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Profile Details
Subject Matter Expertise
Services
Writing
Technical Writing
Research
Scientific and Technical Research
Consulting
Scientific and Technical Consulting
Data & AI
Statistical Analysis,
Data Visualization
Work Experience
Assistant professor
Albert Einstein College of Medicine
February 2019 - Present 
Postdoctoral Fellow
University of Pennsylvania
April 2014 - February 2019
Graduate Research Assistant / Research Assistant
University of Southern Denmark
October 2013 - March 2014
Associate Research Fellow
University of Parma
February 2010 - October 2010
Education
PhD (Biochemistry and Molecular Biology)
University of Southern Denmark
October 2010 - March 2014
MS (Analytical Chemistry)
University of Parma
September 2004 - February 2010
BSc
University of Parma
September 2004 - June 2007
Certifications
- Certification details not provided.
Publications
JOURNAL ARTICLE
Simone Sidoli, John Barbaro, Ana Maria Cuervo, Joan W. Berman (2022). Methamphetamine Dysregulates Macrophage Functions and Autophagy to Mediate HIV Neuropathogenesis . Biomedicines.
Simone Sidoli, Stephanie Stransky, Jennifer Aguilan, Jake Lachowicz, Carlos Madrid-Aliste, Edward Nieves (2020). Mass Spectrometry to Study Chromatin Compaction . Biology.
Coradin, M., Mendoza, M.R., Sidoli, S., Alpert, A.J., Lu, C., Garcia, B.A.(2020). Bullet points to evaluate the performance of the middle-down proteomics workflow for histone modification analysis . Methods.
Gehre, M., Bunina, D., Sidoli, S., Lübke, M.J., Diaz, N., Trovato, M., Garcia, B.A., Zaugg, J.B., Noh, K.-M.(2020). Lysine 4 of histone H3.3 is required for embryonic stem cell differentiation, histone enrichment at regulatory regions and transcription accuracy . Nature Genetics. 52. (3). p. 273-282.
Lu, C., Sidoli, S., Kulej, K., Ross, K., Wu, C.H., Garcia, B.A.(2019). Coordination between TGF-β cellular signaling and epigenetic regulation during epithelial to mesenchymal transition . Epigenetics and Chromatin. 12. (1).
Sidoli, S., Lopes, M., Lund, P.J., Goldman, N., Fasolino, M., Coradin, M., Kulej, K., Bhanu, N.V., Vahedi, G., Garcia, B.A.(2019). A mass spectrometry-based assay using metabolic labeling to rapidly monitor chromatin accessibility of modified histone proteins . Scientific Reports. 9. (1).
et al., Carrer, A., Trefely, S., Zhao, S., Campbell, S.L., Norgard, R.J., Schultz, K.C., Sidoli, S., Parris, J.L.D., Affronti, H.C., Sivanand, S.(2019). Acetyl-CoA metabolism supports multistep pancreatic tumorigenesis . Cancer Discovery. 9. (3). p. 416-435.
Mews, P., Egervari, G., Nativio, R., Sidoli, S., Donahue, G., Lombroso, S.I., Alexander, D.C., Riesche, S.L., Heller, E.A., Nestler, E.J., et al.(2019). Alcohol metabolism contributes to brain histone acetylation . Nature. 574. (7780). p. 717-721.
Agosto, L.M., Gazzara, M.R., Radens, C.M., Sidoli, S., Baeza, J., Garcia, B.A., Lynch, K.W.(2019). Deep profiling and custom databases improve detection of proteoforms generated by alternative splicing . Genome Research. 29. (12). p. 2046-2055.
Klein, B.J., Jang, S.M., Lachance, C., Mi, W., Lyu, J., Sakuraba, S., Krajewski, K., Wang, W.W., Sidoli, S., Liu, J., et al.(2019). Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation . Nature Communications. 10. (1).
Wojcik, J.B., Marchione, D.M., Sidoli, S., Djedid, A., Lisby, A., Majewski, J., Garcia, B.A.(2019). Epigenomic reordering induced by polycomb loss drives oncogenesis but leads to therapeutic vulnerabilities in malignant peripheral nerve sheath tumors . Cancer Research. 79. (13). p. 3205-3219.
