Here, we keep you updated on the products of our research at Einstein! This page includes all the publications that include the Albert Einstein College of Medicine as affiliation (sorted from newest to oldest). If you are interested in our preprints or full bibliography of the PI, please click the buttons.
Older publications: 2022
Investigation of reversible histone acetylation and dynamics in gene expression regulation using 3D liver spheroid model
Stransky S, Cutler R, Aguilan J, Nieves E and Sidoli S (Epigenetics & Chromatin, 2022)
Endocrine resistance and breast cancer plasticity are controlled by CoREST
Garcia-Martinez L, Chan HL, Weich N, Stransky S, Alshalalfa M, Sarria L, Celia-Terrassa T, Mahal BA, Minucci S, Sidoli S, Bilbao D, Verdun RE and Morey L (Nature Structural and Molecular Biology, 2022)
Morphine disrupts macrophage functions even during HIV infection
Barbaro J, Jaureguiberry-Bravo M, Sidoli S and Berman J Morphine disrupts macrophage functions even during HIV infection (Journal of Leukocyte Biology, 2022)
Autophagic state prospectively identifies facultative stem cells in the intestinal epithelium
Johnson NM, Parham LR, Na J, Monaghan KE, Kolev HM, Klochkova A, Kim MS, Danan CH, Cramer Z, Simon LA, Naughton KE, Adams-Tzivelekidis S, Tian Y, Williams PA, Sidoli S, Whelan KA, Li N, Lengner CJ and Hamilton KE (EMBO Reports, 2022)
Reduced endosomal microautophagy activity in aging associates with enhanced exocyst-mediated protein secretion
Krause GJ, Diaz A, Jafari M, Khawaja RR, Agullo-Pascual E, Santiago-Fernández O, Chen KH, Dmitriev P, Sun Y, Krogan NJ, Swaney D, Sidoli S, Bravo-Cordero JJ, Kampmann M and Cuervo AM (Aging Cell, 2022)
CRISPR screening uncovers a central requirement for HHEX in pancreatic lineage commitment and plasticity restriction
Yang D, Cho H, Tayyebi Z, Shukla A, Luo R, Dixon G, Ursu V, Stransky S, Tremmel DM, Sackett SD, Koche R, Kaplan S, Li QV, Park J, Zhu Z, Rosen BP, Pulecio J, Shi ZD, Bram Y, Schwartz RE, Odorico JS, Sidoli S, Wright CV, Leslie C and Huangfu D (Nature Cell Biology, 2022)
Dense granule protein, GRA64 interacts with host cell ESCRT proteins during Toxoplasma gondii infection
Mayoral J, Guevara R, Rivera-Cuevas Y, Tu V, Tomita T, Romano J, Gunther-Cummins L, Sidoli S, Coppens I, Carruthers V and Weiss L (mBio, 2022)
Methamphetamine Dysregulates Macrophage Functions and Autophagy to Mediate HIV Neuropathogenesis
Barbaro JM, Sidoli S, Cuervo AM and Berman JW Methamphetamine Dysregulates Macrophage Functions and Autophagy to Mediate HIV Neuropathogenesis (Biomedicines, 2022)
Global Level Quantification of Histone Post-Translational Modifications in a 3D Cell Culture Model of Hepatic Tissue
Joseph-Chowdhury JSN, Stransky S, Graff S, Cutler R, Young D, Kim J, Madrid-Aliste C, Aguilan JT, Nieves E, Sun Y, Yoo EJ and Sidoli S (Journal of Visualized Experiments, 2022)
Altered abundances of human immunoglobulin M and immunoglobulin G subclasses in Alzheimer’s disease frontal cortex
Lekhraj R, Lalezari S, Aguilan JT, Qin J, Sidoli S, Mowrey W, Gollamudi S and Lalezari P (Scientific Reports, 2022)
PAX8 orchestrates an angiogenic program through interaction with SOX17
Chaves-Moreira D, Mitchell MA, Arruza C, Rawat P, Sidoli S, Nameki R, Reddy J, Corona RI, Afeyan LK, Klein IA, ma S, Winterhoff B, Konecny GE, Garcia BA, Brady DC, Lawrenson K, Morin PJ and Drapkin R (Science Signaling, 2022)
Macrophages Use Apoptotic Cell-Derived Methionine and DNMT3A During Efferocytosis to Promote Tissue Resolution
