Methods for generating barcoded combinatorial libraries
Abstract
Provided herein are methods and composition for trackable genetic variant libraries. Further provided herein are methods and compositions for recursive engineering. Further provided herein are methods and compositions for multiplex engineering. Further provided herein are methods and compositions for enriching for editing and trackable engineered sequences and cells using nucleic acid-guided nucleases.
- Inventors:
- Issue Date:
- Research Org.:
- Inscripta, Inc., Boulder, CO (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1463088
- Patent Number(s):
- 10017760
- Application Number:
- 15/632,222
- Assignee:
- Inscripta, Inc. (Boulder, CO); The Regents of the University of Colorado, a Body Corporate (Denver, CO)
- Patent Classifications (CPCs):
-
C - CHEMISTRY C12 - BIOCHEMISTRY C12N - MICROORGANISMS OR ENZYMES
C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS
- DOE Contract Number:
- SC0008812
- Resource Type:
- Patent
- Resource Relation:
- Patent File Date: 2017 Jun 23
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Gill, Ryan T., Garst, Andrew, Lipscomb, Tanya Elizabeth Warnecke, Bassalo, Marcelo Colika, and Zeitoun, Ramsey Ibrahim. Methods for generating barcoded combinatorial libraries. United States: N. p., 2018.
Web.
Gill, Ryan T., Garst, Andrew, Lipscomb, Tanya Elizabeth Warnecke, Bassalo, Marcelo Colika, & Zeitoun, Ramsey Ibrahim. Methods for generating barcoded combinatorial libraries. United States.
Gill, Ryan T., Garst, Andrew, Lipscomb, Tanya Elizabeth Warnecke, Bassalo, Marcelo Colika, and Zeitoun, Ramsey Ibrahim. Tue .
"Methods for generating barcoded combinatorial libraries". United States. https://www.osti.gov/servlets/purl/1463088.
@article{osti_1463088,
title = {Methods for generating barcoded combinatorial libraries},
author = {Gill, Ryan T. and Garst, Andrew and Lipscomb, Tanya Elizabeth Warnecke and Bassalo, Marcelo Colika and Zeitoun, Ramsey Ibrahim},
abstractNote = {Provided herein are methods and composition for trackable genetic variant libraries. Further provided herein are methods and compositions for recursive engineering. Further provided herein are methods and compositions for multiplex engineering. Further provided herein are methods and compositions for enriching for editing and trackable engineered sequences and cells using nucleic acid-guided nucleases.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Tue Jul 10 00:00:00 EDT 2018},
month = {Tue Jul 10 00:00:00 EDT 2018}
}
Works referenced in this record:
Mutant Cas9 Proteins
patent-application, October 2016
- Chavez, Alejandro; Poelwijk, Franck; Church, George M.
- US Patent Application 15/037696; 20160298097
An updated evolutionary classification of CRISPR–Cas systems
journal, September 2015
- Makarova, Kira S.; Wolf, Yuri I.; Alkhnbashi, Omer S.
- Nature Reviews Microbiology, Vol. 13, Issue 11, p. 722-736
Mass spectrometry-based metabolomics of single yeast cells
journal, May 2013
- Ibanez, A. J.; Fagerer, S. R.; Schmidt, A. M.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 22, p. 8790-8794
Tuning Microbial Populations with Programmable Nucleases
patent-application, March 2015
- Lu, Timothy Kuan-Ta; Citorik, Robert James; Mimee, Mark Kyle
- US Patent Application 14/475785; 20150064138
Regulatory Network of Escherichia coli: Consistency Between Literature Knowledge and Microarray Profiles
journal, November 2003
- Gutierrez-Rios, R. M.
- Genome Research, Vol. 13, Issue 11, p. 2435-2443
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
Metabolic engineering of Escherichia coli for high-specificity production of isoprenol and prenol as next generation of biofuels
journal, January 2013
- Zheng, Yanning; Liu, Qiang; Li, Lingling
- Biotechnology for Biofuels, Vol. 6, Article No. 57
CRISPR Interference Can Prevent Natural Transformation and Virulence Acquisition during In Vivo Bacterial Infection
journal, August 2012
- Bikard, David; Hatoum-Aslan, Asma; Mucida, Daniel
- Cell Host & Microbe, Vol. 12, Issue 2, p. 177-186
Engineering Yeast Transcription Machinery for Improved Ethanol Tolerance and Production
journal, December 2006
- Alper, H.; Moxley, J.; Nevoigt, E.
