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Robert M. Dirks, Ph.D. - Publications

Affiliations: 
Chemistry California Institute of Technology, Pasadena, CA 
Area:
Engineering Molecular Devices
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13 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Tan D, Piana S, Dirks RM, Shaw DE. RNA force field with accuracy comparable to state-of-the-art protein force fields. Proceedings of the National Academy of Sciences of the United States of America. PMID 29378935 DOI: 10.1073/Pnas.1713027115  0.322
2017 Wolfe BR, Porubsky NJ, Zadeh JN, Dirks RM, Pierce NA. Constrained Multistate Sequence Design for Nucleic Acid Reaction Pathway Engineering. Journal of the American Chemical Society. PMID 28191938 DOI: 10.1021/Jacs.6B12693  0.674
2013 Dirks RM, Ueda CT, Pierce NA. Retraction for Venkataraman et al., Selective cell death mediated by small conditional RNAs. Proceedings of the National Academy of Sciences of the United States of America. 110: 384. PMID 23248321 DOI: 10.1073/Pnas.1221212110  0.59
2012 Piana S, Lindorff-Larsen K, Dirks RM, Salmon JK, Dror RO, Shaw DE. Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations. Plos One. 7: e39918. PMID 22768169 DOI: 10.1371/Journal.Pone.0039918  0.314
2011 Zadeh JN, Steenberg CD, Bois JS, Wolfe BR, Pierce MB, Khan AR, Dirks RM, Pierce NA. NUPACK: Analysis and design of nucleic acid systems. Journal of Computational Chemistry. 32: 170-3. PMID 20645303 DOI: 10.1002/Jcc.21596  0.632
2011 Beck VA, Bois JS, Dirks RM, Pierce NA. Elucidation and Control of the Hybridization Chain Reaction Biophysical Journal. 100: 522a. DOI: 10.1016/J.Bpj.2010.12.3051  0.73
2010 Venkataraman S, Dirks RM, Ueda CT, Pierce NA. Selective cell death mediated by small conditional RNAs. Proceedings of the National Academy of Sciences of the United States of America. 107: 16777-82. PMID 20823260 DOI: 10.1073/Pnas.1006377107  0.602
2007 Venkataraman S, Dirks RM, Rothemund PW, Winfree E, Pierce NA. An autonomous polymerization motor powered by DNA hybridization. Nature Nanotechnology. 2: 490-4. PMID 18654346 DOI: 10.1038/Nnano.2007.225  0.614
2007 Dirks RM, Bois JS, Schaeffer JM, Winfree E, Pierce NA. Thermodynamic analysis of interacting nucleic acid strands Siam Review. 49: 65-88. DOI: 10.1137/060651100  0.761
2004 Dirks RM, Pierce NA. Triggered amplification by hybridization chain reaction. Proceedings of the National Academy of Sciences of the United States of America. 101: 15275-8. PMID 15492210 DOI: 10.1073/Pnas.0407024101  0.729
2004 Dirks RM, Pierce NA. An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. Journal of Computational Chemistry. 25: 1295-304. PMID 15139042 DOI: 10.1002/Jcc.20057  0.745
2004 Dirks RM, Lin M, Winfree E, Pierce NA. Paradigms for computational nucleic acid design. Nucleic Acids Research. 32: 1392-403. PMID 14990744 DOI: 10.1093/Nar/Gkh291  0.774
2003 Dirks RM, Pierce NA. A partition function algorithm for nucleic acid secondary structure including pseudoknots. Journal of Computational Chemistry. 24: 1664-77. PMID 12926009 DOI: 10.1002/Jcc.10296  0.746
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