2021
15 Dec 2021 Retina
Predicted protein structure variations indicate the clinical presentation of CYP4V2-related Bietti crystalline dystrophy

Li-Wei Chan, Yu-Chi Sung, Dung-Chi Wu, Chien-Yu Chen, Chang-Hao Yang, Chung-May Yang, Pei-Lung Chen, and Ta-Ching Chen*

                                                   

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18 Oct 2021 Communications Biology, 4:1194
Connecting MHC-I-binding motifs with HLA alleles via deep learning

Ko-Han Lee, Yu-Chuan Chang, Ting-Fu Chen, Hsueh-Fen Juan, Huai-Kuang Tsai, and Chien-Yu Chen*

                                                   

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16 Aug 2021 Bioinformatics, btab588
ezGeno: An Automatic Model Selection Package for Genomic Data Analysis

Jun-Liang Lin#, Tsung-Ting Hsieh# (equal contribution), Yi-An Tung# (equal contribution), Xuan-Jun Chen, Yu-Chun Hsiao, Chia-Lin Yang*, Tyng-Luh Liu*, Chien-Yu Chen*

                                                   

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25 May 2021 Blood Advances, 5(10):2456-2466
Clinical implications of sequential MRD monitoring by NGS at two time points after chemotherapy in AML patients

Cheng-Hong Tsai, Jih-Luh Tang, Feng-Ming Tien, Yuan-Yeh Kuo, Dung-Chi Wu, Chien-Chin Lin, Mei-Hsuan Tseng, Yen-Ling Peng, Mei-Fang Hou, Yi-Kuang Chuang, Min Liu, Chia-Wen Liu, Ming Yao, Liang-In Lin, Wen-Chien Chou, Chien-Yu Chen, Hsin-An Hou, and Hwei-Fang Tien*

                                                                             

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2020
09 Oct 2020 Nucleic Acids Research, 49(D1):D1152-D1159
DockCoV2: a drug database against SARS-CoV-2

Ting-Fu Chen#, Yu-Chuan Chang#, Yi Hsiao#, Ko-Han Lee#, Yu-Chun Hsiao, Yu-Hsiang Lin, Yi-Chin Ethan Tu, Hsuan-Cheng Huang, Chien-Yu Chen*, and Hsueh-Fen Juan*

                                                                                     

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24 Feb 2020 BMC Bioinformatics, 21:68
GenEpi: gene-based epistasis discovery using machine learning

Yu-Chuan Chang, June-Tai Wu, Ming-Yi Hong, Yi-An Tung, Ping-Han Hsieh, Sook Wah Yee, Kathleen M. Giacomini, Yen-Jen Oyang, Chien-Yu Chen* & for the Alzheimer’s Disease Neuroimaging Initiativeon Here

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2019
19 Dec 2019 Nucleic Acids Research, 48(3):1175-1191
Integrative analyses of noncoding RNAs reveal the potential mechanisms augmenting tumor malignancy in lung adenocarcinoma

Jou-Ho Shih, Hsin-Yi Chen, Shin-Chih Lin, Yi-Chen Yeh, Roger Shen, Yaw-Dong Lang, Dung-Chi Wu, Chien-Yu Chen, Ruey-Hwa Chen, Teh-Ying Chou, and Yuh-Shan Jou*

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27 Nov 2019 Scientific Reports, 9:8304
Effect of de novo transcriptome assembly on transcript quantification

Ping-Han Hsieh, Yen-Jen Oyang, and Chien-Yu Chen*

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2018
30 Oct 2018 PeerJ, 6:e5852
HAHap: a read-based haplotyping method using hierarchical assembly

Yu-Yu Lin, Ping Chun Wu, Pei-Lung Chen, Yen-Jen Oyang, Chien-Yu Chen*

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2 May 2018 GigaScience, 7(5):giy044
Whole-genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant

Chien-Yueh Lee#, Ping-Han Hsieh# (equal contribution), Li-Mei Chiang, Amrita Chattopadhyay, Kuan-Yi Li, Yi-Fang Lee, Tzu-Pin Lu, Liang-Chuan Lai, En-Chung Lin, Hsinyu Lee, Shih-Torng Ding, Mong-Hsun Tsai, Chien-Yu Chen*, Eric Y. Chuang*