- Science, Vol. 314, Issue 5805, p. 1565-1568
Microbial Strain Improvement by a HTP Genomic Engineering Platform
patent-application, June 2017
- Serber, Zach; Dean, Jed; Manchester, Shawn
- US Patent Application 15/396230; 20170159045
Consensus DNA site for the Escherichia coli catabolite gene activator protein (CAP): CAP exhibits a 450-fold higher affinity for the consensus DNA site than for the E.coli lac DNA site
journal, January 1989
- Ebright, Richard H.; Ebright, Yon W.; Gunasekera, Angelo
- Nucleic Acids Research, Vol. 17, Issue 24, p. 10295-10305
CRISPR/CAS Systems for Genomic Modification and Gene Modulation
patent-application, September 2014
- Wu, Fangting
- US Patent Application 14/216655; 20140273226
Bacterium
patent-application, July 2015
- Fremaux, Christohe; Horvath, Philippe; Schwobe, Joachim
- US Patent Application 14/478969; 20150201634
CRISPR-Based Genome Modification and Regulation
patent-application, March 2017
- Chen, Fuqiang; Davis, Gregory D.; Kang, Qiaohua
- US Patent Application 15/342976; 20170073705
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
Crisper-Cas Component Systems, Methods and Compositions for Sequence Manipulation
patent-application, April 2016
- Zhang, Feng; Cox, David Benjamin Turitz; Marraffini, Luciano
- US Patent Application 14/990444; 20160115488
Divergent evolution of protein conformational dynamics in dihydrofolate reductase
journal, September 2013
- Bhabha, Gira; Ekiert, Damian C.; Jennewein, Madeleine
- Nature Structural & Molecular Biology, Vol. 20, Issue 11, p. 1243-1249
Functional Assay for Identification of Loss-of-Function Mutations in Genes
patent-application, December 2010
- Kern, Scott E.; Gallmeier, Eike; Hucl, Tomas
- US Patent Application 12/675968; 20100305001
DNA targeting specificity of RNA-guided Cas9 nucleases
journal, July 2013
- Hsu, Patrick D.; Scott, David A.; Weinstein, Joshua A.
- Nature Biotechnology, Vol. 31, Issue 9, p. 827-832
Genome Engineering
patent-application, January 2015
- Church, George M.; Yang, Luhan; Cargol, Marc Guell
- US Patent Application 14/319498; 20150031133
Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression
journal, February 2013
- Qi, Lei S.; Larson, Matthew H.; Gilbert, Luke A.
- Cell, Vol. 152, Issue 5, p. 1173-1183
Evolutional Design of a Hyperactive Cysteine- and Methionine-free Mutant of Escherichia coli Dihydrofolate Reductase
journal, March 2006
- Iwakura, Masahiro; Maki, Kosuke; Takahashi, Hisashi
- Journal of Biological Chemistry, Vol. 281, Issue 19, p. 13234-13246
Crystal structure of AcrB complexed with linezolid at 3.5 Å resolution
journal, May 2013
- Hung, Li-Wei; Kim, Heung-Bok; Murakami, Satoshi
- Journal of Structural and Functional Genomics, Vol. 14, Issue 2, p. 71-75
Engineered Nucleic-Acid Targeting Nucleic Acids
patent-application, April 2017
- Donohoue, Paul Daniel; May, Andrew Paul
- US Patent Application 15/331676; 20170114369
Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes
journal, August 2008
- Brouns, S. J. J.; Jore, M. M.; Lundgren, M.
- Science, Vol. 321, Issue 5891, p. 960-964
Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis
journal, March 2015
- Chen, Sidi; Sanjana, Neville E.; Zheng, Kaijie
- Cell, Vol. 160, Issue 6, p. 1246-1260
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
Compensatory Evolution of Gene Regulation in Response to Stress by Escherichia coli Lacking RpoS
journal, October 2009
- Stoebel, Daniel M.; Hokamp, Karsten; Last, Michael S.
- PLoS Genetics, Vol. 5, Issue 10, Article No. e1000671
Multiplex automated genome engineering
patent, October 2013
- Church, George M.; Wang, Harris H.; Isaacs, Farren J.
- US Patent Document 8,569,041
Methods and Compositions for Sequences Guiding CAS9 Targeting
patent-application, January 2017
- Barrangou, Rodolphe; Selle, Kurt M.; Briner, Alexandra E.
- US Patent Application 15/113656; 20170002339
CRISPR-Based Genome Modification and Regulation
patent-application, October 2016
- Chen, Fuqiang; Davis, Gregory D.; Kang, Qiaohua
- US Patent Application 15/188911; 20160298134
RNA-Guided Human Genome Engineering via Cas9
journal, January 2013
- Mali, P.; Yang, L.; Esvelt, K. M.
- Science, Vol. 339, Issue 6121, p. 823-826
Role of reactive oxygen species in antibiotic action and resistance
journal, October 2009
- Dwyer, Daniel J.; Kohanski, Michael A.; Collins, James J.
- Current Opinion in Microbiology, Vol. 12, Issue 5, p. 482-489
Comparison of genome-wide selection strategies to identify furfural tolerance genes in Escherichia coli: Genome-Wide Mapping of Furfural Tolerance Alleles
journal, September 2014
- Glebes, Tirzah Y.; Sandoval, Nicholas R.; Gillis, Jacob H.
- Biotechnology and Bioengineering, Vol. 112, Issue 1, p. 129-140
Genome Editing Using Campylobacter Jejuni CRISPR/Cas System-Derived RGEN
patent-application, May 2017
- Kim, Eun Ji; Kim, Seok Joong
- US Patent Application 15/420936; 20170145425
Crisper-Based Genome Modification and Regulation
patent-application, October 2016
- Chen, Fuqiang; Davis, Gregory D.; Kang, Qiaohua
- US Patent Application 15/188933; 20160298138
Broad-host-range vectors for protein expression across gram negative hosts
journal, January 2010
- Prior, Jamie E.; Lynch, Michael D.; Gill, Ryan T.
