Jia-Ming Chang 張家銘
Jia-Ming Chang 張家銘
Department of Computer Science, National Chengchi University
Verified email at - Homepage
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T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension
P Di Tommaso, S Moretti, I Xenarios, M Orobitg, A Montanyola, JM Chang, ...
Nucleic acids research 39 (suppl_2), W13-W17, 2011
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
N Zhou, Y Jiang, TR Bergquist, AJ Lee, BZ Kacsoh, AW Crocker, ...
Genome Biology 20, 244, 2019
TADs are 3D structural units of higher-order chromosome organization in Drosophila
Q Szabo, D Jost, JM Chang, DI Cattoni, GL Papadopoulos, B Bonev, ...
Science advances 4 (2), eaar8082, 2018
TCS: A new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction
JM Chang, P Di Tommaso, C Notredame
Molecular biology and evolution 31 (6), 1625-1637, 2014
Multiple sequence alignment modeling: methods and applications
M Chatzou, C Magis, JM Chang, C Kemena, G Bussotti, I Erb, ...
Briefings in bioinformatics 17 (6), 1009-1023, 2016
Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development
Y Ogiyama, B Schuettengruber, GL Papadopoulos, JM Chang, G Cavalli
Molecular Cell 71 (1), 73-88, 2018
Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions
DI Cattoni, AM Cardozo Gizzi, M Georgieva, M Di Stefano, A Valeri, ...
Nature communications 8 (1), 1753, 2017
Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee
JM Chang, P Di Tommaso, JF Taly, C Notredame
BMC Bioinformatics 13 (Suppl 4), S1, 2012
Alignathon: A competitive assessment of whole genome alignment methods
D Earl, NK Nguyen, G Hickey, RS Harris, S Fitzgerald, K Beal, I Seledtsov, ...
Genome Research 24, 2077-2089, 2014
Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures
JF Taly, C Magis, G Bussotti, JM Chang, P Di Tommaso, I Erb, ...
Nature protocols 6 (11), 1669-1682, 2011
Constrained multiple sequence alignment tool development and its application to RNase family alignment
CY Tang, CL Lu, MDT Chang, YT Tsai, YJ Sun, KM Chao, JM Chang, ...
Bioinformatics Conference, 2002. Proceedings. IEEE Computer Society, 127-137, 2002
HYPROSP II-A knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence
HN Lin, JM Chang, KP Wu, TY Sung, WL Hsu
Bioinformatics 21 (15), 3227-3233, 2005
T-Coffee: Tree-based consistency objective function for alignment evaluation
C Magis, JF Taly, G Bussotti, JM Chang, P Di Tommaso, I Erb, ...
Multiple Sequence Alignment Methods, 117-129, 2014
PSLDoc: protein subcellular localization prediction based on gapped‐dipeptides and probabilistic latent semantic analysis
JM Chang, ECY Su, A Lo, HS Chiu, TY Sung, WL Hsu
Proteins: Structure, Function, and Bioinformatics 72 (2), 693-710, 2008
PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases
EW Floden, PD Tommaso, M Chatzou, C Magis, C Notredame, JM Chang
Nucleic acids research 44 (W1), W339-W343, 2016
Expression divergence of chemosensory genes between Drosophila sechellia and its sibling species and its implications for host shift
MS Shiao, JM Chang, WL Fan, MYJ Lu, C Notredame, S Fang, R Kondo, ...
Genome biology and evolution 7 (10), 2843-2858, 2015
TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction
JM Chang, P Di Tommaso, V Lefort, O Gascuel, C Notredame
Nucleic acids research 43 (W1), W3–W6, 2015
RIBRA—an error-tolerant algorithm for the NMR backbone assignment problem
KP Wu, JM Chang, JB Chen, CF Chang, WJ Wu, TH Huang, TY Sung, ...
Journal of Computational Biology 13 (2), 229-244, 2006
HYPROSP: a hybrid protein secondary structure prediction algorithm—a knowledge-based approach
KP Wu, HN Lin, JM Chang, TY Sung, WL Hsu
Nucleic Acids Research 32 (17), 5059-5065, 2004
GANA—a genetic algorithm for NMR backbone resonance assignment
HN Lin, KP Wu, JM Chang, TY Sung, WL Hsu
Nucleic acids research 33 (14), 4593-4601, 2005
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