Emerging strengths in Asia Pacific bioinformatics (2009)
Bmc Bioinformatics, Shoba Ranganathan, Wen-lian Hsu, Ueng-cheng Yang, Wee Tan
Tsou, Chih-Chiang, Tsui, Yin-Hao, Yian, Yi-Hwa, Chen, Yi-Ju, Yang, Han-Yin, Yu, Chuan-Yih, ...
Isotope labeling combined with liquid chromatography–mass spectrometry (LC–MS) provides a robust platform for analyzing differential protein expression in proteomics research. We present a web...
Predicting helix-helix interactions from residue contacts in membrane proteins (2009)
Lo, Allan, Chiu, Yi-Yuan, Rødland, Einar Andreas, Lyu, Ping-Chiang, Sung, Ting-Yi, Hsu, Wen-Lian
Motivation: Helix–helix interactions play a critical role in the structure assembly, stability and function of membrane proteins. On the molecular level, the interactions are mediated by one or...
Lynn, Ke-Shiuan, Li, Li-Lan, Lin, Yen-Ju, Wang, Chiuen-Huei, Sheng, Shu-Hui, Lin, Ju-Hwa, ...
Motivation: Identification of disease-related genes using high-throughput microarray data is more difficult for complex diseases as compared with monogenic ones. We hypothesized that an endophenotype...
Using Maximum Entropy to Extract Biomedical Named Entities without Dictionaries (2008)
Tzong-han Tsai, Chia-wei Wu, Wen-lian Hsu
Current NER approaches include: dictionary-based, rule-based, or machine learning. Since there is no consolidated nomenclature for most biomedical NEs, most NER systems relying on limited...
Chia-yu Su, Allan Lo, Chin-chin Lin, Fu Chang, Wen-lian Hsu
We present a novel method to address multi-labeled protein subcellular localization prediction in Gram-negative bacteria using support vector machines (SVM) as classifiers. For a given protein...
Cheng, Cheng-Wei, Su, Emily, Hwang, Jenn-Kang, Sung, Ting-Yi, Hsu, Wen-Lian
Abstract Background RNA-protein interaction plays an essential role in several biological processes, such as protein synthesis, gene expression, posttranscriptional regulation and viral infectivity....
Semi-automatic conversion of BioProp semantic annotation to PASBio annotation (2008)
Tsai, Richard, Dai, Hong-Jie, Huang, Chi-Hsin, Hsu, Wen-Lian
Abstract Background Semantic role labeling (SRL) is an important text analysis technique. In SRL, sentences are represented by one or more predicate-argument structures (PAS). Each PAS is composed of...
Emerging strengths in Asia Pacific bioinformatics (2008)
Ranganathan, Shoba, Hsu, Wen-Lian, Yang, Ueng-Cheng, Tan, Tin Wee
Abstract The 2008 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998, was organized as the 7 th International Conference...
Cheng-wei Lee, Shih-hung Wu, Chorng-shyong Ong, Wen-lian Hsu
Integration of the bibliographical information of scholarly publications available on the Internet is an important task in academic research. To accomplish this task, accurate reference metadata...
A KNOWLEDGE-BASED APPROACH TO PROTEIN LOCAL STRUCTURE PREDICTION * (2008)
Ching-tai Chen, Hsin-nan Lin, Kun-pin Wu, Ting-yi Sung, Wen-lian Hsu
Local structure prediction can facilitate ab initio structure prediction, protein threading, and remote homology detection. However, previous approaches to local structure prediction suffer from poor...
A Society of Natural Language Agents on the Internet (2008)
Wen-lian Hsu, Yi-shiou Chen, Yuan-kai Wang
As the Internet is flooded with different types of documents (unstructured, semi-structured texts) and heterogeneous databases, information retrieval and extraction become increasingly difficult. To...
Auto-Discovery of NVEF Word-Pairs in Chinese Abstract (2008)
Jia-lin Tsai, Gladys Hsieh, Wen-lian Hsu
A meaningful noun-verb word-pair in a sentence is called a noun-verb event-frame (NVFE). Previously, we have developed an NVEF word-pair identifier to demonstrate that NVEF knowledge can be used...
