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BOOK CHAPTERS
1. G.R. Hart and A.L. Ferguson "Viral fitness landscapes: A physical sciences perspective" in "Systems Immunology: An introduction to modeling methods for scientists" J. Das, C. Jayaprakash (eds.) Taylor and Francis (in press, 2017) [ISBN-10: 1498717403]
CONFERENCE PAPERS
1. R.A. Mansbach, G.L. Herman, M. West, D.R. Trinkle, A.L. Ferguson, and A. Schleife "WORK IN PROGRESS: Computational Modules for the MatSE Undergraduate Curriculum" Paper presented at American Society for Engineering Education (ASEE) 123rd Annual Conference & Exposition, New Orleans, LA, June 26-29 2016 [pdf] [http://dx.doi.org/10.18260/p.27214]
JOURNAL ARTICLES
* Designates corresponding author.
2017
37. E.Y. Lee, G.C.L. Wong, and A.L. Ferguson* "Machine learning discovery and design of membrane-active peptides" Bioorganic and Medicinal Chemistry (submitted, 2017)
Invited mini-review for "Peptide Therapeutics" symposium-in-print

36. W.F. Reinhart, A.W. Long, M.P. Howard, A.L. Ferguson, and A.Z. Panagiotopoulos "Machine learning for autonomous crystal structure identification" Soft Matter (in press, 2017) [http://dx.doi.org/10.1039/c7sm00957g]

35. Z. Song, R.A. Mansbach, R. Baumgartner, K.-C. Shih, H. He, N. Zheng, X. Ba, Y. Huang, D. Mani, Y. Lin, M.-P. Nieh, A.L. Ferguson*, L. Yin, and J. Cheng "Modulation of polypeptide conformation through donor-acceptor transformation of side-chain hydrogen bonding ligands" Nat. Commun. (accepted, 2017)

34. A.W. Long and A.L. Ferguson* "Landmark diffusion maps (L-dMaps): Accelerated manifold learning out-of-sample extension" Appl. Comput. Harmon. Anal. (under review, 2017)

33. E.Y. Lee, M.W. Lee, B.M. Fulan, A.L. Ferguson*, and G.C.L. Wong "What can machine learning do for antimicrobial peptides, and what can antimicrobial peptides do for machine learning?" Interface Focus (accepted, 2017)
RSC Interface Focus invited mini-review

32. R.A. Mansbach and A.L. Ferguson* "Control of the hierarchical assembly of π-conjugated optoelectronic peptides by pH and flow" Organic & Biomolecular Chemistry (in press, 2017) [http://dx.doi.org/10.1039/C7OB00923B]
Invited submission for "Peptide Materials" special issue
Selected as 2017 HOT Article in Organic and Biomolecular Chemistry

31. J. Wang, M. Gayatri, and A.L. Ferguson* "Mesoscale simulation and machine learning of asphaltene aggregation phase behavior and molecular assembly landscapes" J. Phys. Chem. B 121 18 4923-4944 (2017) [pdf] [SI] [http://dx.doi.org/10.1021/acs.jpcb.7b02574]

30. A.L. Ferguson* "BayesWHAM: A Bayesian approach for free energy estimation, reweighting, and uncertainty quantification in the weighted histogram analysis method" J. Comput. Chem. 38 18 1583-1605 (2017) [pdf] [code] [http://dx.doi.org/10.1002/jcc.24800]

29. R.A. Mansbach and A.L. Ferguson* "Coarse-grained molecular simulation of the hierarchical self-assembly of π-conjugated optoelectronic peptides" J. Phys. Chem. B 121 7 1684-1706 (2017) [pdf] [SI] [forcefield] [http://dx.doi.org/10.1021/acs.jpcb.6b10165]
2016
28. E.Y. Lee, B.M. Fulan, G.C.L. Wong, and A.L. Ferguson* "Mapping membrane activity in undiscovered peptide sequence space using machine learning" Proc. Natl. Acad. Sci. USA 113 48 13588-13593 (2016) [pdf] [SI] [http://dx.doi.org/10.1073/pnas.1609893113]

27. C.D. Allen, M.Y. Chen, A.Y. Trick, D. Thanh Le, A.L. Ferguson*, and A.J. Link "Thermal unthreading of the lasso peptides astexin-2 and astexin-3" ACS Chem. Biol. 11 11 3043-3051 (2016) [pdf] [SI] [movieS1] [movieS2] [movieS3] [movieS4] [http://dx.doi.org/10.1021/acschembio.6b00588]

26. J. Wang and A.L. Ferguson* "Mesoscale simulation of asphaltene aggregation" J. Phys. Chem. B 120 32 8016-8035 (2016) [pdf] [SI] [http://dx.doi.org/10.1021/acs.jpcb.6b05925]

