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1. G.R. Hart and A.L. Ferguson* "Chapter 17: 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 pp. 279-298 (2019) [ISBN-10: 1498717403] []
3. X. Zhang, A. Schleife, A.L. Ferguson, P. Bellon, T. Bretl, G.L. Herman, J.A. Krogstad, C.R. Maass, C. Leal, D.R. Trinkle, and M. West "Computational Curriculum for MatSE Undergraduates and the Influence on Senior Classes" Paper presented at 2018 American Society for Engineering Education (ASEE) 125th Annual Conference & Exposition, Salt Lake City, UT, June 24-27 2018 []

2. A. Kononov, P. Bellon, T. Bretl, A.L. Ferguson, G.L. Herman, K.A. Kilian, J.A. Krogstad, C. Leal, C.R. Maass, A. Schleife, J.K. Shang, D.R. Trinkle, and M. West "Computational Curriculum for MatSE Undergraduates" Paper presented at 2017 American Society for Engineering Education (ASEE) 124th Annual Conference & Exposition, Columbus, OH, June 25-28 2017 []

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 []
* Designates corresponding author.
73. B.L. Peters, J. Deng, and A.L. Ferguson* "Free-energy calculations of LSD and lisuride binding to 5-HT2B G protein coupled receptor" (submitted, 2020)

72. E. Jira, K. Shmilovich, T. Kale, A.L. Ferguson, J.D. Tovar, and C. Schroeder "Effect of core oligomer length on the phase behavior and assembly of π-conjugated peptides" (submitted, 2020)

71. K. Shmilovich, R.A. Mansbach, H. Sidky, O.E. Dunne, S.S. Panda, J.D. Tovar, and A.L. Ferguson* "Discovery of self-assembling π-conjugated peptides by active learning-directed coarse-grained molecular simulation" J. Phys. Chem. B (in press, 2020) []
Invited submission to the "Machine Learning in Physical Chemistry" special issue

70. Y. Xia, Z. Song, T. Xue, S. Wei, L. Zhu, Z. Tan, Y. Yang, H. Fu, Y. Jiang, Y. Lin, Y. Lu, A.L. Ferguson*, and J. Cheng "Accelerated polymerization of N-carboxyanhydrides catalyzed by crown ether" (submitted, 2020)
69. M.R. Shirts and A.L. Ferguson* "Statistically optimal continuous potentials of mean force from umbrella sampling and multistate reweighting" (submitted, 2019) []

68. H. Sidky, W. Chen, and A.L. Ferguson* "Machine learning for collective variable discovery and enhanced sampling in biomolecular simulation" Molecular Physics e1737742 (2020) []
Invited New Views article in Molecular Physics

67. M. Magana, M. Pushpanathan, A. Santos, L. Lense, M. Fernandez, A. Ioannidis, M.A. Giulianotti, Y. Apidianakis, S. Bradfute, A.L. Ferguson, A. Cherkasov, M.N. Seleem, C. Pinilla, C. de la Fuente-Nunez, T. Lazaridis, T. Dai, R.A. Houghten, R.E.W. Hancock, and G.P. Tegos "Antimicrobial peptides revisited: Reasons to insist" (submitted, 2019)

66. Y. Yang; H. Ying, Z. Li, J. Wang, A.L. Ferguson, Y. Zhang, and J. Cheng "Quantitative synthesis of urea macrocycles enabled by bulky N-substituent" (submitted, 2019)

65. B.A. Thurston, E.P. Shapera, J.D. Tovar, A. Schleife, and A.L. Ferguson* "Revealing the sequence-structure-electronic property relation of self-assembling π-conjugated oligopeptides by molecular and quantum mechanical modeling" Langmuir 35 47 15221-15231 (2019) []

64. S. Panda, K. Shmilovich, A.L. Ferguson*, and J.D. Tovar "Controlling supramolecular chirality in peptide-π-peptide networks by variation of alkyl spacer length" Langmuir 35 43 14060-14073 (2019) []

E.Y. Lee, L.C. Chan, H. Wang, J. Lieng, M. Hung, Y. Srinivasan, J. Wang, J. Waschek, A.L. Ferguson, K.-F. Lee, N.Y. Yount, M.R. Yeaman, and G.C.L. Wong "Mood-modulating neuropeptide PACAP is potently induced during infection" (submitted, 2019)