- Biotechnology and Bioengineering, Vol. 106, Issue 2, p. 326-332
Methods And Compositions For Rna-Directed Target Dna Modification And For Rna-Directed Modulation Of Transcription
patent-application, March 2014
- Doudna, Jennifer A.; Jinek, Martin; Charpentier, Emmanuelle
- US Patent Application 13/842859; 20140068797
Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex
journal, February 2008
- Hamady, Micah; Walker, Jeffrey J.; Harris, J. Kirk
- Nature Methods, Vol. 5, Issue 3, p. 235-237
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
One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering
journal, May 2013
- Wang, Haoyi; Yang, Hui; Shivalila, Chikdu S.
- Cell, Vol. 153, Issue 4, p. 910-918
A set of recombineering plasmids for gram-negative bacteria
journal, September 2006
- Datta, Simanti; Costantino, Nina; Court, Donald L.
- Gene, Vol. 379, p. 109-115
Efficient genome editing in filamentous fungus Trichoderma reesei using the CRISPR/Cas9 system
journal, May 2015
- Liu, Rui; Chen, Ling; Jiang, Yanping
- Cell Discovery, Vol. 1, Article No. 15007
Methods of Depleting Target Sequences Using CRISPR
patent-application, February 2016
- Wurtzel, Omri; LoCascio, Samuel; Reddien, Peter
- US Patent Application 14/802886; 20160053304
Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining
journal, March 2015
- Maruyama, Takeshi; Dougan, Stephanie K.; Truttmann, Matthias C.
- Nature Biotechnology, Vol. 33, Issue 5, p. 538-542
Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System
journal, October 2015
- Zetsche, Bernd; Gootenberg, Jonathan S.; Abudayyeh, Omar O.
- Cell, Vol. 163, Issue 3, p. 759-771
Methods of In Vivo Engineering of Large Sequences Using Multiple CRISPR/Cas Selections of Recombineering Events
patent-application, January 2016
- Carstens, Carsten-Peter
- US Patent Application 14/773466; 20160024529
Engineering of Systems, Methods and Optimized Guide Compositions for Sequence Manipulation
patent-application, September 2014
- Zhang, Feng; Cong, Le; Hsu, Patrick
- US Patent Application 14/290575; 20140273232
CRISPR/Cas9-Targeted Mutagenesis in Caenorhabditis elegans
journal, August 2013
- Waaijers, Selma; Portegijs, Vincent; Kerver, Jana
- Genetics, Vol. 195, Issue 3, p. 1187-1191
A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity
journal, June 2012
- Jinek, M.; Chylinski, K.; Fonfara, I.
- Science, Vol. 337, Issue 6096, p. 816-821
Engineering furfural tolerance in Escherichia coli improves the fermentation of lignocellulosic sugars into renewable chemicals
journal, February 2013
- Wang, X.; Yomano, L. P.; Lee, J. Y.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 10, p. 4021-4026
Structural Basis of Transcription Initiation: RNA Polymerase Holoenzyme at 4 Å Resolution
journal, May 2002
- Murakami, Katsuhiko S.; Masuda, Shoko; Darst, Seth A.
- Science, Vol. 296, Issue 5571, p. 1280-1284
Metabolic engineering of Escherichia coli using CRISPR–Cas9 meditated genome editing
journal, September 2015
- Li, Yifan; Lin, Zhenquan; Huang, Can
- Metabolic Engineering, Vol. 31, p. 13-21
Bacterium
patent-application, February 2010
- Fremaux, Christophe; Horvath, Philippe; Schwobe, Joachim
- US Patent Application 12/304913; 20100034924
Secure Processor and a Program for a Secure Processor
patent-application, March 2014
- Goto, Seiji; Kamada, Jun; Tamiya, Taijji
- US Patent Application 14/091488; 20140089681
Using Truncated Guide RNAs (tru-gRNAs) to Increase Specificity for RNA-Guided Genome Editing
patent-application, January 2016
- Joung, J. Keith; Sander, Jeffry D.; Fu, Yan-Fang
- US Patent Application 14/775930; 20160024523
Engineering of systems, methods and optimized guide compositions for sequence manipulation
patent, December 2014
- Zhang, Feng; Cong, Le; Hsu, Patrick D.
- US Patent Document 8,906,616
Structural basis for the inhibition of bacterial multidrug exporters
journal, June 2013
- Nakashima, Ryosuke; Sakurai, Keisuke; Yamasaki, Seiji
- Nature, Vol. 500, Issue 7460, p. 102-106
Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain.
journal, February 1996
- Kim, Y. G.; Cha, J.; Chandrasegaran, S.
