Preprints
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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