A KNOWLEDGE-BASED APPROACH TO PROTEIN LOCAL STRUCTURE PREDICTION * (2008)
Ching-tai Chen, Hsin-nan Lin, Kun-pin Wu, Ting-yi Sung, Wen-lian Hsu
Local structure prediction can facilitate ab initio structure prediction, protein threading, and remote homology detection. However, previous approaches to local structure prediction suffer from poor...
Hsi-chuan Hung, Hong-jie Dai, Wen-lian Hsu
The application of text-to-speech (TTS) conversion has become widely used in recent years. Chinese TTS faces several unique difficulties. The most critical is caused by the lack of word delimiters in...
Designing an Ontology-based Intelligent Tutoring Agent with Instant (2008)
Min-yuh Day, Chun-hung Lu, Guey-fa Chiou, Chorng-shyong Ong, Wen-lian Hsu
The rapid growth of the Internet and Instant Messaging (IM) offers new opportunities as well as challenges to both educators and students. In this paper, we propose an Intelligent Tutoring Agent...
Baseball League. Green’s BASEBALL system... (2008)
Cheng-wei Lee, Cheng-wei Shih, Min-yuh Day, Tzong-han Tsai, Tian-jian Jiang, Chia-wei Wu, ...
Question Answering (QA) is becoming an increasingly important research area in natural language processing. Since 1999, many international question answering contests have been held at conferences...
Chiu-chen Hsieh, Tzong-han Tsai, David Wible, Wen-lian Hsu
Generally, Intelligent Tutoring Systems (ITSs) rely heavily on the hand-construction and design of the domain knowledge provided for learners. In this paper we attempt to illustrate a central role...
compartment-specific features (2008)
Hua-sheng Chiu, Allan Lo, Jenn-kang Hwang, Ting-yi Sung, Wen-lian Hsu
Protein subcellular localization prediction based on
Ontological Support in Modeling Learners ' Problem Solving Process (2008)
Chun-hung Lu, Chia-wei Wu, Shih-hung Wu, Guey-fa Chiou, Wen-lian Hsu
This paper presents a new model for simulating procedural knowledge in the problem solving process with our ontological system, InfoMap. The method divides procedural knowledge into two parts:...
Chia-wei Wu, Tzong-han Tsai, Wen-lian Hsu
Abstract. As web taxonomy integration is an emerging issue on the Internet, many research topics, such as personalization, web searches, and electronic markets, would benefit from further development...
Auto-Generation of NVEF Knowledge in Chinese Abstract (2008)
Jia-lin Tsai, Gladys Hsieh, Wen-lian Hsu
Noun-verb event frame (NVEF) knowledge in conjunction with an NVEF word-pair iden-tifier [Tsai et al. 2002] comprises a system to support natural language processing (NLP) and natural language...
Multi-Q Web Server provides an automated data analysis tool for multiplexed protein quantitation based on the iTRAQ labeling method. Multi-Q is designed as a generic platform that can accommodate...
Tzong-han Tsai, Wen-chi Chou, Shih-hung Wu, Ting-yi Sung, Sunita Sarawagi, Jieh Hsiang, ...
Elsevier use only: Received date here; revised date here; accepted date here As new high-throughput technologies have created an explosion of biomedical literature, there arises a pressing need for...
ON THE ACCURACY OF TRANSMEMBRANE HELIX PREDICTION METHODS USING AN UPDATED BENCHMARK (2008)
Allan Lo, Hua-sheng Chiu, Ting-yi Sung, Wen-lian Hsu, Allan Lo, Hua-sheng Chiu, ...
The prediction of transmembrane (TM) helix and topology is an important field of bioinformatics owing to the difficulties in obtaining high-resolution structures of membrane proteins. Many methods...
Chapter FAQ-Centered Organizational Memory (2008)
Shih-hung Wu, Min-yuh Day, Tzong-han Tsai, Wen-lian Hsu
Abstract: The value of a piece of information in an organization is related to its retrieval (or requested) frequency. Therefore, collecting the answers to the frequently asked questions (FAQs) and...
Jia-lin Tsai, Tien-jien Chiang, Wen-lian Hsu
Syllable-to-word (STW) conversion is a frequently used Chinese input method that is fundamental to syllable/speech understanding. The two major problems with STW conversion are the segmentation of...
