H. C. (Paul) LEE  

Selected papers
Articles in Chinese
All publications
- Books

Temporary References

**** Apoptosis ****

Proliferation, cell cycle and apoptosis in cancer
Gerard I. Evan1 and Karen H. Vousden
Nature 411, 342-348 (17 May 2001)

**** Systems Biology ****

Gene_Regulatory_Networks and the Evolution of Animal Body Plans
Eric H. Davidson and Douglas H. Erwin
Science 311:796-800 (2006) Supporting Online Material

Genome Downsizing During Ciliate Development: Nuclear Division of Labor through Chromosome Restructuring
Robert S. Coyne et al.
Annu. Rev. Genet. 1996. 30:557-78.

The yeast cell-cycle network is robustly designed
Fangting Li, Tao Long, Ying Lu, Qi Ouyang, and Chao Tang
PNAS April 6, 2004 vol. 101 no.14, 4781-4786.

**** Evolution and genomics ****

Archaeal Genomics: An Overview
Gary J. Olsen and Carl R. Woese
Cell, 89:991-994, June 27, 1997 Online  PDF

Gene duplication in saccharomyces cerevisiae
P. E. Hansche 1, V. Beres 1, and P. Lange
Genetics 88: 673-687 (1978). PDF

Transposable Elements in Prokaryotes
N Kleckner
Annual Review of Genetics 15:341-404 (1981)

Gene amplification and genomic plasticity in prokaryotes.
David Romero and Rafael Palacios
Ann. Rev. Genet. 31:91-111 (1997). PDF

The CspA family in Escherichia coli: multiple gene duplication for stress adaptation
Yamanaka K., Fang L., Inouye M
Mol. Microbiology, 27:247-255 (1998).

Three views of microbial genomes
Lars Juhl Jensen, Carsten Friis, David W. Ussery.
Res. Microbiol. 150 (1999) 773-777.

The Origins of Eukaryotic Gene Structure
Michael Lynch
Molecular Biology and Evolution 2006 23(2):450-468; Online

The altered evolutionary trajectories of gene duplicates
Michael Lynch and Vaishali Katju
TRENDS in Genetic s Vol. 20:544-549, No.11 November 2006 Online

High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome
Dee R. Denver1, Krystalynne Morris2, Michael Lynch1 and W. Kelley Thomas
Nature 430, 679-682 (5 August 2004) Online

Chromosome evolution in eukaryotes: a multi-kingdom perspective
Avril Coghlana, E. Eichlerc, G. Oliverd, H. Patersone, and Lincoln Steinf
Trends in Genetics Volume 21, Issue 12 , December 2005, Pages 673-682 Online

A genome-wide comparison of recent chimpanzee and human segmental duplications
Ze Cheng, Mario Ventura, Xinwei She, Philipp Khaitovich, Tina Graves, Kazutoyo Osoegawa, Deanna Church, Pieter DeJong, Richard K. Wilson, Svante Paabo, Mariano Rocchi \& Evan E. Eichler
Nature Vol 437:88-93, 1 September 2005 Online  PDF

The Sequence of the Human Genome
J. Craig Venter et al.
Science 16 February 2001: Vol. 291. no. 5507, pp. 1304 - 1351  Online

Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium (Eric S. Lander et al.)
Nature 409, 860-921 (15 February 2001)  Online

The finished DNA sequence of human genome chromosome 12
Steven E.Scherer et al.
Nature, Vol 440, Issue 7082, 346-351, 16 March 2006. Online   PDF

DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage
Michael C. Zody et al.
Nature 440, 1045-1049 (20 April 2006) Online   PDF

Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts
Devin R. Scannell, Kevin P. Byrne1, Jonathan L. Gordon, Simon Wong & Kenneth H. Wolfe
Nature, Vol 440, Issue 7082, 341-345, 16 March 2006. Online   PDF

Prokaryote Phylogeny without Sequence Alignment: From Avoidance Signature to Composition Distance
Bailin Hao and Ji Qi
J. Mol. Evolution, 2003

Recent Segmental Duplications in the Human Genome
Jeffrey A. Bailey, et al. (Eichler group)
Science, Vol 297, Issue 5583, 1003-1007, 9 August 2002

Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome.
Ge Liu, et al (Eichler group)
Genome Res. 2003 March 1; 13(3):358-368.

Gene Duplication and Evolution.
Michael Lynch
Science, Vol 297, Issue 5583, 945-947, 9 August 2002

The Evolutionary Fate and Consequences of Duplicate Genes
Michael Lynch and John S. Conery
Science, Vol 290, Issue 5494, 1151-1155, 10 November 2000

Evolution of genome size: new approaches to an old problem
Dmitri A. Petrov
TRENDS in Genetics Vol.17 No.1 January 2001, 23-28.