The PLUMED Consortium (M. Bonomi, G. Bussi, C. Camilloni, G.A. Tribello, P. Banáš, A. Barducci, M. Bernetti, P.G. Bolhuis, S. Bottaro, D. Branduardi, R. Capelli, P. Carloni, M. Ceriotti, A. Cesari, H. Chen, W. Chen, F. Colizzi, S. De, M. De La Pierre, D. Donadio, V. Drobot, B. Ensing, A.L. Ferguson, M. Filizola, J.S. Fraser, H. Fu, P. Gasparotto, F. Luigi Gervasio, F. Giberti, A. Gil-Ley, T. Giorgino, G.T. Heller, G.M. Hocky, M. Iannuzzi, M. Invernizzi, K.E. Jelfs, A. Jussupow, E. Kirilin, A. Laio, V. Limongelli, K. Lindorff-Larsen, T. Löhr, F. Marinelli, L. Martin-Samos, M. Masetti, R. Meyer, A. Michaelides, C. Molteni, T. Morishita, M. Nava, C. Paissoni, E. Papaleo, M. Parrinello, J. Pfaendtner, P. Piaggi, G. Piccini, A. Pietropaolo, F. Pietrucci, S. Pipolo, D. Provasi, D. Quigley, P. Raiteri, S. Raniolo, J. Rydzewski, M. Salvalaglio, G. Cesare Sosso, V. Spiwok, J. Šponer, D.W.H. Swenson, P. Tiwary, O. Valsson, M. Vendruscolo, G.A. Voth, and A. White) "A community effort to promote transparency and reproducibility in enhanced molecular simulations" Nature Methods 16 8 670-673 (2019) []

H. Sidky, W. Chen, and A.L. Ferguson* "High-resolution Markov state models for the dynamics of Trp-cage miniprotein constructed over slow folding modes identified by state-free reversible VAMPnets" J. Phys. Chem. B 123 38 7999-8009 (2019) []

W. Chen, H. Sidky, and A.L. Ferguson* "Capabilities and limitations of time-lagged autoencoders for slow mode discovery in dynamical systems" J. Chem. Phys. 151 064123 (2019) []

Y. Ma and A.L. Ferguson* "Inverse design of self-assembling colloidal crystals with omnidirectional photonic bandgaps" Soft Matter 15 8808-8826 (2019) []

58. A.L. Ferguson*, T. Mueller, S. Rajasekaran, and B.J. Reich "Conference report: 2018 materials and data science hackathon (MATDAT18)" Mol. Syst. Des. Eng. 4 462-468 (2019) []

57. J. Chen, J. Wang, K. Li, Y. Wang, M. Gruebele, A.L. Ferguson, and S.C. Zimmerman "Polymeric 'clickase' accelerate the copper click reaction of small molecules, proteins, and cells" J. Am. Chem. Soc. 141 9693-9700 (2019) []

56. W. Chen, H. Sidky, and A.L. Ferguson* "Nonlinear discovery of slow molecular modes using state-free reversible VAMPnets" J. Chem. Phys. 150 214114 (2019) []
Selected as J. Chem. Phys. "Editor's Pick"

55. Z. Song, H. Fu, J. Wang, J. Hui, T. Xue, L.A. Pacheco, H. Yan, R. Baumgartner, Z. Wang, Y. Xia, X. Wang, L. Yin, C. Chen, J. Rodríguez-López, A.L. Ferguson, Y. Lin, and J. Cheng "Synthesis of polypeptides via bio inspired polymerization of in situ purified N-carboxyanhydrides" Proc. Natl. Acad. Sci. USA 116 22 10658-10663 (2019) []
54. M.W. Lee, E.Y. Lee, A.L. Ferguson, and G.C.L. Wong "Machine learning antimicrobial peptide sequences: Some surprising variations on the theme of amphiphilic assembly" Curr. Opin. Colloid Interface Sci. 38 204-213 (2018) []

53. J. Wang and A.L. Ferguson* "Recovery of protein folding funnels from single-molecule time series by delay embeddings and manifold learning" J. Phys. Chem. B 122 50 11931–11952 (2018) [ ]
Invited submission to the "Deciphering Molecular Complexity in Dynamics and Kinetics from the Single Biomolecule to Single Cell Levels" issue

52. A.L. Ferguson* "Editorial: ACS Central Science Virtual Issue on Machine Learning" ACS Cent. Sci. 4 8 938-941 (2018) []
Invited editorial for the "Virtual Issue on Machine Learning" issue

51. G.R. Hart and A.L. Ferguson* "Computational design of hepatitis C virus immunogens from host-pathogen dynamics over empirical viral fitness landscapes" Physical Biology 16 016004 (2018) []

50. J. Chen, J. Wang, Y. Bai, K. Li, E.S. Garcia, A.L. Ferguson, and S.C. Zimmerman "Enzyme-like click catalysis by a copper-containing single-chain organic nanoparticle" J. Am. Chem. Soc. 140 42 13695-13702 (2018) []

49. R.A. Mansbach and A.L. Ferguson* "A patchy particle model of the hierarchical self-assembly of π-conjugated optoelectronic peptides" J. Phys. Chem. B 122 44 10219-10236 (2018) []

48. B.A. Thurston and A.L. Ferguson* "Machine learning and molecular design of self-assembling π-conjugated oligopeptides" Mol. Sim. 44 11 930-945 (2018) []

