The SSAHA Trace Server. - Zemin Ning; William Spooner; Adam Spargo; Steven Leonard; Mark Rae; Antony J. Cox (CSB, 2004)

ssahaSNP A Polymorphism Detection Tool on a Whole Genome Scale. - Zemin Ning; Mario Cáccamo; James C. Mullikin (CSB Workshops, 2005)

HI: haplotype improver using paired-end short reads. - Quan Long; Daniel G. MacArthur; Zemin Ning; Chris Tyler-Smith (Bioinform., 2009)

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. - Kai Ye 001; Marcel H. Schulz; Quan Long; Rolf Apweiler; Zemin Ning (Bioinform., 2009)

PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data. - Yanju Zhang; Eric-Wubbo Lameijer; Peter A. C. 't Hoen; Zemin Ning; P. Eline Slagboom; Kai Ye 001 (Bioinform., 2012)

Oxford Nanopore MinION Sequencing and Genome Assembly. - Hengyun Lu; Francesca Giordano; Zemin Ning (Genom. Proteom. Bioinform., 2016)

scanPAV: a pipeline for extracting presence-absence variations in genome pairs. - Francesca Giordano; Maximilian R. Stammnitz; Elizabeth P. Murchison; Zemin Ning (Bioinform., 2018)

Efficient iterative Hi-C scaffolder based on N-best neighbors. - Dengfeng Guan; Shane A. McCarthy; Zemin Ning; Guohua Wang; Yadong Wang; Richard Durbin (BMC Bioinform., 2021)

Correction to: Efficient iterative Hi-C scaffolder based on N-best neighbors. - Dengfeng Guan; Shane A. McCarthy; Zemin Ning; Guohua Wang; Yadong Wang; Richard Durbin (BMC Bioinform., 2021)

Ongoing Work to Study the Underlying Statistical Patterns of Oesophageal Chromothripsis. - Jack Fraser-Govil; Zemin Ning (BIOINFORMATICS, 2023)

GenCHORD: A Pipeline for Genomic Rearrangement Analysis. - Jack Fraser-Govil; Ronnie Crawford; Maximilian R. Stammnitz; Elizabeth P. Murchison; Zemin Ning (ICCBB, 2024)

The Bioinformatic Applications of Hi-C and Linked Reads. - Libo Jiang; Michael A Quail; Jack Fraser-Govil; Haipeng Wang; Xuequn Shi; Karen Oliver; Esther Mellado Gomez; Fengtang Yang; Zemin Ning (Genom. Proteom. Bioinform., 2024)