Information Theory in Molecular Biology
Christoph Adami
Arxiv preprint q-bio.BM/0405004, 2004

Finding Borders between Coding and Noncoding DNA Regions by an Entropic Segmentation Method
Pedro Bernaola-Galván, Ivo Grosse, Pedro Carpena, José L. Oliver, Ramón Román-Roldán, and H. Eugene Stanley
Phys. Rev. Lett. 85, 1342-1345 (2000)

Analysis of symbolic sequences using the Jensen-Shannon divergence
Ivo Grosse, Pedro Bernaola-Galván, Pedro Carpena, Ramón Román-Roldán, Jose Oliver, and H. Eugene Stanley
Phys. Rev. E 65, 041905 (2002)

Segmentation of genomic DNA through entropic divergence: Power laws and scaling
Rajeev K. Azad, Pedro Bernaola-Galván, Ramakrishna Ramaswamy, and J. Subba Rao
Phys. Rev. E 65, 051909 (2002)

Long-Range Correlation and Partial 1/f Spectrum in a Noncoding DNA Sequence
W Li and K Kaneko
[ Euro. Lett. 17:655-660 (1992)]

Generating Non-trivial Long-Range Correlation and 1/f Spectra by replication and mutation
W Li
[ Int'l J. Bifurcation and Chaos 2:137-154 (1992)]

Complexity of DNA
W Li
[ Complexity 3:33-37 (1997)]

The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties
Nicholas M Luscombe, Jiang Qian, Zhaolei Zhang, Ted Johnson and Mark Gerstein
[ Genome Biology 2002, 3(8):research0040.1­0040.7]

Linguistic features of noncoding DNA sequences
RN Mantegna, SV Buldryev, AL Goldberger, S Havlin, C-K Peng, M Simons and HE Stanley
[ Phy Rev Lett 23:3619-3622 (1994)]

An evolutionary model for the origin of non-randomness, long-range order and fractality in the genome
Yannis Almirantis and Astero Provata
[ BioEssays 23.7:647-656 (2001)] The persistence exponent of DNA
Douglas Poland
[ Biophysical Chemistry 110:59­72 (2004)]

Compressing DNA sequence
Ming Li, et al.
Current Topics in Computational Molecular Biology Edited by Tao Jiang, Ying Xu and Michael Q. Zhang.
[ Chapter 7:157-171 (MIT Press, 2002) ]

Information Entropy Study of Multilingual News Reports
Clive Best, Erik Van der Goot, Joint Research Centre, Ispra, Italy
[ Information Entropy, Best et al.]

Recuurrence time statistics: Versatile tools... By Ying Cao et al.
[ Recuurrence time, Cao et al.]

A Compression Algorithm for DNA Sequences and Its Applications in Genome Comparison
Xin Chen, S.Kwong and Ming Li
[ Proc. 4th Annual Intl Conf. Comp. Molecular Biology (RECOMB4), R. Shamir et al., Eds. 107-117 (2000)]

An information-based sequence distance and its application to whole mitochondrial genome
M. Li, J.H. Badger, X. Chen, S. Kwong, P. Kearney and HY Zhang
[ Bioinformatics, 17:149-154 (2001)]

The Modulation of DNA Content: Proximate Causes and Ultimate Consequences
T. Ryan Gregory1 and Paul D.N. Hebert
[ Genome Research 9:317­324 (1999)]

The Deep Roots of Eukaryotes
S. L. Baldauf
[ Science 300:1703-1706 (2003)]

The Origins of Genome Complexity
Michael Lynch and John S. Conery
[ Science 302:1401-1404 (2003)]

The Evolutionary Fate and Consequences of Duplicate Genes
Michael Lynch and John S. Conery
[ Science 290:1152-1155 (2000)]

Structural Dynamics of Eukaryotic Chromosome Evolution Evan E. Eichler and David Sankoff
[ Science 301:973-979 (2003)]

Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome G Liu et al.
[ Gen. Res. 13:358-368 (2003)]

Intron evolution as a population-genetic process Michael Lynch
[ PNAS 99:6119-6123 (2002)]

An Alu Transposition Model for the Origin and Expansion of Human Segmental Duplications Jeffrey A. Bailey, Ge Liu, and Evan E. Eichler
[ Am. J. Hum. Genet. 73:823-834 (2003)]

**** Protein folding and structure ****

Evidence for the role of PrPC helix 1 in the hydrophilic seeding of prion aggregates
MP Morrissey and EI Shakhnovich
Proc. Natl . Acad . Sci . USA, Vol. 96, pp. 11293­11298, September 1999 (PDF)

Identification and Characterization of an Equilibrium Intermediate in the Unfolding Pathway of an All Beta-Barrel Protein
Dharmaraj Samuel et al.
[ J. Biol. Chem., Vol. 275, Issue 45, 34968-34975, November 10, 2000]