47. J. Wang, M. Gayatri, and A.L. Ferguson* "Coarse-grained molecular simulation and nonlinear manifold learning of archipelago asphaltene aggregation and folding" J. Phys. Chem. B 122 25 6627-6647 (2018) []

46. L. Valverde, B.A. Thurston, A.L. Ferguson, and W.L. Wilson "Evidence for prenucleated fibrilogenesis of acid-mediated self-assembling oligopeptides via molecular simulation and fluorescence correlation spectroscopy" Langmuir 34 25 7346-7354 (2018) []

45. W. Chen, A.R. Tan, and A.L. Ferguson* "Collective variable discovery and enhanced sampling using autoencoders: Innovations in network architecture and error function design" J. Chem. Phys. 149 072312 (2018) []
Invited submission to the "Enhanced Sampling for Molecular Simulations issue" []

44. W. Chen and A.L. Ferguson* "Molecular enhanced sampling with autoencoders: On-the-fly nonlinear collective variable discovery and accelerated free energy landscape exploration" J. Comput. Chem. 39 25 2079-2102 (2018) []

43. A.L. Ferguson* and J. Hachmann "Machine learning and data science in materials design: a themed collection" Mol. Syst. Des. Eng. 3 429-430 (2018) []
Editorial for invited themed collection "Machine Learning and Data Science in Materials Design"

J. Wang and A.L. Ferguson "A study of the morphology, dynamics, and folding pathways of ring polymers with supramolecular topological constraints using molecular simulation and nonlinear manifold learning" Macromolecules 51 2 598-616 (2018) []
41. A.L. Ferguson* "Machine learning and data science in soft materials engineering" J. Phys.: Condens. Matter 30 4 043002 (2017) []
Invited review article

40. J. Wang and A.L. Ferguson* "Nonlinear machine learning in simulations of soft and biological materials" Mol. Sim. 44 13-14 1090-1107 (2018) []
Invited review article for the “Free Energy Simulations” special issue

39. A.W. Long and A.L. Ferguson* "Rational design of patchy colloids via landscape engineering" Mol. Syst. Des. Eng. 3 1 49-65 (2018) []
Invited submission to the 2018 Emerging Investigators issue
[] []
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38. M.W. Lee, E.Y. Lee, G.H. Lai, N.W. Kennedy, A.E. Posey, W. Xian, A.L. Ferguson, R.B. Hill, and G.C.L. Wong "Molecular motor Dnm1 synergistically induces membrane curvature to facilitate mitochondrial fission" ACS Cent. Sci. 3 11 1156-1167 (2017) []
Featured as the cover article of ACS Central Science
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37. A.W. Long and A.L. Ferguson* "Landmark diffusion maps (L-dMaps): Accelerated manifold learning out-of-sample extension" Appl. Comput. Harmon. Anal. 47 1 190-211 (2019) []

36. 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 7 20160153 (2017) []
RSC Interface Focus invited mini-review

35. E.Y. Lee, G.C.L. Wong, and A.L. Ferguson* "Machine learning-enabled discovery and design of membrane-active peptides" Bioorg. Med. Chem. 26 10 2708-2718 (2018) []
Invited mini-review for "Peptide Therapeutics" symposium-in-print

34. 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. 92 8 1-8 (2017) []

33. 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 13 4733-4745 (2017) []
Featured work in Soft Matter promotional flyer [pdf]

32. R.A. Mansbach and A.L. Ferguson* "Control of the hierarchical assembly of π-conjugated optoelectronic peptides by pH and flow" Org. Biomol. Chem. 15 26 5484-5502 (2017) []
Invited submission for "Peptide Materials" special issue (
Selected as 2017 HOT Article in Organic and Biomolecular Chemistry
Featured as the cover article of Organic and Biomolecular Chemistry 15 26 (2017)
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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) []

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) []

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) []
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) []

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) []

26. J. Wang and A.L. Ferguson* "Mesoscale simulation of asphaltene aggregation" J. Phys. Chem. B 120 32 8016-8035 (2016) []

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) []

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)

23. J. Hu and A.L. Ferguson* "Global graph matching using diffusion maps" Intelligent Data Analysis 20 3 637-654 (2016) []

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) []

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) []
20. G.R. Hart and A.L. Ferguson* "Empirical fitness models for hepatitis C virus immunogen design" Physical Biology 12 066006 (2015) []

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) []

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) []

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) []
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) []
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) []

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) []

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) []

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) []

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) []
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) []

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) []

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) []
Immunity Preview: N. Goonetilleke and A.J. McMichael "HIV-1 Vaccines: Let’s Get Physical” Immunity 38 410-413 (2013) []
Cell Leading Edge Select: L. Gay and N. Neuman "Antiviral Strategies: Building a Better Defense” Cell 153 727-728 (2013) []


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) []
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


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) []
Featured on the cover of Chem. Phys. Lett. 509 1 (2011)


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) []

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) []

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) []
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) []
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) []