Simone Sidoli - Publications

Affiliations: 
2014-2018 University of Pennsylvania School of Medicine, Philadelphia, PA, United States 

95 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Fels JM, Maurer DP, Herbert AS, Wirchnianski AS, Vergnolle O, Cross RW, Abelson DM, Moyer CL, Mishra AK, Aguilan JT, Kuehne AI, Pauli NT, Bakken RR, Nyakatura EK, Hellert J, ... ... Sidoli S, et al. Protective neutralizing antibodies from human survivors of Crimean-Congo hemorrhagic fever. Cell. PMID 34077751 DOI: 10.1016/j.cell.2021.05.001  0.48
2021 Kronman H, Torres-Berrío A, Sidoli S, Issler O, Godino A, Ramakrishnan A, Mews P, Lardner CK, Parise EM, Walker DM, van der Zee YY, Browne CJ, Boyce BF, Neve R, Garcia BA, et al. 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. PMID 33833436 DOI: 10.1038/s41593-021-00848-y  0.96
2021 Dixon G, Pan H, Yang D, Rosen BP, Jashari T, Verma N, Pulecio J, Caspi I, Lee K, Stransky S, Glezer A, Liu C, Rivas M, Kumar R, Lan Y, ... ... Sidoli S, et al. QSER1 protects DNA methylation valleys from de novo methylation. Science (New York, N.Y.). 372. PMID 33833093 DOI: 10.1126/science.abd0875  0.4
2021 Lu C, Coradin M, Janssen KA, Sidoli S, Garcia BA. Combinatorial Histone H3 Modifications Are Dynamically Altered in Distinct Cell Cycle Phases. Journal of the American Society For Mass Spectrometry. PMID 33818074 DOI: 10.1021/jasms.0c00451  0.96
2021 Kronman H, Torres-Berrío A, Sidoli S, Issler O, Godino A, Ramakrishnan A, Mews P, Lardner CK, Parise EM, Walker DM, van der Zee YY, Browne CJ, Boyce BF, Neve R, Garcia BA, et al. Long-term behavioral and cell-type-specific molecular effects of early life stress are mediated by H3K79me2 dynamics in medium spiny neurons. Nature Neuroscience. PMID 33723435 DOI: 10.1038/s41593-021-00814-8  0.96
2020 Bhanu NV, Sidoli S, Garcia BA. A Workflow for Ultra-rapid Analysis of Histone Post-translational Modifications with Direct-injection Mass Spectrometry. Bio-Protocol. 10: e3756. PMID 33659415 DOI: 10.21769/BioProtoc.3756  0.96
2020 Mayoral J, Tomita T, Tu V, Aguilan JT, Sidoli S, Weiss LM. Toxoplasma gondii PPM3C, a secreted protein phosphatase, affects parasitophorous vacuole effector export. Plos Pathogens. 16: e1008771. PMID 33370417 DOI: 10.1371/journal.ppat.1008771  0.48
2020 Willcockson MA, Healton SE, Weiss CN, Bartholdy BA, Botbol Y, Mishra LN, Sidhwani DS, Wilson TJ, Pinto HB, Maron MI, Skalina KA, Toro LN, Zhao J, Lee CH, Hou H, ... ... Sidoli S, et al. H1 histones control the epigenetic landscape by local chromatin compaction. Nature. PMID 33299182 DOI: 10.1038/s41586-020-3032-z  0.96
2020 Nativio R, Lan Y, Donahue G, Sidoli S, Berson A, Srinivasan AR, Shcherbakova O, Amlie-Wolf A, Nie J, Cui X, He C, Wang LS, Garcia BA, Trojanowski JQ, Bonini NM, et al. Author Correction: An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer's disease. Nature Genetics. PMID 33033384 DOI: 10.1038/s41588-020-00733-7  0.96
2020 Nativio R, Lan Y, Donahue G, Sidoli S, Berson A, Srinivasan AR, Shcherbakova O, Amlie-Wolf A, Nie J, Cui X, He C, Wang LS, Garcia BA, Trojanowski JQ, Bonini NM, et al. An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer's disease. Nature Genetics. PMID 32989324 DOI: 10.1038/s41588-020-0696-0  0.96