Ampomah PB, Cai B, Gerlach B, Yrdagul Jr A, Wang X, Kuriakose G, Darville LN, Sun Y, Sidoli S, Koomen JM, Tall AR and Tabas I (Nature Metabolism, 2022)
Lamiable-Oulaidi F, Harijan RK, Shaffer KJ, Crump DR, Sun Y, Carson G, Du Q, Gulab SA, Khan AA, Luxenbuger A, Woolhouse AD, Sidoli S, Tyler PC and Schramm VL (Journal of Medicinal Chemistry, 2022)
CpG island reconfiguration for the establishment and synchronization of Polycomb functions upon exit from naïve pluripotency
Huo D, Yu Z, Li R, Gong M, Sidoli S, Lu X, Hou Y, Dai Z, Kong Y, Liu G, Jensen ON, Xie W, Helin K, Xiong C, Li G, Zhang Y and Wu X (Molecular Cell, 2022)
Enzymatic transfer of acetate on histones from lysine reservoir sites to lysine activating sites
Mendoza M, Egervari G, Donahue G, Sidoli S, Alexander DC, Sen P, Garcia BA and Berger SL Enzymatic transfer of acetate on histones from lysine reservoir sites to lysine activating sites (Science Advances, 2022)
A dynamic and combinatorial histone code drives malaria parasite asexual and sexual development
Von Gruning H, Coradin M, Mendoza M, Sidoli S, Garcia BA and Birkholtz LM A dynamic and combinatorial histone code drives malaria parasite asexual and sexual development (Molecular and Cellular Proteomics, 2022)
Multi-omic profiling of histone variant H3.3 lysine 27 methylation reveals a distinct role from canonical H3 in stem cell differentiation
Kori Y, Lund PJ, Trovato M, Sidoli S, Yuan ZF, Noh KM and Garcia BA (Molecular Omics, 2022)
Genotype-specific Features Reduce the Susceptibility of South American Yellow Fever Virus Strains to Vaccine-Induced Antibodies
Haslwanter D, Lasso G, Wec AZ, Furtado ND, Raphael MDS, Sun Y, Stransky S, Pedreño-Lopez N, Tse A, Correia CA, Bornholdt ZA, Sakharkar M, Avelino-Silva VI, Moyer CL, Watkins DI, Kallas EG, Sidoli S, Walker LM, Bonaldo MC and Chandran K (Cell Host & Microbe, 2022)
Type I PRMTs and PRMT5 Inversely Regulate Post-Transcriptional Intron Detention
Maron MI, Casill A, Gupta V, Sidoli S, Query C, Gamble M and Shechter D (eLife, 2022)
2021
Pipecolic acid, a putative mediator of the encephalopathy of cerebral malaria and the experimental model of cerebral malaria
Keswani T, Obeidallah A, Nieves E, Sidoli S, Fazzari M, Taylor T, Seydel K and Daily JP (Journal of Infectious Diseases, 2021)
Quantitative subcellular acyl-CoA analysis reveals distinct nuclear metabolism and isoleucine-dependent histone propionylation
Trefely S, Huber K, Liu J, Noji M, Stransky S, Singh J, Doan MT, Lovell CD, von Krusenstiern E, Jiang H, Bostwick A, Pepper HL, Izzo L, Zhao S, Xu JP, Bedi Jr KC, Rame JE, Bogner-Strauss JG, Mesaros C, Sidoli S, Wellen KE and Snyder NW (Molecular Cell, 2021)
DNA methylation and hydroxymethylation analysis using a high throughput and low bias direct injection mass spectrometry platform
Sun Y, Stransky S, Aguilan J, Brenowitz M and Sidoli S (MethodsX, 2021)
A key silencing histone mark on chromatin is lost when colorectal adenocarcinoma cells are depleted of methionine by methionine gamma-lyase
Raboni S, Montalbano S, Stransky S, Garcia BA, Buschini A, Bettati S, Sidoli S and Mozzarelli A (Frontiers in Molecular Biosciences (2021)
The Polycomb protein RING1B enables estrogen-mediated gene expression by promoting enhancer-promoter interaction and R-loop formation
Zhang Y, Liu T, Yuan F, Garcia-Martinez L, Lee K, Stransky S, Sidoli S, Verdun RE, Zhang Y, Wang Z and Morey L (Nucleic Acid Research, 2021)
Independent transcriptomic and proteomic regulation by type I and II protein arginine methyltransferases
