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2018

The development of functional mapping by three sex-related loci on the third whorl of different sex types of Carica papaya L.

Lee CY, Lin HJ, Viswanath KK, Lin CP, Chang BC, Chiu PH, Chiu CT, Wang RH, Chin SW, Chen FC.

Journal: PLoS One. (2018 Mar 22)

A 1204-single nucleotide polymorphism and insertion–deletion polymorphism panel for massively parallel sequencing analysis of DNA mixtures

Hsiao-Lin Hwa, Wan-Chia Chung, Pei-Lung Chen, Chih-Peng Lin, Huei-Ying Li, Hsiang-I Yin, James Chun-I Lee.

Journal: Forensic Science International: Genetics (January 2018)

2017 

Identification of a c.544C>T mutation in WDR34 as a deleterious recessive allele of short rib-polydactyly syndrome

Shu-Han You, Yun-Shien Lee, Chueh-Pai Lee, Chih-Peng Lin, Chiao-Yun Lin, Chia-Lung Tsai, Yao-Lung Chang, Po-Jen Cheng, Tzu-Hao Wang, Shuenn-Dyh Chang

Journal: Taiwanese Journal of Obstetrics & Gynecology (December 2017)

Hepatocellular carcinoma-associated single-nucleotide variants and deletions identified by the use of genome-wide high-throughput analysis of hepatitis B virus.

Liu WC, Wu IC, Lee YC, Lin CP, Cheng JH, Lin YJ, Yen CJ, Cheng PN, Li PF, Cheng YT, Cheng PW, Sun KT, Yan SL, Lin JJ, Yang JC, Chang KC, Ho CH, Tseng VS, Chang BC, Wu JC, Chang TT.
Journal: J Pathol. (2017)

Deguelin exerts potent nematocidal activity via the mitochondrial respiratory chain.

Preston S, Korhonen PK, Mouchiroud L, Cornaglia M, McGee SL, Young ND, Davis RA, Crawford S, Nowell C, Ansell BRE, Fisher GM, Andrews KT, Chang BCH, Gijs MAM, Sternberg PW, Auwerx J, Baell J, Hofmann A, Jabbar A, Gasser RB.

Journal: FASEB J.  (2017 Jul 7)

Whipworm kinomes reflect a unique biology and adaptation to the host animal.

Stroehlein AJ, Young ND, Korhonen PK, Chang BCH, Nejsum P, Pozio E, La Rosa G, Sternberg PW, Gasser RB.

Journal: Int J Parasitol.  (2017 Jun 10)

A panel of 130 autosomal single-nucleotide polymorphisms for ancestry assignment in five Asian populations and in Caucasians.

Hwa HL, Lin CP, Huang TY, Kuo PH, Hsieh WH, Lin CY, Yin HI, Tseng LH, Lee JC.

Journal: Forensic Sci Med Pathol. (2017 Jun)

2016 

Setting Up of First NIPT Service Laboratory in a Thailand Hospital

Bill CH Chang, Takol Chareonsirisuthigul, Pareena Janchompoo, Chutatip Srichunrusami, Ekawat Pasomsub, Thipparat Nasrisuk, Insee Sensorn, Panyu Panburana and Wasun Chantratita*

Journal: Journal of Next Generation Sequencing & Applications. (2016 Oct 19)

Analyses of Compact Trichinella Kinomes Reveal a MOS-like Protein Kinase with a Unique N-terminal Domain

Andreas Stroehlein, Neil D. Young, Pasi K. Korhonen, Bill C. H. Chang, Paul W. Sternberg, Giuseppe La Rosa, Edoardo Pozio and Robin B. Gasser,

Journal: G3: Genes, Genomes, Genetics (2016)

The genome and transcriptome of Phalaenopsis yield insights into floral organ development and flowering regulation

Jian-Zhi Huang, Chih-Peng Lin, Ting-Chi Cheng, Ya-Wen Huang, Yi-Jung Tsai, Shu-Yun Cheng, Yi-Wen Chen, Chueh-Pai Lee, Wan-Chia Chung, Bill Chia-Han Chang​ , Shih-Wen Chin​, Chen-Yu Lee, Fure-Chyi Chen​

Jornal：Peer-reviewed (2016)

2015

Jian-Zhi Huang， Chih-Peng Lin，Ting-Chi Cheng，Bill Chia-Han Chang，Shu-Yu Cheng，Yi-Wen Chen，Chen-Yu Lee，* Shih-Wen Chin，* and Fure-Chyi Chen*

A De Novo Floral Transcriptome Reveals Clues into Phalaenopsis Orchid Flower Development

PLoS One. 2015; 10(5): e0123474.

