Jia-Ming Chang

发表

Alignathon: a competitive assessment of whole-genome alignment methods

David Haussler, Inna Dubchak, Ngan Nguyen, 2014, bioRxiv.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Jari Björne, Tapio Salakoski, Giorgio Valentini, 2019, Genome Biology.

MS2CNN: predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks

Ching-Tai Chen, Jia-Ming Chang, Y. Lin, 2019, BMC Genomics.

T-Coffee: Tree-based consistency objective function for alignment evaluation.

Paolo Di Tommaso, Jia-Ming Chang, Jean-François Taly, 2014, Methods in molecular biology.

Efficient and Interpretable Prediction of Protein Functional Classes by Correspondence Analysis and Compact Set Relations

C. Tang, C. Notredame, W. Hsu, 2013, PloS one.

High-throughput protein functional prediction by data science approach

Jia-Ming Chang, Wen-Hung Liao, Yi-Wei Liu, 2017 .

Pattern recognition of topologically associating domains using deep learning

Jia-Ming Chang, Jhen Yuan Yang, 2022, BMC Bioinform..

Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures

Carsten Kemena, Paolo Di Tommaso, Ionas Erb, 2011, Nature Protocols.

TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction.

Paolo Di Tommaso, Jia-Ming Chang, Cedric Notredame, 2014, Molecular biology and evolution.

Multiple sequence alignment modeling: methods and applications

Cédric Notredame, Carsten Kemena, Jia-Ming Chang, 2016, Briefings Bioinform..

Expression Divergence of Chemosensory Genes between Drosophila sechellia and Its Sibling Species and Its Implications for Host Shift

C. Notredame, Shu Fang, R. Kondo, 2015, Genome biology and evolution.

PSLDoc: Protein subcellular localization prediction based on gapped‐dipeptides and probabilistic latent semantic analysis

Wen-Lian Hsu, Emily Chia-Yu Su, Ting-Yi Sung, 2008, Proteins.

Incorporating alignment uncertainty into Felsenstein’s phylogenetic bootstrap to improve its reliability

Olivier Gascuel, Paolo Di Tommaso, Jia-Ming Chang, 2019, Bioinform..

Improving the Alignment Quality of Consistency Based Aligners with an Evaluation Function Using Synonymous Protein Words

Wen-Lian Hsu, Ting-Yi Sung, Cédric Notredame, 2011, PloS one.

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

Ioannis Xenarios, Sébastien Moretti, Cédric Notredame, 2011, Nucleic Acids Res..

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Tapio Salakoski, Feng Zhang, Paolo Fontana, 2019, Genome Biology.

GODoc: high-throughput protein function prediction using novel k-nearest-neighbor and voting algorithms

Che-Yu Chang, Wen-Hung Liao, Jia-Ming Chang, 2020, BMC Bioinformatics.

Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee

Paolo Di Tommaso, C. Notredame, Jean-François Taly, 2012, BMC Bioinformatics.

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction

Olivier Gascuel, Vincent Lefort, Cédric Notredame, 2015, Nucleic Acids Res..

Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee

Cédric Notredame, Jia-Ming Chang, Paolo Di Tommaso, 2012, BMC Bioinformatics.

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, Cédric Notredame, Jia-Ming Chang, 2016, Nucleic Acids Res..

PSLCNN: Protein Subcellular Localization Prediction for Eukaryotes and Prokaryotes Using Deep Learning

Che-Yu Chang, Jia-Ming Chang, Tz-Wei Hsu, 2019, 2019 International Conference on Technologies and Applications of Artiﬁcial Intelligence (TAAI).

HYPROSP II-A knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence

Wen-Lian Hsu, Ting-Yi Sung, Kuen-Pin Wu, 2005, Bioinform..

HiCmapTools: a tool to access HiC contact maps

Giacomo Cavalli, Jia-Ming Chang, Wei-Ting Chang, 2022, BMC Bioinformatics.

Prediction of nuclear proteins using nuclear translocation signals proposed by probabilistic latent semantic indexing

Wen-Lian Hsu, Emily Chia-Yu Su, Ting-Yi Sung, 2012, BMC Bioinformatics.

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, 2019, 2019 International Conference on Machine Learning and Cybernetics (ICMLC).

HYPROSP: a hybrid protein secondary structure prediction algorithm--a knowledge-based approach.

Wen-Lian Hsu, Ting-Yi Sung, Kuen-Pin Wu, 2004, Nucleic acids research.

Constrained multiple sequence alignment tool development and its application to RNase family alignment

Yin-Te Tsai, Chuan Yi Tang, Kun-Mao Chao, 2002, Proceedings. IEEE Computer Society Bioinformatics Conference.

RIBRA - An Error-Tolerant Algorithm for the NMR Backbone Assignment Problem

Wen-Lian Hsu, Ting-Yi Sung, Kuen-Pin Wu, 2006, J. Comput. Biol..

GANA—a genetic algorithm for NMR backbone resonance assignment

Wen-Lian Hsu, Ting-Yi Sung, Kuen-Pin Wu, 2005, 2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05).

RIBRA-An Error-Tolerant Algorithm for the NMR Backbone Assignment Problem

Wen-Lian Hsu, Ting-Yi Sung, Kuen-Pin Wu, 2005, RECOMB.