25. A.W. Long, C.L. Phillips, E. Jankowski, and A.L. Ferguson* "Nonlinear machine learning and design of reconfigurable digital colloids" Soft Matter 12 7119-7135 (2016) [pdf] [SI] [movieS1] [movieS2] [movieS3] [http://dx.doi.org/10.1039/C6SM01156J]

24. R.A. Mansbach, A.L. Ferguson, K.A. Kilian, J.A. Krogstad, C. Leal, A. Schleife, D.R. Trinkle, M. West, and G.L. Herman "Reforming an undergraduate materials science curriculum with computational modules" J. Mater. Educ. 38 3-4 161-174 (2016) [pdf]

23. J. Hu and A.L. Ferguson* "Global graph matching using diffusion maps" Intelligent Data Analysis 20 3 637-654 (2016) [pdf] [http://dx.doi.org/10.3233/IDA-160824]

22. J. Wang and A.L. Ferguson* "Nonlinear reconstruction of single-molecule free energy surfaces from univariate time series" Phys. Rev. E 93 032412 (2016) [pdf] [http://link.aps.org/doi/10.1103/PhysRevE.93.032412]

21. B.A. Thurston, J.D. Tovar, and A.L. Ferguson* "Thermodynamics, morphology, and kinetics of early-stage self-assembly of pi-conjugated oligopeptides" Mol. Sim. 42 12 955-975 (2016) [pdf] [movie1] [movie2] [http://dx.doi.org/10.1080/08927022.2015.1125997]
2015
20. G.R. Hart and A.L. Ferguson* "Empirical fitness models for hepatitis C virus immunogen design" Physical Biology 12 066006 (2015) [pdf] [SI] [http://dx.doi.org/10.1088/1478-3975/12/6/066006]

19. M. Xiong, M.W. Lee, R. Mansbach, Z. Song, Y. Bao, R.M. Peek Jr., C. Yao, L.-F. Chen, A.L. Ferguson*, G.C.L. Wong, and J. Cheng "Helical antimicrobial polypeptides with radial amphiphilicity" Proc. Natl. Acad. Sci. USA 112 43 13155-13160 (2015) [pdf] [appendix] [SI] [movieS1] [movieS2] [movieS3] [http://dx.doi.org/10.1073/pnas.1507893112]

18. A.W. Long, J. Zhang, S. Granick, and A.L. Ferguson* "Machine learning assembly landscapes from particle tracking data" Soft Matter 11 8141-8153 (2015) [pdf] [SI] [movieS1] [movieS2] [http://dx.doi.org/10.1039/C5SM01981H]

17. R.A. Mansbach and A.L. Ferguson* "Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics" J. Chem. Phys. 142 105101 (2015) [pdf] [SI] [http://dx.doi.org/10.1063/1.4914144]
Ranked as one of the most read Biological Molecules and Networks articles of the year

16. G.R. Hart and A.L. Ferguson* "Error catastrophe and phase transition in the empirical fitness landscape of HIV" Phys. Rev. E 91 032705 (2015) [pdf] [http://dx.doi.org/10.1103/PhysRevE.91.032705]
2014
15. L. Tang, X. Yang, I. Chaudhury, C. Yao, Q. Yin, Q. Zhou, M. Kwon, L.W. Dobrucki, L.B. Borst, S. Lezmi, W.G. Helferich, A.L. Ferguson*, T.M. Fan and J. Cheng "Investigating the optimal size of anticancer nanomedicine" Proc. Natl. Acad. Sci. USA 111 43 15344-15349 (2014) [pdf] [SI] [http://dx.doi.org/10.1073/pnas.1411499111]

14. B.D. Wall, Y. Zhou, S. Mei, H.A.M. Ardona, A.L. Ferguson and J.D. Tovar "Variation of formal hydrogen bonding networks within electronically delocalized pi-conjugated oligopeptide nanostructures" Langmuir 30 38 11375-11385 (2014) [pdf] [SI] [http://dx.doi.org/10.1021/la501999g]

13. J.K. Mann, J.P. Barton, A.L. Ferguson, S. Omarjee, B.D. Walker, A.K. Chakraborty and T. Ndung’u "The fitness landscape of HIV-1 gag: Advanced modeling approaches and validation of model predictions by in vitro testing" PLOS Comput. Biol. 10 8 e1003776 (2014) [pdf] [SI] [code] [http://dx.doi.org/10.1371/journal.pcbi.1003776]

