skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Authors:
ORCiD logo; ORCiD logo; ORCiD logo; ; ORCiD logo
Publication Date:
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.
Plesa, Calin, Sidore, Angus M., Lubock, Nathan B., Zhang, Di, & Kosuri, Sriram. Multiplexed gene synthesis in emulsions for exploring protein functional landscapes. United States. doi:10.1126/science.aao5167.
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. doi:10.1126/science.aao5167.
@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 = {2018},
month = {1}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1126/science.aao5167

Citation Metrics:
Cited by: 13 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

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

  • Pédelacq, Jean-Denis; Cabantous, Stéphanie; Tran, Timothy
  • Nature Biotechnology, Vol. 24, Issue 1, p. 79-88
  • DOI: 10.1038/nbt1172

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

  • Kosuri, Sriram; Church, George M.
  • Nature Methods, Vol. 11, Issue 5
  • DOI: 10.1038/nmeth.2918

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

  • Ma, Siying; Tang, Nicholas; Tian, Jingdong
  • Current Opinion in Chemical Biology, Vol. 16, Issue 3-4
  • DOI: 10.1016/j.cbpa.2012.05.001

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

  • Hughes, Randall A.; Ellington, Andrew D.
  • Cold Spring Harbor Perspectives in Biology, Vol. 9, Issue 1
  • DOI: 10.1101/cshperspect.a023812

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

  • Kim, Hwangbeom; Han, Hyojun; Ahn, Jinwoo
  • Nucleic Acids Research, Vol. 40, Issue 18
  • DOI: 10.1093/nar/gks546

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

  • Sarkisyan, Karen S.; Bolotin, Dmitry A.; Meer, Margarita V.
  • Nature, Vol. 533, Issue 7603
  • DOI: 10.1038/nature17995

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

  • Fowler, Douglas M.; Fields, Stanley
  • Nature Methods, Vol. 11, Issue 8
  • DOI: 10.1038/nmeth.3027

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

  • Schwartz, Jerrod J.; Lee, Choli; Shendure, Jay
  • Nature Methods, Vol. 9, Issue 9
  • DOI: 10.1038/nmeth.2137

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

  • Hopf, Thomas A.; Ingraham, John B.; Poelwijk, Frank J.
  • Nature Biotechnology, Vol. 35, Issue 2
  • DOI: 10.1038/nbt.3769

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

  • Baba, Tomoya; Ara, Takeshi; Hasegawa, Miki
  • Molecular Systems Biology, Vol. 2, Article No. 2006.0008
  • DOI: 10.1038/msb4100050

Protein structure prediction from sequence variation
journal, November 2012

  • Marks, Debora S.; Hopf, Thomas A.; Sander, Chris
  • Nature Biotechnology, Vol. 30, Issue 11
  • DOI: 10.1038/nbt.2419

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

  • Quan, Jiayuan; Saaem, Ishtiaq; Tang, Nicholas
  • Nature Biotechnology, Vol. 29, Issue 5
  • DOI: 10.1038/nbt.1847

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

  • Kuhlman, Thomas E.; Cox, Edward C.
  • Nucleic Acids Research, Vol. 38, Issue 6
  • DOI: 10.1093/nar/gkp1193

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

  • Lubock, Nathan B.; Zhang, Di; Sidore, Angus M.
  • Nucleic Acids Research, Vol. 45, Issue 15
  • DOI: 10.1093/nar/gkx691

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

  • Butland, Gareth; Peregrín-Alvarez, José Manuel; Li, Joyce
  • Nature, Vol. 433, Issue 7025
  • DOI: 10.1038/nature03239

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


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

  • Yu, Guangchuang; Smith, David K.; Zhu, Huachen
  • Methods in Ecology and Evolution, Vol. 8, Issue 1
  • DOI: 10.1111/2041-210X.12628

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

  • Datsenko, K. A.; Wanner, B. L.
  • Proceedings of the National Academy of Sciences, Vol. 97, Issue 12, p. 6640-6645
  • DOI: 10.1073/pnas.120163297

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

  • Borovkov, Alex Y.; Loskutov, Andrey V.; Robida, Mark D.
  • Nucleic Acids Research, Vol. 38, Issue 19
  • DOI: 10.1093/nar/gkq677

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


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

  • Lou, Chunbo; Stanton, Brynne; Chen, Ying-Ja
  • Nature Biotechnology, Vol. 30, Issue 11
  • DOI: 10.1038/nbt.2401

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

  • Gasperini, Molly; Starita, Lea; Shendure, Jay
  • Nature Protocols, Vol. 11, Issue 10
  • DOI: 10.1038/nprot.2016.135

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

  • Rocklin, Gabriel J.; Chidyausiku, Tamuka M.; Goreshnik, Inna
  • Science, Vol. 357, Issue 6347
  • DOI: 10.1126/science.aan0693

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

  • Klein, Jason C.; Lajoie, Marc J.; Schwartz, Jerrod J.
  • Nucleic Acids Research, Vol. 44, Issue 5
  • DOI: 10.1093/nar/gkv1177

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

  • Notredame, Cédric; Higgins, Desmond G.; Heringa, Jaap
  • Journal of Molecular Biology, Vol. 302, Issue 1
  • DOI: 10.1006/jmbi.2000.4042

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

  • Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
  • Journal of Computational Chemistry, Vol. 25, Issue 13
  • DOI: 10.1002/jcc.20084

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

  • Kosuri, Sriram; Eroshenko, Nikolai; LeProust, Emily M.
  • Nature Biotechnology, Vol. 28, Issue 12, p. 1295-1299
  • DOI: 10.1038/nbt.1716

Decoding enhancers using massively parallel reporter assays
journal, September 2015


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

  • de Jonge, Boudewijn L. M.; Walkup, Grant K.; Lahiri, Sushmita D.
  • Antimicrobial Agents and Chemotherapy, Vol. 57, Issue 12
  • DOI: 10.1128/AAC.01661-13

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

  • Cox, Robert; Dunlop, Mary J.; Elowitz, Michael B.
  • Journal of Biological Engineering, Vol. 4, Issue 1
  • DOI: 10.1186/1754-1611-4-10

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

  • Geerlof, Arie; Lewendon, Ann; Shaw, William V.
  • Journal of Biological Chemistry, Vol. 274, Issue 38
  • DOI: 10.1074/jbc.274.38.27105

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

  • Finn, Robert D.; Attwood, Teresa K.; Babbitt, Patricia C.
  • Nucleic Acids Research, Vol. 45, Issue D1
  • DOI: 10.1093/nar/gkw1107