Wen-Chun Liu，Chih-Peng Lin，Chun-Pei Cheng，Cheng-Hsun Ho，Kuo-Lun Lan，Ji-Hong Cheng，Chia-Jui Yen，Pin-Nan Cheng，I-Chin Wu，I-Chen Li，Bill Chia-Han Chang，Vincent S. Tseng，Yen-Cheng Chiu，Ting-Tsung Chang.

Aligning to the sample-specific reference sequence to optimize the accuracy of next-generation sequencing analysis for hepatitis B virus. 

Hepatology International (2015): 9645

• Huang YY, Cho ST, Lo WS, Wang YC, Lai EM and Kuo CH. 

• Complete genome sequence of Agrobacterium tumefaciens Ach5.

Genome Announc. (2015) 3：e00570-15.

• Yao-Shen Chen, Hsi-Hsun Lin, Pei-Tan Hsueh, Pei-Ju Liu, Wen-Fan Ni, Wan-Chia Chung, Chih-Peng Lin, and Ya-Lei Chen

Whole-Genome Sequence of an Epidemic Strain of Burkholderia pseudomallei vgh07 in Taiwan.     

Genome Announc. (2015) 3(2): e00345-15. 

• Tsunglin Liu, Ching-Min Li, Yue-Lun Han, Tzen-Yuh Chiang, Yu-Chung Chiang, Huang-Mo Sung

Highly diversified fungi are associated with the achlorophyllous orchid Gastrodia flavilabella.    

BMC Genomics. (2015)16:185.

• Cristian A Alvarez Rojas,Brendan RE Ansell, Ross S Hall, Robin B Gasser, Neil D Young, Aaron R Jex, and Jean-Pierre Y Scheerlinck

Transcriptional analysis identifies key genes involved in metabolism, fibrosis/tissue repair and the immune response against Fasciola hepatica in sheep liver.    

Parasit Vectors. (2015) 8: 124. 

• Kuo-Wang Tsai, Bill Chang, Cheng-Tsung Pan, Wei-Chen Lin, Ting-Wen Chen, and Sung-Chou Li

Evaluation and Application of the Strand-Specific Protocol for Next-Generation Sequencing    

BioMed Research International.  Article ID 182389

2014 

• Li-Fang Chou, Ting-Wen Chen, Yi-Ching Ko, Ming-Jeng Pan, Ya-Chung Tian, Cheng-Hsun Chiu, Petrus Tang, Cheng-Chieh Hung, Chih-Wei Yang

Potential impact on kidney infection: a whole-genome analysis of Leptospira santarosai serovar Shermani 

Emerg Microbes Infect. (2014) 3(11): e82.

• Duleepa Jayasundara1, I. Saeed, Suhinthan Maheswararajah, B.C. Chang, S-L. Tang and Saman K. Halgamuge

ViQuaS: An improved reconstruction pipeline for viral quasispecies spectra generated by next-generation sequencing. 

Bioinformatics. (2014) pii: btu754.

• Wen-Sui Lo, Hwajiun Chen, Chun-Yao Chen, and Chih-Horng Kuo

Complete Genome Sequence of Vibrio vulnificus 93U204, a Bacterium Isolated from Diseased Tilapia in Taiwan. 

Genome Announc. 2014 Oct 2;2(5). pii: e01005-14.

• Namitha Mohandas, Edoardo Pozio, Giuseppe La Rosa, Pasi K. Korhonen, Neil D. Young, Anson V. Koehler, Ross S. Hall, Paul W. Sternberg, Peter R. Boag, Aaron R. Jex, Bill Chang, Robin B. Gasser 

Mitochondrial genomes of Trichinella species and genotypes - a basis for diagnosis, and systematic and epidemiological explorations. 

Int J Parasitol. (2014) pii: S0020-7519(14)00232-X. 

• Ya-Yi Huang, Chueh-Pai Lee, Jason L. Fu, Bill Chia-Han Chang, Antonius J.M. Matzke and Marjori Matzke

De Novo Transcriptome Sequence Assembly from Coconut Leaves and Seeds with a Focus on Factors Involved in RNA-Directed DNA Methylation. 

