Recent Publications

Richard M Searfoss, Rashmi Karki, Zongtao Lin, Faith Robison & Benjamin A Garcia (2023). “An Optimized and High-Throughput Method for Histone Propionylation and Data-Independent Acquisition Analysis for the Identification and Quantification of Histone Post-translational Modifications” J Am Soc Mass Spectrom. 2023 Nov 1;34(11):2508-2517. doi: 10.1021/jasms.3c00223. Epub 2023 Oct 18. (Abstract)

Yixuan Xie, Francisca N. De Luna Vitorino, Ye Chen, Joanna K. Lempiäinen, Chenfeng Zhao, Robert T. Steinbock, Zongtao Lin, Xingyu Liu, Emily Zahn, Arabella L. Garcia, Matthew D. Weitzmancd & Benjamin A Garcia (2023). “SWAMNA: a comprehensive platform for analysis of nucleic acid modifications” Chem Commun. 2023, 59(83):12499-12502. (Abstract)

Peder J Lund, Leah A Gates, Marylene Leboeuf, Sarah A Smith, Lillian Chau, Mariana Lopes, Elliot S Friedman, Yedidya Saiman, Min Soo Kim, Clarissa A Shoffler, Christopher Petucci, C David Allis, Gary D Wu & Benjamin A Garcia (2022). “Stable isotope tracing in vivo reveals a metabolic bridge linking the microbiota to host histone acetylation” Cell Rep. 2022 Dec 13;41(11):111809. doi: 10.1016/j.celrep.2022.111809. (Abstract)

Yixuan Xie, Kevin A Janssen, Alessandro Scacchetti, Elizabeth G Porter, Zongtao Lin, Roberto Bonasio & Benjamin A Garcia (2022). “Permethylation of Ribonucleosides Provides Enhanced Mass Spectrometry Quantification of Post-Transcriptional RNA Modifications” Anal Chem. 2022 May 24;94(20):7246-7254. doi: 10.1021/acs.analchem.2c00471. Epub 2022 May 12. (Abstract)

John B Wojcik, Dylan M Marchione, Simone Sidoli, Anissa Djedid, Amanda Lisby, Jacek Majewski & Benjamin A Garcia (2019). “Epigenomic Reordering Induced by Polycomb Loss Drives Oncogenesis but Leads to Therapeutic Vulnerabilities in Malignant Peripheral Nerve Sheath Tumors” Cancer Res. 2019 Jul 1;79(13):3205-3219. doi: 10.1158/0008-5472.CAN-18-3704. Epub 2019 Mar 21. (Abstract)

Simone Sidoli, Yekaterina Kori, Mariana Lopes, Zuo-Fei Yuan, Hee Jong Kim, Katarzyna Kulej, Kevin A Janssen, Laura M Agosto, Julia Pinheiro Chagas da Cunha, Andrew J Andrews & Benjamin A Garcia (2019). “One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometry” Genome Res. 2019 Jun;29(6):978-987. doi: 10.1101/gr.247353.118. Epub 2019 May 23. (Abstract)

Anumita Saha-Shah, Melody Esmaeili, Simone Sidoli, Hyojeong Hwang, Jing Yang, Peter S Klein & Benjamin A Garcia (2019). “Single Cell Proteomics by Data-Independent Acquisition To Study Embryonic Asymmetry in Xenopus laevis” Anal Chem. 2019 Jul 16;91(14):8891-8899. doi: 10.1021/acs.analchem.9b00327. Epub 2019 Jun 27. (Abstract)

Natarajan V Bhanu, Simone Sidoli, Zuo-Fei Yuan, Rosalynn C Molden & Benjamin A Garcia (2019). “Regulation of proline-directed kinases and the trans-histone code H3K9me3/H4K20me3 during human myogenesis” J Biol Chem. 2019 May 17;294(20):8296-8308. doi: 10.1074/jbc.RA118.004977. Epub 2019 Mar 14. (Abstract)