- Proceedings of the National Academy of Sciences, Vol. 93, Issue 3, p. 1156-1160
Evolutionary paths to antibiotic resistance under dynamically sustained drug selection
journal, December 2011
- Toprak, Erdal; Veres, Adrian; Michel, Jean-Baptiste
- Nature Genetics, Vol. 44, Issue 1, p. 101-105
Methods and Apparatus for Transformation of Naturally Competent Cells
patent-application, February 2017
- Dalia, Ankur B.; Camilli, Andrew
- US Patent Application 15/308329; 20170051311
Methods of Depleting a Target Molecule form an Initial Collection of Nucleic Acids, and Compositions and Kits for Practicing the Same
patent-application, August 2015
- Farmer, Andrew Alan; Betts, Craig
- US Patent Application 14/582081; 20150225773
Multiplexed in Vivo His-Tagging of Enzyme Pathways for in Vitro Single-Pot Multienzyme Catalysis
journal, November 2011
- Wang, Harris H.; Huang, Po-Yi; Xu, George
- ACS Synthetic Biology, Vol. 1, Issue 2, p. 43-52
Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket
journal, November 2011
- Nakashima, Ryosuke; Sakurai, Keisuke; Yamasaki, Seiji
- Nature, Vol. 480, Issue 7378, p. 565-569
A Common Mechanism of Cellular Death Induced by Bactericidal Antibiotics
journal, September 2007
- Kohanski, Michael A.; Dwyer, Daniel J.; Hayete, Boris
- Cell, Vol. 130, Issue 5, p. 797-810
Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons
journal, May 2015
- Wetmore, Kelly M.; Price, Morgan N.; Waters, Robert J.
- mBio, Vol. 6, Issue 3, Article No. e00306-15
Identification of factors influencing strand bias in oligonucleotide‐mediated recombination in Escherichia coli
journal, November 2003
- Li, Xin‐tian; Costantino, Nina; Lu, Lin‐yu
- Nucleic Acids Research, Vol. 31, Issue 22, p. 6674-6687
[23] Manipulating yeast genome using plasmid vectors
book, January 1990
- Stearns, Tim; Ma, Hong; Botstein, David
- Gene Expression Technology, p. 280-297
CRISPR/Cas Transcriptional Modulation
patent-application, July 2017
- Gilbert, Luke A.; Horlbeck, Max; Kampmann, Martin
- US Patent Application 15/326428; 20170204407
Regulators of oxidative stress response genes in Escherichia coli and their functional conservation in bacteria
journal, September 2012
- Chiang, Sarah M.; Schellhorn, Herb E.
- Archives of Biochemistry and Biophysics, Vol. 525, Issue 2, p. 161-169
Evolution and classification of the CRISPR–Cas systems
journal, May 2011
- Makarova, Kira S.; Haft, Daniel H.; Barrangou, Rodolphe
- Nature Reviews Microbiology, Vol. 9, Issue 6, p. 467-477
CRISPR-Cas System Materials and Methods
patent-application, October 2016
- Charpentier, Emmanuelle; Chylinski, Krzysztof; Fontara, Ines
- US Patent Application 15/037371; 20160298096
Cell-Based Genomic Recorded Accumulative Memory
patent-application, May 2015
- Jacobson, Joseph M.; Jakimo, Noah; Kanarek, Naama
- US Patent Application 14/536128; 20150133315
Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence
journal, June 2011
- Semenova, E.; Jore, M. M.; Datsenko, K. A.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 25, p. 10098-10103
The Pfam protein families database
journal, January 2004
- Bateman, Alex; Coin, Lachlan; Durbin, Richard
- Nucleic Acids Research, Vol. 32, Issue S1, p. D138-D141
Guide RNA with Chemical Modifications
patent-application, October 2016
- Ryan, Daniel E.; Dellinger, Douglas J.; Sampson, Jeffrey R.
- US Patent Application 14/757204; 20160289675
Yeast Arrays, Methods of Making Such Arrays, and Methods of Analyzing Such Arrays
patent-application, November 2008
- Boone, Charles
- US Patent Application 11/484201; 20080287317
Compositions And Methods Of Nucleic Acid-Targeting Nucleic Acids
patent-application, February 2017
- May, Andrew Paul; Haurwitz, Rachel E.; Doudna, Jennifer A.
- US Patent Application 15/344487; 20170051276
Use
patent-application, July 2014
- Barrangou, Rodolphe; Boyaval, Patrick; Fremaux, Christophe
- US Patent Application 13/960796; 20140199767
CAS9-Nucleic Acid Complexes and Uses Related Thereto
patent-application, December 2015
- Weiss, David S.; Grakoui, Aradh; Sampson, Timothy R.
- US Patent Application 14/760113; 20150353905
Functional optimization of gene clusters by combinatorial design and assembly
journal, November 2014
- Smanski, Michael J.; Bhatia, Swapnil; Zhao, Dehua
- Nature Biotechnology, Vol. 32, Issue 12, p. 1241-1249
Methods and Compositions for RNA-Directed Target DNA Modification and for RNA-Directed Modulation of Transcription
patent-application, March 2016
- Doudna, Jennifer A.; Jinek, Martin; Charpentier, Emmanuelle
- US Patent Application 14/685516; 20160068864
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
Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems
journal, November 2015
- Shmakov, Sergey; Abudayyeh, Omar O.; Makarova, Kira S.
