Preprints
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
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
DropSynth 2.0: high-fidelity multiplexed gene synthesis in emulsions
Angus M Sidore*, Calin Plesa*, Joyce A Samson, Sriram Kosuri
bioRxiv 740977; doi: 10.1101/740977
Multiplexed dissection of a model human transcription factor binding site architecture
Jessica E Davis, Kimberly D Insigne, Eric M Jones, Quinn Hastings, Sriram Kosuri
bioRxiv 625434; doi: 10.1101/625434
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
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
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
DropSynth 2.0: high-fidelity multiplexed gene synthesis in emulsions
Angus M Sidore*, Calin Plesa*, Joyce A Samson, Sriram Kosuri
bioRxiv 740977; doi: 10.1101/740977
Multiplexed dissection of a model human transcription factor binding site architecture
Jessica E Davis, Kimberly D Insigne, Eric M Jones, Quinn Hastings, Sriram Kosuri
bioRxiv 625434; doi: 10.1101/625434
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
Published
A Scalable, Multiplexed Assay for Decoding GPCR-Ligand Interactions with RNA Sequencing
Eric M Jones*, Rishi Jajoo*, Daniel Cancilla, Nathan B Lubock, Jeffrey Wang, Megan Satyadi, Rocky Cheung, Claire de March, Joshua S Bloom, Hiroaki Matsunami, Sriram Kosuri
bioRxiv 358739; doi: 10.1101/358739
Cell Systems (2019), doi: 10.1016/j.cels.2019.02.009
A Multiplexed Assay for Exon Recognition Reveals That an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Disruptions to Splicing
Rocky Cheung*, Kimberly D. Insigne*, David Yao, Christina P. Burghard, Jeffrey Wang, Yun-hua E. Hsiao, Eric M. Jones, Daniel B. Goodman, Xinshu Xiao, Sriram Kosuri
bioRxiv 199927; doi: 10.1101/199927
Molecular Cell (2019), doi: 10.1016/j.molcel.2018.10.037
Highly parallel genome variant engineering with CRISPR/Cas9 in eukaryotic cells
Meru J. Sadhu*, Joshua S. Bloom*, Laura Day, Jake J. Siegel, Sriram Kosuri, Leonid Kruglyak
bioRxiv 147637; doi: 10.1101/147637
Nature Genetics, (2018), doi: 10.1038/s41588-018-0087-y
Metagenomic mining of regulatory elements enables programmable species-selective gene expression
Nathan I. Johns, Antonio L.C. Gomes, Sung Sun Yim, Anthony Yang, Tomasz Blazejewski, Christopher S. Smillie, Mark B. Smith, Eric J. Alm, Sriram Kosuri, Harris H Wang
Nature Methods, (2018) doi: 10.1038/nmeth.4633
Systematic Dissection of Sequence Elements Controlling σ70 Promoters Using a Genomically-Encoded Multiplexed Reporter Assay in E. coli
Guillaume Urtecho, Arielle D. Tripp, Kimberly Insigne, Hwangbeom Kim, Sriram Kosuri
bioRxiv 207332; doi: 10.1101/207332
Biochemistry, (2018); doi: 10.1021/acs.biochem.7b01069
Multiplexed Gene Synthesis in Emulsions for Exploring Protein Functional Landscapes
Calin Plesa*, Angus M. Sidore*, Nathan Lubock, Di Zhang, Sriram Kosuri
bioRxiv 163550; doi: 10.1101/163550
Science (2018) doi: 10.1126/science.aao5167 Free PDF HTML
A systematic comparison of error correction enzymes by next-generation sequencing
Nathan B Lubock, Di Zhang, George M Church, Sriram Kosuri
bioRxiv 100685; doi: 10.1101/100685
Nucleic Acids Research, (2017) doi: 10.1093/nar/gkx691
Genetic Engineering: Lassoing Genomic Libraries (Perspective)
Nathan B. Lubock & Sriram Kosuri
Nature Biomedical Engineering, (2017) doi: 10.1038/s41551-017-0098
What Have the Principles of Engineering Taught Us about Biological Systems? (Perspective)
Sriram Kosuri, et al.
