Biological Chemistry seminar: John S. Schneekloth

Thu, 2018-03-22 15:00 - 16:00
Location: 
Carolyn Hoff Lynch Room
Topic: Small molecule tools

Jing Yang Honored by Molecular Sciences Software Institute

Graduate student Jing Yang of the Rappe group has been selected as one of just 11 recipients of this year's Phase-I MolSSI Software Fellowship. Recipients of this fellowship receive six months of support and are eligible for the Phase-II competition later this year. For more information on the program, please click here.

Physical Chemistry Seminar: Dr. Herr vander Zant, (TUDelft)

Mon, 2018-04-23 15:00 - 16:00
Speaker: 
Host:Gai
Location: 
Carol Lynch Lecture Hall Chemistry Complex

Single-molecule quantum transport for electronic component s

 


Physical Chemistry Seminar: Dr. Alexander Sodt (NIH/ NICHD)

Thu, 2018-03-01 13:00 - 14:00
Speaker: 
Host: Baumgart
Location: 
Carol Lynch Lecture Hall Chemistry Complex

Title: Simulating and modeling the molecular mechanisms of biological lipid membrane reshaping

 

Biological Chemistry seminar: Eriks Rozners

Thu, 2018-02-08 15:00
Location: 
Carolyn Hoff Lynch Room
CANCELED---"Amide-modified RNA: Synthesis, structure and RNA interference activity"

CANCELED: Biological Chemistry seminar: Thomas Pologruto, Kepos Capital

Thu, 2018-02-22 15:00 - 16:00
Location: 
Carolyn Hoff Lynch Room
Topic: Biophysics and finance

Ben Garcia joins Chemistry as Secondary Appointment

Professor Benjamin Garcia, Presidential Professor in the Department of Biochemistry and Biophysics in Perelman School of Medicine, received a secondary appointment in Chemistry. Ben received his B.S. in Chemistry from UC Davis, where he was an undergraduate researcher with Prof. Carlito Lebrilla and was first introduced to the field of mass spectrometry. He received his PhD in Chemistry from the University of Virginia under the supervision of Prof. Donald Hunt , and then was an NIH NRSA Postdoctoral Fellow at the University of Illinois with Prof. Neil Kelleher.

Benjamin Garcia

Photo: 
First Name: 
Benjamin
Last Name: 
Garcia
Official Title: 
Presidential Professor of Biochemistry and Biophysics
Contact Information
Office Location: 
9-124 Smilow Center for Translational Research
Email: 
bgarci@mail.med.upenn.edu
Phone: 
215-573-9423
Education: 

B.S. University of California, Davis (2000) Chemistry

Ph.D. University of Virginia (2005) Chemistry

NIH NRSA Postdoctoral Fellow, Institute for Genomic Biology Postdoctoral Fellow, University of Illinois, Urbana-Champaign (2008)

Research Interests: 

The Garcia Lab utilizes high-resolution mass spectrometry to explore cellular signaling, epigenetic mechanisms and chromatin regulation. We are especially interested in understanding how protein and nucleic acid modifications mediate their canonical functions and regulate nuclear processes. Mass spectrometry has become an unparalleled tool in the analysis of these biological molecules and allows us to obtain quantitative information about modifications as well as their co-occurrence. These modifications are critical for nuclear stability and transcription; and dysregulation of these pathways underlie several human diseases such as cancer. Our work aims to reveal the roles of these modifications in the cell cycle, proliferation, differentiation, signaling pathways and metabolism, to consequently help elucidate the mechanisms of various diseases.

Selected Publications: 

Characterization of histone acylations links chromatin modifications with metabolism. 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. Nat Commun. 2017 Oct 26;8(1):1141. doi: 10.1038/s41467-017-01384-9.

 

The nucleosomal surface is the main target of histone ADP-ribosylation in response to DNA damage. Karch KR, Langelier MF, Pascal JM, Garcia BA. Mol Biosyst. 2017 Nov 21;13(12):2660-2671.

 

Proteome-wide acetylation dynamics in human cells. Kori Y, Sidoli S, Yuan ZF, Lund PJ, Zhao X, Garcia BA. Sci Rep. 2017 Aug 31;7(1):10296.

 

Metabolic labeling in middle-down proteomics allows for investigation of the dynamics of the histone code. Sidoli S, Lu C, Coradin M, Wang X, Karch KR, Ruminowicz C, Garcia BA. Epigenetics Chromatin. 2017 Jul 6;10(1):34.

 

Differential quantification of isobaric phosphopeptides using data-independent acquisition mass spectrometry. Sidoli S, Fujiwara R, Kulej K, Garcia BA. Mol Biosyst. 2016 Jul 19;12(8):2385-8.

 

Preferential Phosphorylation on Old Histones during Early Mitosis in Human Cells. Lin S, Yuan ZF, Han Y, Marchione DM, Garcia BA. J Biol Chem. 2016 Jul 15;291(29):15342-57.

 

A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics. Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA. Mol Cell Proteomics. 2016 Jul;15(7):2462-75.

 

Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells. Gonzales-Cope M, Sidoli S, Bhanu NV, Won KJ, Garcia BA. BMC Genomics. 2016 Feb 4;17:95.

 

Bioorthogonal Chemistry for the Isolation and Study of Newly Synthesized Histones and Their Modifications. Arnaudo AM, Link AJ, Garcia BA. ACS Chem Biol. 2016 Mar 18;11(3):782-91.

 

Monitoring Cellular Phosphorylation Signaling Pathways into Chromatin and Down to the Gene Level. Han Y, Yuan ZF, Molden RC, Garcia BA. Mol Cell Proteomics. 2016 Mar;15(3):834-53.

 

Low Resolution Data-Independent Acquisition in an LTQ-Orbitrap Allows for Simplified and Fully Untargeted Analysis of Histone Modifications. Sidoli S, Simithy J, Karch KR, Kulej K, Garcia BA. Anal Chem. 2015 Nov 17;87(22):11448-54.

 

Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH) Analysis for Characterization and Quantification of Histone Post-translational Modifications. Sidoli S, Lin S, Xiong L, Bhanu NV, Karch KR, Johansen E, Hunter C, Mollah S, Garcia BA. Mol Cell Proteomics. 2015 Sep;14(9):2420-8.

 

Characterization of histone post-translational modifications during virus infection using mass spectrometry-based proteomics. Kulej K, Avgousti DC, Weitzman MD, Garcia BA. Methods. 2015 Nov 15;90:8-20.

Special Biological Chemistry seminar: Adrian Ferre-D'Amare, NIH

Thu, 2018-03-08 15:00 - 16:00
Speaker: 
Host Rhoades
Location: 
Carolyn Hoff Lynch Room

RNA mimics of fluorescent proteins: new tools for the in vivo study of noncoding RNAs

 

Adrian R. Ferré-D'Amaré Laboratory of RNA Biophysics and Cellular Physiology National Heart, Lung and Blood Institute Bethesda, MD 20892-8012

 

Matthew Loh

Photo: 
First Name: 
Matthew
Last Name: 
Loh
Official Title: 
Grants Manager
Contact Information
Office Location: 
Room 132, 1973 Building
Email: 
lohm@sas.upenn.edu
Phone: 
215-898-2371

Department of Chemistry

231 S. 34 Street, Philadelphia, PA 19104-6323

215.898.8317 voice | 215.573.2112 fax | web@chem.upenn.edu

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