- Molecular Cell, Vol. 60, Issue 3, p. 385-397
Compositions, Methods and Uses for Multiplex Protein Sequence Activity Relationship Mapping
patent-application, December 2015
- Gill, Ryan T.; Lynch, Sean Andrew; Warner, Joseph R.
- US Patent Application 14/110072; 20150368639
Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria
journal, June 2014
- Farasat, I.; Kushwaha, M.; Collens, J.
- Molecular Systems Biology, Vol. 10, Issue 6, p. 731-731
Ultrahigh-throughput screening in drop-based microfluidics for directed evolution
journal, February 2010
- Agresti, J. J.; Antipov, E.; Abate, A. R.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 9, p. 4004-4009
The Acetate Switch
journal, March 2005
- Wolfe, Alan
- Microbiology and Molecular Biology Reviews, Vol. 69, Issue 1, p. 12-50
Activity and Specificity of the Bacterial PD-(D/E)XK Homing Endonuclease I-Ssp6803I
journal, February 2009
- Zhao, Lei; Pellenz, Stefan; Stoddard, Barry L.
- Journal of Molecular Biology, Vol. 385, Issue 5, p. 1498-1510
GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries
journal, May 2008
- Firth, A. E.; Patrick, W. M.
- Nucleic Acids Research, Vol. 36, Issue S2, p. W281-W285
Optimized Small Guide RNAs and Methods of Use
patent-application, October 2016
- Huang, Bo; Chen, Baohui; Qi, Lei
- US Patent Application 15/025217; 20160289673
The Molecular Diversity of Adaptive Convergence
journal, January 2012
- Tenaillon, O.; Rodriguez-Verdugo, A.; Gaut, R. L.
- Science, Vol. 335, Issue 6067, p. 457-461
Codon Compression Algorithms for Saturation Mutagenesis
journal, September 2014
- Pines, Gur; Pines, Assaf; Garst, Andrew D.
- ACS Synthetic Biology, Vol. 4, Issue 5, p. 604-614
Methods, systems and compositions regarding multiplex construction protein amino-acid substitutions and identification of sequence-activity relationships, to provide gene replacement such as with tagged mutant genes, such as via efficient homologous recombination
patent-application, May 2014
- Warner, Joseph R.
- US Patent Application 14/080519; 20140121118
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
Methods and Compositions for Nuclease Design
patent-application, December 2015
- Miller, Jeffrey C.
- US Patent Application 14/731821; 20150353917
Compositions and Methods for Modifying a Predetermined Target Nucleic Acid Sequence
patent-application, August 2017
- Shiboleth, Yoel Moshe; Weinthal, Dan Michael
- US Patent Application 15/582384; 20170233752
Vector for Nucleic Acid Insertion
patent-application, September 2016
- Yamamoto, Takashi; Suzuki, Kenichi; Sakuma, Tetsushi
- US Patent Application 15/032544; 20160264995
Methods of Modifying a Sequence Using CRISPR
patent-application, February 2016
- Wurtzel, Omri; LoCascio, Samuel; Reddien, Peter
- US Patent Application 14/801133; 20160053272
Methods and Compositions for RNA-Directed Target DNA Modification and RNA-Directed Modulation of Transcription
patent-application, March 2016
- Doudna, Jennifer A.; Jinek, Martin; Charpentier, Emmanuelle
- US Patent Application 14/685513; 20160060653
CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation
journal, December 2011
- Bhaya, Devaki; Davison, Michelle; Barrangou, Rodolphe
- Annual Review of Genetics, Vol. 45, Issue 1, p. 273-297
Argonaute of the archaeon Pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA
journal, April 2015
- Swarts, Daan C.; Hegge, Jorrit W.; Hinojo, Ismael
- Nucleic Acids Research, Vol. 43, Issue 10, p. 5120-5129
Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination
journal, September 2013
- Dickinson, Daniel J.; Ward, Jordan D.; Reiner, David J.
- Nature Methods, Vol. 10, Issue 10, p. 1028-1034
Methods, Cells & Organisms
patent-application, March 2015
- Bradley, Allan; Ani, Hanif; Lee, E-Chiang
- US Patent Application 14/490549; 20150079680
Enhancing E. coli Tolerance towards Oxidative Stress via Engineering Its Global Regulator cAMP Receptor Protein (CRP)
journal, December 2012
- Basak, Souvik; Jiang, Rongrong; Ojcius, David M.
- PLoS ONE, Vol. 7, Issue 12, Article No. e51179
Methods and Compositions for RNA-Directed Target Data Modification and for RNA-Directed Modulation of Transcription
patent-application, February 2017
- Doudna, Jennifer A.; Jack, Martin; Chylinski, Kryzysztof
- US Patent Application 15/138604; 20170051310
Strategies for the multiplex mapping of genes to traits
journal, January 2013
- Garst, Andrew; Lynch, Michael; Evans, Ron
- Microbial Cell Factories, Vol. 12, Issue 1, Article No. 99
Saturation editing of genomic regions by multiplex homology-directed repair
journal, September 2014
- Findlay, Gregory M.; Boyle, Evan A.; Hause, Ronald J.