2020 Aguilan JT, Kulej K, Sidoli S. Guide for protein fold change and -value calculation for non-experts in proteomics. Molecular Omics. PMID 32968743 DOI: 10.1039/d0mo00087f  0.52
2020 Ren W, Medeiros N, Warneford-Thomson R, Wulfridge P, Yan Q, Bian J, Sidoli S, Garcia BA, Skordalakes E, Joyce E, Bonasio R, Sarma K. Disruption of ATRX-RNA interactions uncovers roles in ATRX localization and PRC2 function. Nature Communications. 11: 2219. PMID 32376827 DOI: 10.1038/S41467-020-15902-9  0.96
2020 Chen M, Yan T, Ji L, Yu D, Sidoli S, Yuan Z, Cai C, Chen J, Tang Y, Shen Q, Pan Q, Fu X, Xin K, Liao L, Garcia BA, et al. Comprehensive Map of the Artemisia annua Proteome and Quantification of Differential Protein Expression in Chemotypes Producing High vs Low Content of Artemisinin. Proteomics. e1900310. PMID 32311217 DOI: 10.1002/Pmic.201900310  0.96
2020 Gehre M, Bunina D, Sidoli S, Lübke MJ, Diaz N, Trovato M, Garcia BA, Zaugg JB, Noh KM. Lysine 4 of histone H3.3 is required for embryonic stem cell differentiation, histone enrichment at regulatory regions and transcription accuracy. Nature Genetics. 52: 273-282. PMID 32139906 DOI: 10.1038/S41588-020-0586-5  0.96
2020 Coradin M, Mendoza MR, Sidoli S, Alpert AJ, Lu C, Garcia BA. Bullet points to evaluate the performance of the middle-down proteomics workflow for histone modification analysis. Methods (San Diego, Calif.). PMID 32070774 DOI: 10.1016/J.Ymeth.2020.01.013  0.96
2019 Janssen KA, Coradin M, Lu C, Sidoli S, Garcia BA. 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. 30: 2449-2459. PMID 31944722 DOI: 10.1021/jasms.8b06274  0.96
2019 Agosto LM, Gazzara MR, Radens CM, Sidoli S, Baeza J, Garcia BA, Lynch KW. Deep profiling and custom databases improve detection of proteoforms generated by alternative splicing. Genome Research. PMID 31727681 DOI: 10.1101/Gr.248435.119  0.96
2019 Mews P, Egervari G, Nativio R, Sidoli S, Donahue G, Lombroso SI, Alexander DC, Riesche SL, Heller EA, Nestler EJ, Garcia BA, Berger SL. Alcohol metabolism contributes to brain histone acetylation. Nature. PMID 31645761 DOI: 10.1038/S41586-019-1700-7  0.96
2019 Klein BJ, Jang SM, Lachance C, Mi W, Lyu J, Sakuraba S, Krajewski K, Wang WW, Sidoli S, Liu J, Zhang Y, Wang X, Warfield BM, Kueh AJ, Voss AK, et al. Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation. Nature Communications. 10: 4724. PMID 31624313 DOI: 10.1038/S41467-019-12551-5  0.96
2019 Sidoli S, Lopes M, Lund PJ, Goldman N, Fasolino M, Coradin M, Kulej K, Bhanu NV, Vahedi G, Garcia BA. A mass spectrometry-based assay using metabolic labeling to rapidly monitor chromatin accessibility of modified histone proteins. Scientific Reports. 9: 13613. PMID 31541121 DOI: 10.1038/S41598-019-49894-4  0.96
2019 Janssen KA, Coradin M, Lu C, Sidoli S, Garcia BA. 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. PMID 31512222 DOI: 10.1007/S13361-019-02303-6  0.96
2019 Saha-Shah A, Esmaeili M, Sidoli S, Hwang H, Yang J, Klein PS, Garcia BA. Single Cell Proteomics to Study Embryonic Asymmetry in Xenopus laevis Embryos. Analytical Chemistry. PMID 31194517 DOI: 10.1021/Acs.Analchem.9B00327  0.96
2019 Sidoli S, Kori Y, Lopes M, Yuan ZF, Kim HJ, Kulej K, Janssen KA, Agosto LM, Cunha JPC, Andrews AJ, Garcia BA. One minute analysis of 200 histone post-translational modifications by direct injection mass spectrometry. Genome Research. PMID 31123082 DOI: 10.1101/Gr.247353.118  0.96