Nicetto, D., Donahue, G., Jain, T., Peng, T., Sidoli, S., Sheng, L., Montavon, T., Becker, J.S., Grindheim, J.M., Blahnik, K., et al.(2019). H3K9me3-heterochromatin loss at protein-coding genes enables developmental lineage specification . Science. 363. (6424). p. 294-297.
Sen, P., Lan, Y., Li, C.Y., Sidoli, S., Donahue, G., Dou, Z., Frederick, B., Chen, Q., Luense, L.J., Garcia, B.A., et al.(2019). Histone Acetyltransferase p300 Induces De Novo Super-Enhancers to Drive Cellular Senescence . Molecular Cell. 73. (4). p. 684-698.e8.
Wimmer, M.E., Vassoler, F.M., White, S.L., Schmidt, H.D., Sidoli, S., Han, Y., Garcia, B.A., Pierce, R.C.(2019). Impaired cocaine-induced behavioral plasticity in the male offspring of cocaine-experienced sires . European Journal of Neuroscience. 49. (9). p. 1115-1126.
Behera, V., Stonestrom, A.J., Hamagami, N., Hsiung, C.C., Keller, C.A., Giardine, B., Sidoli, S., Yuan, Z.-F., Bhanu, N.V., Werner, M.T., et al.(2019). Interrogating Histone Acetylation and BRD4 as Mitotic Bookmarks of Transcription . Cell Reports. 27. (2). p. 400-415.e5.
Sidoli, S., Kori, Y., Lopes, M., Yuan, Z.-F., Kim, H.J., Kulej, K., Janssen, K.A., Agosto, L.M., Da Cunha, J.P.C., Andrews, A.J., et al.(2019). One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometry . Genome Research. 29. (6). p. 978-987.
Janssen, K.A., Coradin, M., Lu, C., Sidoli, S., Garcia, B.A.(2019). 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. (12). p. 2449-2459.
Bhanu, N.V., Sidoli, S., Yuan, Z.-F., Molden, R.C., Garcia, B.A.(2019). Regulation of proline-directed kinases and the trans-histone code H3K9me3/H4K20me3 during human myogenesis . Journal of Biological Chemistry. 294. (20). p. 8296-8308.
Saha-Shah, A., Esmaeili, M., Sidoli, S., Hwang, H., Yang, J., Klein, P.S., Garcia, B.A.(2019). Single Cell Proteomics by Data-Independent Acquisition to Study Embryonic Asymmetry in Xenopus laevis . Analytical Chemistry. 91. (14). p. 8891-8899.
Guo, Q., Sidoli, S., Garcia, B.A., Zhao, X.(2018). Assessment of Quantification Precision of Histone Post-Translational Modifications by Using an Ion Trap and down to 50000 Cells as Starting Material . Journal of Proteome Research. 17. (1). p. 234-242.
Kreher, J., Takasaki, T., Cockrum, C., Sidoli, S., Garcia, B.A., Jensen, O.N., Strome, S.(2018). Distinct roles of two histone methyltransferases in transmitting h3k36me3-based epigenetic memory across generations in caenorhabditis elegans . Genetics. 210. (3). p. 969-982.
Grevet, J.D., Lan, X., Hamagami, N., Edwards, C.R., Sankaranarayanan, L., Ji, X., Bhardwaj, S.K., Face, C.J., Posocco, D.F., Abdulmalik, O., et al.(2018). Domain-focused CRISPR screen identifies HRI as a fetal hemoglobin regulator in human erythroid cells . Science. 361. (6399). p. 285-290.
Yuan, Z.-F., Sidoli, S., Marchione, D.M., Simithy, J., Janssen, K.A., Szurgot, M.R., Garcia, B.A.(2018). EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data . Journal of Proteome Research. 17. (7). p. 2533-2541.
