Publications


A full list of Julius’ publications can be found at his Google Scholar page.

E. J. Strobel, K. E. Watters, Y. Nedialkov, I. Artismovitch, J. B. Lucks. "Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding." Nucleic Acids Research, 2017.
DOI:10.1093/nar/gkx233 
bioRxiv (Open Access): 10.1101/100073 
SHAPE-Seq DataSets: RMDB Entries 
Sequencing Reads: SRA Entries
A. M. Westbrook, J. B. Lucks. "Achieving large dynamic range control of gene expression with a compact RNA transcription-translation regulator." Nucleic Acids Research, 2017.
DOI:10.1093/nar/gkx215 
bioRxiv (Open Access): 10.1101/055327
J. Chappell, J. B. Lucks. "Turning it up to 11: Modular proteins amplify RNA sensors for sophisticated circuitry." Cell Systems, 2016.
DOI: 10.1016/j.cels.2016.12.004
K. E. Watters*, E. J. Strobel*, A. M. Yu, J. B. Lucks. "Cotranscriptional folding of a riboswitch at nucleotide resolution." Nature Structure and Molecular Biology, 2016.
DOI: 10.1038/nsmb.3316
SHAPE-Seq DataSets: RMDB Entries 
Sequencing Reads: SRA Entries
K. E. Watters, J. B. Lucks. "Mapping RNA structure in vitro with SHAPE chemistry and next-generation sequencing (SHAPE-Seq)." in RNA Structure Determination: Methods and Protocols, D. H. Turner, D. H. Mathews (eds.), Methods in Molecular Biology, 2016, 1490, 135-162.
DOI: 10.1007/978-1-4939-6433-8_9
M. K. Takahashi, K. E. Watters, P. M. Gaspar, T. R. Abbott, P. D. Carlson, A. A. Chen, J. B. Lucks. "Using in-cell SHAPE-Seq and simulations to probe structure-function design principles of RNA transcriptional regulators." RNA, 2016, 22, 920-933.
DOI: 10.1261/rna.054916.115
SHAPE-Seq DataSets: RMDB Entries
E. J. Strobel, K. E. Watters, D. Loughrey, J. B. Lucks. "RNA systems biology: uniting functional discoveries and structural tools to understand global roles of RNAs." Current Opinion in Biotechnology, 2016 
DOI: 10.1016/j.copbio.2016.03.019
K. E. Watters, A. M. Yu, E. J. Strobel, A. H. Settle, J. B. Lucks. "Characterizing RNA structures in vitro and in vivo with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)." Methods, 2016
DOI (Open Access):10.1016/j.ymeth.2016.04.002 
bioRxiv (Open Access): 10.1101/034470
SHAPE-Seq DataSets: RMDB Entries
C. J. Glasscock, J. B. Lucks, M. P. DeLisa. "Engineered Protein Machines: Emergent Tools for Synthetic Biology." Cell Chemical Biology, 2016
DOI: 10.1016/j.chembiol.2015.12.004
K. E. Watters, Timothy R. Abbott, J. B. Lucks. "Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq." Nucleic Acids Research, 2015. 
DOI (Open Access):10.1093/nar/gkv879
SHAPE-Seq DataSets: RMDB Entries
S. Meyer, J. Chappell, S. Sankar, R. Chew, J. B. Lucks. "Improving fold activation of small transcription activating RNAs (STARs) with rational RNA engineering strategies."Biotechnology and Bioengineering, 2015. 
DOI:10.1002/bit.25693
bioRxiv (Open Access): 10.1101/022772
J. Chappell, K. E. Watters, M. K. Takahashi, J. B. Lucks. "A renaissance in RNA synthetic biology: new mechanisms, applications and tools for the future." Current Opinion in Chemical Biology, 2015. 
DOI (Open Access):10.1016/j.cbpa.2015.05.018
M. K. Takahashi*, C. A. Hayes*, J. Chappell, Z. Z. Sun, R. M. Murray, V. Nouireaux*, J. B. Lucks*. "Characterizing and prototyping genetic networks with cell-free transcription-translation reactions.", Methods, 2015. (* Co-first/corresponding author)
DOI:10.1016/j.ymeth.2015.05.020
bioRxiv (Open Access): 10.1101/019620
C. Y. Hu, J. D. Varner, J. B. Lucks. "Generating effective models and parameters for RNA genetic circuits.", ACS Synthetic Biology, 2015. 
