J. Lucks

发表

Toward scalable parts families for predictable design of biological circuits.

Weston R. Whitaker, A. Arkin, J. Lucks, 2008, Current opinion in microbiology.

Multiplexed RNA structure characterization with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

Cole Trapnell, A. Arkin, J. Lucks, 2011, Proceedings of the National Academy of Sciences.

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

Zachary Z. Sun, Clarmyra A. Hayes, J. Lucks, 2015, Methods.

Modeling and automation of sequencing-based characterization of RNA structure

Cole Trapnell, A. Arkin, J. Lucks, 2011, Proceedings of the National Academy of Sciences.

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

J. Lucks, J. Chappell, Sarai Meyer, 2015, bioRxiv.

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

Kyle E. Watters, J. Lucks, S. Aviran, 2017, Nucleic acids research.

Computational design of three-dimensional RNA structure and function

Paul D. Carlson, Erik D. Carlson, Alexandra N. Ooms, 2019, Nature Nanotechnology.

Versatile RNA-sensing transcriptional regulators for engineering genetic networks

Adam P Arkin, Vivek K. Mutalik, Julius B Lucks, 2011, Proceedings of the National Academy of Sciences.

Pause point spectra in DNA constant-force unzipping.

J B Lucks, J. Lucks, M. Prentiss, 2004, Biophysical journal.

Design and optimization of a cell-free atrazine biosensor.

Julius B. Lucks, Adam D. Silverman, Michael C. Jewett, 2020, ACS synthetic biology.

Computationally Reconstructing Cotranscriptional RNA Folding Pathways from Experimental Data Reveals Rearrangement of Non-Native Folding Intermediates

Kyle E. Watters, Eric J. Strobel, Angela M. Yu, 2018, bioRxiv.

Computational design of Small Transcription Activating RNAs (STARs) for versatile and dynamic gene regulation

Julius B. Lucks, Alexandra Westbrook, James Chappell, 2017 .

Creating small transcription activating RNAs.

James Chappell, Julius B Lucks, J. Lucks, 2015, Nature chemical biology.

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

Julius B. Lucks, James Chappell, J. Lucks, 2015 .

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

Kyle E. Watters, James Chappell, Julius B Lucks, 2015, Current opinion in chemical biology.

The centrality of RNA for engineering gene expression

Kyle E. Watters, James Chappell, Julius Lucks, 2013, Biotechnology journal.

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

Julius B. Lucks, Adam P. Arkin, Vivek K. Mutalik, 2012, Nucleic acids research.

Supplementary information for Rationally designed families of orthogonal RNA regulators of translation

Adam P Arkin, Vivek K. Mutalik, Julius B Lucks, 2012 .

Design and optimization of a cell-free atrazine biosensor

Khalid K. Alam, J. Lucks, M. Jewett, 2019, bioRxiv.

Deconstructing cell-free extract preparation for in vitro activation of transcriptional genetic circuitry

J. Lucks, M. Jewett, A. Silverman, 2018, bioRxiv.

A primer on emerging field-deployable synthetic biology tools for global water quality monitoring

Jaeyoung K. Jung, Khalid K. Alam, J. Lucks, 2020, npj Clean Water.

Rapid, Low-Cost Detection of Water Contaminants Using Regulated In Vitro Transcription

Jaeyoung K. Jung, Khalid K. Alam, Jeong Wook Lee, 2019, bioRxiv.

Why On Earth?: Evaluating Hypotheses About The Physiological Functions Of Human Geophagy

J. Lucks, P. Sherman, S. Young, 2011, The Quarterly Review of Biology.

SnapShot: RNA Structure Probing Technologies

Angela M Yu, Eric J. Strobel, Julius B. Lucks, 2018, Cell.

Chemical roadblocking of DNA transcription for nascent RNA display

Eric J. Strobel, J. Lucks, J. Lis, 2020 .

Chemical roadblocking of DNA transcription for nascent RNA display

Eric J. Strobel, J. Lucks, J. Lis, 2020, The Journal of Biological Chemistry.

Chemical transcription roadblocking for nascent RNA display

Eric J. Strobel, J. Lucks, J. Lis, 2019, bioRxiv.

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

Kyle E. Watters, Paul D. Carlson, J. Lucks, 2016, RNA.

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

J. Lucks, Alexandra Westbrook, 2016, bioRxiv.

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

Jeffrey M. Skerker, A. Arkin, J. Lucks, 2009, Genome Biology.

Dynamic control of pathway expression with riboregulated switchable feedback promoters

Keith E. J. Tyo, J. Lucks, John T Lazar, 2019, bioRxiv.

Widespread global concern over harm from drinking water

J. Lucks, W. B. de Bruin, C. Staddon, 2021 .

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

Paul D. Carlson, J. Lucks, Sarai Meyer, 2017, Biochemistry.

