Julius B Lucks

Julius B Lucks

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Julius B Lucks

Julius B Lucks

Publications by authors named "Julius B Lucks"

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Computational design of three-dimensional RNA structure and function.

Nat Nanotechnol 2019 Sep 19;14(9):866-873. Epub 2019 Aug 19.

Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.

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http://dx.doi.org/10.1038/s41565-019-0517-8DOI Listing
September 2019

DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data.

Bioinformatics 2019 Aug 7. Epub 2019 Aug 7.

Department of Chemical & Biological Engineering, Evanston, Illinois United States.

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http://dx.doi.org/10.1093/bioinformatics/btz449DOI Listing
August 2019

Tracking RNA structures as RNAs transit through the cell.

Nat Struct Mol Biol 2019 Apr;26(4):256-257

Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.

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http://dx.doi.org/10.1038/s41594-019-0213-2DOI Listing
April 2019

Elements of RNA Design.

Biochemistry 2019 Mar 15;58(11):1457-1459. Epub 2018 Nov 15.

Center for Synthetic Biology , Northwestern University , Evanston , Illinois 60208 , United States.

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http://pubs.acs.org/doi/10.1021/acs.biochem.8b01129
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http://dx.doi.org/10.1021/acs.biochem.8b01129DOI Listing
March 2019

Deconstructing Cell-Free Extract Preparation for in Vitro Activation of Transcriptional Genetic Circuitry.

ACS Synth Biol 2019 02 29;8(2):403-414. Epub 2019 Jan 29.

Interdisciplinary Biological Sciences Program , Northwestern University , Evanston , Illinois 60208 , United States.

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http://dx.doi.org/10.1021/acssynbio.8b00430DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6584022PMC
February 2019

High-throughput determination of RNA structures.

Nat Rev Genet 2018 10;19(10):615-634

Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.

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http://dx.doi.org/10.1038/s41576-018-0034-xDOI Listing
October 2018

SnapShot: RNA Structure Probing Technologies.

Cell 2018 10;175(2):600-600.e1

Center for Synthetic Biology, Northwestern University, Evanston IL; Department of Chemical and Biological Engineering, Northwestern University, Evanston IL.

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https://linkinghub.elsevier.com/retrieve/pii/S00928674183123
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http://dx.doi.org/10.1016/j.cell.2018.09.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582637PMC
October 2018

Engineering a Functional Small RNA Negative Autoregulation Network with Model-Guided Design.

ACS Synth Biol 2018 06 22;7(6):1507-1518. Epub 2018 May 22.

School of Chemical and Biological Engineering , Northwestern University , Evanston , Illinois 60208 , United States.

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http://pubs.acs.org/doi/10.1021/acssynbio.7b00440
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http://dx.doi.org/10.1021/acssynbio.7b00440DOI Listing
June 2018

A flow cytometric approach to engineering Escherichia coli for improved eukaryotic protein glycosylation.

Metab Eng 2018 05 25;47:488-495. Epub 2018 Apr 25.

Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY 14853 USA. Electronic address:

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http://dx.doi.org/10.1016/j.ymben.2018.04.014DOI Listing
May 2018

Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements.

Nucleic Acids Res 2018 03;46(5):2573-2584

Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.

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http://dx.doi.org/10.1093/nar/gkx1273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5861449PMC
March 2018

Mapping RNA Structure In Vitro with SHAPE Chemistry and Next-Generation Sequencing (SHAPE-Seq).

Methods Mol Biol 2016 ;1490:135-62

Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14850, USA.

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http://dx.doi.org/10.1007/978-1-4939-6433-8_9DOI Listing
January 2018

Characterizing the Structure-Function Relationship of a Naturally Occurring RNA Thermometer.

Biochemistry 2017 12 14;56(51):6629-6638. Epub 2017 Dec 14.

Department of Chemical and Biological Engineering, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States.

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http://dx.doi.org/10.1021/acs.biochem.7b01170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5807002PMC
December 2017

Computational design of small transcription activating RNAs for versatile and dynamic gene regulation.

Nat Commun 2017 10 19;8(1):1051. Epub 2017 Oct 19.

Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, IL, 60208, USA.

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http://dx.doi.org/10.1038/s41467-017-01082-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5648800PMC
October 2017

Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding.

Nucleic Acids Res 2017 Jul;45(12):e109

Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60201, USA.

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http://dx.doi.org/10.1093/nar/gkx233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5499547PMC
July 2017

Achieving large dynamic range control of gene expression with a compact RNA transcription-translation regulator.

Nucleic Acids Res 2017 May;45(9):5614-5624

Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.

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http://dx.doi.org/10.1093/nar/gkx215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5435934PMC
May 2017

Cotranscriptional folding of a riboswitch at nucleotide resolution.

Nat Struct Mol Biol 2016 Dec 31;23(12):1124-1131. Epub 2016 Oct 31.

Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA.

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http://dx.doi.org/10.1038/nsmb.3316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5497173PMC
December 2016

Turning It Up to 11: Modular Proteins Amplify RNA Sensors for Sophisticated Circuitry.

Cell Syst 2016 Dec;3(6):509-511

Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2016.12.004DOI Listing
December 2016

Characterizing RNA structures in vitro and in vivo with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).

Methods 2016 07 12;103:34-48. Epub 2016 Apr 12.

School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, United States. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2016.04.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4921265PMC
July 2016

Using in-cell SHAPE-Seq and simulations to probe structure-function design principles of RNA transcriptional regulators.

RNA 2016 06 21;22(6):920-33. Epub 2016 Apr 21.

School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14850, USA.

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http://dx.doi.org/10.1261/rna.054916.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878617PMC
June 2016

RNA systems biology: uniting functional discoveries and structural tools to understand global roles of RNAs.