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2017
19 Sep 2017 Molecular Ecology, 26(22):6301-6316
Comparative and population genomic landscape of Phellinus noxius: A hypervariable fungus causing root rot in trees

Chia-Lin Chung, Jiaye Lee, Mitsuteru Akiba, Hsin-Han Lee, Tzu-Hao Kuo, Dang Liu, Huei-Mien Ke, Toshiro Yokoi, Marylette Roa, Meiyeh Lu, Ya-Yun Chang, Pao-Jen Ann, Jyh-Nong Tsai, Chien-Yu Chen, Shean-Shong Tzean, Yuko Ota, Tsutomu Hattori, Norio Sahashi, Ruey-Fen Liou, Taisei Kikuchi, Isheng J. Tsai

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24 Feb 2017 Science, 355(6327):820-826
Predicting human olfactory perception from chemical features of odor molecules

Andreas Keller, Richard C. Gerkin, Yuanfang Guan, Amit Dhurandhar, Gabor Turu, Bence Szalai, Joel D. Mainland, Yusuke Ihara, Chung Wen Yu, Russ Wolfinger, Celine Vens, Leander Schietgat, Kurt De Grave, Raquel Nore, DREAM Olfaction Prediction Consortium (..., Bor-Wei Cherng, Chien-Yu Chen, Ming-Yi Hong, Ping-Han Hsieh, Yen-Jen Oyang, Yi-An Tung, Yu-Chuan Chang, ...), Gustavo Stolovitzky, Guillermo A. Cecchi, Leslie B. Vosshall, Pablo Meyer*

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2016
10 Aug 2016 J. Agric. Food Chem, 64(34):6648-6658
Transcriptomic and Proteomic Research To Explore Bruchid-Resistant Genes in Mungbean Isogenic Lines

Wu-Jui Lin, Chia-Yun Ko, Mao-Sen Liu, Chien-Yen Kuo, Dung-Chi Wu, Chien-Yu Chen, Roland Schafleitner, Long-Fang O. Chen, and Hsiao-Feng Lo*

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15 Jul 2016 BMC Plant Biology, 16:159
Identification of single nucleotide polymorphism markers associated with resistance to bruchids (Callosobruchus spp.) in wild mungbean (Vigna radiata var. sublobata) and cultivated V. radiata through genotyping by sequencing and quantitative trait locus analysis

Roland Schafleitner, Shu-Mei Huang, Shui-Hui Chu, Jo-Yi Yen, Chen-Yu Lin, Miao-Rong Yan, Bharath Krishnan, Mao-Sen Liu, Hsiao-Feng Lo, Chien-Yu Chen, Long-Fang O. Chen, Dung-Chi Wu, Thu-Giang Thi Bui, Srinivasan Ramasamy, Chih-Wei Tung and Ramakrishnan Nair

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28 Jun 2016 Parkinsonism & Related Disorders, 33:36-43
Clinical heterogeneity of LRRK2 p.I2012T mutation

Tian-Sin Fan, Ruey-Meei Wu, Pei-Lung Chen, Ta-Fu Chen, Huei-Ying Li, Yin-Hung Lin, Chien-Yu Chen, Meng-Ling Chen, Chun-Hwei Tai, Hang-I. Lin, Chin-Hsien Lin*

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22 Apr 2016 Journal of Economic Entomology, 109(3):1378-1386
Discovery of Organophosphate Resistance-Related Genes Associated With Well-known Resistance Mechanisms of Plutella xylostella (L.) (Lepidoptera: Plutellidae) by RNA-Seq

Ju-Chun Hsu, Yu-Yu Lin, Chia-Che Chang, Kuo-Hsun Hua, Mei-Ju May Chen, Li-Hsin Huang, and Chien-Yu Chen

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11 Apr 2016 Alzheimer's & Dementia, 12(6):645-653
Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease

Genevera I Allen, …Yu-Chuan Chang, …, Chien-Yu Chen, …, Ting-Ying Chien, …, Ming-Yi Hong, …, Yen-Jen Oyang, …, Yi-An Tung, …, and Alzheimer's Disease Neuroimaging Initiative*

