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

Title: Optimizing complex phenotypes through model-guided multiplex genome engineering

ORCiD logo; ; ; ; ; ; ;
Publication Date:
Research Org.:
Harvard Univ., Boston, MA (United States). Harvard Medical School; Harvard Univ., Cambridge, MA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Contributing Org.:
AWS Cloud Credits for Research Program
OSTI Identifier:
Alternate Identifier(s):
OSTI ID: 1371697; OSTI ID: 1389296
Grant/Contract Number:  
Resource Type:
Published Article
Journal Name:
Genome Biology (Online)
Additional Journal Information:
Journal Name: Genome Biology (Online) Journal Volume: 18 Journal Issue: 1; Journal ID: ISSN 1474-760X
Springer Science + Business Media
Country of Publication:
United Kingdom
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; Genome engineering; Predictive modeling; Synthetic organisms; Genome engineering, Predictive modeling, Synthetic organisms

Citation Formats

Kuznetsov, Gleb, Goodman, Daniel B., Filsinger, Gabriel T., Landon, Matthieu, Rohland, Nadin, Aach, John, Lajoie, Marc J., and Church, George M. Optimizing complex phenotypes through model-guided multiplex genome engineering. United Kingdom: N. p., 2017. Web. doi:10.1186/s13059-017-1217-z.
Kuznetsov, Gleb, Goodman, Daniel B., Filsinger, Gabriel T., Landon, Matthieu, Rohland, Nadin, Aach, John, Lajoie, Marc J., & Church, George M. Optimizing complex phenotypes through model-guided multiplex genome engineering. United Kingdom. doi:10.1186/s13059-017-1217-z.
Kuznetsov, Gleb, Goodman, Daniel B., Filsinger, Gabriel T., Landon, Matthieu, Rohland, Nadin, Aach, John, Lajoie, Marc J., and Church, George M. Thu . "Optimizing complex phenotypes through model-guided multiplex genome engineering". United Kingdom. doi:10.1186/s13059-017-1217-z.
title = {Optimizing complex phenotypes through model-guided multiplex genome engineering},
author = {Kuznetsov, Gleb and Goodman, Daniel B. and Filsinger, Gabriel T. and Landon, Matthieu and Rohland, Nadin and Aach, John and Lajoie, Marc J. and Church, George M.},
abstractNote = {},
doi = {10.1186/s13059-017-1217-z},
journal = {Genome Biology (Online)},
number = 1,
volume = 18,
place = {United Kingdom},
year = {2017},
month = {5}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1186/s13059-017-1217-z

Citation Metrics:
Cited by: 6 works
Citation information provided by
Web of Science

Figures / Tables:

Fig. 1 Fig. 1: Workflow for improving phenotypes through model-guided multiplex genome editing. First, an initial set of target alleles (hundreds to thousands) is chosen for testing based on starting hypotheses. These targets may be designed based on differences from a reference strain, synthesis or design errors, or biophysical modeling. Multiplex genomemore » editing creates a set of modified clones enriched with combinations of the targeted changes. Clones are screened for genotype and phenotype and predictive modeling is used to quantify allele effects. The workflow is repeated to validate and test new alleles. Beneficial alleles are combined to create an optimized genotype« less

Save / Share:

Works referenced in this record:

Design, synthesis, and testing toward a 57-codon genome
journal, August 2016

Genomic Recoding Broadly Obstructs the Propagation of Horizontally Transferred Genetic Elements
journal, August 2016

Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation
journal, June 2011

Multiplexed tracking of combinatorial genomic mutations in engineered cell populations
journal, March 2015

  • Zeitoun, Ramsey I.; Garst, Andrew D.; Degen, George D.
  • Nature Biotechnology, Vol. 33, Issue 6, p. 631-637
  • DOI: 10.1038/nbt.3177

Enhanced levels of λ Red-mediated recombinants in mismatch repair mutants
journal, December 2003

  • Costantino, N.; Court, D. L.
  • Proceedings of the National Academy of Sciences, Vol. 100, Issue 26, p. 15748-15753
  • DOI: 10.1073/pnas.2434959100

Biocontainment of genetically modified organisms by synthetic protein design
journal, January 2015

  • Mandell, Daniel J.; Lajoie, Marc J.; Mee, Michael T.
  • Nature, Vol. 518, Issue 7537
  • DOI: 10.1038/nature14121

Rational optimization of tolC as a powerful dual selectable marker for genome engineering
journal, January 2014

  • Gregg, Christopher J.; Lajoie, Marc J.; Napolitano, Michael G.
  • Nucleic Acids Research, Vol. 42, Issue 7
  • DOI: 10.1093/nar/gkt1374

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

Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement
journal, July 2011

  • Isaacs, Farren J.; Carr, Peter A.; Wang, Harris H.
  • Science, Vol. 333, Issue 6040, p. 348-353
  • DOI: 10.1126/science.1205822

Programming cells by multiplex genome engineering and accelerated evolution
journal, July 2009

  • Wang, Harris H.; Isaacs, Farren J.; Carr, Peter A.
  • Nature, Vol. 460, Issue 7257, p. 894-898
  • DOI: 10.1038/nature08187

Direct Mutagenesis of Thousands of Genomic Targets Using Microarray-Derived Oligonucleotides
journal, June 2014

