Publications
SpatialNP: Gridded Transformer Neural Processes for Probabilistic Spatial Proteomics in Multiplexed Tissue Imaging
Juho Kim
International Conference on Machine Learning (ICML) Workshop on Structured Probabilistic Inference & Generative Modeling, 2026
Personalizing Cancer Models under Data Scarcity via Parameter Decomposition
Logan Rose, Jonathan Martinez, Juho Kim, Jing Qin, Boris Aguilar, David Murrugarra
Preprint, 2026
Using spatial multi-omic assays to explore sequential therapy approaches for melanoma
Juho Kim*, Chong Xia*, Shuo Wang, Jianjun Jiang, Yin Tang, Sarah Li, David L Gibbs, Boris Aguilar, Heber L Rocha, Paul Macklin, Claudia M Ludwig, Ilya Shmulevich, Wei Wei, Vésteinn Thorsson, James R Heath
Cancer Systems Biology Consortium (CSBC) Annual Meeting, 2025
Characterizing the tumor microenvironment and designing predictive modeling of melanoma using spatial multi-omic and imaging data
Juho Kim, Chong Xia, Muna Yase, Shuo Wang, Sai Manikonda, Pelin Garbioglu, Mohitveer Kahlon, Jianjun Jiang, Yin Tang, Sarah Li, David L Gibbs, Boris Aguilar, Heber L Rocha, Paul Macklin, Claudia M Ludwig, James R Heath, Wei Wei, Vésteinn Thorsson
Cancer Systems Biology Consortium (CSBC) Annual Meeting, 2024
Experimental Methods and Computational Pipelines for Spatial ATAC-seq Profiling of Tumor Tissues
Juho Kim*, Chong Xia*, Shuo Wang, Muna Yase, Sai Manikonda, Pelin Garbioglu, Mohitveer Kahlon, Jianjun Jiang, Yin Tang, Sarah Li, David L Gibbs, Boris Aguilar, Claudia M Ludwig, Wei Wei, Vésteinn Thorsson, James R Heath, Rong Fan, Zhentao Yang, Gatien Moriceau, Roger S. Lo
Cancer Systems Biology Consortium (CSBC) Annual Meeting, 2024
Detection of More than 400 CD Biomarkers and Pathway Proteins in Single Immune Cells by Cyclic MIST for Single-Cell Proteomic Studies
Liwei Yang*, Juho Kim*, Wei Wei and Jun Wang (*Equal Contribution)
Analytical Chemistry, 2024
Using spatial multiomic assays to characterize the tumor immune microenvironment and to guide predictive modeling
Juho Kim, Chong Xia, Jianjun Jiang, Yin Tang, Sarah Li, Boris Aguilar, David L Gibbs, Claudia M Ludwig, Wei Wei, Vésteinn Þórsson, Ilya Shmulevich, James R Heath
Cancer Systems Biology Consortium (CSBC) Annual Meeting, 2023
Reconstructing the clonal evolution of tumors via probabilistic machine learning
Juho Kim, Nicholas Chia, Oluwasanmi Koyejo and Mohammed El-Kebir
Preprint, 2022
Probabilistic Subclonal Reconstruction for Cancer
Juho Kim
Ph.D. Thesis, 2022
Detecting Evolutionary Patterns of Cancers using Consensus Trees
Sarah Christensen, Juho Kim, Nicholas Chia, Oluwasanmi Koyejo and Mohammed El-Kebir
Bioinformatics, 2020
Also presented in European Conference on Computational Biology (ECCB), 2020
Teaching Syntax by Adversarial Distraction
Juho Kim, Christopher Malon and Asim Kadav
Conference on Empirical Methods in Natural Language Processing (EMNLP) Workshop on Fact Extraction and Verifiaction (FEVER), 2018
Kapre: On-GPU Audio Preprocessing Layers for a Quick Implementation of Deep Neural Network Models with Keras
Keunwoo Choi, Deokjin Joo, and Juho Kim
International Conference on Machine Learning (ICML) Workshop on Machine Learning for Music Discovery, 2017
Inferring developmental trajectories from single-cell RNA sequencing data via variational auto-encoder
Juho Kim
Tech Report, 2017
Scalable visualization of high-dimensional single-cell data
Juho Kim, Nate Russell, and Jian Peng
Pacific Symposium on Biocomputing (PSB), 2017
Ensemble learning can significantly improve human microRNA target prediction
Seunghak Yu, Juho Kim, Hyeyoung Min, and Sungroh Yoon
Methods, 2014
Ensemble Learning for Robust Prediction of microRNA-mRNA Interactions
Seunghak Yu, Juho Kim, Hyeyoung Min, and Sungroh Yoon
International Conference on Big Data and Smart Computing, 2014
Ensemble Algorithms for DNA Motif Finding
Juho Kim, Seunghak Yu, and Sungroh Yoon
International Conference on Electronics, Information and Communication, 2014