2019 Lund PJ, Kori Y, Zhao X, Sidoli S, Yuan ZF, Garcia BA. Isotopic Labeling and Quantitative Proteomics of Acetylation on Histones and Beyond. Methods in Molecular Biology (Clifton, N.J.). 1977: 43-70. PMID 30980322 DOI: 10.1007/978-1-4939-9232-4_5  0.96
2019 Behera V, Stonestrom AJ, Hamagami N, Hsiung CC, Keller CA, Giardine B, Sidoli S, Yuan ZF, Bhanu NV, Werner MT, Wang H, Garcia BA, Hardison RC, Blobel GA. Interrogating Histone Acetylation and BRD4 as Mitotic Bookmarks of Transcription. Cell Reports. 27: 400-415.e5. PMID 30970245 DOI: 10.1016/J.Celrep.2019.03.057  0.96
2019 Wojcik JB, Marchione DM, Sidoli S, Djedid A, Lisby A, Majewski J, Garcia BA. Epigenomic reordering induced by Polycomb loss drives oncogenesis but leads to therapeutic vulnerabilities in malignant peripheral nerve sheath tumors. Cancer Research. PMID 30898839 DOI: 10.1158/0008-5472.Can-18-3704  0.96
2019 Bhanu NV, Sidoli S, Yuan ZF, Molden RC, Garcia BA. Regulation of proline-directed kinases and the trans-histone code H3K9me3/H4K20me3 during human myogenesis. The Journal of Biological Chemistry. PMID 30872405 DOI: 10.1074/Jbc.Ra118.004977  0.96
2019 Sen P, Lan Y, Li CY, Sidoli S, Donahue G, Dou Z, Frederick B, Chen Q, Luense LJ, Garcia BA, Dang W, Johnson FB, Adams PD, Schultz DC, Berger SL. Histone Acetyltransferase p300 Induces De Novo Super-Enhancers to Drive Cellular Senescence. Molecular Cell. PMID 30773298 DOI: 10.1016/J.Molcel.2019.01.021  0.96
2019 Lu C, Sidoli S, Kulej K, Ross K, Wu CH, Garcia BA. Coordination between TGF-β cellular signaling and epigenetic regulation during epithelial to mesenchymal transition. Epigenetics & Chromatin. 12: 11. PMID 30736855 DOI: 10.1186/S13072-019-0256-Y  0.96
2019 Sidoli S, Trefely S, Garcia BA, Carrer A. Integrated Analysis of Acetyl-CoA and Histone Modification via Mass Spectrometry to Investigate Metabolically Driven Acetylation. Methods in Molecular Biology (Clifton, N.J.). 1928: 125-147. PMID 30725455 DOI: 10.1007/978-1-4939-9027-6_9  0.96
2019 Carrer A, Trefely S, Zhao S, Campbell S, Norgard RJ, Schultz KC, Sidoli S, Parris JLD, Affronti HC, Sivanand S, Egolf S, Sela Y, Trizzino M, Gardini A, Garcia BA, et al. Acetyl-CoA metabolism supports multi-step pancreatic tumorigenesis. Cancer Discovery. PMID 30626590 DOI: 10.1158/2159-8290.Cd-18-0567  0.96
2019 Nicetto D, Donahue G, Jain T, Peng T, Sidoli S, Sheng L, Montavon T, Becker JS, Grindheim JM, Blahnik K, Garcia BA, Tan K, Bonasio R, Jenuwein T, Zaret KS. H3K9me3-heterochromatin loss at protein-coding genes enables developmental lineage specification. Science (New York, N.Y.). PMID 30606806 DOI: 10.1126/Science.Aau0583  0.96
2019 Carrer A, Trefely S, Zhao S, Campbell S, Sela Y, Sidoli S, Garcia BA, Snyder NW, Stanger BZ, Wellen KE. Abstract A03: All the roads bring to Rome: How acetyl-CoA metabolism supports multistep pancreatic carcinogenesis Cancer Research. 79. DOI: 10.1158/1538-7445.Panca19-A03  0.96
2019 Weiner AK, Radaoui AB, Kendsersky NM, Harenza-Rokita JL, Sidoli S, Conkrite KL, Vaksman Z, Rathi K, Raman P, Martinez D, Bhatti T, Tsang M, Pawel B, Garcia BA, Maris JM, et al. Abstract 3650: Integrative mass spectrometry and RNA-sequencing identifies DLK1 as a candidate immunotherapeutic target in neuroblastoma Cancer Research. 79: 3650-3650. DOI: 10.1158/1538-7445.Am2019-3650  0.96
