Shang-Jung Wen;Jia-Ming Chang;David Jing-Wei Chen;Fang Yu*, 2025.07, 'scGHSOM: A Hierarchical Framework for Single-Cell Data Clustering and Visualization, ' IEEE Transactions on Computational Biology and Bioinformatics, pp.1 - 17.(SCIE)(*為通訊作者)
Tatyana G Kahn;Mikhail Savitsky;Chikuan Kuong;Caroline Jacquer;Giacomo Cavalli;Jia-Ming Chang*;Yuri B Schwartz*, 2023.02, 'Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements, ' Science Advances, Vol.9, No.5, pp.eade0090.(SCIE)(*為通訊作者)
Jhen Yuan Yang;Jia-Ming Chang*, 2022.10, 'Pattern recognition of topologically associating domains using deep learning, ' BMC Bioinformatics, Vol.22, No.Suppl 10, pp.634.(SCIE)(*為通訊作者)
Jia-Ming Chang*;Yi-Fu Weng;Wei-Ting Chang;Fu-An Lin;Giacomo Cavalli, 2022.02, 'HiCmapTools: a tool to access HiC contact maps, ' BMC Bioinformatics, Vol.23, No.64, pp.1.(SCIE)(*為通訊作者)
Yi-Wei Liu;Tz-Wei Hsu;Che-Yu Chang;Wen-Hung Liao*;Jia-Ming Chang*, 2020.11, 'GODoc: high-throughput protein function prediction using novel k-nearest-neighbor and voting algorithms, ' BMC Bioinformatics, Vol.21, pp.276.(SCIE)(*為通訊作者)
Yang Ming Lin;Ching-Tai Chen;Jia-Ming Chang*, 2019.12, 'MS2CNN: Predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks, ' BMC Genomics, Vol.20, pp.906.(SCIE)(*為通訊作者)
CAFA3 organization;張家銘, 2019.11, 'The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens, ' Genome Biology, pp.1-1.(SCIE)
Jia-Ming Chang*;Evan W. Floden;Javier Herrero;Olivier Gascuel;Paolo Di Tommaso;Cedric Notredame*, 2019.02, 'Incorporating alignment uncertainty into Felsenstein’s phylogenetic bootstrap to improve its reliability, ' Bioinformatics, pp.1-1.(SCIE)(*為通訊作者)
Yuki Ogiyama;Bernd Schuettengruber;Giorgio L. Papadopoulos;Jia-Ming Chang;Giacomo Cavalli*, 2018.07, 'Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development, ' Molecular Cell, Vol.71, No.1, pp.73-88.(SCIE)(*為通訊作者)
Quentin Szabo;Marcelo Nollmann;Frédéric Bantignies*;Giacomo Cavalli*;Daniel Jost;Jia-Ming Chang;Diego I Cattoni;Giorgio L Papadopoulos;Boyan Bonev;Tom Sexton;Julian Gurgo;Caroline Jacquier, 2018.02, 'TADs are 3D structural units of higher-order chromosome organization in Drosophila, ' Science Advances, Vol.4, No.2, pp.eaar8082.(SCIE)(*為通訊作者)
Diego I. Cattoni;Inma González;Jia-Ming Chang;Thomas Sexton;Marc A. Marti-Renom;Frédéric Bantignies, 2017.11, 'Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions, ' Nature communications, Vol.8, No.1, pp.1753.(SCIE)
Maria Chatzou;Cedrik Magis;張家銘;Carsten Kemena;Giovanni Bussotti;Ionas Erb, 2016.11, 'Multiple sequence alignment modeling: methods and applications, ' Briefings in Bioinformatics, Vol.17, No.6, pp.1009-1023.(SCIE)
Evan Floden;Paolo Di Tommaso;Maria Chatzou;Cedrik Magis;Cedric Notredame;張家銘*, 2016.07, 'PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases, ' Nucleic Acids Research, Vol.44, No.W1, pp.W339-W343.(SCIE, SCI)(*為通訊作者)
Meng-Shin Shiao;張家銘;Wen-Lang Fan;Mei-Yeh Jade Lu;Cedric Notredame;Shu Fang, 2015.10, 'Expression divergence of chemosensory genes between Drosophila sechellia and its sibling species and its implications for host shift, ' Genome Biology and Evolution, Vol.7, No.10, pp.2843-2858.(SCIE)
張家銘;Paolo Di Tommaso;Vincent Lefort;Olivier Gascuel;Cedric Notredame*, 2015.07, 'TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction, ' Nucleic Acids Research, Vol.43, No.W1, pp.W3-6.(SCIE)(*為通訊作者)
張家銘, 2014.10, 'Alignathon: A competitive assessment of whole genome alignment methods, ' Genome Research, Vol.24, pp.2077-2089.(SCIE)