Kelly R Karch, Mariel Coradin, Levani Zandarashvili, Zhong-Yuan Kan, Morgan Gerace, S Walter Englander, Ben E Black & Benjamin A Garcia (2018). “Hydrogen-Deuterium Exchange Coupled to Top- and Middle-Down Mass Spectrometry Reveals Histone Tail Dynamics before and after Nucleosome Assembly” Structure. 2018 Dec 4;26(12):1651-1663.e3. doi: 10.1016/j.str.2018.08.006. Epub 2018 Oct 4. (Abstract)

Johayra Simithy, Simone Sidoli, Zuo-Fei Yuan, Mariel Coradin, Natarajan V Bhanu, Dylan M Marchione, Brianna J Klein, Gleb A Bazilevsky, Cheryl E McCullough, Robert S Magin, Tatiana G Kutateladze, Nathaniel W Snyder, Ronen Marmorstein & Benjamin A Garcia (2017). “Characterization of histone acylations links chromatin modifications with metabolism” Nat Commun. 2017 Oct 26;8(1):1141. doi: 10.1038/s41467-017-01384-9. (Abstract)

Richard Lauman, Hee Jong Kim, Lindsay K Pino, Alessandro Scacchetti, Yixuan Xie, Faith Robison, Simone Sidoli, Roberto Bonasio & Benjamin A Garcia (2023). “Expanding the Epitranscriptomic RNA Sequencing and Modification Mapping Mass Spectrometry Toolbox with Field Asymmetric Waveform Ion Mobility and Electrochemical Elution Liquid Chromatography” Anal Chem. 2023 Mar 28;95(12):5187-5195. doi: 10.1021/acs.analchem.2c04114. Epub 2023 Mar 14. (Abstract)

Josue Baeza, Barbara E. Coons, Zongtao Lin, John Riley, Mariel Mendoza, William H. Peranteau & Benjamin A Garcia (2024). “In utero pulse injection of isotopic amino acids quantifies protein turnover rates during murine fetal development” Cell Rep Methods. 2024 Feb 26;4(2):100713. doi: 10.1016/j.crmeth.2024.100713. (Abstract)

Matthew W Mahoney, Jonathan Helander, Anoopjit S Kooner, Mariah Norman, Vishnu C Damalanka, Paolo De Bona, Paulina Kasperkiewicz, Wioletta Rut, Marcin Poreba, Maithri M Kashipathy, Kevin P Battaile, Scott Lovell, Anthony J O’Donoghue, Charles S Craik, Marcin Drag & James W Janetka (2024). “Use of protease substrate specificity screening in the rational design of selective protease inhibitors with unnatural amino acids: Application to HGFA, matriptase, and hepsin” Protein Sci. 2024 Aug;33(8):e5110. doi: 10.1002/pro.5110. (Abstract)

Michael J Greenberg (2024). “Super Relaxed or Super Stressed: Modeling Length-Dependent Activation in Cardiac Muscle” Biophys J.2024 Jul 26:S0006-3495(24)00492-2. doi: 10.1016/j.bpj.2024.07.033. (Abstract)

Meng Gao, Long Chen, Jinlong Yang, Shixia Dong, Qing Cao, Zihan Cui, Yanyan Dong, Hongli Liu, Yan Shen, Haiping Yang, Zhenyu Hao, Lei Zhang, Weikai Li, Jian-Ke Tie & Guomin Shen (2024). “Multimodal mechanisms of pathogenic variants in the signal peptide of FIX leading to hemophilia B” Blood Adv.2024 Aug 13;8(15):3893-3905. doi: 10.1182/bloodadvances.2023012432. (Abstract)

Jiyeon Lee, Julie M Dimitry, Jong Hee Song, Minsoo Son, Patrick W Sheehan, Melvin W King, G Travis Tabor, Young Ah Goo, Mitchell A Lazar, Leonard Petrucelli, Erik S Musiek (2023). “Microglial REV-ERBα regulates inflammation and lipid droplet formation to drive tauopathy in male mice” Nat Commun. 2023 Aug 25;14(1):5197. doi: 10.1038/s41467-023-40927-1. (Abstract)