2018 Wimmer ME, Vassoler FM, White SL, Schmidt HD, Sidoli S, Han Y, Garica BA, Pierce RC. Impaired cocaine-induced behavioral plasticity in the male offspring of cocaine-experienced sires. The European Journal of Neuroscience. PMID 30565761 DOI: 10.1111/Ejn.14310  0.32
2018 Kreher J, Takasaki T, Cockrum C, Sidoli S, Garcia BA, Jensen ON, Strome S. Distinct Roles of Two Histone Methyltransferases in Transmitting H3K36me3-Based Epigenetic Memory Across Generations in . Genetics. PMID 30217796 DOI: 10.1534/Genetics.118.301353  0.96
2018 Greer SM, Sidoli S, Coradin M, Schack Jespersen M, Schwämmle V, Jensen ON, Garcia BA, Brodbelt JS. Extensive Characterization of Heavily Modified Histone Tails by 193 nm Ultraviolet Photodissociation Mass Spectrometry via a Middle-Down Strategy. Analytical Chemistry. PMID 30063333 DOI: 10.1021/Acs.Analchem.8B02320  0.96
2018 Grevet JD, Lan X, Hamagami N, Edwards CR, Sankaranarayanan L, Ji X, Bhardwaj SK, Face CJ, Posocco DF, Abdulmalik O, Keller CA, Giardine B, Sidoli S, Garcia BA, Chou ST, et al. Domain-focused CRISPR screen identifies HRI as a fetal hemoglobin regulator in human erythroid cells. Science (New York, N.Y.). 361: 285-290. PMID 30026227 DOI: 10.1126/Science.Aao0932  0.96
2018 Yuan ZF, Sidoli S, Marchione DM, Simithy J, Janssen KA, Szurgot MR, Garcia BA. EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data. Journal of Proteome Research. PMID 29790754 DOI: 10.1021/Acs.Jproteome.8B00133  0.96
2018 Simithy J, Sidoli S, Garcia BA. Integrating Proteomics and Targeted Metabolomics to Understand Global Changes in Histone Modifications. Proteomics. PMID 29512899 DOI: 10.1002/Pmic.201700309  0.96
2018 Wojcik JB, Sidoli S, Cooper K, Garcia BA. Abstract A10: Integrated proteome and epigenetic analysis reveals crosstalk between chromatin and cancer pathways in malignant peripheral nerve sheath tumors Clinical Cancer Research. 24. DOI: 10.1158/1557-3265.Sarcomas17-A10  0.96
2017 Becker JS, McCarthy RL, Sidoli S, Donahue G, Kaeding KE, He Z, Lin S, Garcia BA, Zaret KS. Genomic and Proteomic Resolution of Heterochromatin and Its Restriction of Alternate Fate Genes. Molecular Cell. 68: 1023-1037.e15. PMID 29272703 DOI: 10.1016/J.Molcel.2017.11.030  0.96
2017 Guo Q, Sidoli S, Garcia BA, Zhao X. Assessment of quantification precision of histone post-translational modifications by using an ion trap and down to 50,000 cells as starting material. Journal of Proteome Research. PMID 29121770 DOI: 10.1021/Acs.Jproteome.7B00544  0.96
2017 Weiner AK, Sidoli S, Diskin SJ, Garcia B. GiaPronto: a one-click graph visualization software for proteomics datasets. Molecular & Cellular Proteomics : McP. PMID 29118029 DOI: 10.1074/Mcp.Tir117.000438  0.48
2017 Simithy J, Sidoli S, Yuan ZF, Coradin M, Bhanu NV, Marchione DM, Klein BJ, Bazilevsky GA, McCullough CE, Magin RS, Kutateladze TG, Snyder NW, Marmorstein R, Garcia BA. Characterization of histone acylations links chromatin modifications with metabolism. Nature Communications. 8: 1141. PMID 29070843 DOI: 10.1038/S41467-017-01384-9  0.96
