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Terry Clark and J.Andrew McCammon:
Parallelization of a molecular dynamics non-bonded force algorithm
for MIMD architecture. Computers and Chemistry, 14(3):219-224, 1990.
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Terry Clark, J.Andrew McCammon and L.Ridgway Scott:
Parallel molecular dynamics. Proceedings of the Fifth SIAM Conference on
Parallel Processing for Scientific Computing, J. Dongarra, et al.,
Philadelphia: SIAM, March, pp. 338-344, 1991.
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Terry Clark, Reinhard von Hanxleden, Ken Kennedy, Charles Koelbel,
and L.Ridgway Scott:
Evaluating parallel languages for molecular dynamics computations.
Proceedings of the Scalable High Performance Computing Conference,
Williamsburg, VA, April, pp. 98-105, 1992.
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Babak Bagheri, Terry Clark, and L.Ridgway Scott:
Pfortran: A Parallel dialect of Fortran. Fortran Forum, ACM Press, 11:3-20, 1992.
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Yat Ting Wong, Terry Clark, Jian Shen, and J.Andrew McCammon:
Molecular dynamics simulation of substrate-enzyme interactions in the active
site channel of superoxide dismutase. Molecular Simulation, 10(2-6):277-289, 1993.
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Terry Clark, Reinhard von Hanxleden, J.Andrew McCammon, and L.Ridgway Scott:
Parallelization using spatial decomposition for molecular dynamics.
Proceedings of the Scalable High Performance Computing Conference,
Knoxville, TN, May, 1994.
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Stanislaw Wlodek, Jan Antosiewicz, Michael K. Gilson,
J.Andrew McCammon, Terry Clark, and L.Ridgway Scott:
Computer modeling of acetylcholinesterase and acetylcholinesterase-ligand
complexes. Enzymes of the Cholinesterase Family.
editors: D.M. Quinn, et al., Plenum, pp. 97-104, 1995.
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Terry Clark, J.Andrew McCammon, L.Ridgway Scott, and Stanislaw Wlodek.
I/O limitations in parallel molecular dynamics. Proceedings of Supercomputing 1995,
San Diego, November, 1995.
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Piotr Bala, Terry Clark, Palo Grochowski, Bogdan Lesyng and J.Andrew McCammon:
A Parallel version of the combined quantum classical molecular dynamics
code for complex molecular and biomolecular systems.
In Recent Advances in Parallel Virtual Machine and Message Passing Interface,
Lecture Notes in Computer Science 1332,
editors: M. Bubak, J. Dongarra, J. Wasniewski,
Springer-Verlag Berlin-Heidelberg, pp. 409-416, 1997.
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Terry Clark,
Attributes of molecular dynamics calculations: accounting for CPU cycles:
Proceedings of the Eighth SIAM Conference on
Parallel Processing for Scientific Computing, March, 1997.
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Stanislaw Wlodek, Terry Clark, L.Ridgway Scott, and J.Andrew McCammon:
Molecular dynamics of acetylcholinesterase dimer complexed with tacrine.
Journal of the American Chemical Society, 119(40):9513-9522, 1997.
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Terry Clark, Reinhard von Hanxleden, and Ken Kennedy:
Experiences in Data-Parallel Programming.
Scientific Programming, 6:153-158, 1997.
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P. Bala, T. Clark, P. Grochowski, K. Nowinski, B. Lesyng and J.A. McCammon:
Advanced simulations and visualization of enzymatic reactions
using a combined quantum-classical molecular dynamics. Recent Advances,
Applied Parallel Computing Lecture Notes in Computer Science 1541,
editors: B. Kaagstrom, J. Dongarra, E. Elmroth, and J. Wasniewski
Springer-Verlag Berlin-Heidelberg, pp. 20-26, 1998.
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J.A. McCammon, S. Wlodek, T. Clark, P. Kirchhoff, L.R. Scott, and S. Tara:
Computer simulation studies of acetylcholinesterase dynamics and activity.
Structure and Function of Cholinesterases and Related Proteins,
editors: B.P. Doctor, P. Taylor, D.M. Quinn, R.L. Rotundo, and M.K. Gentry,
Plenum Press, New York, pp. 327-329, 1998.
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Piotr Bala and Terry Clark:
Experiences with Co-Array Fortran and Pfortran as Tools for Parallelization of
a Large-Scale Scientific Application.
Proceedings of the Third International Conference on Parallel
Processing & Applied Mathematics,
editors: R. Wyrzykowski and B. Mochnacki and H. Piech and J. Szopa,
Technical University of Czestochowa, pp. 367-377, 1999.
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Piotr Bala, Terry Clark, and L. Ridgway Scott:
Application of Pfortran and Co-Array Fortran in the parallelization
of the GROMOS96 molecular dynamics module.
Proceedings of the SGI Users Conference, Krakow, Poland, October 11-24, 2000
(distinguished paper).
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Sanggyu Lee, Guolin Zhou, Terry Clark, Jianjun Chen, Janet D. Rowley,
and San Ming Wang:
The pattern of gene expression in human CD15+ myleoid progenitor cells.