A data structure called PC-tree is introduced as a generalization of PQ-trees. PC-trees were originally introduced in a planarity test of Shih and Hsu [7] where they represent partial embeddings of...
In this survey we focus on bioinformatics literature involving computational algo-rithms from authors in Taiwan. In a typical scenario of discrete algorithm design we have a single objective to...
Using Instant Messaging to Provide an Intelligent Learning Environment (2008)
Chun-hung Lu, Guey-fa Chiou, Min-yuh Day, Chorng-shyong Ong, Wen-lian Hsu
Abstract. Instant Messaging enables learners and educators to interact in an on-line environment. In this paper, we propose an intelligent ChatBot system, based on instant messaging, for student...
A mobile environment for Chinese language learning (2008)
Chang-chih Tseng, Chun-hung Lu, Wen-lian Hsu
Chinese language was usually considered difficult to learn, because of its complicated shape, different pronunciations and multiple meanings. In recent years, the amount of female spouses from...
Cheng-wei Lee, Shih-hung Wu, Chorng-shyong Ong, Wen-lian Hsu
The integration of bibliographical information of scholarly publications available on the Internet is an important task in academic research. Accurate reference metadata extraction for scholarly...
Cheng-wei Lee, Cheng-wei Shih, Min-yuh Day, Tzong-han Tsai, Tian-jian Jiang, Chia-wei Wu, ...
We propose a hybrid architecture for the NTCIR-5 CLQA C-C (Cross Language Question Answering from Chinese to Chinese) Task. Our system, the
Chinese Word Auto-Confirmation System using a Hybrid Approach Abstract (2008)
Jia-lin Tsai, Cheng-lung Sung, Wen-lian Hsu
In this paper, we present a Chinese word auto-confirmation (CWAC) system that uses a hybrid approach to take advantage of statistical and linguistic techniques. The task of our CWAC system is to...
Chiu-chen Hsieh, Tzong-han Tsai, David Wible, Wen-lian Hsu
Generally, Intelligent Tutoring Systems (ITSs) rely heavily on the hand-construction and design of the domain knowledge provided for learners. In this paper we attempt to illustrate a central role...
PC trees and circular-ones arrangements (2008)
Wen-lian Hsu, Ross M. Mcconnell
A 0-1 matrix has the consecutive-ones property if its columns can be ordered so that the ones in every row are consecutive. It has the circular-ones property if its columns can be ordered so that, in...
On Using Wiki in an English as a Second Language Course: An Empirical Study (2008)
Chun-hung Lu, Hao-chuan Wang, Wen-lian Hsu, Jun-yi Yang, Hsin-wen Hu, Guey-fa Chiou, ...
Abstract. In this poster, we concisely summarize and present our recent results of an empirical study of using Wiki in a freshman-level English as a second language (ESL) course in Taiwan. In this...
Tsai, Richard, Hung, Hsi-Chuan, Dai, Hong-Jie, Lin, Yi-Wen, Hsu, Wen-Lian
Abstract Background Experimentally verified protein-protein interactions (PPI) cannot be easily retrieved by researchers unless they are stored in PPI databases. The curation of such databases can be...
Tzong-han Tsai, Chia-wei Wu, Hsieh-chuan Hung, Yu-chun Wang, Ding He, Yi-feng Lin, ...
The rapid increase of biomedical literature available on the web has made it increasingly difficult to find precise information. To implement an accurate biomedical information retrieval (IR) system,...
Chun-nan Hsu, Jin-mei Lai, Chia-hung Liu, Huei-hun Tseng, Chih-yun Lin, Kuan-ting Lin, ...
Taipei 112, Taiwan, R. O. C. *These authors contribute equally to this work.
Exploitation of Linguistic Features Using a CRF-Based Biomedical Named Entity Recognizer (2008)
Tzong-han Tsai, Shih-hung Wu, Wen-lian Hsu
As new high-throughput technologies have created an explosion of biomedical literature, there arises a pressing need for automatic information extraction from the literature bank. To this end,...