Cell Systems, (2016) doi: 10.1016/j.cels.2016.01.008
Engineering an allosteric transcription factor to respond to new ligands
Noah D Taylor, Alexander S Garruss, Rocco Moretti, Sum Chan, Mark A Arbing, Duilio Cascio, Jameson K Rogers, Farren J Isaacs, Sriram Kosuri, David Baker, Stanley Fields, George M Church and Srivatsan Raman
Nature Methods, (2016) doi:10.1038/nmeth.3696
Direct Mutagenesis of Thousands of Genomic Targets Using Microarray-Derived Oligonucleotides
Mads T Bonde*, Sriram Kosuri*, Hans J Genee, Kira Sarup-Lytzen, George M Church, Morten OA Sommer, and Harris H Wang
ACS Synthetic Biology, (2014) doi:10.1021/sb5001565
Large-scale de novo DNA synthesis: technologies and applications (Review)
Sriram Kosuri and George M Church
Nature Methods, (2014) doi:10.1038/nmeth.2918
Causes and effects of N-terminal codon bias in bacterial genes
Daniel B Goodman, George M Church, Sriram Kosuri
Science, (2013) doi:10.1126/science.1241934 Free: PDF HTML
Probing the Limits of Genetic Recoding in Essential Genes
Marc Lajoie*, Sriram Kosuri*, Joshua Mosberg, Christopher Gregg, Di Zhang, George M Church
Science, (2013) doi:10.1126/science.1241460
Composability of regulatory sequences controlling transcription and translation in E. coli
Sriram Kosuri*, Daniel B Goodman*, Guillaume Cambray, Vivek K Mutalik, Yuan Gao, Adam P. Arkin, Drew Endy, George M Church
PNAS, (2013) doi:10.1073/pnas.1301301110
CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering
Prashant Mali, John Aach, P Benjamin Stranges, Kevin M Esvelt, Mark Moosburner, Sriram Kosuri, Luhan Yang, George M Church
Nature Biotechnology, (2013) doi:10.1038/nbt.2675
Next-Generation Digital Information Storage in DNA
George M. Church, Yuan Gao, Sriram Kosuri
Science (2012) doi:10.1126/science.1226355 Free: PDF HTML
When It Rains, It Pores (Perspective)
Sriram Kosuri & A. Michael Sismour
ACS Synthetic Biology (2012) doi:10.1021/sb300015f
Gene Assembly from Chip-Synthesized Oligonucleotides
Nikolai Eroshenko*, Sriram Kosuri*, Adam H Marblestone, Nicholas Conway, & George Church
Current Protocols in Chemical Biology (2012) doi:10.1002/9780470559277.ch110190
Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription
Feng Zhang*, Le Cong*, Simona Lodato, Sriram Kosuri, George Church & Paola Arlotta
Nature Biotechnology (2011) doi:10.1038/nbt.1775
Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips
Sriram Kosuri*, Nikolai Eroshenko*, Emily LeProust, Michael Super, Jeffrey Way, Jin Billy Li & George Church
Nature Biotechnology (2010) 28:1295 doi:10.1038/nbt.1716
TABASCO: A single molecule, base-pair resolved gene expression simulator
Sriram Kosuri, Jason Kelly, & Drew Endy
BMC Bioinformatics 2007, 8:480 doi:10.1186/1471-2105-8-480
Refactoring bacteriophage T7
Leon Y. Chan*, Sriram Kosuri* & Drew Endy
Molecular Systems Biology 13 September 2005 doi:10.1038/msb4100025
A Scalable, Multiplexed Assay for Decoding GPCR-Ligand Interactions with RNA Sequencing
Eric M Jones*, Rishi Jajoo*, Daniel Cancilla, Nathan B Lubock, Jeffrey Wang, Megan Satyadi, Rocky Cheung, Claire de March, Joshua S Bloom, Hiroaki Matsunami, Sriram Kosuri
bioRxiv 358739; doi: 10.1101/358739
Cell Systems (2019), doi: 10.1016/j.cels.2019.02.009
A Multiplexed Assay for Exon Recognition Reveals That an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Disruptions to Splicing
Rocky Cheung*, Kimberly D. Insigne*, David Yao, Christina P. Burghard, Jeffrey Wang, Yun-hua E. Hsiao, Eric M. Jones, Daniel B. Goodman, Xinshu Xiao, Sriram Kosuri
bioRxiv 199927; doi: 10.1101/199927
Molecular Cell (2019), doi: 10.1016/j.molcel.2018.10.037
Highly parallel genome variant engineering with CRISPR/Cas9 in eukaryotic cells
Meru J. Sadhu*, Joshua S. Bloom*, Laura Day, Jake J. Siegel, Sriram Kosuri, Leonid Kruglyak
bioRxiv 147637; doi: 10.1101/147637
Nature Genetics, (2018), doi: 10.1038/s41588-018-0087-y
Metagenomic mining of regulatory elements enables programmable species-selective gene expression
Nathan I. Johns, Antonio L.C. Gomes, Sung Sun Yim, Anthony Yang, Tomasz Blazejewski, Christopher S. Smillie, Mark B. Smith, Eric J. Alm, Sriram Kosuri, Harris H Wang
Nature Methods, (2018) doi: 10.1038/nmeth.4633
Systematic Dissection of Sequence Elements Controlling σ70 Promoters Using a Genomically-Encoded Multiplexed Reporter Assay in E. coli
Guillaume Urtecho, Arielle D. Tripp, Kimberly Insigne, Hwangbeom Kim, Sriram Kosuri
bioRxiv 207332; doi: 10.1101/207332
Biochemistry, (2018); doi: 10.1021/acs.biochem.7b01069
Multiplexed Gene Synthesis in Emulsions for Exploring Protein Functional Landscapes
Calin Plesa*, Angus M. Sidore*, Nathan Lubock, Di Zhang, Sriram Kosuri
bioRxiv 163550; doi: 10.1101/163550
Science (2018) doi: 10.1126/science.aao5167 Free PDF HTML
A systematic comparison of error correction enzymes by next-generation sequencing
Nathan B Lubock, Di Zhang, George M Church, Sriram Kosuri
bioRxiv 100685; doi: 10.1101/100685
Nucleic Acids Research, (2017) doi: 10.1093/nar/gkx691
Genetic Engineering: Lassoing Genomic Libraries (Perspective)
Nathan B. Lubock & Sriram Kosuri
Nature Biomedical Engineering, (2017) doi: 10.1038/s41551-017-0098
What Have the Principles of Engineering Taught Us about Biological Systems? (Perspective)
Sriram Kosuri, et al.