- Nature, Vol. 513, Issue 7516, p. 120-123
Therapeutic Uses of Genome Editing with CRISPR/Cas Systems
patent-application, June 2015
- Musunuru, Kiran; Cowan, Chad A.; Rossi, Derrick J.
- US Patent Application 14/509787; 20150176013
Global transcription machinery engineering: A new approach for improving cellular phenotype
journal, May 2007
- Alper, H.; Stephanopoulos, G.
- Metabolic Engineering, Vol. 9, Issue 3, p. 258-267
Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA
journal, May 2000
- Kwon, Hyock Joo; Bennik, Marjon H. J.; Demple, Bruce
- Nature Structural Biology, Vol. 7, Issue 5, p. 424-430
Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: library construction methods for directed evolution
journal, February 2004
- Neylon, C.
- Nucleic Acids Research, Vol. 32, Issue 4, p. 1448-1459
Compositions Comprising Synthetic Polynucleotides Encoding Crisper Related Proteins and Synthetic SGRNAS and Methods of Use
patent-application, December 2016
- Hoge, Stephen; Yi-chun, Eric; Chakraborty, Tirtha
- US Patent Application 14/903869; 20160367702
Method for Editing a Genetic Sequence
patent-application, June 2017
- Tolar, Jakub; Blazar, Bruce Robert; Voytas, Daniel Francis
- US Patent Application 15/311685; 20170175143
X-ray Crystal Structures of the Escherichia coli RNA Polymerase in Complex with Benzoxazinorifamycins
journal, May 2013
- Molodtsov, Vadim; Nawarathne, Irosha N.; Scharf, Nathan T.
- Journal of Medicinal Chemistry, Vol. 56, Issue 11, p. 4758-4763
Identification of Isopentenol Biosynthetic Genes from Bacillus subtilis by a Screening Method Based on Isoprenoid Precursor Toxicity
journal, August 2007
- Withers, S. T.; Gottlieb, S. S.; Lieu, B.
- Applied and Environmental Microbiology, Vol. 73, Issue 19, p. 6277-6283
Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli
journal, June 2013
- Chang, R. L.; Andrews, K.; Kim, D.
- Science, Vol. 340, Issue 6137, p. 1220-1223
Multiplex Genome Engineering Using CRISPR/Cas Systems
journal, January 2013
- Cong, L.; Ran, F. A.; Cox, D.
- Science, Vol. 339, Issue 6121, p. 819-823
Maximizing the potential of functional genomics
journal, March 2004
- Steinmetz, Lars M.; Davis, Ronald W.
- Nature Reviews Genetics, Vol. 5, Issue 3, p. 190-201
Efficient Reassignment of a Frequent Serine Codon in Wild-Type Escherichia coli
journal, November 2015
- Ho, Joanne M.; Reynolds, Noah M.; Rivera, Keith
- ACS Synthetic Biology, Vol. 5, Issue 2, p. 163-171
CRISPR-Based Genome Modification and Regulation
patent-application, October 2016
- Chen, Fuqiang; Davis, Gregory D.; Kang, Qiaohua
- US Patent Application 15/188924; 20160298135
Processes and Host Cells for Genome, Pathway, and Biomolecular Engineering
patent-application, June 2016
- Konieczka, Jay H.; Spoonamore, James E.; Wapinski, Ilan N.
- US Patent Application 14/909184; 20160186168
Saturation mutagenesis in directed evolution
patent, May 2003
- Short, Jay M.
- US Patent Document 6,562,594
Enhancing Tolerance to Short-Chain Alcohols by Engineering the Escherichia coli AcrB Efflux Pump to Secrete the Non-native Substrate n-Butanol
journal, September 2013
- Fisher, Michael A.; Boyarskiy, Sergey; Yamada, Masaki R.
- ACS Synthetic Biology, Vol. 3, Issue 1, p. 30-40
Multiplex automated genome engineering
patent, April 2012
- Church, George M.; Wang, Harris H.; Isaacs, Farren J.
- US Patent Document 8,153,432
Methods and Compositions for the Targeted Modification of a Genome
patent-application, June 2015
- Frendewey, David; Auerbach, Wojtek; Lai, Ka-Man Venus
- US Patent Application 14/515503; 20150159174
Using Truncated Guide RNAs (tru-gRNAs) to Increase Specificity for RNA-Guided Genome Editing
patent-application, October 2014
- Joung, J. Keith; Sander, Jeffry D.; Maeder, Morgan
- US Patent Application 14/213723; 20140295557
CRMAGE: CRISPR Optimized MAGE Recombineering
journal, January 2016
- Ronda, Carlotta; Pedersen, Lasse Ebdrup; Sommer, Morten O. A.
- Scientific Reports, Vol. 6, Article No. 19452
ProDy: Protein Dynamics Inferred from Theory and Experiments
journal, April 2011
- Bakan, A.; Meireles, L. M.; Bahar, I.
- Bioinformatics, Vol. 27, Issue 11, p. 1575-1577
The Dynamic Energy Landscape of Dihydrofolate Reductase Catalysis
journal, September 2006
- Boehr, D. D.; McElheny, D.; Dyson, H. J.
