LEE, JULIAN

CONTACT PHONE: 820-0453
e-mail: jul@ssu.ac.kr
RESEARCH INTEREST BIOINFORMATICS AND BIOPHYSICS
PROTEIN FOLDING
PROTEIN STRUCTURE PREDICTION
GLOBAL OPTIMIZATION
STATISTICAL PHYSICS
EDUCATION 1989.8 : Bachelor, Dept. of Physics, Seoul National University
1991. 5 : Science Master, Dept. of Physics, Brown University, USA
1994. 5 : Philosophy Doctor (High Energy Physics), Dept. of Physics, Brown University, USA 
CAREER 2015.3 - PRESENT : Professor, School of Systems Biomedical Science and Dept. of Bioinformatics and Life Science, Soongsil University
2009.4 - 2015.2 : Associate Professor, School of Systems Biomedical Science and Dept. of Bioinformatics and Life Science, Soongsil University
2010. 3 - 2011.2 : Visiting Associate Professor, Dept. of Pharmaceutical Chemistry and Graduate Group in Biophysics, University of California San Francisco, USA
2003. 3 - 2009. 3 : Assistant Professor, Dept. of Bioinformatics and Life Science, Soongsil University
2003. 2. :   Assistant Professor, School of Computational Sciences, Korea Institute for Advanced Study
2001. 7 - 2003. 2 : Research Fellow, School of Computational Sciences, Korea Institute for Advanced Study
2000. 1 - 2001. 6 : Foreign Research Fellow, Japan Society for Promotion of Sciences (Univ. of Tokyo)
1998. 1 - 1999. 12 : Research Fellow, School of Physics, Korea Institute for Advanced Study
1997. 6 - 1997. 12 : Research Fellow, Korean Society fir Promotion of Sciences (Hanyang Univ.)
1997. 5                   : Visiting Scholar, Asia-Pacific Center for Theoretical Physics
1994. 6 - 1997 4 : Research Fellow, Center for Theretical Physics, Seoul National University

PUBLICATION LIST (selected)

49. "Derivation of Markov processes that violate detailed balance"
      Julian Lee
      Physical Review E 97 (2018) 032110. (pdf)

48. "Transfer matrix algorithm for computing the exact partition function of a square lattice polymer"
      Julian Lee
      Computer Physics Communications 228 (2018) 11-21. (pdf)

47. "Stability analysis of an autocatalytic protein model"
      Julian Lee
      AIP advances 6 (2016) 055013. (link)

46. "Microcanonical analysis of a nonequilibrium phase transition"
      Julian Lee
      Physical Review E 93 (2016) 052148. (pdf)

45. "D-Galactose as an autoinducer 2 inhibitor to control the biofilm formation of periodontopathogens"
       Eun-Ju Ryu, Jaehyun Sim, Jun Sim, Julian Lee, and Bong-Kyu Choi
       Journal of Microbiology 54 (2016) 632. (pdf)

44. "Study on collapse and folding transitions of a lattice protein using exact enumeration"
      Jae Hwan Lee, Seung-Yeon Kim, and Julian Lee
      AIP advances 5 (2015) 127211. (link)

43. "Method for identification of rigid domains and hinge residues in proteins based on exhaustive enumeration"
      Jaehyun Sim, Jun Sim, Eunsung Park, and Julian Lee
      Proteins:Structure,Function,and Bioinformatics 83 (2015) 1054-1067. (pdf)

42. "Reply to C. Tsallis’«Conceptual Inadequacy of the Shore and Johnson Axioms for Wide Classes of Complex
      Systems»"
      Steve Pressé, Kingsuk Ghosh, Julian Lee, and Ken Dill
      Entropy 17 (2015) 5043-5046. (pdf)

41. "Single Molecule Conformational Memory Extraction: P5ab RNA Hairpin
      Steve Pressé, Jack Peterson, Julian Lee, Phillip Elms, Justin MacCallum, Susan Marqusee,
      Carlos Bustamante, and Ken Dill
      Journal of Physical Chemistry B 118 (2014) 6597-6603. (pdf)

40. "Nonadditive Entropies Yield Probability Distributions with Biases not Warranted by the Data"
     Steve Pressé, Kingshukl Ghosh, Julian Lee, and Ken Dill
      Physical Review Letters 111 (2013) 180604. (pdf)

39. "Exact Partition Function Zeros of the Wako-Saito-Muñoz-Eaton beta hairpin Model"
     Julian Lee
      Physical Review E 88 (2013) 022710.
     abstract    pdf

38. "Exact Partition Function Zeros of the Wako-Saito-Muñoz-Eaton Protein Model"
     Julian Lee
      Physical Review Letters 110 (2013) 248101.
     abstract    pdf

