Multiplexed gene synthesis in emulsions for exploring protein functional landscapes

Plesa, Calin; Sidore, Angus M.; Lubock, Nathan B.; Zhang, Di; Kosuri, Sriram

doi:10.1126/science.aao5167

Title: Multiplexed gene synthesis in emulsions for exploring protein functional landscapes

Authors:

;

; Zhang, Di;

Publication Date:: Thu Jan 04 00:00:00 EST 2018

Sponsoring Org.:: USDOE

OSTI Identifier:: 1455110

Grant/Contract Number:: FC02-02ER63421

Resource Type:: Published Article

Journal Name:: Science

Additional Journal Information:: Journal Name: Science Journal Volume: 359 Journal Issue: 6373; Journal ID: ISSN 0036-8075

Publisher:: American Association for the Advancement of Science (AAAS)

Country of Publication:: United States

Language:: English

Citation Formats


                    Plesa, Calin, Sidore, Angus M., Lubock, Nathan B., Zhang, Di, and Kosuri, Sriram. Multiplexed gene synthesis in emulsions for exploring protein functional landscapes.  United States: N. p., 2018. 
Web.  doi:10.1126/science.aao5167.

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                    Plesa, Calin, Sidore, Angus M., Lubock, Nathan B., Zhang, Di, & Kosuri, Sriram. Multiplexed gene synthesis in emulsions for exploring protein functional landscapes.  United States.  https://doi.org/10.1126/science.aao5167

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                    Plesa, Calin, Sidore, Angus M., Lubock, Nathan B., Zhang, Di, and Kosuri, Sriram. Thu .  
"Multiplexed gene synthesis in emulsions for exploring protein functional landscapes".  United States.  https://doi.org/10.1126/science.aao5167.

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@article{osti_1455110,

  title        = {Multiplexed gene synthesis in emulsions for exploring protein functional landscapes},

  author       = {Plesa, Calin and Sidore, Angus M. and Lubock, Nathan B. and Zhang, Di and Kosuri, Sriram},

  abstractNote = {},

  doi          = {10.1126/science.aao5167},

  journal      = {Science},

  number       = 6373,

  volume       = 359,

  place        = {United States},

  year         = {Thu Jan 04 00:00:00 EST 2018},

  month        = {Thu Jan 04 00:00:00 EST 2018}

}

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Title: Multiplexed gene synthesis in emulsions for exploring protein functional landscapes

Citation Formats

Engineering and characterization of a superfolder green fluorescent protein journal, December 2005

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies journal, January 2014

Large-scale de novo DNA synthesis: technologies and applications journal, April 2014

BLAT---The BLAST-Like Alignment Tool journal, March 2002

DNA synthesis, assembly and applications in synthetic biology journal, August 2012

Synthetic DNA Synthesis and Assembly: Putting the Synthetic in Synthetic Biology journal, January 2017

From Genetic Footprinting to Antimicrobial Drug Targets: Examples in Cofactor Biosynthetic Pathways journal, August 2002

‘Shotgun DNA synthesis’ for the high-throughput construction of large DNA molecules journal, June 2012

Local fitness landscape of the green fluorescent protein journal, May 2016

Deep mutational scanning: a new style of protein science journal, July 2014

Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules journal, August 2012

Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features journal, December 1983

Mutation effects predicted from sequence co-variation journal, January 2017

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants the Keio collection journal, February 2006

Protein structure prediction from sequence variation journal, November 2012

Parallel on-chip gene synthesis and application to optimization of protein expression journal, April 2011

Predicting functionally important residues from sequence conservation journal, May 2007

Protein Sectors: Evolutionary Units of Three-Dimensional Structure journal, August 2009

An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit journal, May 2014

Precrec: fast and accurate precision–recall and ROC curve calculations in R journal, September 2016

Starcode: sequence clustering based on all-pairs search journal, January 2015

Site-specific chromosomal integration of large synthetic constructs journal, January 2010

A systematic comparison of error correction enzymes by next-generation sequencing journal, August 2017

Interaction network containing conserved and essential protein complexes in Escherichia coli journal, February 2005

Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins journal, April 2009

The crystal structures of phosphopantetheine adenylyltransferase with bound substrates reveal the enzyme’s catalytic mechanism 1 1Edited by K. Nagai journal, January 2002

A Method for Multiplex Gene Synthesis Employing Error Correction Based on Expression journal, March 2015

ggtree : an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data journal, September 2016

One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products journal, May 2000

High-quality gene assembly directly from unpurified mixtures of microarray-synthesized oligonucleotides journal, August 2010

Levenshtein error-correcting barcodes for multiplexed DNA sequencing journal, September 2013

