Department of Biochemistry and Molecular Biophysics

Author: Conrad Weiland

All Publications / Garcia Publications

Single Cell Proteomics by Data-Independent Acquisition To Study Embryonic Asymmetry in Xenopus laevis

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)

All Publications / Garcia Publications

Regulation of proline-directed kinases and the trans-histone code H3K9me3/H4K20me3 during human myogenesis

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)

All Publications / Garcia Publications

Hydrogen-Deuterium Exchange Coupled to Top- and Middle-Down Mass Spectrometry Reveals Histone Tail Dynamics before and after Nucleosome Assembly

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)

All Publications / Garcia Publications

Characterization of histone acylations links chromatin modifications with metabolism

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)

All Publications / Garcia Publications

Expanding the Epitranscriptomic RNA Sequencing and Modification Mapping Mass Spectrometry Toolbox with Field Asymmetric Waveform Ion Mobility and Electrochemical Elution Liquid Chromatography

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)

All Publications / Garcia Publications

In utero pulse injection of isotopic amino acids quantifies protein turnover rates during murine fetal development

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)

All Research / Garcia Lab

Spotlight on Research – Garcia Lab

The Garcia Lab is focused on the development and application of quantitative mass spectrometry (MS) based proteomics and related computation for understanding dynamic protein and proteome post-translational modifications (PTMs). One particular interest is in investigating epigenetic histone PTMs and their role in regulating gene expression in normal and disease physiology. Our lab utilizes high resolution and high-throughput mass spectrometry and further develops improved sample preparation approaches and advanced instrument methods to sequence intact proteins (Top Down MS) and peptides (Bottom Up MS) with high sensitivity. All of these advances have been employed to study several epigenetic targets involved in processes such as cancer, neurological development, viral infection and cellular reprogramming.

Adhikari Lab / All Research

Spotlight on Research – Adhikari Lab

The Adhikari Lab focuses on interrogating RAS oncoprotein signaling networks through the lens of interactomes in cancer, based on an innovative functional proteomics platform combining proximity labeling technology coupled to CRISPR/Cas9 screening. We employ a multifaceted approach by leveraging biochemistry, cell signaling, proteomics, genomics into a range of experimental systems including cell culture, three-dimensional organoids and genetically engineered mouse models. The overarching goal of our laboratory is to elucidate mechanistic underpinnings of reprogramming of oncoprotein signaling networks in space and time to transduce aberrant signaling and promote cancer initiation and tumorigenesis, as a discovery point to reveal new actionable targets that can counter therapeutic resistance.

2024 Events / 2024 News / All Events / All News

2024 BMB SURGE Poster Session

Featured are six individuals chosen for the Department of Biochemistry & Molecular Biophysics’ Summer Undergraduate Group Experience (SURGE) program. Gavin Ghafoori (Dr. Hema Adhikari’s Lab), Alec Garasimowicz (Dr. Andrea Soranno’s Lab), Maxine Akunnakwe and Baika Erdenepurev (Dr. Natalie Niemi’s Lab), and Kylie Villadolid (Dr. Eric Galburt’s Lab) showcase their remarkable lab research during the annual SURGE poster session. These photos encapsulate the culmination of their dedicated 8-week journey of lab experience and study.

You can click here to view photos from the event.

All Publications / Janetka Publications

Use of protease substrate specificity screening in the rational design of selective protease inhibitors with unnatural amino acids: Application to HGFA, matriptase, and hepsin

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)