Greer, S.M., Sidoli, S., Coradin, M., Schack Jespersen, M., Schwämmle, V., Jensen, O.N., Garcia, B.A., Brodbelt, J.S.(2018). Extensive Characterization of Heavily Modified Histone Tails by 193 nm Ultraviolet Photodissociation Mass Spectrometry via a Middle-Down Strategy . Analytical Chemistry. 90. (17). p. 10425-10433.
Di Marcantonio, D., Martinez, E., Sidoli, S., Vadaketh, J., Nieborowska-Skorska, M., Gupta, A., Meadows, J.M., Ferraro, F., Masselli, E., Challen, G.A., et al.(2018). Protein kinase C epsilon is a key regulator of mitochondrial redox homeostasis in acute myeloid leukemia . Clinical Cancer Research. 24. (3). p. 608-618.
Weiner, A.K., Sidoli, S., Diskin, S.J., Garcia, B.A.(2018). Graphical interpretation and analysis of proteins and their ontologies (GiaPronto): A one-click graph visualization software for proteomics data sets . Molecular and Cellular Proteomics. 17. (7). p. 1426-1431.
Tahir, M., Arshid, S., Fontes, B., Castro, M.S., Luz, I.S., Botelho, K.L.R., Sidoli, S., Schwämmle, V., Roepstorff, P., Fontes, W.(2018). Analysis of the effect of intestinal ischemia and reperfusion on the rat neutrophils proteome . Frontiers in Molecular Biosciences. 5. (NOV).
Weissmann, S., Cloos, P.A., Sidoli, S., Jensen, O.N., Pollard, S., Helin, K.(2018). The tumor suppressor CIC directly regulates MAPK pathway genes via histone deacetylation . Cancer Research. 78. (15). p. 4114-4125.
Simithy, J., Sidoli, S., Garcia, B.A.(2018). Integrating Proteomics and Targeted Metabolomics to Understand Global Changes in Histone Modifications . Proteomics. 18. (18).
Sidoli, S.(2018). Middle-Down MS is Ready to Answer Complex Questions in Chromatin Biology . Proteomics. 18. (13).
Juan, A.H., Wang, S., Ko, K.D., Zare, H., Tsai, P.-F., Feng, X., Vivanco, K.O., Ascoli, A.M., Gutierrez-Cruz, G., Krebs, J., et al.(2017). Erratum: Roles of H3K27me2 and H3K27me3 Examined during Fate Specification of Embryonic Stem Cells (Cell Reports (2016) 17(5) (1369–1382)(S2211124716313638)(10.1016/j.celrep.2016.09.087) . Cell Reports. 18. (1). p. 297.
Armour, S.M., Remsberg, J.R., Damle, M., Sidoli, S., Ho, W.Y., Li, Z., Garcia, B.A., Lazar, M.A.(2017). An HDAC3-PROX1 corepressor module acts on HNF4α to control hepatic triglycerides . Nature Communications. 8. (1).
Becker, J.S., McCarthy, R.L., Sidoli, S., Donahue, G., Kaeding, K.E., He, Z., Lin, S., Garcia, B.A., Zaret, K.S.(2017). Genomic and Proteomic Resolution of Heterochromatin and Its Restriction of Alternate Fate Genes . Molecular Cell. 68. (6). p. 1023-1037.e15.
Simithy, J., Sidoli, S., Yuan, Z.-F., Coradin, M., Bhanu, N.V., Marchione, D.M., Klein, B.J., Bazilevsky, G.A., McCullough, C.E., Magin, R.S., et al.(2017). Characterization of histone acylations links chromatin modifications with metabolism . Nature Communications. 8. (1).
Alečković, M., Wei, Y., LeRoy, G., Sidoli, S., Liu, D.D., Garcia, B.A., Kang, Y.(2017). Identification of Nidogen 1 as a lung metastasis protein through secretome analysis . Genes and Development. 31. (14). p. 1439-1455.
Arshid, S., Tahir, M., Fontes, B., de Souza Montero, E.F., Castro, M.S., Sidoli, S., Roepstorff, P., Fontes, W.(2017). High performance mass spectrometry based proteomics reveals enzyme and signaling pathway regulation in neutrophils during the early stage of surgical trauma . Proteomics - Clinical Applications. 11. (1-2).