Abhay K Singh, Calvin D Lewis, Cristian A W V Boas, Philipp Diebolder, Prashant N Jethva, Aaron Rhee, Jong Hee Song, Young Ah Goo, Shunqian Li, Michael L Nickels, Yongjian Liu, Buck E Rogers, Vaishali Kapoor & Dennis E Hallahan (2024). “Development of a [89Zr]Zr-labeled Human Antibody using a Novel Phage-displayed Human scFv Library” Clin Cancer Res. 2024 Apr 1;30(7):1293-1306. doi: 10.1158/1078-0432.CCR-23-3647. (Abstract)

Tusar Giri, Susan E Maloney, Saswat Giri, Young Ah Goo, Jong Hee Song, Minsoo Son, Eric Tycksen, Sara B Conyers, Annie Bice, Xia Ge, Joel R Garbow, James D Quirk, Adam Q Bauer & Arvind Palanisamy (2024). “Oxytocin-induced birth causes sex-specific behavioral and brain connectivity changes in developing rat offspring” iScience. 2024 Jan 22;27(2):108960. doi: 10.1016/j.isci.2024.108960. eCollection 2024 Feb 16. (Abstract)

Meaghan S Jankowski, Daniel Griffith, Divya G Shastry, Jacqueline F Pelham, Garrett M Ginell, Joshua Thomas, Pankaj Karande, Alex S Holehouse & Jennifer M Hurley (2024). “Disordered clock protein interactions and charge blocks turn an hourglass into a persistent circadian oscillator” Nat Communn. 2024 Apr 25;15(1):3523. doi: 10.1038/s41467-024-47761-z. (Abstract)

Zongru Li, Qionghua Shen, Emery T Usher, Andrew P Anderson, Manuel Iburg, Richard Lin, Brandon Zimmer, Matthew D Meyer, Alex S Holehouse, Lingchong You, Ashutosh Chilkoti, Yifan Dai & George J Lu (2024). “Phase transition of GvpU regulates gas vesicle clustering in bacteria” Nat Microbiol. 2024 Apr;9(4):1021-1035. doi: 10.1038/s41564-024-01648-3. Epub 2024 Mar 29. (Abstract)

S Sanchez-Martinez, K Nguyen, S Biswas, V Nicholson, A V Romanyuk, J Ramirez, S Kc, A Akter, C Childs, E K Meese, E T Usher, G M Ginell, F Yu, E Gollub, M Malferrari, F Francia, G Venturoli, E W Martin, F Caporaletti, G Giubertoni, S Woutersen, S Sukenik, D N Woolfson, A S Holehouse & T C Boothby (2024). “Labile assembly of a tardigrade protein induces biostasis” Protein Sci.2024 Apr;33(4):e4941. doi: 10.1002/pro.4941. (Abstract)

Jeffrey M Lotthammer, Garrett M Ginell, Daniel Griffith, Ryan J Emenecker & Alex S Holehouse (2024). “Direct prediction of intrinsically disordered protein conformational properties from sequence” Nat Methods. 2024 Mar;21(3):465-476. doi: 10.1038/s41592-023-02159-5. Epub 2024 Jan 31. (Abstract)

Sourav Biswas, Edith Gollub, Feng Yu, Garrett Ginell, Alex Holehouse, Shahar Sukenik & Thomas C Boothby 1 (2024). “Helicity of a tardigrade disordered protein contributes to its protective function during desiccation” Protein Sci. 2024 Feb;33(2):e4872. doi: 10.1002/pro.4872. (Abstract)

David Moses, Karina Guadalupe, Feng Yu, Eduardo Flores, Anthony R Perez, Ralph McAnelly, Nora M Shamoon, Gagandeep Kaur, Estefania Cuevas-Zepeda, Andrea D Merg, Erik W Martin, Alex S Holehouse & Shahar Sukenik (2024). “Structural biases in disordered proteins are prevalent in the cell” Nat Struct Mol Biol. 2024 Feb;31(2):283-292. doi: 10.1038/s41594-023-01148-8. Epub 2024 Jan 4. (Abstract)

Alex S Holehouse & Birthe B Kragelund (2024). “The molecular basis for cellular function of intrinsically disordered protein regions” Nat Rev Mol Cell Biol. 2024 Mar;25(3):187-211. doi: 10.1038/s41580-023-00673-0. Epub 2023 Nov 13. (Abstract)