Stuart A. Kauffman - Publications

Affiliations: 
Biochemistry University of Calgary, Calgary, Alberta, Canada 
Area:
origin of life and molecular organization
Website:
http://edge.org/memberbio/stuart_a_kauffman

95 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
2022 Mastrogiorgio A, Felin T, Kauffman S, Mastrogiorgio M. More Thumbs Than Rules: Is Rationality an Exaptation? Frontiers in Psychology. 13: 805743. PMID 35282257 DOI: 10.3389/fpsyg.2022.805743  0.609
2020 Xavier JC, Hordijk W, Kauffman S, Steel M, Martin WF. Autocatalytic chemical networks at the origin of metabolism. Proceedings. Biological Sciences. 287: 20192377. PMID 32156207 DOI: 10.1098/Rspb.2019.2377  0.3
2020 Cazzolla Gatti R, Koppl R, Fath BD, Kauffman S, Hordijk W, Ulanowicz RE. On the emergence of ecological and economic niches Journal of Bioeconomics. 22: 99-127. DOI: 10.1007/S10818-020-09295-4  0.334
2019 Hordijk W, Steel M, Kauffman SA. Molecular Diversity Required for the Formation of Autocatalytic Sets. Life (Basel, Switzerland). 9. PMID 30823659 DOI: 10.3390/Life9010023  0.304
2019 Bornholdt S, Kauffman S. Ensembles, dynamics, and cell types: Revisiting the statistical mechanics perspective on cellular regulation Journal of Theoretical Biology. 467: 15-22. PMID 30711453 DOI: 10.1016/J.Jtbi.2019.01.036  0.369
2018 Daniels BC, Kim H, Moore D, Zhou S, Smith HB, Karas B, Kauffman SA, Walker SI. Criticality Distinguishes the Ensemble of Biological Regulatory Networks. Physical Review Letters. 121: 138102. PMID 30312104 DOI: 10.1103/Physrevlett.121.138102  0.343
2018 Cazzolla Gatti R, Fath B, Hordijk W, Kauffman S, Ulanowicz R. Niche emergence as an autocatalytic process in the evolution of ecosystems. Journal of Theoretical Biology. 454: 110-117. PMID 29864429 DOI: 10.1016/J.Jtbi.2018.05.038  0.359
2018 Villani M, Rocca LL, Kauffman SA, Serra R. Dynamical Criticality in Gene Regulatory Networks Complexity. 2018: 1-14. DOI: 10.1155/2018/5980636  0.379
2018 Kauffman S, Pathak SD, Sen PK, Choi TY. Jury Rigging and Supply Network Design: Evolutionary “Tinkering” in the presence of Unknown-Unknowns Journal of Supply Chain Management. 54: 51-63. DOI: 10.1111/Jscm.12146  0.342
2016 Gabora L, Kauffman S. Toward an evolutionary-predictive foundation for creativity : Commentary on "Human creativity, evolutionary algorithms, and predictive representations: The mechanics of thought trials" by Arne Dietrich and Hilde Haider, 2014 (Accepted pending minor revisions for publication in Psychonomic Bulletin & Review). Psychonomic Bulletin & Review. 23: 632-639. PMID 26527351 DOI: 10.3758/S13423-015-0925-1  0.326
2016 Felin T, Kauffman S, Mastrogiorgio A, Mastrogiorgio M. Factor markets, actors, and affordances Industrial and Corporate Change. 25: 133-147. DOI: 10.1093/Icc/Dtv049  0.615
2015 Nghe P, Hordijk W, Kauffman SA, Walker SI, Schmidt FJ, Kemble H, Yeates JA, Lehman N. Prebiotic network evolution: six key parameters. Molecular Biosystems. 11: 3206-17. PMID 26490759 DOI: 10.1039/C5Mb00593K  0.363
2015 Kauffman SA, Gare A. Beyond Descartes and Newton: Recovering life and humanity. Progress in Biophysics and Molecular Biology. PMID 26143598 DOI: 10.1016/J.Pbiomolbio.2015.06.003  0.345
2015 Koppl R, Kauffman S, Felin T, Longo G. Economics for a creative world: A response to comments Journal of Institutional Economics. 11: 61-68. DOI: 10.1017/S1744137414000514  0.646
