| Website | Home URL |
| Division | Biochemistry |
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| skosuri@chem.ucla.edu | |
| Office | 456 Boyer Hall |
| Office Phone | (310) 825-8931 |
Biography
Professor Sriram Kosuri is an Associate Professor at UCLA in the Chemistry and Biochemistry Department. He was previously a member of the Advanced Technology Team in the Synthetic Biology Platform at the Wyss Institute and a postdoc in George Church‘s lab in the Department of Genetics at Harvard Medical School and the Wyss Institute from 2009-2011. From 2007-2009, he was the first employee of a biofuel startup called Joule Unlimited. Kosuri got his ScD in Biological Engineering at MIT in Drew Endy‘s lab and worked on understanding the development of a simple virus (T7) that infects E. coli.
Research Interests
Our laboratory develops methods to vastly increase our ability to empirically explore relationships between DNA sequence and biological function. We do this by developing and combining three related technologies: DNA synthesis, DNA sequencing, and genome engineering. First, we develop methods to build thousands to millions of designed DNA sequences using low-cost DNA microarrays. Second, we develop new ways to link the measurement of some biological function to an output that can be measured in multiplex using next-generation sequencing. Combining the two lets build large numbers of designs/hypothesis regarding a biological function, and testing them all at once in a multiplexed assay. Finally, using new genomic engineering technologies, we can do these large-scale synthesis/sequencing experiments in a wide-variety of cell types and organisms.
Besides this central theme, each of the projects is otherwise seemingly different. We work on organisms such as bacteria, yeast, and human cell lines, and on biological problems that span population genetics, evolution, gene regulation, protein structure-function, and neuroscience. Please see the members page to see what individuals are working on, or the publications page for our latest manuscripts.
Representative Publications
Below is the list of the most recent publications. For the full list, please visit here.
Preprints
Rapid cost-effective viral genome sequencing by V-seq
Longhua Guo, James Boocock, Jacob Tome, Sukantha Chandrasekaran, Evann E. Hilt, Yi Zhang, Laila Sathe, Xinmin Li, Chongyuan Luo, Sriram Kosuri, Jay Shendure, Valerie A. Arboleda, Jonathan Flint, Eleazar Eskin, Omai B. Garner, Shangxin Yang, Joshua S Bloom, Leonid Kruglyak, Yi Yin
bioRxiv 2020.08.15.252510; doi: 10.1101/2020.08.15.252510
Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing
Joshua S. Bloom, Eric M. Jones, Molly Gasperini, Nathan B. Lubock, Laila Sathe, Chetan Munugala, A. Sina Booeshaghi, Oliver F. Brandenberg, Longhua Guo, Scott W. Simpkins, Isabella Lin, Nathan LaPierre, Duke Hong, Yi Zhang, Gabriel Oland, Bianca Judy Choe, Sukantha Chandrasekaran, Evann E. Hilt, Manish J. Butte, Robert Damoiseaux, Aaron R. Cooper, Yi Yin, Lior Pachter, Omai B. Garner, Jonathan Flint, Eleazar Eskin, Chongyuan Luo, Sriram Kosuri, Leonid Kruglyak, Valerie A. Arboleda
medRxiv 2020.08.04.20167874; doi: 10.1101/2020.08.04.20167874
Preliminary support for a “dry swab, extraction free” protocol for SARS-CoV-2 testing via RT-qPCR
Sanjay Srivatsan, Peter D. Han, Katrina van Raay, Caitlin R. Wolf, Denise J. McCulloch, Ashley E. Kim, Elisabeth Brandstetter, Beth Martin, Jase Gehring, Wei Chen, Seattle Flu Study Investigators, Sriram Kosuri, Eric Q. Konnick, Christina M. Lockwood, Mark J. Rieder, Deborah A. Nickerson, Helen Y. Chu, Jay Shendure, Lea M. Starita
bioRxiv 2020.04.22.056283; doi: 10.1101/2020.04.22.056283
Genome-wide Functional Characterization of Escherichia coli Promoters and Regulatory Elements Responsible for their Function
Guillaume Urtecho*, Kimberly D. Insigne*, Arielle D. Tripp, Marcia Brinck, Nathan B. Lubock, Hwangbeom Kim, Tracey Chan, Sriram Kosuri
bioRxiv 2020.01.04.894907; doi: 10.1101/2020.01.04.894907
Published
Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems
Timothy C. Yu*, Winnie L. Liu*, Marcia Brinck, Jessica E. Davis, Jeremy Shek, Grace Bower, Tal Einav, Kimberly D. Insigne, Rob Phillips, Sriram Kosuri, Guillaume Urtecho
bioRxiv 2020.01.31.928689; doi: 10.1101/2020.01.31.928689
Nature Communications (2021) doi: 10.1038/s41467-020-20094-3
Fast and accurate diagnostics from highly multiplexed sequencing assays
A. Sina Booeshaghi, Nathan B. Lubock, Aaron R. Cooper, Scott W. Simpkins, Joshua S. Bloom, Jase Gehring, Laura Luebbert, Sriram Kosuri, Lior Pachter
medRxiv 2020.05.13.20100131; doi: 10.1101/2020.05.13.20100131
Scientific Reports (2020) doi: 10.1038/s41598-020-78942-7
Structural and Functional Characterization of G Protein-Coupled Receptors with Deep Mutational Scanning
Eric M Jones*, Nathan B Lubock*, AJ Venkatakrishnan, Jeffrey Wang, Alex M Tseng, Joseph M Paggi, Naomi R Latorraca, Daniel Cancilla, Megan Satyadi, Jessica Davis, M Madan Babu, Ron O Dror, Sriram Kosuri
bioRxiv 623108; doi: 10.1101/623108
ELife (2020) doi: 10.7554/eLife.54895
Massively parallel identification of causal variants underlying gene expression differences in a yeast cross
Kaushik Renganaath*, Rocky Cheung*, Laura Day, Sriram Kosuri, Leonid Kruglyak, Frank W Albert
bioRxiv 2020.08.31.276337; doi: 10.1101/2020.08.31.276337
Elife (2020) doi: 10.7554/eLife.62669
Common genetic risk variants identified in the SPARK cohort support DDHD2 as a candidate risk gene for autism
Nana Matoba, Dan Liang, Huaigu Sun, Nil Aygün, Jessica C. McAfee, Jessica E. Davis, Laura M. Raffield, Huijun Qian, Joseph Piven, Yun Li, Sriram Kosuri, Hyejung Won, Jason L. Stein
medRxiv 2020.01.13.20017319; doi: 10.1101/2020.01.13.20017319
Translational Psychiatry (2020), doi: 10.1038/s41398-020-00953-9
Dissection of c-AMP Response Element Architecture by Using Genomic and Episomal Massively Parallel Reporter Assays
Jessica E Davis, Kimberly D Insigne, Eric M Jones, Quinn Hastings, W. Clifford Boldrige, Sriram Kosuri
bioRxiv 625434; doi: 10.1101/625434
Cell Systems (2020), doi: 10.1016/j.cels.2020.05.011
DropSynth 2.0: high-fidelity multiplexed gene synthesis in emulsions
Angus M Sidore*, Calin Plesa*, Joyce A Samson, Nathan B Lubock, Sriram Kosuri
bioRxiv 740977; doi: 10.1101/740977
Nucleic Acids Research (2020), doi: 10.1093/nar/gkaa600