Power efficient special processor design for burrows-wheeler-transform-based short read sequence alignment. - Nae-Chyun Chen; Tai-Yin Chiu; Yu-Cheng Li; Yu-Chun Chien; Yi-Chang Lu (BioCAS, 2015)

Step shift: A fast image segmentation algorithm and its hardware implementation for next-generation sequencing fluorescence data. - Xiao-Xuan Huang; Chun-Hsien Ho; Yu-Cheng Li; Nae-Chyun Chen; Yi-Chang Lu (APCCAS, 2016)

An FPGA-based quality filter for de novo sequence assembly pipeline. - Chun-Shen Liu; Nae-Chyun Chen; Yu-Cheng Li; Yi-Chang Lu (APCCAS, 2016)

Queue-based segmentation algorithm for refining depth maps in light field camera applications. - Yi-Hsiang Chen; Nae-Chyun Chen; Yu-Hsiang Kao; Yu-Cheng Li; Yi-Chang Lu (GCCE, 2016)

A special processor design for Nucleotide Basic Local Alignment Search Tool with a new Banded two-hit method. - Chih-Yu Chang; Yu-Cheng Li; Nae-Chyun Chen; Xiao-Xuan Huang; Yi-Chang Lu (NORCAS, 2016)

Adaptively Banded Smith-Waterman Algorithm for Long Reads and Its Hardware Accelerator. - Yi-Lun Liao; Yu-Cheng Li; Nae-Chyun Chen; Yi-Chang Lu (ASAP, 2018)

A Memory-Efficient FM-Index Constructor for Next-Generation Sequencing Applications on FPGAs. - Nae-Chyun Chen; Yu-Cheng Li; Yi-Chang Lu (ISCAS, 2018)

A Hybrid Flow for Multiple Sequence Alignment with a BLASTn Based Pairwise Alignment Processor. - Mao-Jan Lin; Chih-Yu Chang; Yu-Cheng Li; Nae-Chyun Chen; Yi-Chang Lu (ISCAS, 2018)

LevioSAM: fast lift-over of variant-aware reference alignments. - Taher Mun; Nae-Chyun Chen; Ben Langmead (Bioinform., 2021)

Improving variant calling using population data and deep learning. - Nae-Chyun Chen; Alexey Kolesnikov; Sidharth Goel; Taedong Yun; Pi-Chuan Chang; Andrew Carroll (BMC Bioinform., 2023)