2020
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*

                                                                                         

< link >

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


                                                                                          < link >

2019
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*


                                                                                            < link >

Effect of de novo transcriptome assembly on transcript quantification

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


                                                                                          < link >

2018
HAHap: a read-based haplotyping method using hierarchical assembly

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


                                                                                            < link >

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*


                                                                                           read more...

2017
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


                                                                                            read more...

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*

                                                                                           read more...

2016
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*

                                                                                            read more...

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

                                                                                           read more...

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*

                                                                                            read more...

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

                                                                                           read more...

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*

                                                                                            read more...

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*

                                                                                           read more...

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

                                                                                            read more...

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*

                                                                                           read more...

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

                                                                                            read more...

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*

                                                                                           read more...

2015
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*

                                                                                            read more...

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*

                                                                                           read more...

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*

                                                                                            read more...

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*

                                                                                           read more...

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*


                                                                                            read more...

2014
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*

                                                                                           read more...

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*

                                                                                            read more...

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*

                                                                                           read more...

2013
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

                                                                                            read more...

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*

                                                                                           read more...

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*

                                                                                            read more...

PiDNA: predicting protein–DNA interactions with structural models

Chih-Kang Lin and Chien-Yu Chen*

                                                                                           read more...

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*

                                                                                            read more...

2012
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*

                                                                                           read more...

2012
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*


                                                                                            read more...

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*

                                                                                           read more...

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*

                                                                                            read more...

2011
WildSpan: mining structured motifs from protein sequences

Chen-Ming Hsu, Chien-Yu Chen*

                                                                                           read more...

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*

                                                                                            read more...

Predicting DNA-binding locations and orientation on proteins using knowledge-based learning of geometric properties

Chien-Chih Wang and Chien-Yu Chen*

                                                                                           read more...

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*

                                                                                            read more...

2009
seeMotif: exploring and visualizing sequence motifs in 3D structures

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

                                                                                           read more...

2008
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

                                                                                            read more...

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*

                                                                                           read more...

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*

                                                                                            read more...

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

                                                                                           read more...

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*

                                                                                           read more...

2007
iPDA: integrated protein disorder analyzer

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

                                                                                           read more...

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

                                                                                            read more...

2006
Protein disorder prediction by condensed PSSM considering propensity for order or disorder

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

                                                                                           read more...

MAGIIC-PRO: detecting functional signatures by efficient discovery of long patterns in protein sequences

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

                                                                                            read more...

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

                                                                                           read more...

2005
Exploiting homogeneity in protein sequence clusters for construction of protein family hierarchies

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

                                                                                            read more...

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

                                                                                           read more...

A statistics-based approach to control the quality of subclusters in incremental gravitational clustering

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

                                                                                            read more...

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

                                                                                           read more...

2004
Incremental generation of summarized clustering hierarchy for protein family analysis

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

                                                                                            read more...

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

                                                                                          read more...