Curr Opin Biotechnol 2016 06 30;39:182-191. Epub 2016 Apr 30.

School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States. Electronic address:

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http://dx.doi.org/10.1016/j.copbio.2016.03.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5098397PMC
June 2016

Improving fold activation of small transcription activating RNAs (STARs) with rational RNA engineering strategies.

Biotechnol Bioeng 2016 Jan 9;113(1):216-25. Epub 2015 Sep 9.

School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853.

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http://dx.doi.org/10.1002/bit.25693DOI Listing
January 2016

Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq.

Nucleic Acids Res 2016 Jan 8;44(2):e12. Epub 2015 Sep 8.

School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA

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http://dx.doi.org/10.1093/nar/gkv879DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4737173PMC
January 2016

Engineered Protein Machines: Emergent Tools for Synthetic Biology.

Cell Chem Biol 2016 Jan;23(1):45-56

School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chembiol.2015.12.004DOI Listing
January 2016

A renaissance in RNA synthetic biology: new mechanisms, applications and tools for the future.

Curr Opin Chem Biol 2015 Oct 18;28:47-56. Epub 2015 Jun 18.

School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S13675931150005
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http://dx.doi.org/10.1016/j.cbpa.2015.05.018DOI Listing
October 2015

Characterizing and prototyping genetic networks with cell-free transcription-translation reactions.

Methods 2015 Sep 27;86:60-72. Epub 2015 May 27.

School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY 14850, United States. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10462023150022
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http://dx.doi.org/10.1016/j.ymeth.2015.05.020DOI Listing
September 2015

Generating Effective Models and Parameters for RNA Genetic Circuits.

ACS Synth Biol 2015 Aug 2;4(8):914-26. Epub 2015 Jul 2.

School of Chemical and Biomolecular Engineering, Cornell University, Ithaca New York 14850, United States.

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http://www.biorxiv.org/content/biorxiv/early/2015/04/21/0183
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http://pubs.acs.org/doi/abs/10.1021/acssynbio.5b00077
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http://dx.doi.org/10.1021/acssynbio.5b00077DOI Listing
August 2015

Creating small transcription activating RNAs.

Nat Chem Biol 2015 Mar 2;11(3):214-20. Epub 2015 Feb 2.

School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA.

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http://dx.doi.org/10.1038/nchembio.1737DOI Listing
March 2015

A modular strategy for engineering orthogonal chimeric RNA transcription regulators.

Nucleic Acids Res 2013 Aug 12;41(15):7577-88. Epub 2013 Jun 12.

School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1093/nar/gkt452DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753616PMC
August 2013

SHAPE-Seq: High-Throughput RNA Structure Analysis.

Curr Protoc Chem Biol 2012 Dec;4(4):275-97

Department of Molecular and Cell Biology, University of California, Berkeley, California.

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http://dx.doi.org/10.1002/9780470559277.ch120019DOI Listing
December 2012

An RNA Mapping DataBase for curating RNA structure mapping experiments.

Bioinformatics 2012 Nov 12;28(22):3006-8. Epub 2012 Sep 12.

Department of Biochemistry and Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts554DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3496344PMC
November 2012

An adaptor from translational to transcriptional control enables predictable assembly of complex regulation.

Nat Methods 2012 Nov 30;9(11):1088-94. Epub 2012 Sep 30.

Department of Bioengineering, University of California at Berkeley, Berkeley, California, USA.

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http://dx.doi.org/10.1038/nmeth.2184DOI Listing
November 2012

Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals.

Nucleic Acids Res 2012 Jul 1;40(12):5775-86. Epub 2012 Mar 1.

The UC Berkeley & UCSF Graduate Program in Bioengineering, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/nar/gks168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384300PMC
July 2012

Rationally designed families of orthogonal RNA regulators of translation.

Nat Chem Biol 2012 Mar 25;8(5):447-54. Epub 2012 Mar 25.

Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.

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http://dx.doi.org/10.1038/nchembio.919DOI Listing
March 2012

Modeling and automation of sequencing-based characterization of RNA structure.

Proc Natl Acad Sci U S A 2011 Jul 3;108(27):11069-74. Epub 2011 Jun 3.

Department of Bioengineering, University of California, Berkeley, CA 94720, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1106541108
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http://dx.doi.org/10.1073/pnas.1106541108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3131376PMC
July 2011

Why on earth?: Evaluating hypotheses about the physiological functions of human geophagy.

Q Rev Biol 2011 Jun;86(2):97-120

Department of Obstetrics and Gynecology, University of California, San Francisco, California 94105, USA.

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June 2011

Versatile RNA-sensing transcriptional regulators for engineering genetic networks.

Proc Natl Acad Sci U S A 2011 May 9;108(21):8617-22. Epub 2011 May 9.

Department of Bioengineering, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1073/pnas.1015741108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102349PMC
May 2011

Evolution, ecology and the engineered organism: lessons for synthetic biology.

Genome Biol 2009 30;10(11):114. Epub 2009 Nov 30.

Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1186/gb-2009-10-11-114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091310PMC
July 2010

Toward scalable parts families for predictable design of biological circuits.

Curr Opin Microbiol 2008 Dec 12;11(6):567-73. Epub 2008 Nov 12.

Department of Bioengineering, University of California, Berkeley CA, United States.

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http://dx.doi.org/10.1016/j.mib.2008.10.002DOI Listing
December 2008

Genome landscapes and bacteriophage codon usage.

PLoS Comput Biol 2008 Feb 29;4(2):e1000001. Epub 2008 Feb 29.

FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1000001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2266997PMC
February 2008