2014 Kauffman SA. Prolegomenon to patterns in evolution. Bio Systems. 123: 3-8. PMID 24704211 DOI: 10.1016/J.Biosystems.2014.03.004  0.338
2014 Felin T, Kauffman S, Koppl R, Longo G. Economic opportunity and evolution: Beyond landscapes and bounded rationality Strategic Entrepreneurship Journal. 8: 269-282. DOI: 10.2139/Ssrn.2197512  0.644
2014 KOPPL R, KAUFFMAN S, FELIN T, LONGO G. Economics for a creative world Journal of Institutional Economics. 11: 1-31. DOI: 10.1017/S1744137414000150  0.644
2014 Felin T, Kauffman S, Koppl R, Longo G. Economic Opportunity and Evolution: Beyond Landscapes and Bounded Rationality: Economic Opportunity and Evolution Strategic Entrepreneurship Journal. 8: 269-282. DOI: 10.1002/Sej.1184  0.629
2013 Huang S, Kauffman S. How to escape the cancer attractor: rationale and limitations of multi-target drugs. Seminars in Cancer Biology. 23: 270-8. PMID 23792873 DOI: 10.1016/J.Semcancer.2013.06.003  0.306
2013 Gabora L, Scott EO, Kauffman S. A quantum model of exaptation: incorporating potentiality into evolutionary theory. Progress in Biophysics and Molecular Biology. 113: 108-16. PMID 23567156 DOI: 10.1016/J.Pbiomolbio.2013.03.012  0.327
2013 Solée RV, Valverde S, Casals MR, Kauffman SA, Farmer D, Eldredge N. The evolutionary ecology of technological innovations Complexity. 18: 15-27. DOI: 10.1002/Cplx.21436  0.34
2012 Vasas V, Fernando C, Santos M, Kauffman S, Szathmáry E. Evolution before genes Biology Direct. 7. PMID 22221860 DOI: 10.1186/1745-6150-7-1  0.346
2012 Filisetti A, Graudenzi A, Serra R, Villani M, Füchslin RM, Packard N, Kauffman SA, Poli I. A stochastic model of autocatalytic reaction networks. Theory in Biosciences = Theorie in Den Biowissenschaften. 131: 85-93. PMID 21979857 DOI: 10.1007/S12064-011-0136-X  0.351
2011 Labean TH, Butt TR, Kauffman SA, Schultes EA. Protein folding absent selection. Genes. 2: 608-26. PMID 24710212 DOI: 10.3390/Genes2030608  0.701
2011 Hordijk W, Kauffman SA, Steel M. Required levels of catalysis for emergence of autocatalytic sets in models of chemical reaction systems. International Journal of Molecular Sciences. 12: 3085-101. PMID 21686171 DOI: 10.3390/Ijms12053085  0.337
2011 Graudenzi A, Serra R, Villani M, Colacci A, Kauffman SA. Robustness analysis of a Boolean model of gene regulatory network with memory. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 559-77. PMID 21417939 DOI: 10.1089/Cmb.2010.0224  0.323
2011 Damiani C, Serra R, Villani M, Kauffman SA, Colacci A. Cell-cell interaction and diversity of emergent behaviours. Iet Systems Biology. 5: 137-44. PMID 21405202 DOI: 10.1049/Iet-Syb.2010.0039  0.327
2011 Graudenzi A, Serra R, Villani M, Damiani C, Colacci A, Kauffman SA. Dynamical properties of a boolean model of gene regulatory network with memory. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 1291-303. PMID 21214342 DOI: 10.1089/Cmb.2010.0069  0.357
2011 Filisetti A, Graudenzi A, Serra R, Villani M, Lucrezia DD, Füchslin RM, Kauffman SA, Packard N, Poli I. A stochastic model of the emergence of autocatalytic cycles Journal of Systems Chemistry. 2. DOI: 10.1186/1759-2208-2-2  0.348
2010 Andrecut M, Kauffman SA. Phase transition in a class of nonlinear random networks. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 82: 022105. PMID 20866861 DOI: 10.1103/Physreve.82.022105  0.325