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11 Mar 2016 BMC Genomics, 17:220
Integrating RNA-seq and ChIP-seq data to characterize long non-coding RNAs in Drosophila melanogaster

Mei-Ju May Chen#, Li-Kai Chen(#:equal contribution), Yu-Shing Lai, You-Yu Lin, Dung-Chi Wu, Yi-An Tung, Kwei-Yan Liu, Hsueh-Tzu Shih, Yi-Jyun Chen, Yan-Liang Lin, Li-Ting Ma, Jian-Long Huang, Po-Chun Wu, Ming-Yi Hong, Fang-Hua Chu, June-Tai Wu*, Wen-Hsiung Li*, and Chien-Yu Chen*

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8 Mar 2016 New Phytologist, 211(2):599-613
ORA47 (octadecanoid‐responsive AP2/ERF‐domain transcription factor 47) regulates jasmonic acid and abscisic acid biosynthesis and signaling through binding to a novel cis‐element

Hsing-Yu Chen, En-Jung Hsieh, Mei-Chun Cheng, Chien-Yu Chen, Shih-Ying Hwang and Tsan-Piao Lin

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17 Feb 2016 BMC Plant Biology, 16:46
Genomic and transcriptomic comparison of nucleotide variations for insights into bruchid resistance of mungbean (Vigna radiata [L.] R. Wilczek)

Genevera I Allen, …Yu-Chuan Chang, …, Chien-Yu Chen, …, Ting-Ying Chien, …, Ming-Yi Hong, …, Yen-Jen Oyang, …, Yi-An Tung, …, and Alzheimer's Disease Neuroimaging Initiative*

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29 Jan 2016 Cell Death and Differentiation, 23(7):1175-84
Aiolos collaborates with Blimp-1 to regulate the survival of multiple myeloma cells

Kuo-I Lin*, Kuo-Hsuan Hung, Shin-Tang Su, Chien-Yu Chen, Pang-Hung Hsu, Po-Chun Wu, Hsin-Yu Chen, Fan-Ru Lin, Ming-Daw Tsai, Shang-Yi Huang, Wan-Jung Wu, and Mei-Ju May Chen

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11 Jan 2016 Scientific Reports, 6:19112
Identification and preliminary characterization of chemosensory perception-associated proteins in the melon fly Bactrocera cucurbitae using RNA-seq

Samia Elfekih, Chien-Yu Chen, Ju-Chun Hsu, Mahdi Belcaid, and David Haymer*

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2015
10 Aug 2015 Proceedings of the National Academy of Sciences, 112(34):10798-10803
The opportunistic marine pathogen Vibrio parahaemolyticus becomes virulent by acquiring a plasmid that expresses a deadly toxin

Chung-Te Lee, I-Tung Chen, Yi-Ting Yang, Tzu-Ping Ko, Yun-Tzu Huang, Jiun-Yan Huang, Ming-Fen Huang, Shin-Jen Lin, Chien-Yu Chen, Shih-Shun Lin, Donald V. Lightner, Han-Ching Wang, Andrew H.-J. Wang, Hao-Ching Wang, Lien-I Hor, and Chu-Fang Lo*

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12 Jun 2015 BMC Plant Biology, 15:139
The effect of red light and far-red light conditions on secondary metabolism in Agarwood

Tony Chien-Yen Kuo, Chuan-Hung Chen, Shu-Hwa Chen, I-Hsuan Lu, Li-Chun Huang, Chung-Yen Lin, Chien-Yu Chen, Hsiao-Feng Lo, Shih-Tong Jeng, Long-Fang Oliver Chen*

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20 Feb 2015 Insect Molecular Biology, 24(3):338-47
Discovery of genes related to formothion resistance in oriental fruit fly (Bactrocera dorsalis) by a constrained functional genomics analysis

Tony Chien-Yen Kuo, Chia-Cheng Hu, Ting-Ying Chien, Mei-Ju May Chen, Hai-Tung Feng, Long-Fang O. Chen, Chien-Yu Chen* and Ju-Chun Hsu*