DOI (Open Access):10.1021/acssynbio.5b00077
bioRxiv (Open Access): 10.1011/018358
Code: GitHub
J. Chappell, M. K. Takahashi, J. B. Lucks. "Creating Small Transcription Activating RNAs." Nature Chemical Biology, 2015, 11, 214-220.
DOI:10.1038/NCHEMBIO.1737
See Commentary! N. Rusk. "Synthetic biology: RNA that activates transcription.", Nature Methods, 2015, 12, 290.
D. Loughrey*, K. E. Watters*, A. Settle, J. B. Lucks. "SHAPE-Seq 2.0: Systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next-generation sequencing." Nucleic Acids Research, 2014, 42, e01. (* Co-first author)
DOI (Open Access): 10.1093/nar/gku909
SHAPE-Seq DataSets: RMDB Entries.
M. K. Takashashi, J. Chappell, C. A. Hayes, Z. Z. Sun, J. Kim, V. Singhal, K. J. Spring, S. Al-Khabouri, C. P. Fall, V. Noireaux, R. M. Murray, J. B. Lucks. "Rapidly characterizing the fast dynamics of RNA genetic circuitry with cell-free transcription-translation (TX-TL) systems." ACS Synthetic Biology, 2014.
DOI (Open Access): 10.1021/sb400206c
bioRxiv (Open Access): 10.1011/003335
J. Chappell, M. K. Takashashi, S. Meyer, D. Loughrey, K. Watters, J. B. Lucks. "The Centrality of RNA for Engineering Gene Expression." Biotechnology Journal, 2013, 8, 1379-1395.
DOI (Open Access): 10.1002/biot.201300018
M. K. Takashashi, J. B. Lucks. "A modular strategy for engineering orthogonal chimeric RNA transcription regulators." Nucleic Acids Research, 2013, 41, 7577-7588.
DOI (Open Access): 10.1093/nar/gkt452
S. A. Mortimer, C. Trapnell, S. Aviran, L. Pachter, J. B. Lucks. "SHAPE-Seq: High Throughput RNA Structural Analysis." Current Protocols in Chemical Biology, 2012, 4, 275-297.
DOI: 10.1002/9780470559277.ch120019
C. C. Liu, L. Qi, J. B. Lucks, T. H. Segall-Shapiro, D. Wang, V. Mutalik, A. P. Arkin. "An adaptor from translational to transcriptional control yields composable regulators of gene expression." Nature Methods, 2012, 9, 1088-1094.
DOI: 10.1038/nmeth.2184
See Commentary! J. J. Tabor. "Modular gene-circuit design takes two steps forward." Nature Methods, 2012, 9, 1061-1063.
P. Cordero, J. B. Lucks, R. Das. "The Stanford RNA Mapping Database for sharing and visualizing RNA structure mapping experiments. " Bioinformatics, 2012, 28, 3006-3008.
DOI (Open Access): 10.1093/bioinformatics/bts554 
Arxiv: arXiv:1110.0235 (q-bio.BM)
V. K. Mutalik, L. Qi, J. C. Guimaraes, J. B. Lucks, A. P. Arkin. "Rationally designed families of orthogonal RNA regulators of translation." Nature Chemical Biology, 2012, 8, 447-454.
DOI: 10.1038/nchembio.919
L. Qi, J. B. Lucks, C. C. Liu, V. K. Mutalik, A. P. Arkin. "Engineering naturally occurring trans-acting non-coding RNAs to sense cellular signals." Nucleic Acids Research, 2012, 40, 5775-5786.
DOI (Open Access): 10.1093/nar/gks168
S. Aviran, J. B. Lucks, L. Pachter. "RNA Structure Characterization from Chemical Mapping Experiments." Forty-Ninth Allerton Conference, UIUC Illinois, 1743-1750, 2011.