Proc. Natl. Acad. Sci., 98(6):3340-3345, 2001.
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Jianjun Chen, Donald Rowley, Terry Clark, Sanggyu Lee, Guolin Zhou,
Christian Cheers, Janet D. Rowley, and San Ming Wang:
Genome-level identification of expressed genes in mouse Gr-1+
myeloid progenitor cells. Genomics, 77:149-162, 2001.
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Piotr Bala, Terry Clark and L. Ridgway Scott:
Application of Pfortran and Co-Array Fortran in the parallelization of
the GROMOS96 molecular dynamics module.
Scientific Programming, 9(1):61-68, 2001.
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Douglas Kyung Nam, Sanggyu Lee, Guolin Zhou, Xiahong Cao, Clarence Wang,
Terry Clark, Jianjun Chen, Janet D. Rowley, and San Ming Wang:
Oligo(dT) primer generates a high frequency of truncated cDNAs
through internal poly(A) priming during reverse transcription.
Proc. Natl. Acad. Sci. (USA), 99(9):6152-6156, 2002.
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Sanggyu Lee, Terry Clark, Jianjun Chen, Guolin Zhou,
L. Ridgway Scott, Janet D. Rowley, and San Ming Wang:
Correct identification of genes from SAGE tag sequences.
Genomics, 79(4):598-602, 2002.
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Terry Clark, Sanggyu Lee, Ridgway Scott, and Sanming Wang:
Computational analysis of gene identification with SAGE.
Journal of Computational Biology, 9(3):527-540, 2002.
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Guolin Zhou, Jianjun Chen, Sanggyu Lee, Terry Clark, Janet D. Rowley,
and San Ming Wang, book chapter, Perspectives in Gene Expression,
edited by Krishnarao Appasani, 2003.
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L. Ridgway Scott, Terry Clark, and Babak Bagheri:
Education and research challenges in parallel scientific computing.
International Conference on Computational Science (ICCS) 2005,
Emory University, Atlanta, GA, May 22-25, 2005.
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Sanggyu Lee, Jingyue Bao, Guolin Zhou, Joshua Sahpiro, Jinhua Xu,
Run Zhang Shi, Xuemei Lu, Terry Clark, Deborah Johnson, Yeong C. Kim,
Claudia Wing, Charles Tseng, Min Sun, Wei Lin, Jun Wang, Huanming Yang,
Jian Wang, Wei Du, Chung-I Wu, Xiuqing Zhang, and San Ming Wang:
Detecting novel low-level transcripts in Drosophila:
Cold Spring Harbor Laboratory Press, RNA, 11:939-946, 2005.
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Jingue Bao, Sanggyu Lee, Chen Chen, XiuQing Zhang, Yu Zhang, SiQi Liu,
Terry Clark, Jian Wang, MengLiang Cao, HuanMing Yang, San Ming Wang, and Jun Yu:
Serial analysis of gene expression study of
a hybrid rice strain (LYP9) and its parental cultivars.
Plant Physiolology, 138(3):1216-31, 2005.
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Terry Clark, Josef Jurek, Gregory Kettler, and Daphne Preuss:
A structured interface to the object-oriented Genomics Unified Schema
for XML formatted data. Applied Bioinformatics, 4(1):13-24, 2005.
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Robert Swanson, Terry Clark, and Daphne Preuss:
Expression profiling of Arabidopsis stigma tissue identifies
stigma-specific genes. Sexual Plant Reproduction, Oct 2005, pages 1-9.
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Guojie Zhang, Hongsheng Wang, Junjie Shi, Hongkun Zheng, Gane,
Ka-Shu Wong, Terry Clark, Wen Wang, Jun Wang, Le Kang:
Identification and
characterization of insect-specific proteins by genome data analysis,
BMC Genomics, 8:93, 2007.
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Lance Feagan, Justin Rohrer, Alexander Garrett, Heather Amthauer,
Ed Komp, David Johnson, Adam Hock, Terry Clark, Gerald Lushington,
Gary Minden, Victor Frost:
Bioinformatics process management: Information flow
via a computational journal. BMC Source Code for Biology and Medicine, 2007, 2:9.
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Shuqing Xu, Terry Clark, Hongkun Zheng, Soren Vang, Ruiqiang Li,
Gane Ka-Shu Wong, Jun Wang, Xiaoguang Zheng:
Gene Conversion in the Rice Genome,
BMC Genomics, 25 February 2008.
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Junyi Wang, Hongkun Zheng, Terry Clark, Lijuan Cong, Zhike Lu, Junjie Shi,
Zhensheng Li, Yiping Tong, Karsten Kristiansen, Jun Wang: "A high incidence of
new genes and rapid evolution of HSP90 after a burst of gene duplication in mammals,"
Rice Genome, submittted Molecular Biology and Evolution, 2007.
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Yi Jia, Josef Jurek, Kamen Nikolov, Terry Clark,
Integration of genomic data from multiple
sources using XMLGUS, submitted 2007.
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Terry Clark, John Goldsmith, Krishna Priya Kotcherlakota, and L. Ridgway Scott,
Compositional analysis of genome sequences using multigram decompositions,
submitted 2007.
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