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9 Feb 2015 EMBO reports, 16(4):528-38
Intellectual disability‐associated dBRWD3 regulates gene expression through inhibition of HIRA/YEM‐mediated chromatin deposition of histone H3.3

Wei-Yu Chen, Hsueh-Tzu Shih, Kuei-Yan Liu, Zong-Siou Shih, Li-Kai Chen, Tsung-Han Tsai, Mei-Ju Chen, Hsuan Liu, Bertrand Chin-Ming Tan, Chien-Yu Chen, Hsiu-Hsiang Lee, Benjamin Loppin, Ounissa Ait-Ahmed, June-Tai Wu*

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23 Jan 2015 BMC Genomics, 16:22
Emergence of differentially regulated pathways associated with the development of regional specificity in chicken skin

Kai-Wei Chang, Nancy A Huang, I-Hsuan Liu, E-Hui Wang, Ping Wu, Yen-Tzu Tseng, Michael W Hughes, Ting Xin Jiang, Mong-Hsun Tsai, Chien-Yu Chen, Yen-Jen Oyang, En-Chung Lin, Cheng-Ming Chuong and Shau-Ping Lin*


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2014
4 Sep 2014 Genome Announc., 2(5):e00816-14
Draft Genome Sequences of Four Strains of Vibrio parahaemolyticus, Three of Which Cause Early Mortality Syndrome/Acute Hepatopancreatic Necrosis Disease in Shrimp in China and Thailand

Yi-Ting Yang, I-Tung Chen, Chung-Te Lee, Chien-Yu Chen, Shih-Shun Lin, Lien-I Hor, Ta-Chien Tseng, Yun-Tzu Huang, Kallaya Sritunyalucksana, Siripong Thitamadee, Han-Ching Wang, Chu-Fang Lo*

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9 Jul 2014 BMC Genomics, 15:578
Identification of cucurbitacins and assembly of a draft genome for Aquilaria agallocha

Chuan-Hung Chen#, Tony Chien-Yen Kuo#, Meng-Han Yang, Ting-Ying Chien, Mei-Ju Chu, Li-Chun Huang, Chien-Yu Chen, Hsiao-Feng Lo, Shih-Tong Jeng and Long-Fang O. Chen*

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28 Apr 2014 BMC Plant Biology, 14:112
Differential activation of sporamin expression in response to abiotic mechanical wounding and biotic herbivore attack in the sweet potato

SenthilKumar Rajendran, I-Winnie Lin, Mei-Ju Chen, Chien-Yu Chen, and Kai-Wun Yeh*

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2013
15 Aug 2013 Genome Research, 23:1928-1937
Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach

Pablo Meyer, Geoffrey Siwo, Danny Zeevi, Eilon Sharon, Raquel Norel, DREAM6 Promoter Prediction Consortium, Eran Segal and Gustavo Stolovitzky

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1 Jul 2013 BMC Genomics, 14:4342013
De novo transcriptome sequencing of axolotl blastema for identification of differentially expressed genes during limb regeneration

Cheng-Han Wu, Mong-Hsun Tsai, Chia-Chuan Ho, Chien-Yu Chen*, and Hsuan-Shu Lee*

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13 Jun 2013 IEEE/ACM Transactions onComputational Biology <br>and Bioinformatics, 10(3):593-604
Comparison of Feature Selection Methods for Cross-Laboratory Microarray Analysis

Hsi-Che Liu, Pei-Chen Peng, Tzung-Chien Hsieh, Ting-Chi Yeh, Chih-Jen Lin, Chien-Yu Chen, Jen-Yin Hou, Lee-Yung Shih, Der-Cherng Liang*

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22 May 2013 Nucleic Acids Research, 41:W523-530
PiDNA: predicting protein–DNA interactions with structural models

Chih-Kang Lin and Chien-Yu Chen*

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27 Jan 2013 Nature Biotechnology, 31:126-134
Evaluation of methods for modeling transcription factor sequence specificity

Matthew T Weirauch, Atina Cote, Raquel Norel, Matti Annala, Yue Zhao, Todd R Riley, Julio Saez-Rodriguez, Thomas Cokelaer, Anastasia Vedenko, Shaheynoor Talukder, DREAM5 Consortium, Harmen J Bussemaker, Quaid D Morris, Martha L Bulyk, Gustavo Stolovitzky, Timothy R Hughes*

