Jia-Ming Chang

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This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other(More)
Multiple sequence alignment (MSA) is a key modeling procedure when analyzing biological sequences. Homology and evolutionary modeling are the most common applications of MSAs. Both are known to be sensitive to the underlying MSA accuracy. In this work, we show how this problem can be partly overcome using the transitive consistency score (TCS), an extended(More)
In this paper, we design an algorithm of computing a constrained multiple sequence alignment (CMSA for short) for guaranteeing that the generated alignment satisfies the user-specified constraints that some particular residues should be aligned together. If the number of residues needed to be aligned together is a constant alpha, then the time-complexity of(More)
Transmembrane proteins (TMPs) constitute about 20~30% of all protein coding genes. The relative lack of experimental structure has so far made it hard to develop specific alignment methods and the current state of the art (PRALINE™) only manages to recapitulate 50% of the positions in the reference alignments available from the BAliBASE2-ref7. We show how(More)
T-Coffee (Tree-based consistency objective function for alignment evaluation) is a versatile multiple sequence alignment (MSA) method suitable for aligning most types of biological sequences. The main strength of T-Coffee is its ability to combine third party aligners and to integrate structural (or homology) information when building MSAs. The series of(More)
Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark data sets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole-genome alignment (WGA). Using the same model as(More)
Bidens pilosa (B. pilosa) is well known in Taiwan as a traditional Chinese medicine. The purpose of this study was to evaluate the ability of both the ethanol (EtOH) and ethylacetate/ethanol (EA/EtOH) extracts from the whole B. pilosa plant, to protect normal human erythrocytes against oxidative damage in vitro. It was determined that the oxidative(More)
We develop a knowledge-based approach (called PROSP) for protein secondary structure prediction. The knowledge base contains small peptide fragments together with their secondary structural information. A quantitative measure M, called match rate, is defined to measure the amount of structural information that a target protein can extract from the knowledge(More)
Current cytotoxic chemotherapy produces clinical benefit in patients with breast cancer but the survival impact is modest. To explore novel cytotoxic agents for the treatment of advanced disease, we have characterized a new and pharmacokinetically improved Hec1-targeted compound, TAI-95. Nine of 11 breast cancer cell lines tested were sensitive to nanomolar(More)
Cyclooxygenase-2 (COX-2) is an inducible enzyme responsible for high-level prostaglandin production during inflammation and carcinogenesis. In this study, the transcriptional regulation of COX-2 expression induced by epidermal growth factor (EGF) in human epidermoid carcinoma A431 cells was studied. EGF treatment induced the expression of COX-2 mRNA,(More)