RNA sequence and structure determinants of Pol III transcriptional termination in human cells

Taylor B. Dolberg, J. Lucks, J. Leonard, 2020, bioRxiv.

A mechanism for ligand gated strand displacement in ZTP riboswitch transcription regulation

Eric J. Strobel, Paul D. Carlson, J. Lucks, 2019, bioRxiv.

Engineered Protein Machines: Emergent Tools for Synthetic Biology.

Julius B Lucks, J. Lucks, Cameron J Glasscock, 2016, Cell chemical biology.

RNA Engineering for Public Health: Innovations in RNA-Based Diagnostics and Therapeutics.

J. Lucks, Walter Thavarajah, David Z. Bushhouse, 2021, Annual review of chemical and biomolecular engineering.

De novo Design of Translational RNA Repressors

Julius B. Lucks, Paul D. Carlson, J. Lucks, 2018 .

Rapidly Characterizing the Fast Dynamics of RNA Genetic Circuitry with Cell-Free Transcription–Translation (TX-TL) Systems

Richard M. Murray, Julius B. Lucks, Jongmin Kim, 2014, ACS synthetic biology.

PLANT-Dx: A Molecular Diagnostic for Point-of-Use Detection of Plant Pathogens

M Verosloff, J Chappell, K L Perry, 2019, ACS synthetic biology.

High-throughput determination of RNA structures

Angela M Yu, Eric J. Strobel, Julius B Lucks, 2018, Nature Reviews Genetics.

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

Kyle E. Watters, Angela M Yu, Eric J. Strobel, 2016, Methods.

Genome Landscapes and Bacteriophage Codon Usage

Joshua B. Plotkin, Julius B. Lucks, David R. Nelson, 2007, PLoS Comput. Biol..

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

Adam P Arkin, Vivek K. Mutalik, Julius B Lucks, 2012, Nature Methods.

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

Kyle E. Watters, Eric J. Strobel, Julius B Lucks, 2016, Current opinion in biotechnology.

Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates.

Angela M. Yu, J. Lucks, Paul M. Gasper, 2021, Molecular cell.

SHAPE–Seq: High‐Throughput RNA Structure Analysis

Lior Pachter, Cole Trapnell, Sharon Aviran, 2012, Current protocols in chemical biology.

RNA sequence and structure determinants of Pol III transcriptional termination in human cells.

Taylor B. Dolberg, J. Lucks, J. Leonard, 2021, Journal of molecular biology.

A ligand gated strand displacement mechanism for ZTP riboswitch transcription control

Eric J. Strobel, Paul D. Carlson, J. Lucks, 2019, Nature Chemical Biology.

Distributed biotin–streptavidin transcription roadblocks for mapping cotranscriptional RNA folding

Kyle E. Watters, Eric J. Strobel, J. Lucks, 2017, Nucleic acids research.

Distributed Biotin-Streptavidin Transcription Roadblocks for Mapping Cotranscriptional RNA Folding

Kyle E. Watters, Eric J. Strobel, J. Lucks, 2017, bioRxiv.

Cotranscriptional Folding of a Riboswitch at Nucleotide Resolution

Kyle E. Watters, Angela M Yu, Eric J. Strobel, 2016, Nature Structural &Molecular Biology.

Programming cell-free biosensors with DNA strand displacement circuits

Julius B. Lucks, Jaeyoung K. Jung, Khalid K. Alam, 2021, bioRxiv.

Cell-free biosensors for rapid detection of water contaminants

Jaeyoung K. Jung, Khalid K. Alam, Jeong Wook Lee, 2020, Nature Biotechnology.

A primer on emerging field-deployable synthetic biology tools for global water quality monitoring

Jaeyoung K. Jung, Khalid K. Alam, J. Lucks, 2020, npj Clean Water.

Point-of-Use Detection of Environmental Fluoride via a Cell-Free Riboswitch-Based Biosensor

Julius B. Lucks, Adam D. Silverman, Michael C. Jewett, 2019, bioRxiv.

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

Nancy Kelley-Loughnane, Michael C Jewett, Julius B Lucks, 2018, ACS synthetic biology.

Distinct timescales of RNA regulators enable the construction of a genetic pulse generator

Julius B. Lucks, Xun Tang, Vincent Noireaux, 2018, bioRxiv.

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

Kyle E. Watters, Julius B. Lucks, J. Lucks, 2015, Nucleic acids research.

An RNA Mapping DataBase for curating RNA structure mapping experiments

Julius B. Lucks, Pablo Cordero, Rhiju Das, 2012, Bioinform..

Dynamic Control of Gene Expression with Riboregulated Switchable Feedback Promoters.

Keith E. J. Tyo, J. Lucks, John T Lazar, 2021, ACS synthetic biology.

Estimating RNA structure chemical probing reactivities from reverse transcriptase stops and mutations

Angela M. Yu, J. Lucks, M. Evans, 2018, bioRxiv.

