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Ty M. Thomson et al.
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Haijun Gong et al.
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Min K. Roh et al.
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Ofer Feinerman et al.
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Eric Mjolsness et al.
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Alex Dickson et al.
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Basil Bayati et al.
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Melissa Vellela et al.
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Arjun Raj et al.
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Aryeh Warmflash et al.
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Hiroyuki Kuwahara et al.
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Murat Acar et al.
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Y Cao et al.
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E Weinan et al.
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LS Weinberger et al.
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A Chatterjee et al.
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M Samoilov et al.
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RJ Allen et al.
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Parallel tempering: Theory, applications, and new perspectives
DJ Earl et al.
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DM Roma et al.
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BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains
ML Blinov et al.
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JM Raser et al.
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AK Faradjian et al.
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Improved leap-size selection for accelerated stochastic simulation
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Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study
B Zagrovic et al.
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TS van Erp et al.
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JR Faeder et al.
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MB Elowitz et al.
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DM Zuckerman et al.
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MA Gibson et al.
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