User:Julius B. Lucks

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[[Image:JBL.jpg|250px|left|Julius B. Lucks]]
[[Image:JBL.jpg|250px|left|Julius B. Lucks]]
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I am a [http://millerinstitute.berkeley.edu/ Miller Fellow] at the University of California, Berkeley. With [http://genomics.lbl.gov/People.html Adam Arkin], I am working on developing genetic systems that compute.  I am also part of the [http://arxiv.org arXiv.org] project, where I am the lead developer of the [http://export.arxiv.org/api_help applications programming interface].  You can reach me at jblucks at berkeley dot edu.
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I am an Assistant Professor in the [http://www.cheme.cornell.edu/ School of Chemical and Biomolecular Engineering] at Cornell University. Please visit my lab webpage at [http://luckslab.org http://luckslab.org] for more information about my research interests in unraveling the RNA sequence/structure/function code for biology, medicine and biotechnology.
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=== Research/Projects ===
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As a recent [http://millerinstitute.berkeley.edu/ Miller Fellow], I have become interested in studying and developing biological genetic circuits that can perform programmable computations.  While I don't think cellular based computing can rival the speed of silicon computing, I do believe that a cellular system that can be programmed is an extremely powerful tool for applications we can only begin to imagine.  In its simplest incarnation, programmatic control of gene expression would be an invaluable tool for metabolic engineers trying to coax bacteria into producing therapeutics.  More creatively, we might see bacterial cells that can form patterns with each other, and carry out instructions once specific patterns are formed.
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Recent work suggests that these goals are indeed feasible, but that we are in the exciting beginnings of this adventure!  For more information, see the work of Jay Keasling on [http://www.nature.com/nature/journal/v440/n7086/abs/nature04640.html producing anti-malarial drugs inside bacteria], and Ron Weiss on [http://www.pnas.org/content/101/17/6355 pattern-forming bacteria].
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In addition to scientific research, I am involved in projects aimed at improving the general science landscape. 
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* With Lorrie LeJeune, I helped to start OpenWetWare's [[Open_writing_projects|Open Writing Projects]].  As a first article, I have written an introduction to the Python programming language for scientists - [[Julius_B._Lucks/Projects/Python_All_A_Scientist_Needs|Python, All A Scientist Needs]]. 
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* I am also the lead developer of the [http://export.arxiv.org/api_help arXiv.org API], which allows easy, programmatic access to the vast amounts 'open source' scientific information housed at [http://arxiv.org 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.
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For my PhD, I worked in the area of biophysics with [http://www.physics.harvard.edu/people/facpages/nelson.html David Nelson], where we used theoretical physics to study problems related to
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*Unzipping DNA at a constant force
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*Translocating RNA through nanopores
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*Geometrical Defects in curved, two-dimensional crystals (related to viral capsids)
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*Phage genome landscapes - a way to visualize important genomic features
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== CV ==
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===Julius B. Lucks===
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Miller Fellow<br/>
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Department of Bioengineering<br/>
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University of California Berkeley<br/>
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309 Hildebrand Hall<br/>
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mailcode 5230<br/>
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Berkeley, CA 94720<br/>
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510-643-5683<br/>
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jblucks at berkeley dot edu<br/>
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=== Education ===
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* [http://millerinstitute.berkeley.edu/ Miller Fellow], [http://berkeley.edu/ University of California Berkeley] (2008)
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** ''Mentor:'' [http://genomics.lbl.gov/ Adam Arkin]
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* PhD, [http://www.harvard.edu Harvard University] (2002-2007)
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** [http://www.chem.harvard.edu/ Chemical Physics]
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** ''Advisor:'' [http://www.physics.harvard.edu/people/facpages/nelson.html David Nelson]
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** ''Committee:'' [http://nobelprize.org/nobel_prizes/chemistry/laureates/1986/herschbach-autobio.html Dudley Herschbach], [http://www.physics.harvard.edu/people/facpages/heller.html Eric Heller], [http://www-shakh.harvard.edu/ Eugene Shakhnovich]
