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Andrew L Ferguson
Andrew L Ferguson
Associate Professor of Molecular Engineering, University of Chicago
Verified email at uchicago.edu - Homepage
Title
Cited by
Cited by
Year
Investigating the optimal size of anticancer nanomedicine
L Tang, X Yang, Q Yin, K Cai, H Wang, I Chaudhury, C Yao, Q Zhou, ...
Proceedings of the National Academy of Sciences 111 (43), 15344-15349, 2014
5102014
The value of antimicrobial peptides in the age of resistance
M Magana, M Pushpanathan, AL Santos, L Leanse, M Fernandez, ...
The Lancet Infectious Diseases 20 (9), e216-e230, 2020
3802020
Promoting transparency and reproducibility in enhanced molecular simulations
Nature methods 16 (8), 670-673, 2019
3752019
Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design
AL Ferguson, JK Mann, S Omarjee, T Ndung’u, BD Walker, ...
Immunity 38 (3), 606-617, 2013
2292013
Solubility and Molecular Conformations of n-Alkane Chains in Water
AL Ferguson, PG Debenedetti, AZ Panagiotopoulos
The Journal of Physical Chemistry B 113 (18), 6405-6414, 2009
1552009
Helical antimicrobial polypeptides with radial amphiphilicity
M Xiong, MW Lee, RA Mansbach, Z Song, Y Bao, RM Peek Jr, C Yao, ...
Proceedings of the National Academy of Sciences 112 (43), 13155-13160, 2015
1542015
Systematic determination of order parameters for chain dynamics using diffusion maps
AL Ferguson, AZ Panagiotopoulos, PG Debenedetti, IG Kevrekidis
Proceedings of the National Academy of Sciences 107 (31), 13597-13602, 2010
1482010
Molecular enhanced sampling with autoencoders: On‐the‐fly collective variable discovery and accelerated free energy landscape exploration
W Chen, AL Ferguson
Journal of computational chemistry 39 (25), 2079-2102, 2018
1362018
Nonlinear dimensionality reduction in molecular simulation: The diffusion map approach
AL Ferguson, AZ Panagiotopoulos, IG Kevrekidis, PG Debenedetti
Chemical Physics Letters 509 (1), 1-11, 2011
1342011
The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing
JK Mann, JP Barton, AL Ferguson, S Omarjee, BD Walker, A Chakraborty, ...
PLoS computational biology 10 (8), e1003776, 2014
1332014
Machine learning and data science in soft materials engineering
AL Ferguson
Journal of Physics: Condensed Matter 30 (4), 043002, 2017
1312017
Mapping membrane activity in undiscovered peptide sequence space using machine learning
EY Lee, BM Fulan, GCL Wong, AL Ferguson
Proceedings of the National Academy of Sciences 113 (48), 13588-13593, 2016
1242016
Collective variable discovery and enhanced sampling using autoencoders: Innovations in network architecture and error function design
W Chen, AR Tan, AL Ferguson
The Journal of chemical physics 149 (7), 072312, 2018
872018
Machine learning force fields and coarse-grained variables in molecular dynamics: application to materials and biological systems
P Gkeka, G Stoltz, A Barati Farimani, Z Belkacemi, M Ceriotti, JD Chodera, ...
Journal of chemical theory and computation 16 (8), 4757-4775, 2020
852020
Machine learning for autonomous crystal structure identification
WF Reinhart, AW Long, MP Howard, AL Ferguson, AZ Panagiotopoulos
Soft Matter 13 (27), 4733-4745, 2017
852017
What can machine learning do for antimicrobial peptides, and what can antimicrobial peptides do for machine learning?
EY Lee, MW Lee, BM Fulan, AL Ferguson, GCL Wong
Interface focus 7 (6), 20160153, 2017
802017
Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes
K Shekhar, CF Ruberman, AL Ferguson, JP Barton, M Kardar, ...
Physical review E 88 (6), 062705, 2013
802013
Integrating diffusion maps with umbrella sampling: Application to alanine dipeptide
AL Ferguson, AZ Panagiotopoulos, PG Debenedetti, IG Kevrekidis
The Journal of chemical physics 134 (13), 04B606, 2011
742011
Nonlinear machine learning of patchy colloid self-assembly pathways and mechanisms
AW Long, AL Ferguson
The Journal of Physical Chemistry B 118 (15), 4228-4244, 2014
732014
Synthesis of polypeptides via bioinspired polymerization of in situ purified N-carboxyanhydrides
Z Song, H Fu, J Wang, J Hui, T Xue, LA Pacheco, H Yan, R Baumgartner, ...
Proceedings of the National Academy of Sciences 116 (22), 10658-10663, 2019
722019
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