2010 Serra R, Villani M, Barbieri A, Kauffman SA, Colacci A. On the dynamics of random Boolean networks subject to noise: attractors, ergodic sets and cell types. Journal of Theoretical Biology. 265: 185-93. PMID 20399217 DOI: 10.1016/J.Jtbi.2010.04.012  0.334
2009 Foster DV, Foster JG, Huang S, Kauffman SA. A model of sequential branching in hierarchical cell fate determination. Journal of Theoretical Biology. 260: 589-97. PMID 19615382 DOI: 10.1016/J.Jtbi.2009.07.005  0.354
2009 Huang S, Ernberg I, Kauffman S. Cancer attractors: A systems view of tumors from a gene network dynamics and developmental perspective Seminars in Cell and Developmental Biology. 20: 869-876. PMID 19595782 DOI: 10.1016/J.Semcdb.2009.07.003  0.332
2009 Andrecut M, Foster D, Carteret H, Kauffman SA. Maximal information transfer and behavior diversity in Random Threshold Networks. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 909-16. PMID 19580520 DOI: 10.1089/Cmb.2009.0007  0.339
2009 Huang AC, Hu L, Kauffman SA, Zhang W, Shmulevich I. Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation. Bmc Systems Biology. 3: 20. PMID 19222862 DOI: 10.1186/1752-0509-3-20  0.323
2008 Carteret HA, Rose KJ, Kauffman SA. Maximum power efficiency and criticality in random Boolean networks. Physical Review Letters. 101: 218702. PMID 19113460 DOI: 10.1103/Physrevlett.101.218702  0.318
2008 Wilds R, Kauffman SA, Glass L. Evolution of complex dynamics. Chaos (Woodbury, N.Y.). 18: 033109. PMID 19045447 DOI: 10.1063/1.2962223  0.318
2008 Andrecut M, Huang S, Kauffman SA. Heuristic approach to sparse approximation of gene regulatory networks. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 15: 1173-86. PMID 18844584 DOI: 10.1089/Cmb.2008.0087  0.335
2008 Balleza E, Alvarez-Buylla ER, Chaos A, Kauffman S, Shmulevich I, Aldana M. Critical dynamics in genetic regulatory networks: Examples from four kingdoms Plos One. 3. PMID 18560561 DOI: 10.1371/Journal.Pone.0002456  0.391
2008 Nykter M, Price ND, Larjo A, Aho T, Kauffman SA, Yli-Harja O, Shmulevich I. Critical networks exhibit maximal information diversity in structure-dynamics relationships. Physical Review Letters. 100: 058702. PMID 18352443 DOI: 10.1103/Physrevlett.100.058702  0.336
2008 Ribeiro AS, Kauffman SA, Lloyd-Price J, Samuelsson B, Socolar JE. Mutual information in random Boolean models of regulatory networks. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 77: 011901. PMID 18351870 DOI: 10.1103/Physreve.77.011901  0.325
2008 Nykter M, Price ND, Aldana M, Ramsey SA, Kauffman SA, Hood LE, Yli-Harja O, Shmulevich I. Gene expression dynamics in the macrophage exhibit criticality. Proceedings of the National Academy of Sciences of the United States of America. 105: 1897-900. PMID 18250330 DOI: 10.1073/Pnas.0711525105  0.343
2008 Andrecut M, Cloud D, Kauffman SA. Monte Carlo simulation of a simple gene network yields new evolutionary insights. Journal of Theoretical Biology. 250: 468-74. PMID 18061620 DOI: 10.1016/J.Jtbi.2007.10.035  0.333
2008 Serra R, Villani M, Graudenzi A, Colacci A, Kauffman SA. The simulation of gene knock-out in scale-free random boolean models of genetic networks Networks and Heterogeneous Media. 3: 333-343. DOI: 10.3934/Nhm.2008.3.333  0.336
2008 Andrecut M, Kauffman SA. Energy and criticality in random Boolean networks Physics Letters, Section a: General, Atomic and Solid State Physics. 372: 4757-4760. DOI: 10.1016/J.Physleta.2008.05.041  0.303