Ribozyme-based insulator parts buffer synthetic circuits from genetic context journal, October 2012

The power of multiplexed functional analysis of genetic variants journal, September 2016

A Novel Adenylate Binding Site Confers Phosphopantetheine Adenylyltransferase Interactions with Coenzyme A journal, July 2003

Global analysis of protein folding using massively parallel design, synthesis, and testing journal, July 2017

Multiplex pairwise assembly of array-derived DNA oligonucleotides journal, November 2015

T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton journal, September 2000

UCSF Chimera?A visualization system for exploratory research and analysis journal, January 2004

Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips journal, November 2010

Decoding enhancers using massively parallel reporter assays journal, September 2015

The crystal structure of a novel bacterial adenylyltransferase reveals half of sites reactivity journal, April 1999

Discovery of Inhibitors of 4′-Phosphopantetheine Adenylyltransferase (PPAT) To Validate PPAT as a Target for Antibacterial Therapy journal, September 2013

A synthetic three-color scaffold for monitoring genetic regulation and noise journal, January 2010

Purification and Characterization of Phosphopantetheine Adenylyltransferase from Escherichia coli journal, September 1999

InterPro in 2017—beyond protein family and domain annotations journal, November 2016

Engineering and characterization of a superfolder green fluorescent protein
journal, December 2005

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
journal, January 2014

Large-scale de novo DNA synthesis: technologies and applications
journal, April 2014

BLAT---The BLAST-Like Alignment Tool
journal, March 2002

DNA synthesis, assembly and applications in synthetic biology
journal, August 2012

Synthetic DNA Synthesis and Assembly: Putting the Synthetic in Synthetic Biology
journal, January 2017

From Genetic Footprinting to Antimicrobial Drug Targets: Examples in Cofactor Biosynthetic Pathways
journal, August 2002

‘Shotgun DNA synthesis’ for the high-throughput construction of large DNA molecules
journal, June 2012

Local fitness landscape of the green fluorescent protein
journal, May 2016

Deep mutational scanning: a new style of protein science
journal, July 2014

Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules
journal, August 2012

Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
journal, December 1983

Mutation effects predicted from sequence co-variation
journal, January 2017

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants the Keio collection
journal, February 2006

Protein structure prediction from sequence variation
journal, November 2012

Parallel on-chip gene synthesis and application to optimization of protein expression
journal, April 2011

Predicting functionally important residues from sequence conservation
journal, May 2007

Protein Sectors: Evolutionary Units of Three-Dimensional Structure
journal, August 2009

An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit
journal, May 2014

Precrec: fast and accurate precision–recall and ROC curve calculations in R
journal, September 2016

Starcode: sequence clustering based on all-pairs search
journal, January 2015

Site-specific chromosomal integration of large synthetic constructs
journal, January 2010

A systematic comparison of error correction enzymes by next-generation sequencing
journal, August 2017

Interaction network containing conserved and essential protein complexes in Escherichia coli
journal, February 2005

Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins
journal, April 2009

The crystal structures of phosphopantetheine adenylyltransferase with bound substrates reveal the enzyme’s catalytic mechanism 1 1Edited by K. Nagai
journal, January 2002

A Method for Multiplex Gene Synthesis Employing Error Correction Based on Expression
journal, March 2015

ggtree : an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data
journal, September 2016

One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products
journal, May 2000

High-quality gene assembly directly from unpurified mixtures of microarray-synthesized oligonucleotides
journal, August 2010

Levenshtein error-correcting barcodes for multiplexed DNA sequencing
journal, September 2013

Ribozyme-based insulator parts buffer synthetic circuits from genetic context
journal, October 2012

The power of multiplexed functional analysis of genetic variants
journal, September 2016

A Novel Adenylate Binding Site Confers Phosphopantetheine Adenylyltransferase Interactions with Coenzyme A
journal, July 2003

Global analysis of protein folding using massively parallel design, synthesis, and testing
journal, July 2017

Multiplex pairwise assembly of array-derived DNA oligonucleotides
journal, November 2015

T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton
journal, September 2000

UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004

Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips
journal, November 2010

Decoding enhancers using massively parallel reporter assays
journal, September 2015

The crystal structure of a novel bacterial adenylyltransferase reveals half of sites reactivity
journal, April 1999

Discovery of Inhibitors of 4′-Phosphopantetheine Adenylyltransferase (PPAT) To Validate PPAT as a Target for Antibacterial Therapy
journal, September 2013

A synthetic three-color scaffold for monitoring genetic regulation and noise
journal, January 2010

Purification and Characterization of Phosphopantetheine Adenylyltransferase from Escherichia coli
journal, September 1999

InterPro in 2017—beyond protein family and domain annotations
journal, November 2016