COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge. - Yang Young Lu; Ting Chen 006; Jed A. Fuhrman; Fengzhu Sun (Bioinform., 2017)

Improving contig binning of metagenomic data using (d2S) oligonucleotide frequency dissimilarity. - Ying Wang 005; Kun Wang; Yang Young Lu; Fengzhu Sun (BMC Bioinform., 2017)

CAFE: aCcelerated Alignment-FrEe sequence analysis. - Yang Young Lu; Kujin Tang; Jie Ren 006; Jed A. Fuhrman; Michael S. Waterman; Fengzhu Sun (Nucleic Acids Res., 2017)

DeepPINK: reproducible feature selection in deep neural networks. - Yang Young Lu; Yingying Fan; Jinchi Lv; William Stafford Noble (NeurIPS, 2018)

SolidBin: improving metagenome binning with semi-supervised normalized cut. - Ziye Wang; Zhengyang Wang; Yang Young Lu; Fengzhu Sun; Shanfeng Zhu (Bioinform., 2019)

Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features. - David F. Read; Kate Cook; Yang Young Lu; Karine G. Le Roch; William Stafford Noble (PLoS Comput. Biol., 2019)

DANCE: Enhancing saliency maps using decoys. - Yang Young Lu; Wenbo Guo 002; Xinyu Xing 001; William Stafford Noble (ICML, 2021)

ACE: Explaining cluster from an adversarial perspective. - Yang Young Lu; Timothy C. Yu; Giancarlo Bonora; William Stafford Noble (ICML, 2021)

DIAmeter: matching peptides to data-independent acquisition mass spectrometry data. - Yang Young Lu; Jeff A. Bilmes; Ricard A. Rodriguez-Mias; Judit Villén; William Stafford Noble (Bioinform., 2021)

CRAFT: Compact genome Representation toward large-scale Alignment-Free daTabase. - Yang Young Lu; Jiaxing Bai; Yiwen Wang; Ying Wang 005; Fengzhu Sun (Bioinform., 2021)

Metric learning for comparing genomic data with triplet network. - Zhi Ma; Yang Young Lu; Yiwen Wang; Renhao Lin; Zizi Yang; Fang Zhang; Ying Wang 005 (Briefings Bioinform., 2022)

DeepROCK: Error-controlled interaction detection in deep neural networks. - Winston Chen; William Stafford Noble; Yang Young Lu (CoRR, 2023)

Error-controlled non-additive interaction discovery in machine learning models. - Winston Chen; Yifan Jiang; William Stafford Noble; Yang Young Lu (CoRR, 2024)