2017 Warneford-Thomson R, He C, Sidoli S, Garcia BA, Bonasio R. Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions. Journal of Visualized Experiments : Jove. PMID 28994809 DOI: 10.3791/56004  0.96
2017 Armour SM, Remsberg JR, Damle M, Sidoli S, Ho WY, Li Z, Garcia BA, Lazar MA. An HDAC3-PROX1 corepressor module acts on HNF4α to control hepatic triglycerides. Nature Communications. 8: 549. PMID 28916805 DOI: 10.1038/S41467-017-00772-5  0.96
2017 Shinde MY, Sidoli S, Kulej K, Mallory MJ, Radens CM, Reicherter A, Myers RL, Barash Y, Lynch KW, Garcia BA, Klein PS. Phosphoproteomics reveals that glycogen synthase kinase-3 phosphorylates multiple splicing factors and is associated with alternative splicing. The Journal of Biological Chemistry. PMID 28916722 DOI: 10.1074/Jbc.M117.813527  0.96
2017 Kori Y, Sidoli S, Yuan ZF, Lund PJ, Zhao X, Garcia BA. Proteome-wide acetylation dynamics in human cells. Scientific Reports. 7: 10296. PMID 28860605 DOI: 10.1038/S41598-017-09918-3  0.96
2017 Alečković M, Wei Y, LeRoy G, Sidoli S, Liu DD, Garcia BA, Kang Y. Identification of Nidogen 1 as a lung metastasis protein through secretome analysis. Genes & Development. PMID 28827399 DOI: 10.1101/Gad.301937.117  0.96
2017 Sidoli S, Lu C, Coradin M, Wang X, Karch KR, Ruminowicz C, Garcia BA. Metabolic labeling in middle-down proteomics allows for investigation of the dynamics of the histone code. Epigenetics & Chromatin. 10: 34. PMID 28683815 DOI: 10.1186/S13072-017-0139-Z  0.96
2017 Sidoli S, Garcia BA. Middle-down proteomics: a still unexploited resource for chromatin biology. Expert Review of Proteomics. 1-10. PMID 28649883 DOI: 10.1080/14789450.2017.1345632  0.96
2017 Coetzee N, Sidoli S, van Biljon R, Painter H, Llinás M, Garcia BA, Birkholtz LM. Quantitative chromatin proteomics reveals a dynamic histone post-translational modification landscape that defines asexual and sexual Plasmodium falciparum parasites. Scientific Reports. 7: 607. PMID 28377601 DOI: 10.1038/S41598-017-00687-7  0.96
2017 Wimmer ME, Briand LA, Fant B, Guercio LA, Arreola AC, Schmidt HD, Sidoli S, Han Y, Garcia BA, Pierce RC. Paternal cocaine taking elicits epigenetic remodeling and memory deficits in male progeny. Molecular Psychiatry. PMID 28322277 DOI: 10.1038/mp.2017.71  0.96
2017 Wimmer ME, Briand LA, Fant B, Guercio LA, Arreola AC, Schmidt HD, Sidoli S, Han Y, Garcia BA, Pierce RC. Paternal cocaine taking elicits epigenetic remodeling and memory deficits in male progeny. Molecular Psychiatry. PMID 28220045 DOI: 10.1038/Mp.2017.8  0.96
2017 Feist PE, Sidoli S, Liu X, Schroll MM, Rahmy S, Fujiwara R, Garcia BA, Hummon AB. Multicellular Tumor Spheroids Combined with Mass Spectrometric Histone Analysis to Evaluate Epigenetic Drugs. Analytical Chemistry. PMID 28194967 DOI: 10.1021/Acs.Analchem.6B03602  0.96
2017 Kulej K, Avgousti DC, Sidoli S, Herrmann C, Della Fera AN, Kim ET, Garcia BA, Weitzman MD. Time-resolved global and chromatin proteomics during herpes simplex virus (HSV-1) infection. Molecular & Cellular Proteomics : McP. PMID 28179408 DOI: 10.1074/Mcp.M116.065987  0.96
2017 Janssen KA, Sidoli S, Garcia BA. Recent Achievements in Characterizing the Histone Code and Approaches to Integrating Epigenomics and Systems Biology. Methods in Enzymology. 586: 359-378. PMID 28137571 DOI: 10.1016/Bs.Mie.2016.10.021  0.96