G3 (Bethesda). 2014 Sep 4. pii: g3.114.013409.

• Yuzhe Li, I-Son Ng, Xia Zhang, Nan Wang

Draft Genome Sequence of the Dye-Decolorizing and Nanowire-Producing Bacterium Shewanella xiamenensis BC01. 

Genome Announc. 2014 Aug 7;2(4). pii: e00721-14.

• Chih-Yao Hsu, Chung-Shien Wu, and Shu-Miaw Chaw

Ancient Nuclear Plastid DNA in the Yew Family (Taxaceae) 

Genome Biol Evol. ( 2014) 6(8): 2111–2121. 

• Inna S. Kuznetsova, Natascha M. Thevasagayam, Prakki S. R. Sridatta, Aleksey S. Komissarov, Jolly M. Saju, Si Y. Ngoh, Junhui Jiang, Xueyan Shen, László Orbán

Primary analysis of repeat elements of the Asian seabass (Lates calcarifer) transcriptome and genome.   

Front Genet. (2014) 5:223.

• Fang-Mo Chang, Tsong-Yih Ou, Wei-Ning Cheng, Ming-Li Chou, Kai-Cheng Lee, Yi-Ping Chin, Chih-Peng Lin, Kai-Di Chang, Che-Tong Lin, Ching-Hua Su

Short-Term Exposure to Fluconazole Induces Chromosome Loss in Candida albicans: An Approach to Produce Haploid Cells. 

Fungal Genet Biol. (2014) pii: S1087-1845(14)00112-1.

• Hshin-Ping Wu, Yi-shin Su, Hsiu-Chen Chen, Yu-Rong Chen, Chia-Chen Wu, Wen-Dar Lin, Shih-Long Tu

Genome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens. 

Genome Biol. (2014) 15(1):R10.

• Chiung-Yun Chang, Wen-Dar Lin, Shih-Long Tu

Genome-Wide Analysis of Heat-Sensitive Alternative Splicing in Physcomitrella patens. 

Plant Physiol. (2014) 165(2):826-840.

• Jason Li, Maria A. Doyle, Isaam Saeed, Stephen Q. Wong, Victoria Mar, David L. Goode, Franco Caramia, Ken Doig, Georgina L. Ryland, Ella R. Thompson, Sally M. Hunter, Saman K. Halgamuge, Jason Ellul, Alexander Dobrovic, Ian G. Campbell, Anthony T. Papenfuss, Grant A. McArthur, Richard W. Tothill

Bioinformatics Pipelines for Targeted Resequencing and Whole-Exome Sequencing of Human and Mouse Genomes: A Virtual Appliance Approach for Instant Deployment. 

PLoS One. (2014) 9: e95217.

• Han-Qin Zheng,Yi-Fan Chiang-Hsieh, Chia-Hung Chien, Bo-Kai Justin Hsu, Tsung-Lin Liu,Ching-Nen Nathan Chen and Wen-Chi Chang

AlgaePath: comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae. 

 BMC Genomics. 2014 Mar 14;15(1):196. 

• Jiun-Yan Ding, Pei-Wen Chiang, Mei-Jhu Hong, Mike Dyall-Smith, Sen-Lin Tang

Complete Genome Sequence of the Extremely Halophilic Archaeon Haloarcula hispanica Strain N601. 

 Genome Announc. 2014 Mar 13;2(2). pii: e00178-14. 

• Tean-Hsu Chang, Wen-Sui Lo, Chuan Ku, Ling-Ling Chen and Chih-Horng Kuo

Molecular Evolution of the Substrate Utilization Strategies and Putative Virulence Factors in Mosquito-associated Spiroplasma Species. 

Genome Biol Evol. 2014 Mar;6(3):500-9.

• Nan Wang, I-Son Ng, Po Ting Chen, Yuzhe Li, Yi-Chung Chen, Bor-Yann Chen, Yinghua Lu

Draft Genome Sequence of the Bioelectricity-Generating and Dye-Decolorizing Bacterium Proteus hauseri Strain ZMd44.   

Genome Announc. 2014 Jan 16;2(1). pii: e00992-13. doi: 10.1128/genomeA.00992-13.

• Chuan Kua, Wen-Sui Lo, Ling-Ling Chen, Chih-Horng Kuo

Complete Genome Sequence of Spiroplasma apis B31T (ATCC 33834), a Bacterium Associated with May Disease of Honeybees (Apis mellifera).  