Chen, Ching-Tai, Yang, Ei-Wen, Hsu, Hung-Ju, Sun, Yi-Kun, Hsu, Wen-Lian, Yang, An-Suei
Motivation: Regulatory proteases modulate proteomic dynamics with a spectrum of specificities against substrate proteins. Predictions of the substrate sites in a proteome for the proteases would...
BIOSMILE web search: a web application for annotating biomedical entities and relations (2008)
Dai, Hong-Jie, Huang, Chi-Hsin, Lin, Ryan T. K., Tsai, Richard Tzong-Han, Hsu, Wen-Lian
BIOSMILE web search (BWS), a web-based NCBI-PubMed search application, which can analyze articles for selected biomedical verbs and give users relational information, such as subject, object,...
BioMed Central Research Semi-automatic conversion of BioProp semantic annotation to (2008)
Bmc Bioinformatics, Pasbio Annotation, Hong-jie Dai, Chi-hsin Huang, Lian Hsu, ...
This article is available from:
On Physical Mapping Algorithms -- An Error-Tolerant Test for the Consecutive Ones Property (2007)
An important problem in physical mapping is to test the consecutive ones property of a (0,1)-matrix: that is, whether it is possible to permute the columns so that each row of the resulting matrix...
A Context Sensitive Model for Concept Understanding (2007)
Wen-lian Hsu, Yi-shiou Chen, Yuan-kai Wang
In artificial intelligence, knowledge representation is very crucial for simulating human understanding. Several strategies have previously been proposed for natural language understanding. But many...
Su, Emily, Chiu, Hua-Sheng, Lo, Allan, Hwang, Jenn-Kang, Sung, Ting-Yi, Hsu, Wen-Lian
Abstract Background Protein subcellular localization is crucial for genome annotation, protein function prediction, and drug discovery. Determination of subcellular localization using experimental...
Tsai, Richard, Chou, Wen-Chi, Su, Ying-Shan, Lin, Yu-Chun, Sung, Cheng-Lung, Dai, Hong-Jie, ...
Abstract Background Bioinformatics tools for automatic processing of biomedical literature are invaluable for both the design and interpretation of large-scale experiments. Many information...
The Multi-Q web server for multiplexed protein quantitation (2007)
Yu, Chuan-Yih, Tsui, Yin-Hao, Yian, Yi-Hwa, Sung, Ting-Yi, Hsu, Wen-Lian
The Multi-Q web server provides an automated data analysis tool for multiplexed protein quantitation based on the iTRAQ labeling method. The web server is designed as a platform that can accommodate...
Hsu, Chun-Nan, Lai, Jin-Mei, Liu, Chia-Hung, Tseng, Huei-Hun, Lin, Chih-Yun, Lin, Kuan-Ting, ...
Abstract Background The significant advances in microarray and proteomics analyses have resulted in an exponential increase in potential new targets and have promised to shed light on the...
Korean-Chinese Person Name Translation for Cross Language Information Retrieval (2007)
Wang, Yu-Chun, Lee, Yi-Hsun, Lin, Chu-Cheng, Tsai, Tzong-Han Richard, Hsu, Wen-Lian
PACLIC 21 / Seoul National University, Seoul, Korea / November 1-3, 2007
Tsai, Richard, Sung, Cheng-Lung, Dai, Hong-Jie, Hung, Hsieh-Chuan, Sung, Ting-Yi, Hsu, Wen-Lian
Abstract Background Biomedical named entity recognition (Bio-NER) is a challenging problem because, in general, biomedical named entities of the same category (e.g., proteins and genes) do not follow...
Various criteria in the evaluation of biomedical named entity recognition (2006)
Tsai, Richard Tzong-Han, Wu, Shih-Hung, Chou, Wen-Chi, Lin, Yu-Chun, He, Ding, Hsiang, Jieh, ...
Abstract Background Text mining in the biomedical domain is receiving increasing attention. A key component of this process is named entity recognition (NER). Generally speaking, two annotated...
Wen-chi Chou, Yu-chun Lin, Cheng-lung Sung, Wei Ku, Ying-shan Su, ...
In this paper, we construct a biomedical semantic role labeling (SRL) system that can be used to facilitate relation extraction. First, we construct a proposition bank on top of the popular...
Bmc Bioinformatics, Wen-chi Chou, Ying-shan Su, Yu-chun Lin, Cheng-lung Sung, ...