2008 Kauffman S, Logan RK, Este R, Goebel R, Hobill D, Shmulevich I. Propagating organization: An enquiry Biology and Philosophy. 23: 27-45. DOI: 10.1007/S10539-007-9066-X  0.318
2007 Hanel R, Kauffman SA, Thurner S. Towards a physics of evolution: critical diversity dynamics at the edges of collapse and bursts of diversification. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 76: 036110. PMID 17930309 DOI: 10.1103/Physreve.76.036110  0.35
2007 Andrecut M, Kauffman SA. A physical analogy of the genetic toggle switch. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 14: 973-83. PMID 17803374 DOI: 10.1089/Cmb.2007.0038  0.306
2007 Ribeiro AS, Kauffman SA. Noisy attractors and ergodic sets in models of gene regulatory networks. Journal of Theoretical Biology. 247: 743-55. PMID 17543998 DOI: 10.1016/J.Jtbi.2007.04.020  0.346
2007 Zhu R, Ribeiro AS, Salahub D, Kauffman SA. Studying genetic regulatory networks at the molecular level: delayed reaction stochastic models. Journal of Theoretical Biology. 246: 725-45. PMID 17350653 DOI: 10.1016/J.Jtbi.2007.01.021  0.34
2007 Serra R, Villani M, Graudenzi A, Kauffman SA. Why a simple model of genetic regulatory networks describes the distribution of avalanches in gene expression data. Journal of Theoretical Biology. 246: 449-60. PMID 17316697 DOI: 10.1016/J.Jtbi.2007.01.012  0.315
2007 Aldana M, Balleza E, Kauffman S, Resendiz O. Robustness and evolvability in genetic regulatory networks Journal of Theoretical Biology. 245: 433-448. PMID 17188715 DOI: 10.1016/J.Jtbi.2006.10.027  0.351
2007 Kauffman S. Beyond reductionism: Reinventing the sacred Zygon. 42: 903-914. DOI: 10.1111/J.1467-9744.2007.00879.X  0.306
2007 Rämö P, Kauffman S, Kesseli J, Yli-Harja O. Measures for information propagation in Boolean networks Physica D: Nonlinear Phenomena. 227: 100-104. DOI: 10.1016/J.Physd.2006.12.005  0.317
2006 Ribeiro A, Zhu R, Kauffman SA. A general modeling strategy for gene regulatory networks with stochastic dynamics. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 1630-9. PMID 17147485 DOI: 10.1089/Cmb.2006.13.1630  0.354
2006 Kauffman SA. The evolution of future wealth. Scientific American. 295: 44. PMID 17076082 DOI: 10.1038/Scientificamerican1106-44  0.303
2006 Foster DV, Kauffman SA, Socolar JE. Network growth models and genetic regulatory networks. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 73: 031912. PMID 16605563 DOI: 10.1103/Physreve.73.031912  0.315
2006 Grefenstette J, Kim S, Kauffman S. An analysis of the class of gene regulatory functions implied by a biochemical model Biosystems. 84: 81-90. PMID 16384633 DOI: 10.1016/J.Biosystems.2005.09.009  0.36
2006 Kauffman S, Clayton P. On emergence, agency, and organization Biology and Philosophy. 21: 501-521. DOI: 10.1007/S10539-005-9003-9  0.301
2005 Toulouse T, Ao P, Shmulevich I, Kauffman S. Noise in a Small Genetic Circuit that Undergoes Bifurcation. Complexity. 11: 45-51. PMID 16670776 DOI: 10.1002/Cplx.20099  0.331
2005 Hanel R, Kauffman SA, Thurner S. Phase transition in random catalytic networks. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 72: 036117. PMID 16241525 DOI: 10.1103/Physreve.72.036117  0.313
2005 Shmulevich I, Kauffman SA, Aldana M. Eukaryotic cells are dynamically ordered or critical but not chaotic. Proceedings of the National Academy of Sciences of the United States of America. 102: 13439-44. PMID 16155121 DOI: 10.1073/Pnas.0506771102  0.351