Feist, P.E., Sidoli, S., Liu, X., Schroll, M.M., Rahmy, S., Fujiwara, R., Garcia, B.A., Hummon, A.B.(2017). Multicellular Tumor Spheroids Combined with Mass Spectrometric Histone Analysis to Evaluate Epigenetic Drugs . Analytical Chemistry. 89. (5). p. 2773-2781.
Arshid, S., Tahir, M., Fontes, B., Montero, E.F.S., Castro, M.S., Sidoli, S., Schwämmle, V., Roepstorff, P., Fontes, W.(2017). Neutrophil proteomic analysis reveals the participation of antioxidant enzymes, motility and ribosomal proteins in the prevention of ischemic effects by preconditioning . Journal of Proteomics. 151. p. 162-173.
Sidoli, S., Lu, C., Coradin, M., Wang, X., Karch, K.R., Ruminowicz, C., Garcia, B.A.(2017). Metabolic labeling in middle-down proteomics allows for investigation of the dynamics of the histone code . Epigenetics and Chromatin. 10. (1).
Sidoli, S., Garcia, B.A.(2017). Middle-down proteomics: a still unexploited resource for chromatin biology . Expert Review of Proteomics. 14. (7). p. 617-626.
Kori, Y., Sidoli, S., Yuan, Z.-F., Lund, P.J., Zhao, X., Garcia, B.A.(2017). Proteome-wide acetylation dynamics in human cells . Scientific Reports. 7. (1).
Rabiee, A., Schwämmle, V., Sidoli, S., Dai, J., Rogowska-Wrzesinska, A., Mandrup, S., Jensen, O.N.(2017). Nuclear phosphoproteome analysis of 3T3-L1 preadipocyte differentiation reveals system-wide phosphorylation of transcriptional regulators . Proteomics. 17. (6).
Wimmer, M.E., Briand, L.A., Fant, B., Guercio, L.A., Arreola, A.C., Schmidt, H.D., Sidoli, S., Han, Y., Garcia, B.A., Pierce, R.C.(2017). Paternal cocaine taking elicits epigenetic remodeling and memory deficits in male progeny . Molecular Psychiatry. 22. (11). p. 1641-1650.
Shinde, M.Y., Sidoli, S., Kulej, K., Mallory, M.J., Radens, C.M., Reicherter, A.L., Myers, R.L., Barash, Y., Lynch, K.W., Garcia, B.A., et al.(2017). Phosphoproteomics reveals that glycogen synthase kinase-3 phosphorylates multiple splicing factors and is associated with alternative splicing . Journal of Biological Chemistry. 292. (44). p. 18240-18255.
Kulej, K., Avgousti, D.C., Sidoli, S., Herrmann, C., Della Fera, A.N., Kim, E.T., Garcia, B.A., Weitzman, M.D.(2017). Time-resolved global and chromatin proteomics during herpes simplex virus type 1 (HSV-1) infection . Molecular and Cellular Proteomics. 16. (4). p. S92-S107.
Coetzee, N., Sidoli, S., Van Biljon, R., Painter, H., Llinás, M., Garcia, B.A., Birkholtz, L.-M.(2017). Quantitative chromatin proteomics reveals a dynamic histone post-translational modification landscape that defines asexual and sexual Plasmodium falciparum parasites . Scientific Reports. 7. (1).
Thomson, R.W., He, C., Sidoli, S., Garcia, B.A., Bonasio, R.(2017). Sample preparation for mass spectrometry-based identification of RNA-binding regions . Journal of Visualized Experiments. 2017. (127).
Sidoli, S., Kulej, K., Garcia, B.A.(2017). Why proteomics is not the new genomics and the future of mass spectrometry in cell biology . Journal of Cell Biology. 216. (1). p. 21-24.
Wang, W., Sidoli, S., Zhang, W., Wang, Q., Wang, L., Jensen, O.N., Guo, L., Zhao, X., Zheng, L.(2017). Abnormal levels of histone methylation in the retinas of diabetic rats are reversed by minocycline treatment . Scientific Reports. 7.