Research article BIOSMILE: A semantic role labeling system for biomedical verbs using a maximum-entropy model with automatically generated template features
An empirical exploration of using Wiki in an English as a second language course (2005)
Hao-chuan Wang, Chun-hung Lu, Jun-yi Yang, Hsin-wen Hu, Guey-fa Chiou, Yueh-tzu Chiang, ...
In this paper, we present an empirical study of using a new and cost-effective Web-based collaboration software, Wiki, in a freshman-level English as a second language (ESL) course. This paper...
Tzong-han Tsai, Chia-wei Wu, Yu-chun Lin, Wen-lian Hsu
In this paper, we propose a method that exploits full parsing information by representing it as features of argument classification models and as constraints in integer linear learning programs. In...
Tzong-han Tsai, Chia-wei Wu, Yu-chun Lin, Wen-lian Hsu
In this paper, we propose a method that exploits full parsing information by representing it as features of argument classification models and as constraints in integer linear learning programs. In...
Lin, Hsin-Nan, Chang, Jia-Ming, Wu, Kuen-Pin, Sung, Ting-Yi, Hsu, Wen-Lian
Motivation: In our previous approach, we proposed a hybrid method for protein secondary structure prediction called HYPROSP, which combined our proposed knowledge-based prediction algorithm PROSP and...
GANA--a genetic algorithm for NMR backbone resonance assignment (2005)
Lin, Hsin-Nan, Wu, Kun-Pin, Chang, Jia-Ming, Sung, Ting-Yi, Hsu, Wen-Lian
NMR data from different experiments often contain errors; thus, automated backbone resonance assignment is a very challenging issue. In this paper, we present a method called GANA that uses a genetic...
Lin, Hsin-Nan, Chang, Jia-Ming, Wu, Kuen-Pin, Sung, Ting-Yi, Hsu, Wen-Lian
Motivation: In our previous approach, we proposed a hybrid method for protein secondary structure prediction, called HYPROSP, which combined our proposed knowledge-based prediction algorithm PROSP...
Jia-lin Tsai, Tien-jien Chiang, Wen-lian Hsu
Abstract. Syllable-to-word (STW) conversion is a frequently used Chinese input method that is fundamental to syllable/speech understanding. The two major problems with STW conversion are the...
A maximum entropy approach to biomedical named entity recognition (2004)
Yi-feng Lin, Tzong-han Tsai, Wen-chi Chou, Kuen-pin Wu, Ting-yi Sung, Wen-lian Hsu
Machine learning approaches are frequently used to solve name entity (NE) recognition (NER). In this paper we propose a hybrid method that uses maximum entropy (ME) as the underlying machine learning...
Wu, Kuen-Pin, Lin, Hsin-Nan, Chang, Jia-Ming, Sung, Ting-Yi, Hsu, Wen-Lian
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...
An efficient implementation of the PC-trees algorithm of shih and hsu’s planarity test (2003)
In Shih & Hsu [9] a simpler planarity test was introduced utilizing a data structure called PC-trees (generalized from PQ-trees). In this paper we give an efficient implementation of that linear...
Mencius: A Chinese Named Entity Recognizer Using Hybrid Model (2003)
Tzong-han Tsai, Shih-Hung Wu, Wen-lian Hsu
This paper presents a maximum entropy based Chinese named entity recognizer (NER): Mencius. It aims to address Chinese NER problems by combining the advantages of rule-based and machine learning (ML)...
Domain Event Extraction and Representation with Domain Ontology (2003)
Shih-hung Wu, Tzong-han Tsai, Wen-lian Hsu
With domain ontology, a meaningful index of document indexing, such as the domain events structure in this paper, can be defined. Since the construction of domain ontology is costly, an automatic...
Syllable-to-word (STW) conversion is important in Chinese phonetic input methods and speech recognition. There are two major problems in the STW conversion: (1) resolving the ambiguity caused by...
A Cognitive Student Model – An Ontological Approach (2002)
Liongyu Tu, Wen-lian Hsu, Shih-hung Wu
We present an ontological approach to the design of the student model for a tutorial agent system (TAS). Our model emphasizes the classification and detection of error types. If the student has any...