Genome Announc. 2014 Jan 9;2(1). pii: e01151-13. doi: 10.1128/genomeA.01151-13.

• Hshin-Ping Wu, Yi-Shin Su, Hsiu-Chen Chen, Yu-Rong Chen, Chia-Chen Wu, Wen-Dar Lin, Shih-Long Tu

Genome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens.  

Genome Biology. 2014, 15:R10. doi: 10.1186/gb-2014-15-1-r10

2013 

• Yi-Min Chen, Chun-Hui Yu, Chi-Chuan Hwang, Tsunglin Liu

OMACC: an Optical-Map-Assisted Contig Connector for improving de novo genome assembly. 

BMC Syst Biol. (2013) 7(Suppl 6):S7.

• Chien Yu Huang, Pei-Ying Chen, Ming-Der Huang, Chih-Hua Tsou, Wann-Neng Jane, Anthony H. C. Huang

Tandem oleosin genes in a cluster acquired in Brassicaceae created tapetosomes and conferred additive benefit of pollen vigor. 

Proc Natl Acad Sci U S A. 2013 Aug 27;110(35):14480-5.

• Yu-Chieh Liao, Ying-Hsiang Chen, Hsin-Hung Lin, Jung-Jung Mu, Ho-Sheng Wu, Feng-Chi Chen, Chao Agnes Hsiung

Draft Genome Sequence of NDM-1-Producing Klebsiella pneumoniae Clinical Isolate 303K  

Genome Announc. 2013 Nov-Dec; 1(6): e01069-13. Published online 2013 December 19. doi: 10.1128/genomeA.01069-13

• Ming-Jung Liu, Szu-Hsien Wu, Jing-Fen Wu, Wen-Dar Lin, Yi-Chen Wu, Tsung-Ying Tsai, Huang-Lung Tsai, Shu-Hsing Wu

Translational landscape of photomorphogenic Arabidopsis. 

Plant Cell. 2013 Oct;25(10):3699-710.

• Chung-Shien Wu, Shu-Miaw Chaw

Highly rearranged and size-variable chloroplast genomes in conifers II clade (cupressophytes): evolution towards shorter intergenic spacers.  

Plant Biotechnol J. 2013 Nov 28. doi: 10.1111/pbi.12141.

• Helen B. Forrester, Alesia Ivashkevich, Michael J. McKay, Trevor Leong, David M. de Kretser, Carl N. Sprung

Follistatin Is Induced by Ionizing Radiation and Potentially Predictive of Radiosensitivity in Radiation-Induced Fibrosis Patient Derived Fibroblasts 

PLoS One. 2013 Oct 18;8(10):e77119. doi: 10.1371/journal.pone.0077119.

• Ya-Yi Huang, Antonius J. M. Matzke, Marjori Matzke

Complete Sequence and Comparative Analysis of the Chloroplast Genome of Coconut Palm (Cocos nucifera).

PLoS One. 2013 Aug 30;8(8):e74736. doi: 10.1371/journal.pone.0074736.

• Wen-Sui Lo, Chuan Ku, Ling-Ling Chen, Tean-Hsu Chang, Chih-Horng Kuo

Comparison of Metabolic Capacities and Inference of Gene Content Evolution in Mosquito-Associated Spiroplasma diminutum and S. taiwanense  

 Genome Biol Evol. 2013; 5(8): 1512–1523. Published online 2013 July 19. doi: 10.1093/gbe/evt108

• Chuan Ku, Wen-Sui Lo, Ling-Ling Chen, and Chih-Horng Kuo

 Complete Genomes of Two Dipteran-Associated Spiroplasmas Provided Insights into the Origin, Dynamics, and Impacts of Viral Invasion in Spiroplasma   

 Genome Biol Evol. 2013; 5(6): 1151–1164. Published online 2013 May 27. doi: 10.1093/gbe/evt084

•  Chuan Ku, Wan-Chia Chung, Ling-Ling Chen, Chih-Horng Kuo

The Complete Plastid Genome Sequence of Madagascar Periwinkle Catharanthus roseus (L.) G. Don: Plastid Genome Evolution, Molecular Marker Identification, and Phylogenetic Implications in Asterids  

PLoS One. 2013; 8(6): e68518. Published online 2013 June 18. doi: 10.1371/journal.pone.0068518

•  Chuan Ku, Jer-Ming Hu, Chih-Horng Kuo

Complete Plastid Genome Sequence of the Basal Asterid Ardisia polysticta Miq. and Comparative Analyses of Asterid Plastid Genomes