  • Bonde, Mads T.; Kosuri, Sriram; Genee, Hans J.
  • ACS Synthetic Biology, Vol. 4, Issue 1
  • DOI: 10.1021/sb5001565

The Escherichia coli Cpx Envelope Stress Response Regulates Genes of Diverse Function That Impact Antibiotic Resistance and Membrane Integrity
journal, April 2013

  • Raivio, T. L.; Leblanc, S. K. D.; Price, N. L.
  • Journal of Bacteriology, Vol. 195, Issue 12
  • DOI: 10.1128/JB.00105-13

EcoCyc: a comprehensive database of Escherichia coli biology
journal, November 2010

  • Keseler, I. M.; Collado-Vides, J.; Santos-Zavaleta, A.
  • Nucleic Acids Research, Vol. 39, Issue Database
  • DOI: 10.1093/nar/gkq1143

Regularization and variable selection via the elastic net
journal, April 2005

Adaptive laboratory evolution – principles and applications for biotechnology
journal, January 2013

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells
journal, December 2013

  • Shalem, Ophir; Sanjana, Neville E.; Hartenian, Ella
  • Science, Vol. 343, Issue 6166, p. 84-87
  • DOI: 10.1126/science.1247005

Synthetic chromosome arms function in yeast and generate phenotypic diversity by design
journal, September 2011

  • Dymond, Jessica S.; Richardson, Sarah M.; Coombes, Candice E.
  • Nature, Vol. 477, Issue 7365
  • DOI: 10.1038/nature10403

Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population
journal, June 2011

Gene Ontology: tool for the unification of biology
journal, May 2000

  • Ashburner, Michael; Ball, Catherine A.; Blake, Judith A.
  • Nature Genetics, Vol. 25, Issue 1
  • DOI: 10.1038/75556

Codon Bias as a Means to Fine-Tune Gene Expression
journal, July 2015

Use of Adaptive Laboratory Evolution To Discover Key Mutations Enabling Rapid Growth of Escherichia coli K-12 MG1655 on Glucose Minimal Medium
journal, October 2014

  • LaCroix, Ryan A.; Sandberg, Troy E.; O'Brien, Edward J.
  • Applied and Environmental Microbiology, Vol. 81, Issue 1
  • DOI: 10.1128/AEM.02246-14

Genome engineering Escherichia coli for L-DOPA overproduction from glucose
journal, July 2016

  • Wei, Tao; Cheng, Bi-Yan; Liu, Jian-Zhong
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep30080

Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli
journal, September 2016

  • Napolitano, Michael G.; Landon, Matthieu; Gregg, Christopher J.
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 38
  • DOI: 10.1073/pnas.1605856113

Adenylate Cyclase and the Cyclic AMP Receptor Protein Modulate Stress Resistance and Virulence Capacity of Uropathogenic Escherichia coli
journal, October 2012

  • Donovan, Grant T.; Norton, J. Paul; Bower, Jean M.
  • Infection and Immunity, Vol. 81, Issue 1
  • DOI: 10.1128/IAI.00796-12

Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes
journal, May 2015

Evolution-guided optimization of biosynthetic pathways
journal, December 2014

  • Raman, Srivatsan; Rogers, Jameson K.; Taylor, Noah D.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 50, p. 17803-17808
  • DOI: 10.1073/pnas.1409523111

Design and synthesis of a minimal bacterial genome
journal, March 2016

Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations
journal, July 2014

  • Sandberg, Troy E.; Pedersen, Margit; LaCroix, Ryan A.
  • Molecular Biology and Evolution, Vol. 31, Issue 10
  • DOI: 10.1093/molbev/msu209

Emergent Properties of Reduced-Genome Escherichia coli
journal, May 2006

  • Posfai, G.; Plunkett III, Guy; Fehér, Tamás
  • Science, Vol. 312, Issue 5776, p. 1044-1046
  • DOI: 10.1126/science.1126439

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond
journal, November 2015

  • Gama-Castro, Socorro; Salgado, Heladia; Santos-Zavaleta, Alberto
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1156

Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector
journal, August 2014

  • Kabadi, Ami M.; Ousterout, David G.; Hilton, Isaac B.
  • Nucleic Acids Research, Vol. 42, Issue 19
  • DOI: 10.1093/nar/gku749

Recoded organisms engineered to depend on synthetic amino acids
journal, January 2015

  • Rovner, Alexis J.; Haimovich, Adrian D.; Katz, Spencer R.
  • Nature, Vol. 518, Issue 7537
  • DOI: 10.1038/nature14095

Genomically Recoded Organisms Expand Biological Functions
journal, October 2013

  • Lajoie, M. J.; Rovner, A. J.; Goodman, D. B.
  • Science, Vol. 342, Issue 6156, p. 357-360
  • DOI: 10.1126/science.1241459

Yeast Oligo-Mediated Genome Engineering (YOGE)
journal, November 2013

  • DiCarlo, James E.; Conley, Andrew J.; Penttilä, Merja
  • ACS Synthetic Biology, Vol. 2, Issue 12
  • DOI: 10.1021/sb400117c

Millstone: software for multiplex microbial genome analysis and engineering
journal, May 2017

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture
journal, January 2012

Genetic Screens in Human Cells Using the CRISPR-Cas9 System
journal, December 2013

    Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.