID: 40376090	2025
3D Biomimetic Liver Cancer Model: Diethylnitrosamine-Induced Proteomic Dysregulations in Stromal-Epithelial Milieu. bioRxiv : the preprint server for biology\| PubMed ID: 40475465	2025
Multi-Omics Identification of Extracellular Components of the Fetal Monkey and Human Neocortex. Proteomics\| PubMed ID: 40489056	2025
Small molecule disruption of RARα/NCoR1 interaction inhibits chaperone-mediated autophagy in cancer. EMBO molecular medicine\| PubMed ID: 40490560	2025
Collagen hydroxylation couples NAD+/NADH dynamics to tumor dormancy and reactivation. Research square\| PubMed ID: 40671813	2025
PRMT5 activity sustains histone production to maintain genome integrity. bioRxiv : the preprint server for biology\| PubMed ID: 40672221	2025
The SWI/SNF-related protein SMARCA3 is a histone H3K23 ubiquitin ligase that regulates H3K9me3 in cancer. Molecular cell\| PubMed ID: 40680746	2025
Altered Metabolism in Heterozygous Mice With a Mutation in the Motor Domain of Cytoplasmic Dynein, DYNC1H1 (AAA4; c9052C>T(P3018S)). Proteomics\| PubMed ID: 40766986	2025
Exploiting an Epigenetic Resistance Mechanism to PI3 Kinase Inhibition in Leukemic Stem Cells. bioRxiv : the preprint server for biology\| PubMed ID: 40791365	2025
Fabry disease cardiomyopathy: A state-of-the-art review. Progress in cardiovascular diseases\| PubMed ID: 40840785	2025
ACR-16/α7-nicotinic receptor signaling mediates nicotine-induced mitochondrial dysfunction and suppression of host defense against gram-negative bacteria. Environmental pollution (Barking, Essex : 1987)\| PubMed ID: 40846258	2025
Mapping a interactome by crosslinking mass spectrometry and machine learning. mBio\| PubMed ID: 40874616	2025
Protocol for plasma membrane enrichment by ultracentrifugation for mass spectrometry of cell lines, xenografts, and patient tumors. STAR protocols\| PubMed ID: 40884789	2025
Dual EZH1/2 inhibition enhances DNMT inhibitor efficacy in colon cancer through targeting H3K27me1. bioRxiv : the preprint server for biology\| PubMed ID: 41000734	2025
Elevated Clonal Hematopoiesis in 9/11 First Responders Has Distinct Age-related Patterns and Relies on IL1RAP for Clonal Expansion. Cancer discovery\| PubMed ID: 41031953	2025
A needed nomenclature for nucleosomes. Molecular cell\| PubMed ID: 41043390	2025
Reply to Rattanapitoon et al., "Reconsidering the interactome: opportunities beyond crosslinking mass spectrometry". mBio\| PubMed ID: 41065395	2025
Productive mRNA chromatin escape is promoted by PRMT5 activity. Molecular cell\| PubMed ID: 41086806	2025
Chaperone-mediated autophagy regulates neuronal activity by sex-specific remodelling of the synaptic proteome. Nature cell biology\| PubMed ID: 41087566	2025
Identifying space-resolved proteins of the murine thymus, by combining MALDI-MSI and proteomics. Life science alliance\| PubMed ID: 41266110	2026
CoREST complex inhibition alters RNA splicing to promote neoantigen expression and enhance tumor immunity. JCI insight\| PubMed ID: 41364533	2025
Mass spectrometry-based profiling of single-cell histone post-translational modifications to dissect chromatin heterogeneity. Nature communications\| PubMed ID: 41387402	2025
Reduced IGF-1 signaling fails to limit Alzheimer's disease progression in a novel rat model of IGF-1R haploinsufficiency. Scientific reports\| PubMed ID: 41402425	2025
Chromatin architecture reprogramming reveals novel epigenetic dependencies in breast cancer. Genes & development\| PubMed ID: 41412800	2025