LEAP: constructing gene co-expression networks for single-cell RNA-sequencing data using pseudotime ordering. - Alicia T. Specht; Jun Li 052 (Bioinform., 2017)

Widespread position-specific conservation of synonymous rare codons within coding sequences. - Julie L. Chaney; Aaron Steele; Rory Carmichael; Anabel Rodriguez; Alicia T. Specht; Kim Ngo; Jun Li 052; Scott J. Emrich; Patricia L. Clark (PLoS Comput. Biol., 2017)

DiPhiSeq: robust comparison of expression levels on RNA-Seq data with large sample sizes. - Jun Li 052; Alicia T. Lamere (Bioinform., 2019)

Weighted graphlets and deep neural networks for protein structure classification. - Hongyu Guo; Khalique Newaz; Scott J. Emrich; Tijana Milenkovic; Jun Li 052 (CoRR, 2019)

Network analysis of synonymous codon usage. - Khalique Newaz; Gabriel Wright; Jacob Piland; Jun Li 052; Patricia L. Clark; Scott J. Emrich; Tijana Milenkovic (Bioinform., 2020)

Fine-Grained Synonymous Codon Usage Patterns and their Potential Role in Functional Protein Production. - Ashley Babjac; Jun Li 052; Scott J. Emrich (BIBM, 2021)

Variable selection with false discovery rate control in deep neural networks. - Zixuan Song; Jun Li 052 (Nat. Mach. Intell., 2021)

SCIBER: a simple method for removing batch effects from single-cell RNA-sequencing data. - Dailin Gan; Jun Li 052 (Bioinform., 2023)