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** Thesis: ''Biophysics of Polynucleotide Unzipping, Viral Codon Usage and Crystalline Defects''
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* MPhil  [http://www.cam.ac.uk/ Cambridge University] [http://www.chu.cam.ac.uk/ Churchill College] (2001-2002)
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** [http://www-theor.ch.cam.ac.uk/ Theoretical Chemistry]
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** ''Advisor:'' [http://www.ch.cam.ac.uk/staff/nch.html Nicholas Handy]
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** ''Committee:'' [http://www.ch.cam.ac.uk/staff/aa.html Ali Alavi], [http://www.dur.ac.uk/chemistry/staff/?id=202 David Tozer]
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* BS [http://www.chem.unc.edu/ University of North Carolina at Chapel Hill] (1997-2001)
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** Chemistry, Highest Honors
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** Mathematics Minor
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** GPA 3.97
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=== Fellowships ===
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* [http://millerinstitute.berkeley.edu/ Miller Fellowship], University of California Berkeley (2008-present)
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* [http://www.hertzfoundation.org/ John and Fannie Hertz Foundation Graduate Fellowship], Harvard University (2002-2007)
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* [http://www.winstonchurchillfoundation.org/ Winston Churchill Scholarship], Cambridge University Churchill College (2001-2002)
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* [https://www.fastlane-beta.nsf.gov/grfp/Login.do National Science Foundation Graduate Fellowship] (Declined 2001)
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* [https://www.asee.org/ndseg/ Department of Defense Graduate Fellowship] (Declined 2001)
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* [http://www.act.org/goldwater/ Barry M. Goldwater Scholarship], University of North Caroline Chapel Hill (2000-2001)
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* NSF Research Experience for Undergraduates Fellowship, University of Colorado Boulder (2000)
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=== Honors and Awards ===
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* Robert Karplus Prize in Chemical Physics, Harvard University (2002)
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* Francis P. Venable Medal, University of North Carolina Chapel Hill (2001)
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* Academic Excellence in Physical Chemistry, University of North Carolina Chapel Hill (2001)
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* Phi Beta Kappa, University of North Carolina Chapel Hill, 2000
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* American Chemical Society Undergraduate Research Award, University of North Carolina Chapel Hill (1999)
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=== Publications ===
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'''J. B. Lucks''' ''Python - All a Scientist Needs'', 2008.
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:OWW: [[Julius_B._Lucks/Projects/Python_All_A_Scientist_Needs|Article Page]] (FREE)
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:Arxiv: [http://arxiv.org/abs/0803.1838 arXiv:0803.1838 (q-bio.QM)] (FREE)
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'''J. B. Lucks''', D. R. Nelson, G. Kudla, J. B. Plotkin. ''Genome landscapes and bacteriophage codon usage'', PLoS Computational Biology, '''4''', .1000001, 2008.
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:DOI: [http://dx.doi.org/10.1371/journal.pcbi.1000001 10.1371/journal.pcbi.1000001] (FREE)
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:Arxiv: [http://www.arxiv.org/abs/0708.2038 arXiv:0708.2038v1 (q-bio.GN)] (FREE)
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'''J. B. Lucks''', Y. Kafri. ''Dynamics of RNA Translocation through a Nanopore'', 2007.
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:Arxiv: [http://www.arxiv.org/abs/q-bio.BM/0703028 q-bio.BM/0703028] (FREE)
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V. Vitelli, '''J. B. Lucks''', D. R. Nelson. ''Crystallography on Curved Surfaces''. PNAS, '''103''', 12323-12328, 2006.
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:DOI: [http://dx.doi.org/10.1073/pnas.0602755103 10.1073/pnas.0602755103] (FREE)
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:Arxiv: [http://www.arxiv.org/abs/cond-mat/0604203 cond-mat/0604203] (FREE)
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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. 
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:DOI: [http://dx.doi.org/10%2E1529/biophysj%2E104%2E047340 10.1529/biophysj.104.047340],
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:Arxiv: [http://www.arxiv.org/abs/cond-mat/0406246 cond-mat/0406246] (FREE)
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Current revision

Julius B. Lucks

I am an Assistant Professor in the School of Chemical and Biomolecular Engineering at Cornell University. Please visit my lab webpage at http://luckslab.org for more information about my research interests in unraveling the RNA sequence/structure/function code for biology, medicine and biotechnology.








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