Preprints
A Scalable, Multiplexed Assay for Decoding Receptor-Ligand Interactions
Eric M Jones, Rishi Jajoo, Daniel Cancilla, Nathan B Lubock, Jeff Wang, Megan Satyadi, Rocky Cheung, Claire de March, Hiroaki Matsunami, Sriram Kosuri
bioRxiv 358739; doi: 10.1101/358739
Many rare genetic variants have unrecognized large-effect disruptions to exon recognition
bioRxiv 199927; doi: 10.1101/199927
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, Eric M. Jones, Daniel B. Goodman, Sriram Kosuri
Cell Sneak Peak
A Scalable, Multiplexed Assay for Decoding Receptor-Ligand Interactions
Eric M Jones, Rishi Jajoo, Daniel Cancilla, Nathan B Lubock, Jeff Wang, Megan Satyadi, Rocky Cheung, Claire de March, Hiroaki Matsunami, Sriram Kosuri
bioRxiv 358739; doi: 10.1101/358739
Many rare genetic variants have unrecognized large-effect disruptions to exon recognition
bioRxiv 199927; doi: 10.1101/199927
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, Eric M. Jones, Daniel B. Goodman, Sriram Kosuri
Cell Sneak Peak
Published
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
Nature Genetics, (2018), doi: 10.1038/s41588-018-0087-y
bioRxiv 147637; doi: 10.1101/147637
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
Biochemistry, (2018); doi: 10.1021/acs.biochem.7b01069
bioRxiv 207332; doi: 10.1101/207332
Multiplexed Gene Synthesis in Emulsions for Exploring Protein Functional Landscapes
Calin Plesa, Angus M. Sidore, Nathan Lubock, Di Zhang, Sriram Kosuri
Science (2018) doi: 10.1126/science.aao5167 Free PDF HTML
bioRxiv 163550; doi: 10.1101/163550
A systematic comparison of error correction enzymes by next-generation sequencing
Nathan B Lubock, Di Zhang, George M Church, Sriram Kosuri
Nucleic Acids Research, (2017) doi: 10.1093/nar/gkx691
bioRxiv 100685; doi: 10.1101/100685
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
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
Nature Genetics, (2018), doi: 10.1038/s41588-018-0087-y
bioRxiv 147637; doi: 10.1101/147637
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
Biochemistry, (2018); doi: 10.1021/acs.biochem.7b01069
bioRxiv 207332; doi: 10.1101/207332
Multiplexed Gene Synthesis in Emulsions for Exploring Protein Functional Landscapes
Calin Plesa, Angus M. Sidore, Nathan Lubock, Di Zhang, Sriram Kosuri
Science (2018) doi: 10.1126/science.aao5167 Free PDF HTML
bioRxiv 163550; doi: 10.1101/163550
A systematic comparison of error correction enzymes by next-generation sequencing
Nathan B Lubock, Di Zhang, George M Church, Sriram Kosuri
Nucleic Acids Research, (2017) doi: 10.1093/nar/gkx691
bioRxiv 100685; doi: 10.1101/100685
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