Identification of novel multi-transmembrane proteins from genomic databases using quasi-periodic structural properties. - Junhyong Kim; Etsuko N. Moriyama; Coral G. Warr; Peter J. Clyne; John R. Carlson (Bioinform., 2000)

A Tree Obscured By Vines: Horizontal Gene Transfer and the Median Tree Method of Estimating Species Phylogeny. - Junhyong Kim; Benjamin A. Salisbury (Pacific Symposium on Biocomputing, 2001)

Geometry of gene expression dynamics. - S. A. Rifkin; Junhyong Kim (Bioinform., 2002)

Computers Are from Mars, Organisms Are from Venus. - Junhyong Kim (Computer, 2002)

A Combinatorial Toolbox for Protein Sequence Design and Landscape Analysis in the Grand Canonical Model. - James Aspnes; Julia Hartling; Ming-Yang Kao; Junhyong Kim; Gauri Shah (J. Comput. Biol., 2002)

Reconstructing the Temporal Ordering of Biological Samples Using Microarray Data. - Paul M. Magwene; Paul Lizardi; Junhyong Kim (Bioinform., 2003)

Genome Identification and Classification by Short Oligo Arrays. - Stanislav Angelov; Boulos Harb; Sampath Kannan; Sanjeev Khanna; Junhyong Kim; Li-San Wang (WABI, 2004)

Guest Editorial: WABI Special Section Part 1. - Junhyong Kim; Inge Jonassen (IEEE ACM Trans. Comput. Biol. Bioinform., 2004)

Efficiently Supporting Structure Queries on Phylogenetic Trees. - Susan B. Davidson; Junhyong Kim; Yifeng Zheng (SSDBM, 2005)

Guest Editorial: WABI Special Section Part II. - Junhyong Kim; Inge Jonassen (IEEE ACM Trans. Comput. Biol. Bioinform., 2005)

Transcriptional Target Prediction Using Qualitative Reasoning. - Li-San Wang; Doris Wagner; Chang Seob Kwon; Yanhui Su; Junhyong Kim (EMBC, 2006)

Crimson: A Data Management System to Support Evaluating Phylogenetic Tree Reconstruction Algorithms. - Yifeng Zheng; Stephen Fisher; Shirley Cohen; Sheng Guo; Junhyong Kim; Susan B. Davidson (VLDB, 2006)

Phyl-O'Data (POD) from Tree of Life: Integration Challenges from Yellow Slimy Things to Black Crunchy Stuff. - Junhyong Kim (DILS, 2007)

Efficient Enumeration of Phylogenetically Informative Substrings. - Stanislav Angelov; Boulos Harb; Sampath Kannan; Sanjeev Khanna; Junhyong Kim (J. Comput. Biol., 2007)

Self Containment, a Property of Modular RNA Structures, Distinguishes microRNAs. - Miler T. Lee; Junhyong Kim (PLoS Comput. Biol., 2008)

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences. - Siavash Mirarab; Nam Nguyen; Sheng Guo; Li-San Wang; Junhyong Kim; Tandy J. Warnow (J. Comput. Biol., 2015)

Discovering Similar Workflows via Provenance Clustering: A Case Study. - Abdussalam Alawini; Leshang Chen; Susan B. Davidson; Stephen Fisher; Junhyong Kim (IPAW, 2018)

PIVOT: platform for interactive analysis and visualization of transcriptomics data. - Qin Zhu; Stephen A. Fisher; Hannah Dueck; Sarah Middleton; Mugdha Khaladkar; Junhyong Kim (BMC Bioinform., 2018)

Resistant Fit Regression Normalization for Single-cell RNA-seq Data. - Da Kuang; Junhyong Kim (BIBE, 2020)

A subspace clustering method for satisfying stoimetric constraints in scRNA -seq. - Angela Huang; Junhyong Kim (BIBE, 2021)

Reconstructing Cell Lineage Trees from Phenotypic Features with Metric Learning. - Da Kuang; Guanwen Qiu; Junhyong Kim (CoRR, 2025)