Derek Jones

Global Security Computing Applications Division

Lawrence Livermore National Laboratory

Computer Science and Engineering Dept.

University of California, San Diego

Hi, I’m (William) Derek Jones.

I am a PhD candidate in the Department of Computer Science at University of California, San Diego in the Systems Energy Efficiency (SEE) Lab where I am advised by Dr. Tajana S. Rosing and Dr. Niema Moshiri and mentored by Dr. Jonathan E. Allen of Lawrence Livermore National Laboratory (LLNL). My research is focused on molecular representation learning using physics-informed learning algorithms and high performance computing (HPC). I am thankful to have been awarded a UC National Laboratory FEES Research fellowship to support my PhD work.

I graduated from the University of Kentucky in May of 2018 where I earned an M.Sc. in Computer Science with a research focus in Machine Learning/Deep Learning and its applications to Computational Biology and Drug Discovery with the help of HPC. I was advised by Dr. Nathan Jacobs (Computer Science, now at WashU) and Dr. Sally R. Ellingson (Biomedical Informatics).

selected publications

HDBind: encoding of molecular structure with hyperdimensional binary representations

Jones, Derek, Zhang, Xiaohua, Bennion, Brian J, Pinge, Sumukh, Xu, Weihong, Kang, Jaeyoung, Khaleghi, Behnam, Moshiri, Niema, Allen, Jonathan E, and Rosing, Tajana S

Sci. Rep. 2024

Bib
@article{Jones2024-id, title = {{HDBind}: encoding of molecular structure with hyperdimensional binary representations}, author = {Jones, Derek and Zhang, Xiaohua and Bennion, Brian J and Pinge, Sumukh and Xu, Weihong and Kang, Jaeyoung and Khaleghi, Behnam and Moshiri, Niema and Allen, Jonathan E and Rosing, Tajana S}, journal = {Sci. Rep.}, publisher = {Springer Science and Business Media LLC}, volume = {14}, number = {1}, pages = {29025}, month = nov, year = {2024}, bibtex_show = true, selected = true }
Accelerators for Classical Molecular Dynamics Simulations of Biomolecules

Jones, Derek, Jonathan, Allen E, Yang, Yue, Bennett, W F D, Gokhale, Maya, Moshiri, Niema, and Rosing, Tajana

J. Chem. Theory Comput. 2022

Bib
@article{Jones_2022-uq, title = {Accelerators for Classical Molecular Dynamics Simulations of Biomolecules}, author = {Jones, Derek and Jonathan, Allen E and Yang, Yue and Bennett, W F D and Gokhale, Maya and Moshiri, Niema and Rosing, Tajana}, journal = {J. Chem. Theory Comput.}, volume = {}, number = {}, pages = {}, month = {}, year = {2022}, language = {en}, selected = {true}, bibtex_show = true }
Improved Protein-Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference

Jones, Derek, Kim, Hyojin, Zhang, Xiaohua, Zemla, Adam, Stevenson, Garrett, Bennett, W F Drew, Kirshner, Daniel, Wong, Sergio E, Lightstone, Felice C, and Allen, Jonathan E

J. Chem. Inf. Model. 2021

Bib
@article{Jones2021-al, title = {Improved {Protein-Ligand} Binding Affinity Prediction with {Structure-Based} Deep Fusion Inference}, author = {Jones, Derek and Kim, Hyojin and Zhang, Xiaohua and Zemla, Adam and Stevenson, Garrett and Bennett, W F Drew and Kirshner, Daniel and Wong, Sergio E and Lightstone, Felice C and Allen, Jonathan E}, journal = {J. Chem. Inf. Model.}, volume = {61}, number = {4}, pages = {1583--1592}, month = apr, year = {2021}, language = {en}, selected = {true}, doi = {http://dx.doi.org/10.1021/acs.jcim.0c01306}, bibtex_show = true }