Maron MI, Lehman SM, Gayatri S, DeAngelo JD, Hegde S, Lorton B, Sun Y, Bai DL, Sidoli S, Gupta V, Marunde MR, Bone JR, Sun ZW, Bedford MT, Shabanowitz J, Chen H, Hunt DF and Shechter D (iScience, 2021)
High throughput and low bias DNA methylation and hydroxymethylation analysis by direct injection mass spectrometry
Sun Y, Stransky S, Aguilan J, Koul S, Garforth SJ, Brenowitz B and Sidoli S (Analytical Chimica Acta, 2021)
VAL genes regulate vegetative phase change via miR156-dependent and independent mechanisms
Fouracre JP, He J, Chen VJ, Sidoli S and Poethig RS (Pols Genetics, 2021)
FGF-2 induces a failure of cell cycle progression in cells harboring amplified K-Ras, revealing new insights into oncogene-induced senescence
Lund PJ, Lopes M, Sidoli S, Coradin M, Vitorino FNL, da Cunha JPC and Garcia BA (Molecular Omics, 2021)
Protective neutralizing antibodies from human survivors of Crimean-Congo hemorrhagic fever
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, Quevedo G, Lobel L, Balinandi S, Lutwama JJ, Zeitlin L, Geisbert TW, Rey FA, Sidoli S, McLellan JS, Lai JR, Bornholdt ZA, Dye JM, Walker LM and Chandran K (Cell, 2021)
QSER1 protects DNA methylation valleys from De Novo methylation
Dixon G, Pan H, Rosen BP, Yang D, Jashari T, Verma N, Pulecio J, Caspi I, Lee K, Stransky S, Glezer A, Liu C, Rivas M, Kumar R, Lan Y, Torregroza I, He C, Sidoli S, Evans T, Elemento O and Huangfu D (Science, 2021)
Combinatorial Histone H3 Modifications Are Dynamically Altered in Distinct Cell Cycle Phases
Lu C, Coradin M, Janssen K, Sidoli S and Garcia BA (JASMS, 2021)
Long-term behavioral and cell-type-specific molecular effects of early life stress are mediated by H3K79me2 dynamics in medium spiny neurons
Kronman H, Peña CJ, Torres-Berrío A, Sidoli S, Issler O, Godino A, Ramakrishnan A, Mews P, Parise EM, Lardner CK, Walker DM, Van der Zee Y, Boyce BF, Garcia BA, Shen L and Nestler EJ (Nature Neuroscience, 2021)
One-shot analysis of translated mammalian lncRNAs with AHARIBO
Minati L, Peretti A, Firrito C, Del Piano A, Sidoli S, Peroni D, Belli R, Gandolfi F, Romanel A, Bernabò P, Zasso J, Quattrone A, Guella G, Lauria F, Viero G and Clamer M (eLife, 2021)
Toxoplasma gondii PPM3C, a secreted protein phosphatase, affects parasitophorous vacuole effector export
Mayoral, JA, Tomita T, Tu, V, Aguilan JT, Sidoli S and Weiss LM (PloS Pathogens, 2020)
2020
H1 histones control the epigenetic landscape by local chromatin compaction
Willcockson MA, Healton SE, Weiss CN, Bartholdy BA, Botbol YM, Mishra LN, Sidhwani DS, Wilson TJ, Pinto HB, Maron MI, Skalina KA, Norwood Toro L, Zhao J, Lee CH, Hou H, Yusufova N, Meydan C, Osunsade A, David Y, Cesarman E, Melnik AM, Sidoli S, Garcia BA, Edelmann W, Macian F and Skoultchi AI (Nature, December 2020)
White adipose remodeling during browning in mice involves YBX1 to drive thermogenic commitment
Rabiee A, Pluciñska K, Isidor MS, Brown EL, Tozzi M, Sidoli S, Petersen PS, Agueda-Oyarzabal M, Torsetnes SB, Chehabi GN, Lundh M, Altıntaş A, Barres R, Jensen ON, Gerhart-Hines Z and Emanuelli B (Molecular Metabolism, 2020)
An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease
Nativio R, Lan Y, Donahue G, Sidoli S, Berson A, Srinivasan A, Shcherbakova O, Amlie-Wolf A, Wang LS, Garcia BA, Trojanowski JQ, Bonini NM and Berger SL (Nature Genetics, 2020)
A Workflow for Ultra-rapid Analysis of Histone Post-translational Modifications with Direct-injection Mass Spectrometry
Bhanu NV, Sidoli S and Garcia BA (Bio-Protocol, 2020)
Guide for protein fold change and p-value calculation for non-experts in proteomics
