Publication List

Topological Repulsion between Polymer Globules.

• Jeffrey Chuang, A. Yu. Grosberg, and T. Tanaka, Journal of Chemical Physics 112, 6434 (2000).
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Frustrations in Polymer Gels and Their Minimization through Molecular Imprinting.

• T. Enoki, Jeffrey Chuang, T. Tanaka, A. Yu. Grosberg, et al., Physical Review Letters, 85, 5000 (2000).
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Free Energy Self-Averaging in Protein-Sized Heteropolymers.

• Jeffrey Chuang, A. Yu. Grosberg, and M. Kardar, Physical Review Letters, 87, 078104 (2001).
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Effect of Reversible Cross-linker, N,N'-Bis(acryloyl)-cystamine, on Calcium Ion Adsorption by Imprinted Gels.

• H. Hiratani, C. Alvarez-Lorenzo, Jeffrey Chuang, O. Guney, A. Yu.Grosberg, and T. Tanaka, Langmuir, 17, 4431 (2001).
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Anomalous Dynamics of Translocation.

• Jeffrey Chuang, Y. Kantor, and M. Kardar, Physical Review E, 65, 011802 (2001).
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Multiple point adsorption in a Heteropolymer Gel and the Tanaka Approach To Imprinting: Experiment and Theory.

• K. Ito, Jeffrey Chuang, C. Alvarez-Lorenzo, T. Watanabe, N. Ando, and A. Yu. Grosberg, Progress in Polymer Science, 28, 1489 (2003).
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Multiple Contact Adsorption of Target Molecules by Heteropolymer Gels.

• K. Ito, J. Chuang, C. Alvarez-Lorenzo, T. Watanabe, N. Ando, and A. Yu. Grosberg, Macromolecular Symposia 207, 1 (2004).
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Functional Bias and Spatial Organization of Genes in Mutational Hot and Cold Regions in the Human Genome.

• Jeffrey Chuang and H. Li, PLOS Biology, 2, 0253, doi:10.1371/journal.pbio (2004).
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• Synopsis

Genome-wide Regulatory Complexity in Yeast Promoters: Separation of Functional and Neutral Sequence.

• C.S. Chin, Jeffrey H. Chuang, and H. Li. Genome Research, 15, 205 (2005).
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• Supplementary Materials Website

Similarity of Synonymous Substitutions Rates Across Mammalian Genomes.

• Jeffrey H. Chuang and H. Li. Journal of Molecular Evolution, 65, 236 (2007).
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Sequences Conserved by Selection across Mouse and Human Malaria Species.

• H. Imamura, J. Persampieri, and Jeffrey H. Chuang. BMC: Genomics, 8, 372 (2007).
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• Supplementary Materials Website

Smart Polymers: Applications in Biotechnology and Biomedicine, Second Edition. Chapter title: Imprinting Using Smart Polymers.

• C. Alvarez-Lorenzo, A. Concheiro, Jeffrey Chuang and A. Yu. Grosberg. CRC Press: Boca Raton (2007).

Lipidomic Analysis and Electron Transport Chain Activities in C57BL/6J Mouse Brain Mitochondria.

• M.A. Kiebish, X. Han, H. Cheng, A. Lunford, C.F. Clarke, H. Moon, Jeffrey H. Chuang, and T.N. Seyfried. Journal of Neurochemistry 106, 299–312(2008).

Measuring the Prevalence of Regional Mutation Rates: An Analysis of Silent Substitutions in Mammals, Fungi, and Insects.

• A.K. Fox, B.B. Tuch, and Jeffrey H. Chuang. BMC: Evolutionary Biology, 8, 186 (2008).

Brain Mitochondrial Lipid Abnormalities in Mice Susceptible to Spontaneous Gliomas.

• M.A. Kiebish, X. Han, H. Cheng, Jeffrey H. Chuang, and T.N. Seyfried. Lipids 43, 951-9 (2008).

cneViewer: A Database of Conserved Noncoding Elements for Studies of Tissue-Specific Gene Regulation

• J. Persampieri, D. I. Ritter, D. Lees, J. Lehoczky, Q. Li, S. Guo, and Jeffrey H. Chuang. Bioinformatics, 24:2418-2419 (2008).
• cneViewer website

Cardiolipin and electron transport chain abnormalities in mouse brain tumor mitochondria: Lipidomic evidence supporting the Warburg theory of cancer

• Michael A. Kiebish, Xianlin Han, Hua Cheng, Jeffrey H. Chuang and Thomas N. Seyfried. Journal of Lipid Research, Vol. 49, 2545-2556 (2008)

Weak preservation of local neutral mutation rates across mammalian genomes

• Hideo Imamura, John E Karro and Jeffrey H. Chuang. BMC Evolutionary Biology (2009), 9:89

The effect of Plasmodium falciparum Sir2a histone deacetylase on clonal and longitudinal variation in expression of the var family of virulence genes

Merrick CJ, Dzikowski R, Imamura H, Chuang J, Deitsch K, Duraisingh MT. Int J Parasitol. 2009 (in press).

A systematic approach to identify functional motifs within vertebrate developmental enhancers

Qiang Li, Deborah Ritter, Nan Yang, Zhiqiang Dong, Hao Li, Jeffrey H. Chuang, Su Guo. Developmental Biology 2009 (in press).

COMIT: Identification of Noncoding Motifs under Selection in Coding Sequences

Deniz Kural, Yang Ding, Jiantao Wu, Alicia M Korpi, Jeffrey H. Chuang. Genome Biology 2009 (in press).