2017 Juan AH, Wang S, Ko KD, Zare H, Tsai PF, Feng X, Vivanco KO, Ascoli AM, Gutierrez-Cruz G, Krebs J, Sidoli S, Knight AL, Pedersen RA, Garcia BA, Casellas R, et al. Roles of H3K27me2 and H3K27me3 Examined during Fate Specification of Embryonic Stem Cells. Cell Reports. 18: 297. PMID 28052258 DOI: 10.1016/j.celrep.2016.12.036  0.96
2017 Sidoli S, Garcia BA. Characterization of Individual Histone Posttranslational Modifications and Their Combinatorial Patterns by Mass Spectrometry-Based Proteomics Strategies. Methods in Molecular Biology (Clifton, N.J.). 1528: 121-148. PMID 27854019 DOI: 10.1007/978-1-4939-6630-1_8  0.96
2017 Weiner AK, Sidoli S, Glisovic-Aplenc T, Maris JM, Garcia BA, Diskin SJ. Abstract 684: Integrative proteomics and transcriptomics to define the cell surface landscape of neuroblastoma Cancer Research. 77: 684-684. DOI: 10.1158/1538-7445.Am2017-684  0.96
2016 Sidoli S, Kulej K, Garcia BA. Why proteomics is not the new genomics and the future of mass spectrometry in cell biology. The Journal of Cell Biology. PMID 27956468 DOI: 10.1083/Jcb.201612010  0.96
2016 Juan AH, Wang S, Ko KD, Zare H, Tsai PF, Feng X, Vivanco KO, Ascoli AM, Gutierrez-Cruz G, Krebs J, Sidoli S, Knight AL, Pedersen RA, Garcia BA, Casellas R, et al. Roles of H3K27me2 and H3K27me3 Examined during Fate Specification of Embryonic Stem Cells. Cell Reports. 17: 1369-1382. PMID 27783950 DOI: 10.1016/J.Celrep.2016.09.087  0.96
2016 He C, Sidoli S, Warneford-Thomson R, Tatomer DC, Wilusz JE, Garcia BA, Bonasio R. High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells. Molecular Cell. 64: 416-430. PMID 27768875 DOI: 10.1016/J.Molcel.2016.09.034  0.96
2016 Karch KR, Sidoli S, Garcia BA. Identification and Quantification of Histone PTMs Using High-Resolution Mass Spectrometry. Methods in Enzymology. 574: 3-29. PMID 27423855 DOI: 10.1016/Bs.Mie.2015.12.007  0.96
2016 Schwämmle V, Sidoli S, Ruminowicz C, Wu X, Lee CF, Helin K, Jensen ON. Systems level analysis of histone H3 post-translational modifications reveals features of PTM crosstalk in chromatin regulation. Molecular & Cellular Proteomics : McP. PMID 27302890 DOI: 10.1074/Mcp.M115.054460  0.4
2016 Sidoli S, Fujiwara R, Kulej K, Garcia BA. Differential quantification of isobaric phosphopeptides using data-independent acquisition mass spectrometry. Molecular Biosystems. PMID 27301801 DOI: 10.1039/C6Mb00385K  0.96
2016 Sidoli S, Bhanu NV, Karch KR, Wang X, Garcia BA. Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis. Journal of Visualized Experiments : Jove. PMID 27286567 DOI: 10.3791/54112  0.64
2016 Sidoli S, Fujiwara R, Garcia BA. Multiplexed data independent acquisition (MSX-DIA) applied by high resolution mass spectrometry improves quantification quality for the analysis of histone peptides. Proteomics. PMID 27193262 DOI: 10.1002/Pmic.201500527  0.96
2016 Gonzales-Cope M, Sidoli S, Bhanu NV, Won KJ, Garcia BA. Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells. Bmc Genomics. 17: 95. PMID 26847871 DOI: 10.1186/S12864-016-2414-Y  0.64
2016 Anderson LC, Karch KR, Ugrin SA, Coradin M, English AM, Sidoli S, Shabanowitz J, Garcia BA, Hunt DF. Analyses of Histone Proteoforms Using Front-End Electron Transfer Dissociation-Enabled Orbitrap Instruments. Molecular & Cellular Proteomics : McP. PMID 26785730 DOI: 10.1074/Mcp.O115.053843  0.64