2005 Dealy S, Kauffman S, Socolar J. Modeling pathways of differentiation in genetic regulatory networks with Boolean networks Complexity. 11: 52-60. DOI: 10.1002/Cplx.20100  0.326
2004 Kauffman S, Peterson C, Samuelsson B, Troein C. Genetic networks with canalyzing Boolean rules are always stable Proceedings of the National Academy of Sciences of the United States of America. 101: 17102-17107. PMID 15572453 DOI: 10.1073/Pnas.0407783101  0.355
2004 Kauffman S. A proposal for using the ensemble approach to understand genetic regulatory networks Journal of Theoretical Biology. 230: 581-590. PMID 15363677 DOI: 10.1016/J.Jtbi.2003.12.017  0.362
2004 Shmulevich I, Kauffman SA. Activities and sensitivities in boolean network models. Physical Review Letters. 93: 048701. PMID 15323803 DOI: 10.1103/Physrevlett.93.048701  0.308
2004 Kauffman S. The ensemble approach to understand genetic regulatory networks Physica a: Statistical Mechanics and Its Applications. 340: 733-740. DOI: 10.1016/J.Physa.2004.05.018  0.361
2003 Solé RV, Fernández P, Kauffman SA. Adaptive walks in a gene network model of morphogenesis: insights into the Cambrian explosion. The International Journal of Developmental Biology. 47: 685-93. PMID 14756344 DOI: 10.1387/Ijdb.14756344  0.361
2003 Kauffman S, Peterson C, Samuelssont B, Troein C. Random Boolean network models and the yeast transcriptional network Proceedings of the National Academy of Sciences of the United States of America. 100: 14796-14799. PMID 14657375 DOI: 10.1073/Pnas.2036429100  0.343
2003 Socolar JE, Kauffman SA. Scaling in ordered and critical random boolean networks. Physical Review Letters. 90: 068702. PMID 12633339 DOI: 10.1103/Physrevlett.90.068702  0.363
2002 Harris SE, Sawhill BK, Wuensche A, Kauffman S. A model of transcriptional regulatory networks based on biases in the observed regulation rules Complexity. 7: 23-40. DOI: 10.1002/Cplx.10022  0.33
1999 Preisler HD, Kauffman S. A proposal regarding the mechanism which underlies lineage choice during hematopoietic differentiation. Leukemia Research. 23: 685-694. PMID 10456665 DOI: 10.1016/S0145-2126(99)00077-6  0.327
1999 Solé RV, Manrubia SC, Benton M, Kauffman S, Bak P. Criticality and scaling in evolutionary ecology. Trends in Ecology and Evolution. 14: 156-160. PMID 10322524 DOI: 10.1016/S0169-5347(98)01518-3  0.317
1995 LaBean TH, Kauffman SA, Butt TR. Libraries of random-sequence polypeptides produced with high yield as carboxy-terminal fusions with ubiquitin. Molecular Diversity. 1: 29-38. PMID 9237192 DOI: 10.1007/Bf01715807  0.703
1995 Kauffman SA, Macready WG. Search strategies for applied molecular evolution. Journal of Theoretical Biology. 173: 427-40. PMID 7783452 DOI: 10.1006/Jtbi.1995.0074  0.301
1993 Goodwin BC, Kauffman S, Murray JD. Is morphogenesis an intrinsically robust process? Journal of Theoretical Biology. 163: 135-44. PMID 8412239 DOI: 10.1006/Jtbi.1993.1112  0.313
1993 LaBean TH, Kauffman SA. Design of synthetic gene libraries encoding random sequence proteins with desired ensemble characteristics. Protein Science : a Publication of the Protein Society. 2: 1249-54. PMID 8401210 DOI: 10.1002/Pro.5560020807  0.593
1991 Kauffman SA, Johnsen S. Coevolution to the edge of chaos: coupled fitness landscapes, poised states, and coevolutionary avalanches. Journal of Theoretical Biology. 149: 467-505. PMID 2062105 DOI: 10.1016/S0022-5193(05)80094-3  0.339
