| 2020 | ICLR | Probabilistic Connection Importance Inference and Lossless Compression of Deep Neural Networks. | Xin Xing, Long Sha, Pengyu Hong, Zuofeng Shang, Jun S. Liu |
| 2020 | ICMLA | NGM: Neural Gaussian Mirror for Controlled Feature Selection in Neural Networks. | Xin Xing, Yu Gui, Chenguang Dai, Jun S. Liu |
| 2007 | BIBE | Statistial Analysis of nucleosome occupancy and histone modification data. | Guo-Cheng Yuan, Jun S. Liu |
| 2002 | RECOMB | Haplotype Inference and Its Application in Linkage Disequilibrium Mapping. | Tianhua Niu, Xin Lu, Hosung Kang, Zhaohui S. Qin, Jun S. Liu |
| 2002 | RECOMB | Dynamic Programming Algorithms for Haplotype Block Partitioning and Tag SNP Selection Using Haplotype Data or Genotype Data. | Kui Zhang, Ting Chen, Michael S. Waterman, Zhaohui S. Qin, Jun S. Liu, Fengzhu Sun |
| 2001 | PSB | BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes. | X. Liu, Douglas L. Brutlag, Jun S. Liu |
| 2000 | ASPDAC | Dynamic weighting Monte Carlo for constrained floorplan designs in mixed signal application. | Jason Cong, Tianming Kong, Faming Liang, Jun S. Liu, Wing Hung Wong, Dongmin Xu |
| 1999 | ASPDAC | Relaxed Simulated Tempering for VLSI Floorplan Designs. | Jason Cong, Tianming Kong, Dongmin Xu, Faming Liang, Jun S. Liu, Wing Hung Wong |
| 1997 | ISMB | Bayesian Adaptive Alignment and Inference. | Jun Zhu, Jun S. Liu, Charles E. Lawrence |