2016 Karch KR, Sidoli S, Garcia BA. Identification and Quantification of Histone PTMs Using High-Resolution Mass Spectrometry Methods in Enzymology. DOI: 10.1016/bs.mie.2015.12.007  0.64
2015 Bhanu NV, Sidoli S, Garcia BA. Histone modification profiling reveals differential signatures associated with human embryonic stem cell self-renewal and differentiation. Proteomics. PMID 26631989 DOI: 10.1002/Pmic.201500231  0.64
2015 Jamieson K, Wiles ET, McNaught KJ, Sidoli S, Leggett N, Shao Y, Garcia BA, Selker EU. Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin. Genome Research. PMID 26537359 DOI: 10.1101/Gr.194555.115  0.64
2015 Sidoli S, Vandamme J, Salcini AE, Jensen ON. Dynamic changes of histone H3 marks during Caenorhabditis elegans lifecycle revealed by middle-down proteomics. Proteomics. PMID 26508544 DOI: 10.1002/Pmic.201500285  0.64
2015 Sidoli S, Simithy J, Karch KR, Kulej K, Garcia BA. Low Resolution Data-Independent Acquisition in an LTQ-Orbitrap Allows for Simplified and Fully Untargeted Analysis of Histone Modifications. Analytical Chemistry. 87: 11448-54. PMID 26505526 DOI: 10.1021/Acs.Analchem.5B03009  0.64
2015 Vandamme J, Sidoli S, Mariani L, Friis C, Christensen J, Helin K, Jensen ON, Salcini AE. H3K23me2 is a new heterochromatic mark in Caenorhabditis elegans. Nucleic Acids Research. PMID 26476455 DOI: 10.1093/Nar/Gkv1063  0.64
2015 Wu X, Bekker-Jensen IH, Christensen J, Rasmussen KD, Sidoli S, Qi Y, Kong Y, Wang X, Cui Y, Xiao Z, Xu G, Williams K, Rappsilber J, Sønderby CK, Winther O, et al. Tumor suppressor ASXL1 is essential for the activation of INK4B expression in response to oncogene activity and anti-proliferative signals. Cell Research. PMID 26470845 DOI: 10.1038/Cr.2015.121  0.64
2015 Chen S, Yang Z, Wilkinson AW, Deshpande AJ, Sidoli S, Krajewski K, Strahl BD, Garcia BA, Armstrong SA, Patel DJ, Gozani O. The PZP Domain of AF10 Senses Unmodified H3K27 to Regulate DOT1L-Mediated Methylation of H3K79. Molecular Cell. PMID 26439302 DOI: 10.1016/J.Molcel.2015.08.019  0.64
2015 Tvardovskiy A, Wrzesinski K, Sidoli S, Fey SJ, Rogowska-Wrzesinska A, Jensen ON. Top-down and middle-down protein analysis reveals that intact and clipped human histones differ in post-translational modification patterns. Molecular & Cellular Proteomics : McP. PMID 26424599 DOI: 10.1074/Mcp.M115.048975  0.64
2015 Önder Ö, Sidoli S, Carroll M, Garcia BA. Progress in epigenetic histone modification analysis by mass spectrometry for clinical investigations. Expert Review of Proteomics. 12: 499-517. PMID 26400466 DOI: 10.1586/14789450.2015.1084231  0.64
2015 Sidoli S, Garcia BA. Properly reading the histone code by MS based proteomics. Proteomics. PMID 26223514 DOI: 10.1002/Pmic.201500298  0.64
2015 Won KJ, Choi I, LeRoy G, Zee BM, Sidoli S, Gonzales-Cope M, Garcia BA. Proteogenomics analysis reveals specific genomic orientations of distal regulatory regions composed by non-canonical histone variants. Epigenetics & Chromatin. 8: 13. PMID 25878728 DOI: 10.1186/S13072-015-0005-9  0.64
2015 Yuan ZF, Lin S, Molden RC, Cao XJ, Bhanu NV, Wang X, Sidoli S, Liu S, Garcia BA. EpiProfile Quantifies Histone Peptides With Modifications by Extracting Retention Time and Intensity in High-resolution Mass Spectra. Molecular & Cellular Proteomics : McP. 14: 1696-707. PMID 25805797 DOI: 10.1074/Mcp.M114.046011  0.64