De-Novo-Designed Translation-Repressing Riboregulators for Multi-Input Cellular Logic

Peng Yin, Friedrich C Simmel, Yu Zhou, 2019, Nature chemical biology.

A modular strategy for engineering orthogonal chimeric RNA transcription regulators

Julius B. Lucks, J. Lucks, Melissa K. Takahashi, 2013, Nucleic acids research.

Organism engineering for the bioproduction of the triaminotrinitrobenzene (TATB) precursor phloroglucinol (PG).

Christopher A. Voigt, Sarah M. Glaven, Matthew W. Lux, 2019, ACS synthetic biology.

Design of a transcriptional biosensor for the portable, on-demand detection of cyanuric acid

Khalid K. Alam, J. Lucks, Srivatsan Raman, 2019, bioRxiv.

De-Novo-Designed Translational Repressors for Multi-Input Cellular Logic

Peng Yin, Julius B. Lucks, Alexander A. Green, 2018 .

Characterizing the structure-function relationship of a naturally-occurring RNA thermometer

J. Lucks, Sarai Meyer, 2017, bioRxiv.

RBS: ribosome binding site ROSE: repression of heat shock gene expression UTR: untranslated region SD: Shine-Dalgarno NMR: nuclear magnetic resonance SHAPE-Seq: Selective 2’-hydroxyl acylation analyzed by primer extension sequencing WT: wild-type SFGFP: superfolder green fluorescent protein LB: Lyso

J. Lucks, Sarai Meyer, 2017 .

SHAPE-Seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing

Kyle E. Watters, Julius B. Lucks, J. Lucks, 2014, Nucleic acids research.

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

Kyle E. Watters, Angela M Yu, Eric J. Strobel, 2015, bioRxiv.

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

Alexandra M. Westbrook, Alexandra Westbrook, James Chappell, 2017, Nature Communications.

Rapidly characterizing the fast dynamics of RNA genetic circuitry with cell-free transcription-translation (TX-TL) systems

Zachary Z. Sun, Clarmyra A. Hayes, Kevin J. Spring, 2014, bioRxiv.

Crystallography on curved surfaces

J. Lucks, D. Nelson, V. Vitelli, 2006, Proceedings of the National Academy of Sciences.

The Stanford RNA Mapping Database for sharing and visualizing RNA structure mapping experiments pdf

Julius B. Lucks, Pablo Cordero, Rhiju Das, 2011, ArXiv.

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

J. Lucks, M. DeLisa, J. H. Merritt, 2018, Metabolic engineering.

Generating effective models and parameters for RNA genetic circuits

Jeffrey D Varner, Julius B Lucks, Chelsea Y. Hu, 2015, bioRxiv.

Generating effective models and parameters for RNA genetic circuits

Julius B. Lucks, Jeffrey D. Varner, Chelsea Y. Hu, 2015, bioRxiv.

Mathematical Modeling of RNA-Based Architectures for Closed Loop Control of Gene Expression.

Xun Tang, Vincent Noireaux, Elisa Franco, 2018, ACS synthetic biology.

Tracking RNA structures as RNAs transit through the cell

Angela M. Yu, J. Lucks, 2019, Nature Structural & Molecular Biology.

Characterizing and Prototyping Genetic Networks with Cell-Free Transcription-Translation Reactions

Richard M. Murray, Julius B. Lucks, Vincent Noireaux, 2015, bioRxiv.

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

Julius B. Lucks, Alexandra M. Westbrook, J. Lucks, 2016, bioRxiv.

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

Kyle E. Watters, Julius B Lucks, J. Lucks, 2016, Methods in molecular biology.

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

J. Lucks, J. Chappell, 2016, Cell systems.

Engineering a Functional small RNA Negative Autoregulation Network with Model-guided Design

Julius B. Lucks, Yan Zhang, Chelsea Y. Hu, 2017, bioRxiv.

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

J. Lucks, M. DeLisa, Cameron J. Glasscock, 2018, Metabolic engineering.

Toward scalable parts families for predictable design of biological circuits.

Weston R. Whitaker, A. Arkin, J. Lucks, 2008, Current opinion in microbiology.

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

Angela M Yu, Neda Bagheri, Albert Y Xue, 2018, bioRxiv.

Python - All a Scientist Needs

Julius B. Lucks, J. Lucks, 2008, 0803.1838.

Supplementary information for Rationally designed families of orthogonal RNA regulators of translation

Vivek K. Mutalik, Joao C. Guimaraes, A. Arkin, 2012 .

Versatile RNA-sensing transcriptional regulators for engineering genetic networks

Vivek K. Mutalik, A. Arkin, J. Lucks, 2011, Proceedings of the National Academy of Sciences.

Computational design of three-dimensional RNA structure and function

Paul D. Carlson, Erik D. Carlson, Alexandra N. Ooms, 2019, Nature Nanotechnology.