37. "Principles of maximum entropy and maximum caliber in statistical physics"
     Steve Pressé, Kingshukl Ghosh, Julian Lee, and Ken Dill
      Review of Modern Physics 85 (2013) 1115-1141.
     abstract   pdf

36. "Partition function zeros of a square-lattice homopolymer with nearest- and next-nearest-neighbor interactions"      Jae Hwan Lee, Seung-Yeon Kim and Julian Lee*
      Physical Review E 87 (2013) 052601.
     abstract    pdf

35. "Extracting Conformational Memory from Single-Molecule Kinetic Data"
     Steve Pressé, Julian Lee, and Ken Dill
      Journal of Physical Chemistry B 117 (2013) 495.
     abstract    pdf

34. "Microcanonical origin of the maximum entropy principle for open systems"
     Julian Lee* and Steve Pressé
      Physical Review E 86 (2012) 041126.
     abstract    pdf

33. "A derivation of the master equation from path entropy maximization"
     Julian Lee* and Steve Pressé
      Journal of Chemical Physics 137 (2012) 074103.
     abstract    pdf

32. "Exact partition function zeros of a polymer on a simple cubic lattice"
     Jae Hwan Lee, Seung-Yeon Kim, and Julian Lee*
      Physical Review E 86 (2012) 011802.
     abstract    pdf

31. "Collapse transition of a square-lattice polymer with next nearest-neighbor interaction "
     Jae Hwan Lee, Seung-Yeon Kim, and Julian Lee*
      Journal of Chemical Physics 135 (2011) 204102.
     abstract    pdf

30 . "The FALC-Loop web server for protein loop modeling"
     Junsu Ko, Dongseon Lee, Hahnbeom Park, Evangelos A. Coutsias, Julian Lee*, and Chaok Seok*
     Nucleic Acid Research 39 (2011) W210-W214.
     abstract    pdf   Server

29. "Refinement of protein termini in template-based modeling using conformational space annealing"
     Hahnbeom Park, Junsu Ko, Keehyung Joo, Julian Lee, Chaok Seok and Jooyoung Lee
     Proteins: Structure, Function, and Bioinformatics 79 (2011) 2725-2734.
     abstract    pdf

28. "Parallel Algorithm for Calculation of the Exact Partition Function of a Lattice Polymer"
     Jae Hwan Lee, Seung-Yeon Kim, and Julian Lee*
     Computer Physics Communications 182 (2011) 1027-1033.
     abstract    pdf

27. "Protein loop modeling by using fragment assembly and analytical loop closure"
     Julian Lee*, Dongseon Lee, Hahnbeom Park, Evangelos A. Coutsias, and Chaok Seok*
     Proteins: Structure, Function, and Bioinformatics 78 (2010) 3428-3436.
     abstract    pdf   Server

26. "Exact partition function zeros and the collapse transition of a two-dimensional lattice polymer"
     Jae Hwan Lee, Seung-Yeon Kim, and Julian Lee*
     Journal of Chemical Physics 133 (2010) 114106.
     abstract    pdf

25. "A new method for prediction of RNA secondary structure with pseudoknots, based on helix removal and refinement
     Bayarbaatar Amgalan and Julian Lee*
     Optimization 58 (2009) 861-869.
     abstract    pdf

24. "Protein Structure Prediction Using the Hybrid Energy Function, Fragment Assembly and Double Optimizaiton"
     Kwang-Hwi Cho
, Taek-Kyun Kim, and Julian Lee*
     J
ournal of the Korean Physical Society 52 (2008) 143-151.
     abstract    pdf

23. "Protein Loop Modeling Using Fragment Assembly "
     
Dongseon Lee, Chaok Seok*, and Julian Lee*
     J
ournal of the Korean Physical Society 52 (2008) 1137-1142.
     abstract    pdf

22. "Protein Folding Using Fragment Assembly and Physical Energy Function"
     Seung-Yeon Kim, Weontae Lee, and Julian Lee*
     Journal of Chemical Physics 125 (2006) 194908.

     abstract    pdf

21. "Measures for the assessment of fuzzy predictions of protein secondary structure",
     Julian Lee
     Proteins: Structure, Function, and Bioinformatics 65 (2006) 453-462.

     abstract    pdf

20. "Double Optimization for Design of Protein Energy Function",
     Seung-Yeon Kim, and Julian Lee*
     Lecture Notes in Bioinformatics 4115 (2006) 562
-570.
     abstract    pdf

