Gabriel Pratt

Post-Doctoral Fellow Alumni
Bioinformatics and Systems Biology
NSF Fellow
gpratt at ucsd.edu

Degrees

B.S Computer Science, University of Washington 2011

Summary

Gabriel Pratt received his B.S. in [Computer Science] (http://www.cs.washington.edu/) from the University of Washington in 2011. During his undergraduate career he had the opportunity to learn bioinformatcs in the labs of Chuck Murry, Martin Tompa and John Stamatoyannopoulos. His projects focused on microarray and high-throughput sequence analysis with a specific focus on epigenetic regulation of cardiovascular differentiation. As a summer intern at Microsoft he learned software engineering and techniques to analyze big data. Additionally he spent a year in the in Japan working with Dr. Yasunori Aizawa at Tokyo Institute of Technology studying functional upstream open reading frames. As a graduate student Gabriel is broadly interested in understanding protein-RNA interactions. Specifically understanding how combinations of RNA binding proteins influence splicing and how that regulates RNA translation and stalling. Gabriel is funded by the NSF GRFP.

Publications

  • Van Nostrand EL, Pratt GA, Yee BA, Wheeler E, Blue SM, Mueller J, Park SS, Garcia KE, Gelboin-Burkhart C, Nguyen TB, Rabano I, Stanton R, Sundararaman B, Wang R, Fu X-D, Graveley BR, Yeo GW. Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins. Genome Biology, 2020.

  • Quinones-Valdez G, Tran SS, Jun HI, Bahn JH, Yang EW, Zhan L, Brümmer A, Wei X, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, Xiao X.Regulation of RNA editing by RNA-binding proteins in human cells. Commun Biol. 2019

  • Tran SS, Jun HI, Bahn JH, Azghadi A, Ramaswami G, Van Nostrand EL, Nguyen TB, Hsiao YE, Lee C, Pratt GA, Martínez-Cerdeño V, Hagerman RJ, Yeo GW, Geschwind DH, Xiao X. Widespread RNA editing dysregulation in brains from autistic individuals. Nat Neurosci. 2018

  • Van Nostrand EL, Shishkin AA, Pratt GA, Nguyen TB, Yeo GW. Variation in single-nucleotide sensitivity of eCLIP derived from reverse transcription conditions. Methods, 2017.

  • Van Nostrand EL , Nguyen TB , Gelboin-Burkhart C, Wang R, Blue SM, Pratt GA, Louie AL, Yeo GW. Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP). Methods Mol Biol. 2017 *Co-authorship.

  • Fernando J Martinez, Gabriel A Pratt, Eric L Van Nostrand, Ranjan Batra, Stephanie C Huelga, Katannya Kapeli, Peter Freese, Seung J Chun, Karen Ling, Chelsea Gelboin-Burkhart, Layla Fijany, Harrison C Wang, Julia K Nussbacher, Sara M Broski, Hong Joo Kim, Rea Lardelli, Balaji Sundararaman, John P Donohue, Ashkan Javaherian, Jens Lykke-Andersen, Steven Finkbeiner, C Frank Bennett, Manuel Ares, Christopher B Burge, J Paul Taylor, Frank Rigo, Gene W Yeo. Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System. Neuron, 2016

  • Kristopher W Brannan, Wenhao Jin, Stephanie C Huelga, Charles AS Banks, Joshua M Gilmore, Laurence Florens, Michael P Washburn, Eric L Van Nostrand, Gabriel A Pratt, Marie K Schwinn, Danette L Daniels, Gene W Yeo. SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes. Molecular Cell, 2016

  • Katannya Kapeli§, Gabriel A. Pratt§, Anthony Q. Vu, Kasey R. Hutt, Fernando J. Martinez, Balaji Sundararaman, Ranjan Batra, Peter Freese, Nicole J. Lambert, Stephanie C. Huelga, Seung J. Chun, Tiffany Y. Liang, Jeremy Chang, John P. Donohue, Lily Shiue, Jiayu Zhang, Haining Zhu, Franca Cambi, Edward Kasarskis, Shawn Hoon, Manuel Ares Jr., Christopher B. Burge, John Ravits, Frank Rigo, Gene W. Yeo. Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses. NATURE COMMUNICATIONS, 2016

  • Stefan Rentas, Nicholas T Holzapfel, Muluken S Belew, Gabriel A Pratt, Veronique Voisin, Brian T Wilhelm, Gary D Bader, Gene W Yeo, Kristin J Hope. Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells. Nature, 2016

  • Anne E Conway, Eric L Van Nostrand, Gabriel A Pratt, Stefan Aigner, Melissa L Wilbert, Balaji Sundararaman, Peter Freese, Nicole J Lambert, Shashank Sathe, Tiffany Y Liang, Anthony Essex, Severine Landais, Christopher B Burge, D Leanne Jones, Gene W Yeo. Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival. Cell Reports, 2016

  • Eric L Van Nostrand§, Gabriel A Pratt §, Alexander A Shishkin, Chelsea Gelboin-Burkhart, Mark Y Fang, Balaji Sundararaman, Steven M Blue, Thai B Nguyen, Christine Surka, Keri Elkins, Rebecca Stanton, Frank Rigo, Mitchell Guttman, Gene W Yeo. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nature Methods, 2016

  • Balaji Sundararaman, Lijun Zhan, Steven M Blue, Rebecca Stanton, Keri Elkins, Sara Olson, Xintao Wei, Eric L Van Nostrand, Gabriel A Pratt, Stephanie C Huelga, Brendan M Smalec, Xiaofeng Wang, Eurie L Hong, Jean M Davidson, Eric Lécuyer, Brenton R Graveley, Gene W Yeo. Resources for the comprehensive discovery of functional RNA elements. Molecular Cell, 2016

  • T. Hung, G. A. Pratt, B. Sundararaman, M. J. Townsend, C. Chaivorapol, T. Bhangale, R. R. Graham, W. Ortmann, L. A. Criswell, G. W. Yeo, T. W. Behrens. The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression. Science, 2015

  • Suzanne R. Lee, Gabriel Pratt, Fernando Martinez, Gene W. Yeo, Jens Lykke-Andersen. Target discrimination in nonsense-mediated mRNA decay requires the ATPase activity of Upf1. Molecular Cell, 2015

  • Singh G, Gabriel Pratt, Yeo GW, Moore MJ. The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion.Annual Review of Biochemistry, 2015

  • Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. Lovci MT, Ghanem D, Marr H, Arnold J, Gee S, Parra M, Liang TY, Stark TJ, Gehman LT, Hoon S, Massirer KB, Gabriel Pratt, Black DL, Gray JW, Conboy JG, Yeo GW. Nature Structural and Molecular Biology, 2013

  • Sharon L. Paige, Sean Thomas, Cristi Stoick-Cooper, Hao Wang, Richard Sandstrom4, Lisa Maves, Lil Pabon, Hans Reinecke, Gabriel Pratt, Gordon Keller, Randall T. Moon, John Stamatoyannopoulos, and Charles E. Murry. A Temporal Chromatin Signature in Human Embryonic Stem Cells Identifies Novel Regulators of Cardiovascular Development. Cell, 2013

  • Golob, J. L., Kumar, R. M., Guenther, M. G., Pabon, L. M., Pratt, G. A., Loring, J. F., Laurent, L. C., Young, R. A., and Murry, C. E. Evidence That Gene Activation and Silencing during Stem Cell Differentiation Requires a Transcriptionally Paused Intermediate State. PLoS ONE, 2011