Characterization of the Structure and Dynamics of a Near-native Equilibrium Intermediate in the Unfolding Pathway of an All beta-Barrel Protein
Thiagarajan Srimathi et al.
[ J. Biol. Chem., Vol. 277, Issue 49, 47507-47516, December 6, 2002]

Specificity of native-like interhelical hydrophobic contacts in the apomyoglobin intermediate
Michael S. Kay*, Carlos H. I. Ramos, and Robert L. Baldwin
[PNAS 96, Issue 5, 2007-2012, March 2, 1999]

The molten globule state is involved in the translocation of proteins across membranes?
Valentina E. Bychkova, Roger H. Pain and Oleg B. Ptitsyn
[FEB 238, number 2, 231-234 October 1988]

**** Protein Networks and Maps ****

Overview of biological networks
Harvard_MIT Ph.D. Program in Bioinformatics and Integrative Genomics
[ 2002 September 12 Lecture 1](html-ppt file)

Structure of biological networks: curcuits, modules and motifs
Harvard_MIT Ph.D. Program in Bioinformatics and Integrative Genomics
[ 2002 September 16 Lecture 2](html-ppt file)

Systems Biology: A Brief Overview
Hiroaki Kitano
[ Science Volume 295, Number 5560, Issue of 1 Mar 2002, pp. 1662-1664.]

A Genomic Regulatory Network for Development
Eric H. Davidson
[ Science 295, 1669 (2002)]

Network Motifs: Simple Building Blocks of Complex Networks
R. Milo et al (Departments of Physics of Complex Systems and Molecular Cell Biology, Weizmann Institute of Science)
[ Science. 2002 Oct 25;298(5594):763-4.]

Automated modelling of signal transduction networks
Martin Steffen et al
[ BMC Bioinformatics. 2002 Nov 1;3(1):34. Epub 2002 Nov 01.]

Hierarchical Organization of Modularity in Metabolic Networks
E. Ravasz et al
[ Science. 2002 Aug 30;297(5586):1551-5.]

Inferring domain-domain interactions from protein-protein interactions
Deng M, Mehta S, Sun F, Chen T.
[ Genome Res. 2002 Oct;12(10):1540-8.]

Transcriptional Regulatory Networks in Saccharomyces cerevisiae
Tong Ihn Lee et al.
[ Science. 2002 Oct 25;298(5594):799-804.]

A Protein Interaction Map of Drosophila melanogaster
L. Giot et al.
[ Science Vol 302, 5 December 2003, 1727-1736.]

Evolution of transcription factors and the gene regulatory network in Escherichia coli
M. Madan Babu* and Sarah A. Teichmann
[ Nucleic Acids Research, 2003, Vol. 31, No. 4 1234-1244.]

Topological structure analysis of the protein-protein interaction network in budding yeast
Dongbo Bu et al. Runsheng Chen
[ Nucleic Acids Research, 2003, Vol. 31, No. 9 2443-2450](.pdf file)

Molecular network modeling and data analysis
R. Somogyi, H. Kitano, S. Miyano and Q. Zheng
[ Harvard_MIT Prog. Bioinformatics \& Integrative Genomics
](.pdf file)

Protein-Protein Interaction
Rain et al
[ Nature 409 2001](.pdf file)

Regulatory Network for_Development
Davidson et al
[ Science 2002](.pdf file)

Protein-Protein Interaction
von Mering et al
[ Nature 417 2002](.pdf file)

**** MD codes: AMBER and GROMACS ****

AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules.
D.A. Pearlman, D.A. Case, J.W. Caldwell, W.S. Ross, T.E. Cheatham, III, S. DeBolt, D. Ferguson, G. Seibel, and P. Kollman
[ Comp. Phys. Commun. 91:1-41 (1995)](.pdf file)

GROMACS: A message-passing parallel molecular dynamics implementation
Berendsen, H. J. C., van der Spoel, D., van Drunen
[ Comp. Phys. Comm. 91:43-56, 1995](.pdf file)

Gromacs 3.0: A package for molecular simulation and trajectory analysis
Lindahl, E., Hess, B., van der Spoel, D.
[ J. Mol. Mod. 7:306-317, 2001](.pdf file)

**** Review on MD simulation of proteins ****

Molecular dynamics simulation of biomolecules
Martin Karplus and J.A. Macammon
[ Nature Struc. Bio. 9, 646-652, September 2002](.pdf file)

**** Results from Folding@home ****

Screen savers of the world, Unite!
Michael Shirts and Vijay Pande
[Science 290, 1903-1904, 8 Dec 2000.](.pdf file)

Absolute comparison of simulated and experimental protein-folding dynamics
Christopher D. Snow, Houbi Nguyen, Vijay S. Pande* & Martin Gruebele
[Nature advance online publication, 20 October 2002, pp1-4](.pdf file)