PLoS One. 2013; 8(4): e62548. Published online 2013 April 30. doi: 10.1371/journal.pone.0062548

•  Wan-Chia Chung, Ling-Ling Chen, Wen-Sui Lo, Chan-Pin Lin, Chih-Horng Kuo

Comparative Analysis of the Peanut Witches'-Broom Phytoplasma Genome Reveals Horizontal Transfer of Potential Mobile Units and Effectors

PLoS One. 2013; 8(4): e62770. Published online 2013 April 23. doi: 10.1371/journal.pone.0062770

• Wan-Chia Chung, Ling-Ling Chen, Wen-Sui Lo, Pei-An Kuo, Jenn Tu, Chih-Horng Kuo

Complete Genome Sequence of Serratia marcescens WW4.  

Genome Announc. 2013 Apr 4;1(2):e0012613. doi: 10.1128/genomeA.00126-13.

•  Nan-Lan Huang, Ming-Der Huang, Tung-Ling L. Chen, Anthony H.C. Huang

Oleosin of subcellular lipid droplets evolved in green algae. 

Plant Physiol. 2013 Feb 7. [Epub ahead of print]

•  Wen-Sui Lo, Ling-Ling Chen, Wan-Chia Chung, Gail E Gasparich, Chih-Horng Kuo

Comparative genome analysis of Spiroplasma melliferum IPMB4A, a honeybee-associated bacterium.

BMC Genomics. 2013 Jan 16;14:22. doi: 10.1186/1471-2164-14-22.

• Chung-Shien Wu, Shu-Miaw Chaw, Ya-Yi Huang

Chloroplast Phylogenomics Indicates that Ginkgo biloba Is Sister to Cycads

Genome Biol Evol. 2013; 5(1): 243–254. Published online 2013 January 12. doi: 10.1093/gbe/evt001

• Po-Xing Zheng, Kun-Ta Chung, Chuan Chiang-Ni, Shu-Ying Wang, Pei-Jane Tsai, Woei-Jer Chuang, Yee-Shin Lin, Ching-Chuan Liu, Jiunn-Jong Wu

Complete Genome Sequence of emm1 Streptococcus pyogenes A20, a Strain with an Intact Two-Component System, CovRS, Isolated from a Patient with Necrotizing Fasciitis

Genome Announc. 2013 Jan-Feb; 1(1): e00149-12. Published online 2013 February 7. doi: 10.1128/genomeA.00149-12

• Silk Yu Lin, Wung Yang Shieh, Jwo-Sheng Chen, Sen-Lin Tang

Complete Genome Sequence of Simiduia agarivorans SA1(T), a Marine Bacterium Able To Degrade a Variety of Polysaccharides.

Genome Announc. 2013 Jan;1(1). pii: e00039-12. doi: 10.1128/genomeA.00039-12. Epub 2013 Jan 15.

2012 

• Ching-Ping Lin, Chung-Shien Wu, Ya-Yi Huang, Shu-Miaw Chaw

The complete chloroplast genome of Ginkgo biloba reveals the mechanism of inverted repeat contraction.

Genome Biol Evol. 2012;4(3):374-81. doi: 10.1093/gbe/evs021. Epub 2012 Mar 8.

• Yu-Rong Chen, Yi-shin Su, Shih-Long Tu

Distinct phytochrome actions in nonvascular plants revealed by targeted inactivation of phytobilin biosynthesis.

Proc Natl Acad Sci U S A. 2012 May 22;109(21):8310-5. doi: 10.1073/pnas.1201744109. Epub 2012 May 7.

• Sung-Chou Li, Yu-Lun Liao, Meng-Ru Ho, Kuo-Wang Tsai, Chun-Hung Lai, Wen-chang Lin

miRNA arm selection and isomiR distribution in gastric cancer.

BMC Genomics. 2012;13 Suppl 1:S13. doi: 10.1186/1471-2164-13-S1-S13. Epub 2012 Jan 17.

 

2011

• Li SC, Liao YL, Chan WC, Ho MR, Tsai KW, Hu LY, Lai CH, Hsu CN, Lin WC.

Interrogation of rabbit miRNAs and their isomiRs.

Genomics. 2011 Dec;98(6):453-9. doi: 10.1016/j.ygeno.2011.08.008. Epub 2011 Sep 10.