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2012
7 Aug 2012 PLoS ONE, 7(8):e40950
Discovery of Genes Related to Insecticide Resistance in Bactrocera dorsalis by Functional Genomic Analysis of a De Novo Assembled Transcriptome

Ju-Chun Hsu, Ting-Ying Chien(§:equal contribution), Chia-Cheng Hu§, Mei-Ju May Chen§, Wen-Jer Wu, Hai-Tung Feng, David S. Haymer and Chien-Yu Chen*

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2012
11 Jun 2012 Nucleic Acids Research, 40:W173-179
DBD2BS: connecting a DNA-binding protein with its binding sites

Ting-Ying Chien, Chih-Kang Lin, Chih-Wei Lin, Yi-Zhong Weng, Chien-Yu Chen*, Darby Tien-Hao Chang*

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1 Feb 2012 PLoS ONE, 7(2):e30446
Predicting Target DNA Sequences of DNA-Binding Proteins Based on Unbound Structures

Chien-Yu Chen, Ting-Ying Chien, Chih-Kang Lin, Chih-Wei Lin, Yi-Zhong Weng, and Darby Tien-Hao Chang*

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11 Jan 2012 Bioinformatics, 28(5):701-708
De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiae

Mei-Ju May Chen, Lih-Ching Chou, Tsung-Ting Hsieh, Ding-Dar Lee, Kai-Wei Liu, Chi-Yuan Yu, Yen-Jen Oyang, Huai-Kuang Tsai*, and Chien-Yu Chen*

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2011
31 Mar 2011 Algorithms for Molecular Biology, 6:6
WildSpan: mining structured motifs from protein sequences

Chen-Ming Hsu and Chien-Yu Chen*

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7 Feb 2011 Cancer Genetics, 204(5):252-259
Expression of HOXB genes is significantly different in acute myeloid leukemia with a partial tandem duplication of MLL vs. a MLL translocation: a cross-laboratory study

Hsi-Che Liu, Lee-Yung Shih, Mei-Ju May Chen, Chien-Chih Wang, Ting-Chi Yeh, Tung-Huei Lin, Chien-Yu Chen, Chih-Jen Lin, and Der-Cherng Liang*

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4 Feb 2011 Proteome Science, 9(Suppl 1):S11
Predicting DNA-binding locations and orientation on proteins using knowledge-based learning of geometric properties

Chien-Chih Wang and Chien-Yu Chen*

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1 Feb 2011 Biological Psychiatry, 70(1):51-58
ANXA7, PPP3CB, DNAJC9, and ZMYND17 Genes at Chromosome 10q22 Associated with the Subgroup of Schizophrenia with Deficits in Attention and Executive Function

Chih-Min Liu, Cathy S-J Fann, Chien-Yu Chen, Yu-Li Liu, Yen-Jen Oyang, Wei-Chih Yang, Chien-Ching Chang, Chun-Chiang Wen, Wei J. Chen, Tzung-Jeng Hwang, Ming-Hsien Hsieh, Chen-Chung Liu, Stephen V. Faraone, Ming T. Tsuang, and Hai-Gwo Hwu*

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2009
28 May 2009 Nucleic Acids Research, 37:W552-558
seeMotif: exploring and visualizing sequence motifs in 3D structures

Darby Tien-Hao Chang, Ting-Ying Chien, and Chien-Yu Chen*

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2008
19 Aug 2008 Journal of Biomedical Informatics, 41(4):570-579
Cross-generation and cross-laboratory predictions of Affymetrix microarrays by rank-based methods

Hsi-Che Liu, Chien-Yu Chen*, Yu-Ting Liu, Cheng-Bang Chu, Der-Cherng Liang, Lee-Yung Shih and Chih-Jen Lin

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23 Jul 2008 BMC Research Notes, 1:51
Prediction of protein secondary structures with a novel kernel density estimation based classifier

Darby Tien-Hao Chang, Yu-Yen Ou, Hao-Geng Hung, Meng-Han Yang, Chien-Yu Chen, and Yen-Jen Oyang*