Absolute comparison of simulated and experimental protein-folding dynamics
Christopher D. Snow, Houbi Nguyen, Vijay S. Pande* & Martin Gruebele
[Nature advance online publication, 20 October 2002, pp1-4](.pdf file)

The Trp Cage: Folding Kinetics and Unfolded State Topology via Molecular Dynamics Simulations
Christopher D. Snow, Bojan Zagrovic, and Vijay S. Pande*
[ J. AM. CHEM. SOC. 124, 14548-14549, 2002](.pdf file)

**** Parallel-tempering ****

Parallel-tempering Monte Carlo simulations of the finite temperature behavior of (H_2O)^-_6
F. Wang and K. D. Jordan
[J. Chemical Physics 119, 11645-11653, 8 December 2003](.pdf file)

Phase changes in 38-atom Lennard-Jones clusters. I. A parallel tempering study in the canonical ensemble
J. P. Neirotti, F. Calvo, David L. Freeman and J.D> Doll
[J. Chemical Physics 112, 10340-10349, 15 June 2000](.pdf file)

**** Miscellaneous ****

The protein trinity - linking function and disorder
A. Keith Dunker and Zoran Obradovic
[Nature Biotechnology, 19, 805-806, September 2001](.pdf file)

How Many Conformations Can a Protein Remember?
Thomas M. A. Fink* and Robin C. Ball
[Physical Review Letters 87, 198103-1, 5 November 2001](.pdf file)

An Amino Code for Protein Folding
Jon Rumbley, Linh Hoang, Leland Mayne, and S. Walter Englander*
[PNAS, 98, no. 1, 105-112, January 2, 2001](.pdf file)

PAC: A massive distributed computing facility for molecular dynamics studies of protein structure and protein function
H.C. Lee
[html version of Powerpoint presentation, 2003]

CBL - Computational Biology Lab at NCU
H.C. Lee
[html version of Powerpoint presentation, 2003]

******* Comparative DNA analysis across diverse genomes ****

Ultraconserved elements in human genome
G. Bejerano et al.
Science Express. Science 6 May 2004.0:1098119(.pdf file)

Comparative DNA analysis across diverse genomes
S. Karlin, A.M. Campbell, and J. Mrazek
Annu. Rev. Genet. 1998. 32:185-225.(.pdf file)

The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes
Skaletsky, H. et al.
Nature, 423:825-837, (2003).(.pdf file)

Abundant gene conversion between arms of palindromes in human and ape Y chromosomes
Rozen, S. et al.
Nature, 423:873-876, (2003).(.pdf file)

******* Papers for Center for Soft and Biological Material ****

Jamming of Granular flow in a two-dimensional hopper
K. To, Pik-Yin Lai and H. K. Pak
Phys. Rev. Lett. 85, 71-74 (2001)(.pdf file)

Nonequilibrium Relaxation in Polymer Knot Groups
Pik-Yin Lai, Y.-J. Sheng and H.-K. Tsao
Phys. Rev. Lett.,85, 175503 (2001)(.pdf file)

Turbulent Drag Reduction and Mechanical Degradation of DNA"
, H.J. Choi, S.T. Lim, Pik-Yin Lai, and C.K. Chan
Phys. Rev. Lett. 89, 088302 (2002)(.pdf file)

Modularized Design for Wrappers/Monitors in Data Warehouse Systems
J.T. Horng and J. Lu
Journal of Systems and Software, 3:185-199 (2000)(.pdf file)

Applying Evolutionary Algorithms to Materialized View Selection in A Data Warehouse
J.T. Horng, Y.J. Chang, and B.J. Liu
Soft Computing, 7:574-581 (2003)(.pdf file)

Computing motif correlations in proteins
J.T. Horng, et al.
J. Comp. Chem. 24:2032-43 (2003)(.pdf file)

Adhesion-induced phase separation of multiple species of membrane junctions
H.Y. Chen
Physical Review E 67, 031919 (2003)(.pdf file)

Subcritical bifurcations and nonlinear balloons in Faraday waves membrane junctions
Peilong Chen and Kuo-An Wu
Physical Review Letters 85, 3813 (2000)(.pdf file)

A Mathematical Theory of Communication
C.E. Shannon
The Bell System Technical Journal, Vol. 27, pp. 379-423 (July); 623-656 (October) (1948)(.pdf file)

Divergence measures based on Shannon Entropy
JH Lin
IEEE Trans. Infor. Theory, 37, 145-151 (1991)(.pdf file)

Self-Organized Criticality: An Explanation of $1/f$ Noise
Per Bak, Chao Tang, Kurt Wiesenfeld
Phys. Rev. Lett. 59 (1987) 831-834 (.pdf file)

H. C. (Paul) Lee