Publications

Selected publications of Jia-Ming Chang, National Chengchi University — 3D genome, bioinformatics methods and protein function prediction.

完整著作列表請見 Google Scholar。以下是精選。

Selected publications

Download BibTeX — 精選著作的引用資料，可直接匯入文獻管理軟體。

Co-corresponding author

2023 · Science Advances

Topological screen identifies hundreds of Cp190- and CTCF-dependent Drosophila chromatin insulator elements

Tatyana G Kahn, Mikhail Savitsky, Chikuan Kuong, Caroline Jacquier, Giacomo Cavalli, Jia-Ming Chang*, Yuri B Schwartz*

A topological screen in Drosophila cells lacking CTCF and Cp190 identifies hundreds of insulator elements that modulate local chromatin interactions without driving global genome folding, suggesting Cp190 functions by promoting insulator protein cobinding rather than loop formation.

First author

2021 · Bioinformatics

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, Cedric Notredame

Sampling alignment columns across alternative aligners enhances the discriminative power of bootstrap support regarding tree topology correctness.

Code Docs

Corresponding author

2019 · BMC Genomics

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

Yang-Ming Lin, Ching-Tai Chen, Jia-Ming Chang*

Predicted MS2 spectra improve the sensitivity and coverage of peptide identification. MS2CNN was among the first deep-learning approaches to this problem, outperforming MS2PIP, matching pDeep overall, and performing best on the hardest 3+ charge peptides.

Code

First author

2014 · Molecular Biology and Evolution

TCS: A New Multiple Sequence Alignment Reliability Measure to Estimate Alignment Accuracy and Improve Phylogenetic Tree Reconstruction

Jia-Ming Chang, Paolo Di Tommaso, Cedric Notredame

The reliability of a multiple sequence alignment can be robustly quantified using the Transitive Consistency Score, derived from the T-Coffee pairwise library.

Web server

First author

2012 · BMC Bioinformatics

Accurate Multiple Sequence Alignment of Transmembrane Proteins with PSI-Coffee

Jia-Ming Chang, Paolo Di Tommaso, Jean-François F Taly, Cedric Notredame

Homology extension combined with a consistency-based approach significantly improves the multiple sequence alignment of alpha-helical transmembrane proteins.

Web server

* co-corresponding authors

科普文章

長達兩公尺的遺傳資訊如何塞進六微米的細胞核？讓我們從染色體上的「拓樸結構域」談起