19. "Fuzzy k-Nearest Neighbor Method for Protein Secondary Structure Prediction and its Parallel      Implementation",
     Seung-Yeon Kim, Jaehyun Sim, and Julian Lee*
     Lecture Notes in Bioinformatics 4115 (2006) 4
44-453.
     abstract    pdf

18. "Prediction of protein solvent accessibility using fuzzy k-nearest neighbor method"
     Jaehyun Sim, Seung-Yeon Kim, and Julian Lee*
     Bioinformatics 21< (2005)
2844-2849.
     abstract    pdf

17. " Protein structure prediction based on fragment assembly and beta-strand pairing energy function",
     Julian Lee, Seung-Yeon Kim, and Jooyoung Lee
     Journal of Korean Physical Society 46  (2005) 707 - 712.
     abstract    pdf

16. "Protein structure prediction based on fragment assembly and parameter optimization"
     Julian Lee, Seung-Yeon Kim, and Jooyoung Lee
     Biophysical Chemistry 115 (2005) 209-214.
     abstract    pdf

15. "Folding simulations of small proteins "
     Seung-Yeon Kim, Julian Lee, and Jooyoung Lee
     Biophysical Chemistry 115 (2005) 195-200.
     abstract    pdf

14. " Conformational space annealing and a lattice model protein "
     Julian Lee
     Journal of Korean Physical Society 45  (2004) 1450 - 1454.
     abstract    pdf

13. " Prediction of the secondary structure of proteins using PREDICT, a nearest neighbor method on pattern space"
     Keehyung Joo, Ilsoo Kim, Julian Lee, Seung-Yeon Kim, Sung Jong Lee, and Jooyoung Lee
     Journal of Korean Physical Society 45  (2004) 1441 - 1449.
     abstract    pdf

12. "Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing"
     Julian Lee, Seung-Yeon Kim, Keehyung Joo, Ilsoo Kim, and Jooyoung Lee
     Proteins: Structure, Function, and Bioinformatics 56 (2004) 704-714.
     abstract    pdf

11. "Design of a protein potential energy landscape by parameter optimization"
    Julian Lee, Seung-Yeon Kim, and Jooyoung Lee

     Journal of Physical Chemistry B 108 (2004) 4525 - 4534.
     abstract    pdf 

10. "Folding of small proteins using a single continuous potential"
    Seung-Yeon Kim, Julian Lee, and Jooyoung Lee
    Journal of Chemical Physics 120 (2004) 8271 - 8276.
    abstract    pdf 

9. "Exact partition function zeros of two-dimensional lattice polymers"
    Julian Lee
   
Journal of Korean Physical Society 44  (2004) 617 - 620.
    abstract    pdf 

8. "Optimization of potential-energy parameters for folding of several proteins"
    Julian Lee, Seung-Yeon Kim, and Jooyoung Lee
    Journal of Korean Physical Society 44 (2004) 594 - 598.
    abstract    pdf 

7. "Profile-based nearest neighbor method for pattern recognition"
Keehyoung Joo, Julian Lee, Seung-Yeon Kim, Ilsoo Kim, Sung Jong Lee, and Jooyoung Lee
Journal of Korean Physical Society 44 (2004) 599 - 604.
abstract    pdf 

 

6. "Unbiased Global Optimization of Lennard-Jones Clusters for N>=201 Using the Conformational Space Annealing Method"
Julian Lee, In-Ho Lee, and Jooyoung Lee
Physical Review Letters 91 (2003) 080201-080204.
abstract    pdf 

 

5. "Prediction of protein tertiary structure using PROFESY, a novel method based on pattern matching and fragment assembly"
     Julian Lee, Seung-Yeon Kim, Keehyoung Joo, Ilsoo Kim, Saejoon Kim,  and Jooyoung Lee
     Fifth Meeting on the Critical Assessment of Techniques for Protein Structure Prediction (2002), p.A97 - A98.

 

4. "Prediction of protein secondary structure using PREDICT, a novel method based on pattern matching"
     Keehyoung Joo, Ilsoo Kim, Julian Lee, Seung-Yeon Kim, Sung Jong Lee, and Jooyoung Lee

      Fifth Meeting on the Critical Assessment of Techniques for Protein Structure Prediction (2002) p.A96 - A97.

 

3. "Full Optimization of Linear Parameters of a United Residue Protein Potential"
    Julian Lee, Kibeom Park, and Jooyoung Lee
    Journal of Physical Chemistry B 106
(2002) 11647.

 

2. "Tunneling between the giant gravitons in AdS5 x S5"
     Julian Lee
     
Physical Review D 64 (2001) 046012.

 

1. "Exact zeros of the partition function for a continuum system with  double Gaussian peaks"
     Julian Lee and Koo-Chul Lee
     
Physical Review E 62 (2000) p.4558.

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