Cell Systems, (2016) doi: 10.1016/j.cels.2016.01.008
Engineering an allosteric transcription factor to respond to new ligands
Noah D Taylor, Alexander S Garruss, Rocco Moretti, Sum Chan, Mark A Arbing, Duilio Cascio, Jameson K Rogers, Farren J Isaacs, Sriram Kosuri, David Baker, Stanley Fields, George M Church and Srivatsan Raman
Nature Methods, (2016) doi:10.1038/nmeth.3696
Direct Mutagenesis of Thousands of Genomic Targets Using Microarray-Derived Oligonucleotides
Mads T Bonde*, Sriram Kosuri*, Hans J Genee, Kira Sarup-Lytzen, George M Church, Morten OA Sommer, and Harris H Wang
ACS Synthetic Biology, (2014) doi:10.1021/sb5001565
Large-scale de novo DNA synthesis: technologies and applications (Review)
Sriram Kosuri and George M Church
Nature Methods, (2014) doi:10.1038/nmeth.2918
Causes and effects of N-terminal codon bias in bacterial genes
Daniel B Goodman, George M Church, Sriram Kosuri
Science, (2013) doi:10.1126/science.1241934 Free: PDF HTML
Probing the Limits of Genetic Recoding in Essential Genes
Marc Lajoie*, Sriram Kosuri*, Joshua Mosberg, Christopher Gregg, Di Zhang, George M Church
Science, (2013) doi:10.1126/science.1241460
Composability of regulatory sequences controlling transcription and translation in E. coli
Sriram Kosuri*, Daniel B Goodman*, Guillaume Cambray, Vivek K Mutalik, Yuan Gao, Adam P. Arkin, Drew Endy, George M Church
PNAS, (2013) doi:10.1073/pnas.1301301110
CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering
Prashant Mali, John Aach, P Benjamin Stranges, Kevin M Esvelt, Mark Moosburner, Sriram Kosuri, Luhan Yang, George M Church
Nature Biotechnology, (2013) doi:10.1038/nbt.2675
Next-Generation Digital Information Storage in DNA
George M. Church, Yuan Gao, Sriram Kosuri
Science (2012) doi:10.1126/science.1226355 Free: PDF HTML
When It Rains, It Pores (Perspective)
Sriram Kosuri & A. Michael Sismour
ACS Synthetic Biology (2012) doi:10.1021/sb300015f
Gene Assembly from Chip-Synthesized Oligonucleotides
Nikolai Eroshenko*, Sriram Kosuri*, Adam H Marblestone, Nicholas Conway, & George Church
Current Protocols in Chemical Biology (2012) doi:10.1002/9780470559277.ch110190
Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription
Feng Zhang*, Le Cong*, Simona Lodato, Sriram Kosuri, George Church & Paola Arlotta
Nature Biotechnology (2011) doi:10.1038/nbt.1775
Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips
Sriram Kosuri*, Nikolai Eroshenko*, Emily LeProust, Michael Super, Jeffrey Way, Jin Billy Li & George Church
Nature Biotechnology (2010) 28:1295 doi:10.1038/nbt.1716
TABASCO: A single molecule, base-pair resolved gene expression simulator
Sriram Kosuri, Jason Kelly, & Drew Endy
BMC Bioinformatics 2007, 8:480 doi:10.1186/1471-2105-8-480
Refactoring bacteriophage T7
Leon Y. Chan*, Sriram Kosuri* & Drew Endy
Molecular Systems Biology 13 September 2005 doi:10.1038/msb4100025