- Science, Vol. 313, Issue 5793, p. 1638-1642
Methods and Compositions for RNA-Directed Target DNA Modification and for RNA-Directed Modulation of Transcription
patent-application, March 2016
- Doudna, Jennifer A.; Jinek, Martin; Charpentier, Emmanuelle
- US Patent Application 14/685514; 20160060654
RNA Modification to Engineer Cas9 Activity
patent-application, April 2017
- May, Andrew Paul; Donohue, Paul Daniel; Nye, Christopher
- US Patent Application 15/390584; 20170114334
A mass spectrometry–guided genome mining approach for natural product peptidogenomics
journal, October 2011
- Kersten, Roland D.; Yang, Yu-Liang; Xu, Yuquan
- Nature Chemical Biology, Vol. 7, Issue 11, p. 794-802
RNA-Guided Human Genome Engineering
patent-application, February 2017
- Church, George M.; Mali, Prashant; Yang, Luhan
- US Patent Application 14/681510; 20170044569
Role of the acrAB locus in organic solvent tolerance mediated by expression of marA, soxS, or robA in Escherichia coli.
journal, October 1997
- White, D. G.; Goldman, J. D.; Demple, B.
- Journal of Bacteriology, Vol. 179, Issue 19, p. 6122-6126
Crisper Oligonucleotides and Gene Editing
patent-application, April 2016
- Ravinder, Namritha; Heil, Korbinian; Guo, Yizhu
- US Patent Application 14/879872; 20160102322
Quantifying Impact of Chromosome Copy Number on Recombination in Escherichia coli
journal, March 2015
- Reynolds, T. Steele; Gill, Ryan T.
- ACS Synthetic Biology, Vol. 4, Issue 7, p. 776-780
Efficient genome editing in zebrafish using a CRISPR-Cas system
journal, January 2013
- Hwang, Woong Y.; Fu, Yanfang; Reyon, Deepak
- Nature Biotechnology, Vol. 31, Issue 3, p. 227-229
CRISPR–Cas9-assisted recombineering in Lactobacillus reuteri
journal, July 2014
- Oh, Jee-Hwan; van Pijkeren, Jan-Peter
- Nucleic Acids Research, Vol. 42, Issue 17, p. e131-e131
Genome-scale promoter engineering by coselection MAGE
journal, April 2012
- Wang, Harris H.; Kim, Hwangbeom; Cong, Le
- Nature Methods, Vol. 9, Issue 6, p. 591-593
Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides
journal, July 2010
- Warner, Joseph R.; Reeder, Philippa J.; Karimpour-Fard, Anis
- Nature Biotechnology, Vol. 28, Issue 8, p. 856-862
CRISPR-Cas Component Systems, Methods and Compositions for Sequence Manipulation
patent-application, January 2015
- Zhang, Feng; Turitz Cox, David Benjamin; Marraffini, Luciano
- US Patent Application 14/497627; 20150031134
Directed evolution of an E. coli inner membrane transporter for improved efflux of biofuel molecules
journal, January 2013
- Foo, Jee Loon; Leong, Susanna Su Jan
- Biotechnology for Biofuels, Vol. 6, Issue 1, Article No. 81
Method for Sensitive Detection of Target DNA Using Target-Specific Nuclease
patent-application, July 2017
- Kim, Jin Soo; Kim, So Jung; Lee, Seung Hwan
- US Patent Application 15/314288; 20170191123
Methods and Systems for Targeted Gene Manipulation
patent-application, July 2017
- Feng, Bo; He, Xiangjun
- US Patent Application 15/354329; 20170198302
Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems
journal, March 2013
- DiCarlo, James E.; Norville, Julie E.; Mali, Prashant
- Nucleic Acids Research, Vol. 41, Issue 7, p. 4336-4343
RNA-Guided Human Genome Engineering
patent-application, June 2016
- Mali, Prashant G.; Church, George M.; Yang, Luhan
- US Patent Application 15/042515; 20160160210
Crisper-Cas Component Systems, Methods and Compositions for Sequence manipulation
patent-application, April 2016
- Zhang, Feng; Cox, David Benjamin Turitz; Marraffini, Luciano
- US Patent Application 14/991083; 20160115489
Multigene Editing in the Escherichia coli Genome via the CRISPR-Cas9 System
journal, January 2015
- Jiang, Yu; Chen, Biao; Duan, Chunlan
- Applied and Environmental Microbiology, Vol. 81, Issue 7, p. 2506-2514
RNA-guided editing of bacterial genomes using CRISPR-Cas systems
journal, January 2013
- Jiang, Wenyan; Bikard, David; Cox, David
- Nature Biotechnology, Vol. 31, Issue 3, p. 233-239
Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering
journal, December 2016
- Garst, Andrew D.; Bassalo, Marcelo C.; Pines, Gur
- Nature Biotechnology, Vol. 35, Issue 1, p. 48-55
Genetic Targeting in Non-Conventional Yeast Using an RNA-Guided Endonuclease
patent-application, August 2017
- Frisch, Ryan; Fan, Xiaochun; Hong, Seung-Pyo
- US Patent Application 15/503383; 20170226533
Multiplex Homology-Directed Repair
patent-application, March 2016
- Shendure, Jay; Boyle, Evan; Findlay, Gregory
- US Patent Application 14/818217; 20160076093
Altered target site specificity variants of the I-PpoI His-Cys box homing endonuclease
journal, July 2007
- Eklund, Jennifer L.; Ulge, Umut Y.; Eastberg, Jennifer
- Nucleic Acids Research, Vol. 35, Issue 17, p. 5839-5850
Life after genetics
journal, October 2014
- Shendure, Jay
- Genome Medicine, Vol. 6, Issue 10, Article No. 86
Compositions and Methods Related to CRISPR Targeting
patent-application, April 2015
- Hyde, Roderick A.; Kindsvogel, Wayne R.; Wood, Lowell L.
