User:Julius B. Lucks



I am a Miller Fellow at the University of California, Berkeley. With Adam Arkin, I am studying and engineering RNA-based systems that control gene expression. I am also part of the Cornell University arXiv.org project, where I am the lead developer of the applications programming interface. You can reach me at jblucks at berkeley dot edu.

Research/Projects
As a Miller Fellow, I have become interested in RNA-based mechanisms that regulate gene expression, and in particular how the interplay between RNA structure and function can be engineered to create a platform for the scalable control of gene expression. One of the most thrilling aspects of this work is that it is at the interface between basic science and engineering. On the basic science side, we use computational structure prediction and in-vivo mutation analysis and screening to uncover RNA-RNA binding and folding pathways that are at the core of the regulatory mechanism. Information gleaned from these mechanistic studies are then used to develop more general engineering principles, where we make targeted changes to the RNA molecules to design functional RNA motifs that have tunable function, can act orthogonally inside the same cell, are both physically and functionally composable, and that ultimately facilitate the design and construction of scalable genetic architectures for controlling gene expression.

In addition to scientific research, I am involved in projects aimed at improving the general science landscape.
 * With Lorrie LeJeune, I helped to start OpenWetWare's Open Writing Projects. As a first article, I have written an introduction to the Python programming language for scientists - Python, All A Scientist Needs.
 * I am also the lead developer of the arXiv.org API, which allows easy, programmatic access to the vast amounts 'open source' scientific information housed at arXiv.org. The API allows software developers to include arXiv.org information, thereby giving scientists easy to use tools to access scientific literature.  It also paves the way for creative uses of the information, and the creation of better search interface tools.

For my PhD, I worked in the area of biophysics with David Nelson, where we used theoretical physics to study problems related to
 * Unzipping DNA at a constant force
 * Translocating RNA through nanopores
 * Geometrical Defects in curved, two-dimensional crystals (related to viral capsids)
 * Phage genome landscapes - a way to visualize important genomic features related to comparative genomics of bacteriophages

Julius B. Lucks
Miller Fellow Department of Bioengineering University of California Berkeley 309 Hildebrand Hall mailcode 5230 Berkeley, CA 94720 510-643-5683 jblucks at berkeley dot edu

Education

 * Miller Fellow, University of California Berkeley (2008)
 * Mentor: Adam Arkin
 * PhD, Harvard University (2002-2007)
 * Chemical Physics
 * Advisor: David Nelson
 * Committee: Dudley Herschbach, Eric Heller, Eugene Shakhnovich
 * Thesis: Biophysics of Polynucleotide Unzipping, Viral Codon Usage and Crystalline Defects
 * MPhil Cambridge University Churchill College (2001-2002)
 * Theoretical Chemistry
 * Advisor: Nicholas Handy
 * Committee: Ali Alavi, David Tozer
 * BS University of North Carolina at Chapel Hill (1997-2001)
 * Chemistry, Highest Honors
 * Mathematics Minor
 * GPA 3.97

Fellowships

 * Miller Fellowship, University of California Berkeley (2008-present)
 * John and Fannie Hertz Foundation Graduate Fellowship, Harvard University (2002-2007)
 * Winston Churchill Scholarship, Cambridge University Churchill College (2001-2002)
 * National Science Foundation Graduate Fellowship (Declined 2001)
 * Department of Defense Graduate Fellowship (Declined 2001)
 * Barry M. Goldwater Scholarship, University of North Caroline Chapel Hill (2000-2001)
 * NSF Research Experience for Undergraduates Fellowship, University of Colorado Boulder (2000)

Honors and Awards

 * Robert Karplus Prize in Chemical Physics, Harvard University (2002)
 * Francis P. Venable Medal, University of North Carolina Chapel Hill (2001)
 * Academic Excellence in Physical Chemistry, University of North Carolina Chapel Hill (2001)
 * Phi Beta Kappa, University of North Carolina Chapel Hill, (2000)
 * American Chemical Society Undergraduate Research Award, University of North Carolina Chapel Hill (1999)

Publications
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 (Not Free)

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)

Presentations
J. B. Lucks, Stanley Qi, Sarah Richardson, Adam P. Arkin Engineering an Antisense-RNA-Mediated Transcription Control System, Selected Presentation, Synthetic Biology 4.0 2008, Hong Kong. (Video)

J. B. Lucks Python - All a Scientist Needs, Pycon 2008, Chicago. (Video)

Posters
J. B. Lucks, Stanley Qi, Adam P. Arkin Toward Scalable Control of Gene Expression Networks with Composable RNA Transcription Attenuator, Gordon Research Conference on Nucleic Acids, June, 2009.