A Cognitive Student Model – An Ontological Approach (2002)
Liongyu Tu, Wen-lian Hsu, Shih-hung Wu
We present an ontological approach to the design of the student model for a tutorial agent system (TAS). Our model emphasizes the classification and detection of error types. If the student has any...
Fast and simple algorithms for recognizing chordal comparability graphs and interval graphs (1999)
Abstract. In this paper, we present a linear-time algorithm for substitution decomposition on chordal graphs. Based on this result, we develop a linear-time algorithm for transitive orientation on...
Given an undirected graph, the planarity testing problem is to determine whether the graph can be drawn in the plane without any crossing edges. Linear time planarity testing algorithms have...
Muchnick S.S.: Advanced compiler design & implementation (1997)
Shih-hung Wu, Tzong-han Tsai, Wen-lian Hsu
In this paper, we describe ontology-based text categorization in which the domain ontologies are automatically acquired through morphological rules and statistical methods. The ontology-based...
Muchnick S.S.: Advanced compiler design & implementation (1997)
Shih-hung Wu, Tzong-han Tsai, Wen-lian Hsu
In this paper, we describe ontology-based text categorization in which the domain ontologies are automatically acquired through morphological rules and statistical methods. The ontology-based...
Muchnick S.S.: Advanced compiler design & implementation (1997)
Shih-hung Wu, Tzong-han Tsai, Wen-lian Hsu
In this paper, we describe ontology-based text categorization in which the domain ontologies are automatically acquired through morphological rules and statistical methods. The ontology-based...
On-Line Recognition of Interval Graphs in O(m + log n) Time (1996)
. Since the invention of PQ-trees by Booth and Lueker in 1976 the recognition of interval graphs has been simplified dramatically. In [7], we presented a very simple linear-time recognition algorithm...
A Linear Time Algorithm For Finding Maximal Planar Subgraphs (1995)
. Given an undirected graph G, the maximal planar subgraph problem is to determine a planar subgraph H of G such that no edge of G-H can be added to H without destroying planarity. Polynomial...
A Linear Time Algorithm for Finding Maximal Planar Subgraphs (1995)
In Shih & Hsu, a planarity test was introduced utilizing a data structure called PC-trees, generalized from PQ-trees. They illustrated that a PC-tree is more natural IN representing planar...
assigned to templates so that the final outcome is not decided by a fixed rule (as in a traditional rule-based system); rather, the accumulated effect of different matched templates makes the desired...
A simple test for interval graphs (1992)
An interval graph is the intersection graph of a collection of intervals. Interval graphs are a special class of chordal graphs. This class of graphs has a wide range of applications. Several linear...
A simple test for the consecutive ones property (1992)
A (0,1)-matrix satisfies the consecutive ones property if there exists a column permutation such that the ones in each row of the resulting matrix are consecutive. Booth and Lueker [1976] designed a...
An approximation algorithm for coloring circular arc graphs (1990)
Consider families of arcs on a circle. The minimum coloring problem on arc families has been shown to be NP-hard by Garey, Johnson, Miller and Papadimitriou. It is easy to show that 2q colors are...
An Approximation Algorithm for Coloring Circular-Arc Graphs (1990)
Consider families of arcs on a circle. The minimum coloring problem on arc families has been shown to be NP-hard by Garey, Johnson, Miller and Papadimitriou. It is easy to show that 2q colors are...
Efficient algorithms for some packing and covering problems on graphs / (1980)
Photocopy of typescript.
HYPROSP: a hybrid protein secondary structure prediction algorithm—a knowledge-based approach
Wu, Kuen-Pin, Lin, Hsin-Nan, Chang, Jia-Ming, Sung, Ting-Yi, Hsu, Wen-Lian
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...
GANA—a genetic algorithm for NMR backbone resonance assignment
Lin, Hsin-Nan, Wu, Kun-Pin, Chang, Jia-Ming, Sung, Ting-Yi, Hsu, Wen-Lian
NMR data from different experiments often contain errors; thus, automated backbone resonance assignment is a very challenging issue. In this paper, we present a method called GANA that uses a genetic...