- US Patent Application 14/048283; 20150098954
Compositions, Methods and Uses for Multiplex Protein Sequence Activity Relationship Mapping
patent-application, March 2017
- Gill, Ryan T.; Lynch, Sean; Warner, Joseph R.
- US Patent Application 15/294356; 20170067046
Allele Selective Gene Editing and Uses Thereof
patent-application, March 2017
- Chivukula, Padmanabh; Wilkie-Grantham, Rachel; Tachikawa, Kiyoshi
- US Patent Application 15/272107; 20170080107
Crystal Structure of an IHF-DNA Complex: A Protein-Induced DNA U-Turn
journal, December 1996
- Rice, Phoebe A.; Yang, Shu-wei; Mizuuchi, Kiyoshi
- Cell, Vol. 87, Issue 7, p. 1295-1306
Nuclease Profiling System
patent-application, November 2016
- Liu, David R.; Pattanayak, Vikram
- US Patent Application 14/911117; 20160333389
Cellulosic hydrolysate toxicity and tolerance mechanisms in Escherichia coli
journal, January 2009
- Mills, Tirzah Y.; Sandoval, Nicholas R.; Gill, Ryan T.
- Biotechnology for Biofuels, Vol. 2, Issue 1, Article No. 26
Search and clustering orders of magnitude faster than BLAST
journal, August 2010
- Edgar, Robert C.
- Bioinformatics, Vol. 26, Issue 19, p. 2460-2461
Engineering of systems, methods and optimized guide compositions for sequence manipulation
patent-application, September 2015
- Zhang, Feng; Cong, Le; Hsu, Patrick
- US Patent Application 14/704551; 20150247150
Modulation of CRP‐dependent transcription at the Escherichia coli acsP2 promoter by nucleoprotein complexes: anti‐activation by the nucleoid proteins FIS and IHF
journal, November 2003
- Browning, Douglas F.; Beatty, Christine M.; Sanstad, Erik A.
- Molecular Microbiology, Vol. 51, Issue 1, p. 241-254
DNA-guided genome editing using the Natronobacterium gregoryi Argonaute
journal, May 2016
- Gao, Feng; Shen, Xiao Z.; Jiang, Feng
- Nature Biotechnology, Vol. 34, Issue 7, p. 768-773
A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase
journal, November 1993
- Ross, W.; Gosink, K.; Salomon, J.
- Science, Vol. 262, Issue 5138, p. 1407-1413
A novel DNA-binding motif in MarA: The first structure for an AraC family transcriptional activator
journal, September 1998
- Rhee, S.; Martin, R. G.; Rosner, J. L.
- Proceedings of the National Academy of Sciences, Vol. 95, Issue 18, p. 10413-10418
Strategy for directing combinatorial genome engineering in Escherichia coli
journal, June 2012
- Sandoval, N. R.; Kim, J. Y. H.; Glebes, T. Y.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 26, p. 10540-10545
Probing Cellular Processes with Oligo-Mediated Recombination and Using the Knowledge Gained to Optimize Recombineering
journal, March 2011
- Sawitzke, James A.; Costantino, Nina; Li, Xin-tian
- Journal of Molecular Biology, Vol. 407, Issue 1, p. 45-59
CRISPR Enabled Multiplexed Genome Engineering
patent-application, August 2017
- Gill, Ryan T.; Garst, Andrew
- US Patent Application 15/116616; 20170240922
Evolution of Escherichia coli rifampicin resistance in an antibiotic-free environment during thermal stress
journal, January 2013
- Rodríguez-Verdugo, Alejandra; Gaut, Brandon S.; Tenaillon, Olivier
- BMC Evolutionary Biology, Vol. 13, Issue 1, Article No. 50
Multiplex RNA-Guided Genome Engineering
patent-application, June 2006
- Church, George M.; Dicarlo, James
- US Patent Application 14/903719; 20160168592
DNA-guided DNA interference by a prokaryotic Argonaute
journal, February 2014
- Swarts, Daan C.; Jore, Matthijs M.; Westra, Edze R.
- Nature, Vol. 507, Issue 7491, p. 258-261
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
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
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
Directed evolution of trimethoprim resistance in Escherichia coli
journal, April 2007
- Watson, Morgan; Liu, Jian-Wei; Ollis, David
- FEBS Journal, Vol. 274, Issue 10, p. 2661-2671