Constrained Multiple Sequence Alignment Tool Development and Its Application to RNase Family Alignment. - Chuan Yi Tang; Chin Lung Lu; Margaret Dah-Tsyr Chang; Yin-Te Tsai; Yuh-Ju Sun; Kun-Mao Chao; Jia-Ming Chang; Yu-Han Chiou; Chia-Mao Wu; Hao-Teng Chang; Wei-I Chou (CSB, 2002)

Constrained Multiple Sequence Alignment Tool Development Andits Application to Rnase Family Alignment. - Chuan Yi Tang; Chin Lung Lu; Margaret Dah-Tsyr Chang; Yin-Te Tsai; Yuh-Ju Sun; Kun-Mao Chao; Jia-Ming Chang; Yu-Han Chiou; Chia-Mao Wu; Hao-Teng Chang; Wei-I Chou (J. Bioinform. Comput. Biol., 2003)

Implementation of robust wavelet-neural-network sliding-mode control for induction servo motor drive. - Rong-Jong Wai; Jia-Ming Chang (IEEE Trans. Ind. Electron., 2003)

An Iterative Relaxation Technique for the NMR Backbone Assignment Problem. - Wen-Lian Hsu; Jia-Ming Chang; Wen-Chi Chou; Jun-Bo Chen; Kuen-Pin Wu; Ting-Yi Sung; Chi-Fon Chang; Wen-Jin Wu; Tai-Huang Huang (BIBE, 2004)

GANAA Genetic Algorithm for NMR Backbone Resonance Assignment. - Hsin-Nan Lin; Kuen-Pin Wu; Jia-Ming Chang; Ting-Yi Sung; Wen-Lian Hsu (CSB Workshops, 2005)

HYPROSP II-A knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence. - Hsin-Nan Lin; Jia-Ming Chang; Kuen-Pin Wu; Ting-Yi Sung; Wen-Lian Hsu (Bioinform., 2005)

RIBRA - An Error-Tolerant Algorithm for the NMR Backbone Assignment Problem. - Kuen-Pin Wu; Jia-Ming Chang; Jun-Bo Chen; Chi-Fon Chang; Wen-Jin Wu; Tai-Huang Huang; Ting-Yi Sung; Wen-Lian Hsu (J. Comput. Biol., 2006)

Novel efficient two-pass algorithm for closed polygonal approximation based on LISE and curvature constraint criteria. - Kuo-Liang Chung; Po-Hsuan Liao; Jia-Ming Chang (J. Vis. Commun. Image Represent., 2008)

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. - Paolo Di Tommaso; Sébastien Moretti; Ioannis Xenarios; Miquel Orobitg; Alberto Montanyola; Jia-Ming Chang; Jean-François Taly; Cédric Notredame (Nucleic Acids Res., 2011)

Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee. - Jia-Ming Chang; Paolo Di Tommaso; Jean-François Taly; Cédric Notredame (BMC Bioinform., 2012)

Prediction of nuclear proteins using nuclear translocation signals proposed by probabilistic latent semantic indexing. - Emily Chia-Yu Su; Jia-Ming Chang; Cheng-Wei Cheng; Ting-Yi Sung; Wen-Lian Hsu (BMC Bioinform., 2012)

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction. - Jia-Ming Chang; Paolo Di Tommaso; Vincent Lefort; Olivier Gascuel; Cédric Notredame (Nucleic Acids Res., 2015)

Multiple sequence alignment modeling: methods and applications. - Maria Chatzou; Cedrik Magis; Jia-Ming Chang; Carsten Kemena; Giovanni Bussotti; Ionas Erb; Cédric Notredame (Briefings Bioinform., 2016)

PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases. - Evan W. Floden; Paolo Di Tommaso; Maria Chatzou; Cedrik Magis; Cédric Notredame; Jia-Ming Chang (Nucleic Acids Res., 2016)

Identification of Alternative Splicing Characteristic Associated with Clear-Cell Ovarian Cancer from Paired Normal and Tumor Tissues. - Yu-Ting Huang; Meng-Shin Shiao; Chen-An Tasi; Kuer-Yuan Lan; Chieh-Hsi Lin; Natini Jianawath; Jia-Ming Chang (ICMLC, 2019)

PSLCNN: Protein Subcellular Localization Prediction for Eukaryotes and Prokaryotes Using Deep Learning. - Che-Yu Chang; Tz-Wei Hsu; Jia-Ming Chang (TAAI, 2019)

GODoc: high-throughput protein function prediction using novel k-nearest-neighbor and voting algorithms. - Yi-Wei Liu; Tz-Wei Hsu; Che-Yu Chang; Wen-Hung Liao; Jia-Ming Chang (BMC Bioinform., 2020)

Stability of single-cell dimension reduction after data shuffling. - Yu Ting Hsu; Jia-Ming Chang (ISPACS, 2021)

Incorporating alignment uncertainty into Felsenstein's phylogenetic bootstrap to improve its reliability. - Jia-Ming Chang; Evan W. Floden; Javier Herrero; Olivier Gascuel; Paolo Di Tommaso; Cédric Notredame (Bioinform., 2021)

Pattern recognition of topologically associating domains using deep learning. - Jhen Yuan Yang; Jia-Ming Chang (BMC Bioinform., 2021)

HiCmapTools: a tool to access HiC contact maps. - Jia-Ming Chang; Yi-Fu Weng; Wei-Ting Chang; Fu-An Lin; Giacomo Cavalli (BMC Bioinform., 2022)

Dual-Objective Personalized Federated Service System With Partially-Labeled Data Over Wireless Networks. - Cheng-Wei Ching; Jia-Ming Chang; Jian-Jhih Kuo; Chih-Yu Wang 001 (IEEE Trans. Serv. Comput., 2023)

scGHSOM: Hierarchical clustering and visualization of single-cell and CRISPR data using growing hierarchical SOM. - Shang-Jung Wen; Jia-Ming Chang; Fang Yu (CoRR, 2024)