Juan, A.H., Wang, S., Ko, K.D., Zare, H., Tsai, P.-F., Feng, X., Vivanco, K.O., Ascoli, A.M., Gutierrez-Cruz, G., Krebs, J., et al.(2016). Roles of H3K27me2 and H3K27me3 Examined during Fate Specification of Embryonic Stem Cells . Cell Reports. 17. (5). p. 1369-1382.
Sidoli, S., Vandamme, J., Salcini, A.E., Jensen, O.N.(2016). Dynamic changes of histone H3 marks during Caenorhabditis elegans lifecycle revealed by middle-down proteomics . Proteomics. 16. (3). p. 459-464.
Anderson, L.C., Karch, K.R., Ugrin, S.A., Coradin, M., English, A.M., Sidoli, S., Shabanowitz, J., Garcia, B.A., Hunt, D.F.(2016). Analyses of histone proteoforms using frontend electron transfer dissociation-enabled orbitrap instruments . Molecular and Cellular Proteomics. 15. (3). p. 975-988.
Sidoli, S., Bhanu, N.V., Karch, K.R., Wang, X., Garcia, B.A.(2016). Complete workflow for analysis of histone post-translational modifications using bottom-up mass spectrometry: From histone extraction to data analysis . Journal of Visualized Experiments. 2016. (111).
Gonzales-Cope, M., Sidoli, S., Bhanu, N.V., Won, K.-J., Garcia, B.A.(2016). Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells . BMC Genomics. 17. (1).
Sidoli, S., Fujiwara, R., Kulej, K., Garcia, B.A.(2016). Differential quantification of isobaric phosphopeptides using data-independent acquisition mass spectrometry . Molecular BioSystems. 12. (8). p. 2385-2388.
Bhanu, N.V., Sidoli, S., Garcia, B.A.(2016). Histone modification profiling reveals differential signatures associated with human embryonic stem cell self-renewal and differentiation . Proteomics. 16. (3). p. 448-458.
He, C., Sidoli, S., Warneford-Thomson, R., Tatomer, D.C., Wilusz, J.E., Garcia, B.A., Bonasio, R.(2016). High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells . Molecular Cell. 64. (2). p. 416-430.
Sidoli, S., Fujiwara, R., Garcia, B.A.(2016). Multiplexed data independent acquisition (MSX-DIA) applied by high resolution mass spectrometry improves quantification quality for the analysis of histone peptides . Proteomics. 16. (15-16). p. 2095-2105.
Schwämmle, V., Sidoli, S., Ruminowicz, C., Wu, X., Lee, C.-F., Helin, K., Jensen, O.N.(2016). Systems level analysis of Histone H3 posttranslational modifications (PTMs) reveals features of PTM crosstalk in chromatin regulation . Molecular and Cellular Proteomics. 15. (8). p. 2715-2729.
Jamieson, K., Wiles, E.T., McNaught, K.J., Sidoli, S., Leggett, N., Shao, Y., Garcia, B.A., Selker, E.U.(2016). Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin . Genome Research. 26. (1). p. 97-107.
Sidoli, S., Lin, S., Karch, K.R., Garcia, B.A.(2015). Bottom-Up and Middle-Down Proteomics Have Comparable Accuracies in Defining Histone Post-Translational Modification Relative Abundance and Stoichiometry . Analytical Chemistry. 87. (6). p. 3129-3133.
Garrigues, J.M., Sidoli, S., Garcia, B.A., Strome, S.(2015). Defining heterochromatin in C. elegans through genome-wide analysis of the heterochromatin protein 1 homolog HPL-2 . Genome Research. 25. (1). p. 76-88.
Kulej, K., Sidoli, S., Palmisano, G., Edwards, A.V.G., Robinson, P.J., Larsen, M.R.(2015). Optimization of calmodulin-affinity chromatography for brain and organelles . EuPA Open Proteomics. 8. p. 55-67.