Aguilan J, Kulej K and Sidoli S (Molecular Omics, 2020)
Caenorhabditis elegans nuclear RNAi factor SET-32 deposits the transgenerational histone modification, H3K23me3
Schwartz-Orbach L, Zhang C, Sidoli S, Amin R, Kaur D, Zhebrun A and Gu SG (eLife, 2020)
Phosphoproteomics of rat neutrophils shows the effect of intestinal ischemia/reperfuson and preconditioning on kinases and phosphatases
Tahir M, Arshid S, Fontes B, Castro MS, Sidoli S, Schwammle V, Luz IS, Roepstorff P and Fontes W (International Journal of Molecular Sciences, 2020)
PR-DUB maintains expression of critical genes through FOXK1/2 and ASXML1/2/3-dependent recruitment to chromatin and H2AK119ub1 deubiquitination
Kolovos, P, Nishimura K, Sankar A, Sidoli S, Cloos P, Helin K and Christensen J (Genome Research, 2020)
Mutant FOXL2C134W Highjacks SMAD4 and SMAD2/3 to Drive Adult Granulosa Cell Tumors
Weis-Banke S, Kleine-Kohlbrecher D, Lerdrup M, Mohammad F, Sidoli S, Jensen ON, Yanase T, Nakamura T, Iwase A, Koche R, Da Cruz Paula A, Weigelt B, Christensen J, Helin K and Cloos PAC (Cancer Research, 2020)
Mass spectrometry to study chromatin compaction
Stransky S, Aguilan J, Lachowicz J, Madrid-Aliste C, Nieves E and Sidoli S (Biology, Chromatin Dynamics special issue, 2020)
The comprehensive map of the Artemisia annua proteome based on Data independent acquisition (DIA) reveals potential key roles for the production of artemisinin
Chen M, Yan T, Ji L, Yu D, Sidoli S, Yuan ZF, Chen J, Fu X, Tang Y, Shen Q, Pan Q, Xin K, Liao L, Garcia BA, Yan W and Tang K (Proteomics, 2020)
Disruption of ATRX-RNA interactions uncovers roles in ATRX localization and PRC2 function
Ren W, Medeiros N, Warneford-Thomson R, Wulfridge P, Yan Q, Bian J, Sidoli S, Garcia BA, Skordalakes E, Joyce E, Bonasio R and Sarma K (Nature Communications, 2020)
Lysine 4 of histone H3.3 is required for embryonic stem cell differentiation, histone enrichment at regulatory regions and transcription accuracy
Gehre M, Bunina D, Sidoli S, Lübke M, Diaz N, Trovato M, Garcia BA, Zaugg JB and Noh KM (Nature Genetics, 2020)
Bullet points to evaluate the performance of the middle-down proteomics workflow for histone modification analysis
Coradin M, Mendoza M, Sidoli S, Alpert AJ, Lu C and Garcia BA (Methods, 2020)
2019
Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation
Klein BJ, Jang SM, Lachance C, Mi W, Lyu J, Sakuraba S, Krajewski K, Wang WW, Sidoli S, Yan K, Liu J, Zhang Y, Roques C, Fournier E, Wang X, Warfield BM, Yang XJ, Garcia BA, Liu WR, Li W, Strahl BD, Kono H, Shi X, Côté J and Kutateladze TG (Nature Communications, 2019)
Quantitation of Single and Combinatorial Histone Modifications by Integrated Chromatography of Bottom-up Peptides and Middle-down Polypeptide Tails
Janssen KA, Coradin M, Lu C, Sidoli S and Garcia BA (Journal of the American Society of Mass Spectrometry, 2019)
A mass spectrometry-based assay using metabolic labeling to rapidly monitor chromatin accessibility of modified histone proteins
Sidoli S, Lopes M, Lund PJ, Goldman N, Fasolino M, Coradin M, Bhanu NV, Kulej K, Vahedi G and Garcia BA (Scientific Reports, 2019)
Alcohol metabolism contributes to brain histone acetylatioN
Mews P, Egervari G, Nativio R, Sidoli S, Donahue G, Lombroso SI, Alexander DC, Riesche SL, Heller EA, Nestler EJ, Garcia BA and Berger SL (Nature, 2019)
One minute analysis of histone post-translational modifications by direct injection mass spectrometry
Sidoli S, Kori Y, Lopes M, Yuan ZF, Kim HJ, Kulej K, Janssen K, Agosto L, Cunha JPC and Garcia BA (Genome Research, 2019)