20 citations · 45 across the 9 of their papers we have counts for
9 papers
SurGBSA: Learning Representations From Molecular Dynamics Simulations
Derek Jones, Yue Yang, Felice C. Lightstone +3
Self-supervised pretraining from static structures of drug-like compounds and proteins enable powerful learned feature representations. Learned features demonstrate state of the ar…
RapidOMS: FPGA-based Open Modification Spectral Library Searching with HD Computing
Sumukh Pinge, Weihong Xu, Wout Bittremieux +3
Mass spectrometry (MS) is essential for protein analysis but faces significant challenges with large datasets and complex post-translational modifications, resulting in difficultie…
SpecHD: Hyperdimensional Computing Framework for FPGA-based Mass Spectrometry Clustering
Sumukh Pinge, Weihong Xu, Jaeyoung Kang +4
Mass spectrometry-based proteomics is a key enabler for personalized healthcare, providing a deep dive into the complex protein compositions of biological systems. This technology…
HD-Bind: Encoding of Molecular Structure with Low Precision, Hyperdimensional Binary Representations
Derek Jones, Jonathan E. Allen, Xiaohua Zhang +5
Publicly available collections of drug-like molecules have grown to comprise 10s of billions of possibilities in recent history due to advances in chemical synthesis. Traditional m…
RAPIDx: High-performance ReRAM Processing in-Memory Accelerator for Sequence Alignment
Weihong Xu, Saransh Gupta, Niema Moshiri +1
Genome sequence alignment is the core of many biological applications. The advancement of sequencing technologies produces a tremendous amount of data, making sequence alignment a…
NiemaGraphGen: A memory-efficient global-scale contact network simulation toolkit
Niema Moshiri
Epidemic simulations require the ability to sample contact networks from various random graph models. Existing methods can simulate city-scale or even country-scale contact network…
Ten Simple Rules for Attending Your First Conference
Elizabeth Leininger, Kelly Shaw, Niema Moshiri +3
Conferences are a mainstay of most scientific disciplines, where scientists of all career stages come together to share cutting-edge ideas and approaches. If you do research, chanc…
The dual-Barabási-Albert model
Niema Moshiri
The ability to sample random networks that can accurately represent real social contact networks is essential to the study of viral epidemics. The Barabási-Albert model and its ext…
Ten Simple Rules for Reproducible Research in Jupyter Notebooks
Adam Rule, Amanda Birmingham, Cristal Zuniga +8
Reproducibility of computational studies is a hallmark of scientific methodology. It enables researchers to build with confidence on the methods and findings of others, reuse and e…