Sidoli, S., Yuan, Z.-F., Lin, S., Karch, K., Wang, X., Bhanu, N., Arnaudo, A.M., Britton, L.-M., Cao, X.-J., Gonzales-Cope, M., et al.(2015). Drawbacks in the use of unconventional hydrophobic anhydrides for histone derivatization in bottom-up proteomics PTM analysis . Proteomics. 15. (9). p. 1459-1469.
Önder, O., Sidoli, S., Carroll, M., Garcia, B.A.(2015). Progress in epigenetic histone modification analysis by mass spectrometry for clinical investigations . Expert Review of Proteomics. 12. (5). p. 499-517.
Yuan, Z.-F., Lin, S., Molden, R.C., Cao, X.-J., Bhanu, N.V., Wang, X., Sidoli, S., Liu, S., Garcia, B.A.(2015). Epiprofile quantifies histone peptides with modifications by extracting retention time and intensity in high-resolution mass spectra . Molecular and Cellular Proteomics. 14. (6). p. 1696-1707.
Vandamme, J., Sidoli, S., Mariani, L., Friis, C., Christensen, J., Helin, K., Jensen, O.N., Salcini, A.E.(2015). H3K23me2 is a new heterochromatic mark in Caenorhabditis elegans . Nucleic Acids Research. 43. (20). p. 9694-9710.
Milioli, M., Ibáñez-Vea, M., Sidoli, S., Palmisano, G., Careri, M., Larsen, M.R.(2015). Quantitative proteomics analysis of platelet-derived microparticles reveals distinct protein signatures when stimulated by different physiological agonists . Journal of Proteomics. 121. p. 56-66.
Chen, S., Yang, Z., Wilkinson, A.W., Deshpande, A.J., Sidoli, S., Krajewski, K., Strahl, B.D., Garcia, B.A., Armstrong, S.A., Patel, D.J., et al.(2015). The PZP Domain of AF10 Senses Unmodified H3K27 to Regulate DOT1L-Mediated Methylation of H3K79 . Molecular Cell. 60. (2). p. 319-327.
Sidoli, S., Garcia, B.A.(2015). Properly reading the histone code by MS-based proteomics . Proteomics. 15. (17). p. 2901-2902.
Won, K.-J., Choi, I., Leroy, G., Zee, B.M., Sidoli, S., Gonzales-Cope, M., Garcia, B.A.(2015). Proteogenomics analysis reveals specific genomic orientations of distal regulatory regions composed by non-canonical histone variants . Epigenetics and Chromatin. 8. (1).
Tvardovskiy, A., Wrzesinski, K., Sidoli, S., Fey, S.J., Rogowska-Wrzesinska, A., Jensen, O.N.(2015). Top-down and middle-down protein analysis reveals that intact and clipped human histones differ in post-translational modification patterns . Molecular and Cellular Proteomics. 14. (12). p. 3142-3153.
Wu, X., Bekker-Jensen, I.H., Christensen, J., Rasmussen, K.D., Sidoli, S., Qi, Y., Kong, Y., Wang, X., Cui, Y., Xiao, Z., et al.(2015). Tumor suppressor ASXL1 is essential for the activation of INK4B expression in response to oncogene activity and anti-proliferative signals . Cell Research. 25. (11). p. 1205-1218.
Sidoli, S., Lin, S., Xiong, L., Bhanu, N.V., Karch, K.R., Johansen, E., Hunter, C., Mollah, S., Garcia, B.A.(2015). Sequential window acquisition of all theoretical mass spectra (SWATH) analysis for characterization and quantification of histone post-translational modifications . Molecular and Cellular Proteomics. 14. (9). p. 2420-2428.
Sidoli, S., Simithy, J., Karch, K.R., Kulej, K., Garcia, B.A.(2015). Low Resolution Data-Independent Acquisition in an LTQ-Orbitrap Allows for Simplified and Fully Untargeted Analysis of Histone Modifications . Analytical Chemistry. 87. (22). p. 11448-11454.
Alabert, C., Barth, T.K., Reverón-Gómez, N., Sidoli, S., Schmidt, A., Jensen, O., Imhof, A., Groth, A.(2015). Two distinct modes for propagation of histone PTMs across the cell cycle . Genes and Development. 29. (6). p. 585-590.