Various criteria in the evaluation of biomedical named entity recognition
Tsai, Richard Tzong-Han, Wu, Shih-Hung, Chou, Wen-Chi, Lin, Yu-Chun, He, Ding, Hsiang, Jieh, ...
HYPROSP: a hybrid protein secondary structure prediction algorithm—a knowledge-based approach
Wu, Kuen-Pin, Lin, Hsin-Nan, Chang, Jia-Ming, Sung, Ting-Yi, Hsu, Wen-Lian
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...
GANA—a genetic algorithm for NMR backbone resonance assignment
Lin, Hsin-Nan, Wu, Kun-Pin, Chang, Jia-Ming, Sung, Ting-Yi, Hsu, Wen-Lian
NMR data from different experiments often contain errors; thus, automated backbone resonance assignment is a very challenging issue. In this paper, we present a method called GANA that uses a genetic...
Various criteria in the evaluation of biomedical named entity recognition
Tsai, Richard Tzong-Han, Wu, Shih-Hung, Chou, Wen-Chi, Lin, Yu-Chun, He, Ding, Hsiang, Jieh, ...
Tsai, Richard Tzong-Han, Sung, Cheng-Lung, Dai, Hong-Jie, Hung, Hsieh-Chuan, Sung, Ting-Yi, Hsu, Wen-Lian
The Multi-Q web server for multiplexed protein quantitation
Yu, Chuan-Yih, Tsui, Yin-Hao, Yian, Yi-Hwa, Sung, Ting-Yi, Hsu, Wen-Lian
The Multi-Q web server provides an automated data analysis tool for multiplexed protein quantitation based on the iTRAQ labeling method. The web server is designed as a platform that can accommodate...
Tsai, Richard Tzong-Han, Chou, Wen-Chi, Su, Ying-Shan, Lin, Yu-Chun, Sung, Cheng-Lung, Dai, Hong-Jie, ...
BIOSMILE web search: a web application for annotating biomedical entities and relations
Dai, Hong-Jie, Huang, Chi-Hsin, Lin, Ryan T. K., Tsai, Richard Tzong-Han, Hsu, Wen-Lian
BIOSMILE web search (BWS), a web-based NCBI-PubMed search application, which can analyze articles for selected biomedical verbs and give users relational information, such as subject, object,...
Emerging strengths in Asia Pacific bioinformatics
Ranganathan, Shoba, Hsu, Wen-Lian, Yang, Ueng-Cheng, Tan, Tin Wee
The 2008 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998, was organized as the 7th International Conference on...
Predicting RNA-binding sites of proteins using support vector machines and evolutionary information
Cheng, Cheng-Wei, Su, Emily Chia-Yu, Hwang, Jenn-Kang, Sung, Ting-Yi, Hsu, Wen-Lian
Semi-automatic conversion of BioProp semantic annotation to PASBio annotation
Tsai, Richard Tzong-Han, Dai, Hong-Jie, Huang, Chi-Hsin, Hsu, Wen-Lian
Object Oriented Concept Representation
way of an English-to-Chinese machine translation (MT) system. Concept representation is a key to natural language understanding. Several strategies have previously been proposed. But many of them...
Lynn, Ke-Shiuan, Li, Li-Lan, Lin, Yen-Ju, Wang, Chiuen-Huei, Sheng, Shu-Hui, Lin, Ju-Hwa, ...
Motivation: Identification of disease-related genes using high-throughput microarray data is more difficult for complex diseases as compared with monogenic ones. We hypothesized that an endophenotype...
Predicting helix–helix interactions from residue contacts in membrane proteins
Lo, Allan, Chiu, Yi-Yuan, Rødland, Einar Andreas, Lyu, Ping-Chiang, Sung, Ting-Yi, Hsu, Wen-Lian
Motivation: Helix–helix interactions play a critical role in the structure assembly, stability and function of membrane proteins. On the molecular level, the interactions are mediated by one or...
Tsou, Chih-Chiang, Tsui, Yin-Hao, Yian, Yi-Hwa, Chen, Yi-Ju, Yang, Han-Yin, Yu, Chuan-Yih, ...
Isotope labeling combined with liquid chromatography–mass spectrometry (LC–MS) provides a robust platform for analyzing differential protein expression in proteomics research. We present a web...