Arxiv: arXiv:1106.5061 (q-bio) (FREE)
Conference PDF DOI: 10.1109/Allerton.2011.6120379 (FREE)
J. B. Lucks*, S. A. Mortimer, C. Trapnell, S. Luo, S. Aviran, G. P. Schroth, L. Pachter, J. A. Doudna, A. P. Arkin*. "Multiplexed RNA structure characterization with selective 2’-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)." PNAS, 108, 11063, 2011. (* Co-corresponding author)
DOI (Open Access): 10.1073/pnas.1106501108
See Commentary! K. M. Weeks. "RNA Structure Probing dash Seq.", PNAS, 108, 10933, 2011.
S. Aviran, C. Trapnell, J. B. Lucks, S. A. Mortimer, S. Luo, G. P. Schroth, J. A. Doudna, A. P. Arkin, L. Pachter. "Modeling and automation of sequencing-based characterization of RNA structure." PNAS, 108, 11069, 2011.
DOI (Open Access): 10.1073/pnas.1106541108
See Commentary! K. M. Weeks. “RNA Structure Probing dash Seq.”, PNAS, 108, 10933, 2011.
J. B. Lucks, L. S. Qi, V. K. Mutalik, D. Wang, A. P. Arkin. "Versatile RNA-sensing transcriptional regulators for engineering genetic networks." PNAS, 108, 8617, 2011.
DOI (Open Access): 10.1073/pnas.1015741108
J. B. Lucks, A. P. Arkin. "Synthetic Biology’s Hunt for the Biological Transistor." IEEE Spectrum, March, 38, 2011 (Coverstory).
Request: jblucks(at)cornell(dot)edu
S. L. Young, P. W. Sherman, J. B. Lucks, G. H. Pelto. "Why on Earth?: Evaluating Hypotheses About the Physiological Functions of Human Geophagy." Quarterly Review of Biology, 86, 97, 2011.
PMID: 21800636
Request: jblucks(at)cornell(dot)edu
Jeffery M. Skerker, J. B. Lucks, A. P. Arkin. "Evolution, ecology and the engineered organism: lessons for synthetic biology." Genome Biology, 10, 114, 2009.
DOI: 10.1186/gb-2009-10-11-114
Request: jblucks(at)cornell(dot)edu
J. B. Lucks, L. S. Qi, W. Whitaker, A. P. Arkin. "Toward scalable parts families for predictable design of biological circuits." Current Opinion in Microbiology, 11, 567-573, 2008.
DOI: 10.1016/j.mib.2008.10.002
Request: jblucks(at)cornell(dot)edu
J. B. Lucks "Python – All a Scientist Needs", 2008.
OWW: Article Page (FREE)
Arxiv: arXiv:0803.1838 (q-bio.QM) (FREE)
Video: Pycon 2008 Presentation
J. B. Lucks, D. R. Nelson, G. Kudla, J. B. Plotkin. "Genome landscapes and bacteriophage codon usage", PLoS Computational Biology, 4, 1000001, 2008.
DOI: 10.1371/journal.pcbi.1000001 (FREE)
Arxiv: arXiv:0708.2038v1 (q-bio.GN) (FREE)
J. B. Lucks, Y. Kafri. "Dynamics of RNA Translocation through a Nanopore", 2007.
Arxiv: q-bio.BM/0703028 (FREE)
V. Vitelli, J. B. Lucks, D. R. Nelson. "Crystallography on Curved Surfaces". PNAS, 103, 12323-12328, 2006.
DOI: 10.1073/pnas.0602755103 (FREE)
Arxiv: cond-mat/0604203 (FREE)
J. D. Weeks, J. B. Lucks, Y. Kafri, C. Danilowicz, D. R. Nelson and M. Prentiss. "Pause Point Spectra in DNA Constant-Force Unzipping", Biophysical Journal, 88, 2752-2765, 2005.
DOI: 10.1529/biophysj.104.047340
Arxiv: cond-mat/0406246 (FREE)
J. B. Lucks, A. J. Cohen, N. C. Handy. "Constructing a map from the electron density to the exchange-correlation potential", Physical Chemistry Chemical Physics, 4, 4612, 2002.
Request: jblucks(at)cornell(dot)edu
P. W. Ayers, J. B. Lucks, R. G. Parr. "Constructing exact density functionals from the moments of the electron density". Acta Univ. Debrecceniensis Series Physica et Chimica, XXXIV-XXXV, 223, 2002.
Request: jblucks(at)cornell(dot)edu