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2 Jul 2008 Mammalian Genome, 19(6):398-405
Gene expression variation increase in trisomy 21 tissues

Ching-Yu Chou, Li-Yu Liu, Chien-Yu Chen, Cheng-Hsien Tsai, Hsiao-Lin Hwa, Li-Yun Chang, Yi-Shing Lin, and Fon-Jou Hsieh*

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4 Jun 2008 Nucleic Acids Research, 36:W291-W296
E1DS: catalytic site prediction based on 1D signatures of concurrent conservation

Ting-Ying Chien, Darby Tien-Hao Chang*, Chien-Yu Chen, Yi-Zhong Weng, and Chen-Ming Hsu

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19 Feb 2008 Proceedings of the National Academy of Sciences, 105(7):2527-2532
Discovering gapped binding sites of yeast transcription factors

Chien-Yu Chen, Huai-Kuang Tsai, Chen-Ming Hsu, Mei-Ju May Chen, Hao-Geng Hung, Grace Tzu-Wei Huang, and Wen-Hsiung Li*

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2007
1 Jul 2007 Nucleic Acids Research, 35:W465-W472
iPDA: integrated protein disorder analyzer

Chung-Tsai Su, Chien-Yu Chen*, and Chen-Ming Hsu

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24 May 2007 BMC Bioinformatics, 8(Suppl 5):S8
Identification of hot regions in protein-protein interactions by sequential pattern mining

Chen-Ming Hsu, Chien-Yu Chen*, Baw-Jhiune Liu, Chih-Chang Huang, Min-Hung Laio, Chien-Chieh Lin, and Tzung-Lin Wu

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2006
23 Jun 2006 BMC Bioinformatics, 7:319
Protein disorder prediction by condensed PSSM considering propensity for order or disorder

Chung-Tsai Su, Chien-Yu Chen*, and Yu-Yen Ou

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11 Apr 2006 Nucleic Acids Research, 34:W356-361
MAGIIC-PRO: detecting functional signatures by efficient discovery of long patterns in protein sequences

Chen-Ming Hsu, Chien-Yu Chen*, Baw-Jhiune Liu

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9 Jan 2006 Pattern Recognition, 39(12):2426-2438
Pattern classification in DNA microarray data of multiple tumor types

Tsun-Chen Lin, Ru-Sheng Liu*, Chien-Yu Chen, Ya-Ting Chao, and Shu-Yuan Chen

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2005
12 Dec 2005 Pattern Recognition, 38(12):2256-2269
Exploiting homogeneity in protein sequence clusters for construction of protein family hierarchies

Chien-Yu Chen*, Wen-Chin Chung, and Chung-Tsai Su

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30 Mar 2005 Intelligent Data Analysis, 9(1):43-58
Analysis and Summarization of Correlations in Data Cubes and its Applications in Microarray Data Analysis

Chien-Yu Chen*, Shien-Ching Hwang, and Yen-Jen Oyang

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21 Mar 2005 Pattern Recognition, 38(12):2256-2269
A statistics-based approach to control the quality of subclusters in incremental gravitational clustering

Chien-Yu Chen*, Shien-Ching Hwang, and Yen-Jen Oyang

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31 Jan 2005 IEEE transactions on neural networks, 16(1):225-236
Data classification with radial basis function networks based on a novel kernel density estimation algorithm

Yen-Jen Oyang*, Shien-Ching Hwang, Yu-Yen Ou, Chien-Yu Chen, and Zhi-Wei Chen

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2004
1 Nov 2004 Bioinformatics, 20(16):2586-2596
Incremental generation of summarized clustering hierarchy for protein family analysis

Chien-Yu Chen*, Yen-Jen Oyang, and Hsueh-Fen Juan

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1 Jul 2004 Nucleic Acids Research, 32:W76-W82
ProteMiner-SSM: a web server for efficient analysis of similar protein tertiary substructures

Darby Tien-Hau Chang, Chien-Yu Chen, Wen-Chin Chung, Yen-Jen Oyang*, Hsueh-Fen Juan, and Hsuan-Cheng Huang

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