1991 Kauffman SA. Antichaos and adaptation. Scientific American. 265: 78-84. PMID 1862333 DOI: 10.1038/Scientificamerican0891-78  0.311
1990 Goodwin BC, Kauffman SA. Spatial harmonics and pattern specification in early Drosophila development. Part I. Bifurcation sequences and gene expression. Journal of Theoretical Biology. 144: 303-19. PMID 2395374 DOI: 10.1016/S0022-5193(05)80078-5  0.317
1990 Hunding A, Kauffman SA, Goodwin BC. Drosophila segmentation: supercomputer simulation of prepattern hierarchy. Journal of Theoretical Biology. 145: 369-84. PMID 2232822 DOI: 10.1016/S0022-5193(05)80116-X  0.318
1990 Kauffman SA. Requirements for evolvability in complex systems: Orderly dynamics and frozen components Physica D: Nonlinear Phenomena. 42: 135-152. DOI: 10.1016/0167-2789(90)90071-V  0.342
1989 Bagley RJ, Farmer JD, Kauffman SA, Packard NH, Perelson AS, Stadnyk IM. Modeling adaptive biological systems. Bio Systems. 23: 113-37; discussion 1. PMID 2627562 DOI: 10.1016/0303-2647(89)90016-6  0.56
1989 Kauffman SA. Cambrian explosion and Permian quiescence: Implications of rugged fitness landscapes Evolutionary Ecology. 3: 274-281. DOI: 10.1007/Bf02270728  0.31
1987 Farmer JD, Kauffman SA, Packard NH, Perelson AS. Adaptive dynamic networks as models for the immune system and autocatalytic sets. Annals of the New York Academy of Sciences. 504: 118-31. PMID 3477111 DOI: 10.1111/J.1749-6632.1987.Tb48728.X  0.561
1987 Kauffman S, Levin S. Towards a general theory of adaptive walks on rugged landscapes. Journal of Theoretical Biology. 128: 11-45. PMID 3431131 DOI: 10.1016/S0022-5193(87)80029-2  0.344
1986 Kauffman SA. Autocatalytic sets of proteins. Journal of Theoretical Biology. 119: 1-24. PMID 3713221 DOI: 10.1016/S0022-5193(86)80047-9  0.302
1986 Kauffman SA, Smith RG. Adaptive automata based on Darwinian selection Physica D: Nonlinear Phenomena. 22: 68-82. DOI: 10.1016/0167-2789(86)90234-4  0.314
1986 Farmer JD, Kauffman SA, Packard NH. Autocatalytic replication of polymers Physica D: Nonlinear Phenomena. 22: 50-67. DOI: 10.1016/0167-2789(86)90233-2  0.302
1985 Kauffman SA. New Questions In Genetics And Evolution Cladistics. 1: 247-265. DOI: 10.1111/J.1096-0031.1985.Tb00426.X  0.31
1985 Smith JM, Burian R, Kauffman S, Alberch P, Campbell J, Goodwin B, Lande R, Raup D, Wolpert L. Developmental Constraints and Evolution: A Perspective from the Mountain Lake Conference on Development and Evolution The Quarterly Review of Biology. 60: 265-287. DOI: 10.1086/414425  0.336
1984 Kauffman SA. Emergent properties in random complex automata Physica D: Nonlinear Phenomena. 10: 145-156. DOI: 10.1016/0167-2789(84)90257-4  0.304
1973 Glass L, Kauffman SA. The logical analysis of continuous, non-linear biochemical control networks. Journal of Theoretical Biology. 39: 103-29. PMID 4741704 DOI: 10.1016/0022-5193(73)90208-7  0.347
1971 Kauffman S. Chapter 5 Gene Regulation Networks: A Theory For Their Global Structure and Behaviors Current Topics in Developmental Biology. 6: 145-182. PMID 5005757 DOI: 10.1016/S0070-2153(08)60640-7  0.303
1969 Kauffman S. Homeostasis and differentiation in random genetic control networks. Nature. 224: 177-178. PMID 5343519 DOI: 10.1038/224177A0  0.302
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