12. B.D. Wall, A.E. Zacca, A.M. Sanders, W.L. Wilson, A.L. Ferguson and J.D. Tovar "Supramolecular polymorphism: Tunable electronic interactions within pi-conjugated peptide nanostructures dictated by primary amino acid sequence" Langmuir 30 20 5946-5956 (2014) [pdf] [SI] [http://dx.doi.org/10.1021/la500222y]

11. A.W. Long and A.L. Ferguson* “Nonlinear machine learning of patchy colloid self-assembly mechanisms and pathways” J. Phys. Chem. B 118 15 4228-4244 (2014) [pdf] [SI] [http://dx.doi.org/10.1021/jp500350b]
2013
10. K. Shekhar, C.F. Ruberman, A.L. Ferguson, J.P. Barton, M. Kardar, A.K. Chakraborty "Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes" Phys. Rev. E 88 062705 (2013) [pdf] [SI] [http://dx.doi.org/10.1103/PhysRevE.88.062705]

9. A.L. Ferguson, E. Falkowska, L.M. Walker, M.S. Seaman, D.R. Burton and A.K. Chakraborty “Computational prediction of broadly neutralizing HIV-1 antibody epitopes from neutralization activity data” PLOS ONE 8 12 e80562 (2013) [pdf] [SI] [http://dx.doi.org/10.1371/journal.pone.0080562]

8. A.L. Ferguson, J.K. Mann, S. Omarjee, T. Ndung’u, B.D. Walker and A.K. Chakraborty “Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design” Immunity 38 606-617 (2013) [pdf] [SI] [http://dx.doi.org/10.1016/j.immuni.2012.11.022]
Immunity Preview: N. Goonetilleke and A.J. McMichael "HIV-1 Vaccines: Let’s Get Physical” Immunity 38 410-413 (2013) [pdf] [http://dx.doi.org/10.1016/j.immuni.2013.02.017]
Cell Leading Edge Select: L. Gay and N. Neuman "Antiviral Strategies: Building a Better Defense” Cell 153 727-728 (2013) [pdf] [http://dx.doi.org/10.1016/j.cell.2013.04.039]

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2012
7. A.L. Ferguson*, N. Giovambattista, P.J. Rossky, A.Z. Panagiotopoulos and P.G. Debenedetti “A computational investigation of the phase behavior and capillary sublimation of water confined between nanoscale hydrophobic plates” J. Chem. Phys. 137 144501 (2012) [pdf] [SI] [movie1] [movie2] [http://dx.doi.org/10.1063/1.4755750]
Featured on the cover of JCP 137 14 (2012)
Most read regular JCP article in October 2012
Selected as a 2012 Editor’s Choice Article

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2011
6. A.L. Ferguson, A.Z. Panagiotopoulos, I.G. Kevrekidis and P.G. Debenedetti “Nonlinear dimensionality reduction in molecular simulation: The diffusion map approach” Chem. Phys. Lett. Frontiers 509 1 1-11 (2011) [pdf] [http://dx.doi.org/10.1016/j.cplett.2011.04.066]
Featured on the cover of Chem. Phys. Lett. 509 1 (2011)

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5. A.L. Ferguson*, A.Z. Panagiotopoulos, P.G. Debenedetti and I.G. Kevrekidis “Integrating diffusion maps with umbrella sampling: Application to alanine dipeptide” J. Chem. Phys. 134 135103 (2011) [pdf] [SI] [http://dx.doi.org/10.1063/1.3574394]

2010
4. A.L. Ferguson, S. Zhang, I. Dikiy, A.Z. Panagiotopoulos, P.G. Debenedetti and A.J. Link “An experimental and computational investigation of lasso formation in microcin J25” Biophys. J. 99 9 3056-3065 (2010) [pdf] [SI] [movie] [http://dx.doi.org/10.1016/j.bpj.2010.08.073]

3. A.L. Ferguson, A.Z. Panagiotopoulos, P.G. Debenedetti and I.G. Kevrekidis “Systematic determination of order parameters for chain dynamics using diffusion maps” Proc. Natl. Acad. Sci. USA 107 31 13597-13602 (2010) [pdf] [SI] [movie] [http://dx.doi.org/10.1073/pnas.1003293107]
2009
2. A.L. Ferguson, P.G. Debenedetti and A.Z. Panagiotopoulos “Solubility and molecular conformations of n-alkane chains in water” J. Phys. Chem. B 113 18 6405-6414 (2009) [pdf] [SI] [http://dx.doi.org/10.1021/jp811229q]
2006
1. E. Guibal, T. Vincent, E. Touraud, S. Colombo, and A.L. Ferguson "Oxidation of hydroquinone to p-benzoquinone catalyzed by Cu(II) supported on chitosan flakes" J. Appl. Polym. Sci. 100 4 3034-3043 (2006) [pdf] [http://dx.doi.org/10.1002/app.23702]