Such-Sanmartín, G., Sidoli, S., Ventura-Espejo, E., Jensen, O.N.(2014). KYSS: Mass spectrometry data quality assessment for protein analysis and large-scale proteomics . Biochemical and Biophysical Research Communications. 445. (4). p. 702-707.
Sidoli, S., Schwämmle, V., Ruminowicz, C., Hansen, T.A., Wu, X., Helin, K., Jensen, O.N.(2014). Middle-down hybrid chromatography/tandem mass spectrometry workflow for characterization of combinatorial post-translational modifications in histones . Proteomics. 14. (19). p. 2200-2211.
Schwämmle, V., Aspalter, C.-M., Sidoli, S., Jensen, O.N.(2014). Large scale analysis of co-existing post-translational modifications in histone tails reveals global fine structure of cross-talk . Molecular and Cellular Proteomics. 13. (7). p. 1855-1865.
Siersbæk, R., Rabiee, A., Nielsen, R., Sidoli, S., Traynor, S., Loft, A., Poulsen, L., Rogowska-Wrzesinska, A., Jensen, O., Mandrup, S.(2014). Transcription factor cooperativity in early adipogenic hotspots and super-enhancers . Cell Reports. 7. (5). p. 1443-1455.
Zhao, X., Sidoli, S., Wang, L., Wang, W., Guo, L., Jensen, O.N., Zheng, L.(2014). Comparative proteomic analysis of histone post-translational modifications upon ischemia/reperfusion-induced retinal injury . Journal of Proteome Research. 13. (4). p. 2175-2186.
Bignardi, C., Mattarozzi, M., Penna, A., Sidoli, S., Elviri, L., Careri, M., Mangia, A.(2013). 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. (4). p. 1144-1152.
Jung, H.R., Sidoli, S., Haldbo, S., Sprenger, R.R., Schwämmle, V., Pasini, D., Helin, K., Jensen, O.N.(2013). Precision mapping of coexisting modifications in histone H3 tails from embryonic stem cells by ETD-MS/MS . Analytical Chemistry. 85. (17). p. 8232-8239.
Sidoli, S., Cheng, L., Jensen, O.N.(2012). Proteomics in chromatin biology and epigenetics: Elucidation of post-translational modifications of histone proteins by mass spectrometry . Journal of Proteomics. 75. (12). p. 3419-3433.
Vandamme, J., Lettier, G., Sidoli, S., Di Schiavi, E., Nørregaard Jensen, O., Salcini, A.E.(2012). The C. elegans H3K27 demethylase UTX-1 is essential for normal development, independent of its enzymatic activity . PLoS Genetics. 8. (5).
BOOK CHAPTER
Sidoli, S., Trefely, S., Garcia, B.A., Carrer, A.(2019). Integrated analysis of acetyl-CoA and histone modification via mass spectrometry to investigate metabolically driven acetylation . Methods in Molecular Biology. 1928. p. 125-147.
Lund, P.J., Kori, Y., Zhao, X., Sidoli, S., Yuan, Z.-F., Garcia, B.A.(2019). Isotopic labeling and quantitative proteomics of acetylation on histones and beyond . Methods in Molecular Biology. 1977. p. 43-70.
Sidoli, S., Garcia, B.A.(2017). Characterization of individual histone posttranslational modifications and their combinatorial patterns by mass spectrometry-based proteomics strategies . Methods in Molecular Biology. 1528. p. 121-148.
Janssen, K.A., Sidoli, S., Garcia, B.A.(2017). Recent Achievements in Characterizing the Histone Code and Approaches to Integrating Epigenomics and Systems Biology . Methods in Enzymology. 586. p. 359-378.
Karch, K.R., Sidoli, S., Garcia, B.A.(2016). Identification and Quantification of Histone PTMs Using High-Resolution Mass Spectrometry . Methods in Enzymology. 574. p. 3-29.
Wang, X., Sidoli, S., Garcia, B.A.(2015). Application of Mass Spectrometry in Translational Epigenetics . Epigenetic Technological Applications. p. 55-78.
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