Jordy Homing Lam

Ph.D. Bioinformatics, University of Southern California

homingla [AT] usc.edu

About

I am a postdoctoral fellow at the University of Southern California, supported by the Croucher Foundation of Hong Kong . I work at the Center for New Technologies in Drug Discovery and Development and the Center for Advanced Research Computing . I am advised by Prof. Aiichiro Nakano and Prof. Vsevolod Katritch. I have extensive experience in Chemical Physics, Numerical Algorithms and Parallel Computing.

"https://estija.github.io/" ============================================= REF here s my current fpcous I work on the foundations of machine learning, and my interests mostly lie in the intersection of machine learning, theoretical computer science and statistics. The goal of my research is to study and discover the underlying principles which govern learning, and to leverage this understanding to build practical machine learning systems which are more efficient, fair and robust. A large part of my work aims to inspect questions which arise from modern applications and challenges of machine learning. If you're interested in learning more, here are some questions I've recently been working on: Maksim is a bioinformatics software engineer at the Irwin Lab. Maksim attained his Bachelor's of Chemistry at the University of California, Berkeley in 2020. At Berkeley, Maksim did undergraduate research in the advanced applications of nuclear magnetic resonance. After Berkeley, Maksim started working as a research chemist at a large corporation. Maksim always had an interest in computer science and that interest drew him to join the Irwin Lab, which merges both his interests in chemistry and software. What is the role of computational and statistical constraints in learning and optimization? Are there inherent trade-offs between the amount of memory required for learning or optimization, and the amount of data or computation required? How do we solve learning tasks with limited data, such as by designing optimal data augmentation and regularization techniques? What are appropriate notions of fairness in various domains, and how do we train models which respect these notions? Similarly, how do we ensure trained models are robust, such as when evaluated on data distributions which differ from the original training distribution? How can we understand deep neural networks and foundation models in the context of some of the above considerations? My research is supported by an NSF CAREER award (2023), and Amazon Research Awards (2022 and 2024). This support is very gratefully acknowledged. Here is my CV

News

Publications

Most recent publications on Google Scholar. (The outbound hyperlinks for the papers/videos may take a little longer to redirect!)
indicates equal contribution.

Scalable computation of anisotropic vibrations for large macromolecular assemblies

Lam JH, Nakano A, Katritch V

Nature Communications. 2024.

Nimrodd: Enhancing multi-resolution geometric neural hierarchy with an expectation maximization kernel

Lam JH, Sadybekov A, Ferrari T, Sadybekov A, Liu Y, Nakano A, Katritch V

In Preparation 2024

Structural insights into inverse agonism of an orphan receptor

Barekatain M, Johansson L, Lam JH, Chang H, Sadybekov A, Han GW, Russo J, Bliesath J, Brice N, Carlton M, Saikatendu K, Murphy S, Monenschein H, Schiffer H, Popov P, Lutomski C, Robinson CV, Liu ZJ, Hua T, Katritch V, Cherezov V

In Review 2024.

Structural details of a class B GPCR-arrestin complex revealed by genetically encoded crosslinkers in living cells

Aydin Y, Böttke T, Lam JH, Ernicke S, Fortmann A, Tretbar M, Zarzycka B, Gurevich VV, Katritch V, Coin I

Nature Communications 2023

A deep learning framework to predict binding preference of RNA constituents on protein surface

Lam JH, Li Y, Zhu L, Umarov R, Jiang H, Héliou A, Sheong FK, Liu T, Long Y, Li Y, Fang L, Altman RB, Chen W, Huang X, Gao X

Nature Communications 2019

Scalable computation of anisotropic vibrations for large macromolecular assemblies

Lam JH, Nakano A, Katritch V

Nature Communications. 2024.

Nimrodd: Enhancing multi-resolution geometric neural hierarchy with an expectation maximization kernel

Lam JH, Sadybekov A, Ferrari T, Sadybekov A, Liu Y, Nakano A, Katritch V

In Preparation 2024

Structural insights into inverse agonism of an orphan receptor

Barekatain M, Johansson L, Lam JH, Chang H, Sadybekov A, Han GW, Russo J, Bliesath J, Brice N, Carlton M, Saikatendu K, Murphy S, Monenschein H, Schiffer H, Popov P, Lutomski C, Robinson CV, Liu ZJ, Hua T, Katritch V, Cherezov V

In Review 2024.

Constitutive activation mechanism of a class C GPCR

Shin J, Park J, Jeong J, Lam JH, Qiu X, Wu D, Kim K, Lee J, Robinson CV, Hyun J, Katritch V, Kim KP, Cho Y

Nature Structural & Molecular Biology. 2024.

Structure of the dopamine D3 receptor bound to a bitopic agonist reveals a new specificity site in an expanded allosteric pocket

Arroyo-Urea S, Nazarova AL, Carrión-Antolí A, Bonifazi A, Battiti FO, Lam JH, Newman AH, Katritch V, García-Nafría J

Nature Communications. 2024. In Review.

Ligand and G-protein selectivity in the κ-opioid receptor

Han J, Zhang J, Nazarova AL, Bernhard SM, Krumm BE, Zhao L, Lam JH, Rangari VA, Majumdar S, Nichols DE, Katritch V, Yuan P, Fay JF, Che T

Nature 2023

Structural details of a class B GPCR-arrestin complex revealed by genetically encoded crosslinkers in living cells

Aydin Y, Böttke T, Lam JH, Ernicke S, Fortmann A, Tretbar M, Zarzycka B, Gurevich VV, Katritch V, Coin I

Nature Communications 2023

Structural basis of GABA reuptake inhibition

Motiwala Z, Aduri NG, Shaye H, Han GW, Lam JH, Katritch V, Cherezov V, Gati C

Nature 2022

Structure of the full-length human Pannexin1 channel and insights into its role in pyroptosis

Zhang S, Yuan B, Lam JH, Zhou J, Zhou X, Ramos-Mandujano G, Tian X, Liu Y, Han R, Li Y, Gao X, Li M, Yang M

Cell Discovery 2021

Structural basis of the activation of a metabotropic GABA receptor

Shaye H, Ishchenko A, Lam JH, Han GW, Xue L, Rondard P, Pin JP, Katritch V, Gati C, Cherezov V

Nature 2020

Self-assembling tetrameric peptides allow in situ 3D bioprinting under physiological conditions

Rauf S, Susapto HH, Kahin K, Alshehri S, Abdelrahman S, Lam JH, Asad S, Jadhav S, Sundaramurthi D, Gao X, Hauser CAE

Journal of Materials Chemistry B 2019

A deep learning framework to predict binding preference of RNA constituents on protein surface

Lam JH, Li Y, Zhu L, Umarov R, Jiang H, Héliou A, Sheong FK, Liu T, Long Y, Li Y, Fang L, Altman RB, Chen W, Huang X, Gao X

Nature Communications 2019

Vitæ

Full Resume (likely not the most updated!) in PDF.

Consultation Request

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