張家銘;Paolo Di Tommaso;Cedric Notredame*, 2014.06, 'TCS: A New Multiple Sequence Alignment Reliability Measure to Estimate Alignment Accuracy and Improve Phylogenetic Tree Reconstruction, ' Molecular Biology and Evolution, Vol.31, No.6, pp.1625-37.(SCIE)(*為通訊作者)
張家銘;Jean-Francois Taly;Ionas Erb; Ting-Yi Sung;Wen-Lian Hsu;Chuan Yi Tang, 2013.10, 'Efficient and interpretable prediction of protein functional classes by correspondence analysis and compact set relations, ' PLoS ONE, Vol.8, No.10, pp.e75542.(SCIE)
Emily CY Su*;張家銘;Cheng-Wei Cheng;Ting-Yi Sung;Wen-Lian Hsu, 2012.12, 'Prediction of nuclear proteins using nuclear translocation signals proposed by probabilistic latent semantic indexing, ' BMC Bioinformatics, Vol.13, No.Suppl 17, pp.S13.(SCIE)(*為通訊作者)
張家銘;Paolo Di Tommaso;Jean-François Taly;Cedric Notredame*, 2012.03, 'Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee, ' BMC Bioinformatics, Vol.13, No.Suppl 4, pp.S1.(SCIE)(*為通訊作者)
Hsin-Nan Lin;Cédric Notredame;張家銘;Ting-Yi Sung*;Wen-Lian Hsu*, 2011.12, 'Improving the alignment quality of consistency based aligners with an evaluation function using synonymous protein words, ' PLoS One, Vol.6, No.12, pp.e27872.(SCIE)(*為通訊作者)
Jean-Francois Taly;Cedrik Magis;Giovanni Bussotti;張家銘;Paolo Di Tommaso;Ionas Erb,, 2011.11, 'Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures, ' Nature Protocols, Vol.6, No.11, pp.1669-1682.(SCIE, SCI)
Paolo Di Tommaso;Sebastien Moretti;Ioannis Xenarios;Miquel Orobitg;Alberto Montanyola;張家銘, 2011.07, 'T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension, ' Nucleic Acids Research, Vol.39, No.2, pp.W13-W17.(SCIE)
Che-Yu Chang;Tz-Wei Hsu;張家銘*, 2019.11, 'PSLCNN: Protein Subcellular Localization Prediction for Eukaryotes and Prokaryotes Using Deep Learning, ' International Conference on Technologies and Applications of Artificial Intelligence, Taiwanese Association for Artificial Intelligence.(EI)(*為通訊作者)
Yang Ming Lin;Ching-Tai Chen;Jia-Ming Chang*, 2019.09, 'MS2CNN: Predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks, ' International Conference on Bioinformatics 2019, Asia-Pacific Bioinformatics Network (APBioNet).(*為通訊作者)
YU-TING HUANG;MENG-SHIN SHIAO;CHEN-AN TSAI;KUER-YUAN LAN;CHIEH-HSI LIN;NATINI JIANAWATH*;張家銘*, 2019.07, 'Identification of alternative splicing characteristic associated with clear-cell ovarian cancer from paired normal and tumor tissues, ' IEEE Xplore and EI, IEEE the Systems, Man, and Cybernetics Society, pp.1-5.(EI)(*為通訊作者)
Yi-Wei Liu;Tz-Wei Hsu;Che-Yu Chang;Wen-Hung Liao*;Jia-Ming Chang*, 2019.06, 'GODoc: A High-Throughput Protein Function Prediction using the Novel k-nearest-neighbor and Voting algorithms, ' 15th International Symposium on Bioinformatics Research and Applications (ISBRA), Georgia State University, Department of Computer Science.(*為通訊作者)
張家銘*;Evan W. Floden;Javier Herrero;Olivier Gascuel;Paolo Di Tommaso;Cedric Notredame*, 2018, 'Incorporating alignment uncertainty into Felsenstein’s phylogenetic bootstrap to improve its reliability, ' The 29th International Conference on Genome Informatics, University of Technology Sydney.(*為通訊作者)
Yi‑Wei Liu;Wen‑Hung Liao;Jia-Ming Chang*, 2017.05, 'High‑throughput Protein Functional Prediction by Data Science Approach, ' The 34th Workshop on Combinatorial Mathematics and Computation Theory, Feng Chia University.(*為通訊作者)
Jia-Ming Chang*;Cedric Notredame, 2017.05, 'Influence of alignment uncertainty on homology modeling, ' The 34th Workshop on Combinatorial Mathematics and Computation Theory, Feng Chia University.(*為通訊作者)
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