2015 Alabert C, Barth TK, Reverón-Gómez N, Sidoli S, Schmidt A, Jensen ON, Imhof A, Groth A. Two distinct modes for propagation of histone PTMs across the cell cycle. Genes & Development. 29: 585-90. PMID 25792596 DOI: 10.1101/Gad.256354.114  0.64
2015 Sidoli S, Lin S, Karch KR, Garcia BA. Bottom-up and middle-down proteomics have comparable accuracies in defining histone post-translational modification relative abundance and stoichiometry. Analytical Chemistry. 87: 3129-33. PMID 25719549 DOI: 10.1021/Acs.Analchem.5B00072  0.64
2015 Sidoli S, Yuan ZF, Lin S, Karch K, Wang X, Bhanu N, Arnaudo AM, Britton LM, Cao XJ, Gonzales-Cope M, Han Y, Liu S, Molden RC, Wein S, Afjehi-Sadat L, et al. Drawbacks in the use of unconventional hydrophobic anhydrides for histone derivatization in bottom-up proteomics PTM analysis. Proteomics. 15: 1459-69. PMID 25641854 DOI: 10.1002/Pmic.201400483  0.64
2015 Sidoli S, Lin S, Xiong L, Bhanu NV, Karch KR, Johansen E, Hunter C, Mollah S, Garcia BA. SWATH Analysis for Characterization and Quantification of Histone Post-translational Modifications. Molecular & Cellular Proteomics : McP. PMID 25636311 DOI: 10.1074/Mcp.O114.046102  0.64
2015 Garrigues JM, Sidoli S, Garcia BA, Strome S. Defining heterochromatin in C. elegans through genome-wide analysis of the heterochromatin protein 1 homolog HPL-2. Genome Research. 25: 76-88. PMID 25467431 DOI: 10.1101/Gr.180489.114  0.64
2015 Kulej K, Sidoli S, Palmisano G, Edwards AVG, Robinson PJ, Larsen MR. Optimization of calmodulin-affinity chromatography for brain and organelles Eupa Open Proteomics. DOI: 10.1016/J.Euprot.2015.05.004  0.64
2014 Sidoli S, Schwämmle V, Ruminowicz C, Hansen TA, Wu X, Helin K, Jensen ON. Middle-down hybrid chromatography/tandem mass spectrometry workflow for characterization of combinatorial post-translational modifications in histones. Proteomics. 14: 2200-11. PMID 25073878 DOI: 10.1002/Pmic.201400084  0.4
2014 Siersbæk R, Rabiee A, Nielsen R, Sidoli S, Traynor S, Loft A, La Cour Poulsen L, Rogowska-Wrzesinska A, Jensen ON, Mandrup S. Transcription factor cooperativity in early adipogenic hotspots and super-enhancers. Cell Reports. 7: 1443-55. PMID 24857652 DOI: 10.1016/J.Celrep.2014.04.042  0.64
2014 Zhao X, Sidoli S, Wang L, Wang W, Guo L, Jensen ON, Zheng L. Comparative proteomic analysis of histone post-translational modifications upon ischemia/reperfusion-induced retinal injury. Journal of Proteome Research. 13: 2175-86. PMID 24628298 DOI: 10.1021/Pr500040A  0.64
2014 Such-Sanmartín G, Sidoli S, Ventura-Espejo E, Jensen ON. KYSS: mass spectrometry data quality assessment for protein analysis and large-scale proteomics. Biochemical and Biophysical Research Communications. 445: 702-7. PMID 24480439 DOI: 10.1016/J.Bbrc.2014.01.066  0.64
2013 Bignardi C, Mattarozzi M, Penna A, Sidoli S, Elviri L, Careri M, Mangia A. A Rapid Size-Exclusion Solid-Phase Extraction Step for Enhanced Sensitivity in Multi-Allergen Determination in Dark Chocolate and Biscuits by Liquid Chromatography-Tandem Mass Spectrometry Food Analytical Methods. 6: 1144-1152. DOI: 10.1007/S12161-012-9521-4  0.64
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