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"PCA and Clustering Reveal Alternate mtDNA Phylogeny of N and M Clades." J Mol Evol 67(5):465-487 (2008).

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"Mitochondrial DNA Haplogroup D4a is a Marker for Extreme Longevity in Japan." PLoS ONE 3(6):e2421.doi:10.1371/journal. pone.0002421 (2008)

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"Structural biology: Modelling collagen diseases." Nature 453:998-999 (2008)

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"Effects of the Nucleoid Protein HU on the Structure, Flexibility, and Ring-Closure Properties of DNA Deduced from Monte Carlo Simulations." J Mol Biol 382:353-370 (2008)

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"Modular cell biology: retroactivity and insulation." Molecular Systems Biology 4:161-176 (2008)

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"Binding cooperativity in phage lambda is not sufficient to produce an effective switch." Biophys J. 94(9):3384-92 (2008)

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"When activators repress and repressors activate: a qualitative analysis of the Shea-Ackers model." Bull Math Biol. 70(6):1660-83 (2008)

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"Patterns of Evolution and Host Gene Mimicry in Influenza and other RNA Viruses." PLoS Pathogens 4(6):e1000079 doi:10.1371/journal.ppat.1000079 (2008)

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"Repression of B-Cell Linker (BLNK) and B-Cell Adaptor for Phosphoinositide 3-Kinase (BCAP) Is Important for Lymphocyte Transformation by Rel Proteins." Cancer Research 68:808-814 (2008)

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"Structure, Dynamics, and Branch Migration of a DNA Holliday Junction: A Single-molecule Fluorescence and Modeling Study." Biophys J. (2008)

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"Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling." Acta Crystallogr D Biol Crystallogr  64(Pt 4):383-96 (2008)

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"3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures." Nat Protoc. 3(7):1213-27 (2008)

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"RNA Ontology Consortium. RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)." RNA 14(3):465-81(2008)

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"The effect of negative feedback loops on the dynamics of Boolean networks." Biophysical Journal 95(2):518-26 (2008)

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"Common interruptions in the repeating tripeptide sequence of non-fibrillar collagens: sequence analysis and structural studies on triple-helix peptide models." J Mol Biol 376:736-48 (2008)

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"Correlation between 13Calpha chemical shifts and helix content of peptide ensembles." Protein Sci 17:950-4 (2008)

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"Characterization of conformational ensemble of natively unfolded human and mouse alpha-synuclein: implication for aggregation." J Mol Biol 378:1104-1115 (2008) 

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"Simple continuous and discrete models for simulating replica exchange simulations of protein folding." J Phys Chem B 112:6083-6093 (2008)