Works by Wei-Sheng Wu

Results: 51

CLASH Analyst: A Web Server to Identify In Vivo RNA–RNA Interactions from CLASH Data.

Published in:

Non-Coding RNA, 2022, v. 8, n. 1, p. 6, doi. 10.3390/ncrna8010006

By:

Wu, Wei-Sheng;
Brown, Jordan S.;
Chen, Pin-Hao;
Shiue, Sheng-Cian;
Lee, Dong-En;
Lee, Heng-Chi

Publication type:

Article

Epidemiology profile and outcomes of oral potentially malignant disorders among different geographic regions of Taiwan: A retrospective observational nationwide population database study.

Published in:

Journal of Medical Sciences (1011-4564), 2021, v. 41, n. 6, p. 286, doi. 10.4103/jmedsci.jmedsci_257_20

By:

Chiu, Sheng-Fu;
Ho, Chung-Han;
Chen, Yi-Chen;
Wu, Li-Wha;
Chen, Yuh-Ling;
Wu, Jer-Horng;
Wu, Wei-Sheng;
Hung, Hui-Kun;
Chiang, Wei-Fan

Publication type:

Article

Elucidating the regulatory mechanism of Swi1 prion in global transcription and stress responses.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-77993-0

By:

Du, Zhiqiang;
Regan, Jeniece;
Bartom, Elizabeth;
Wu, Wei-Sheng;
Zhang, Li;
Goncharoff, Dustin Kenneth;
Li, Liming

Publication type:

Article

Comparable bidirectional neutrophil immune dysregulation between Kawasaki disease and severe COVID-19.

Published in:

Frontiers in Immunology, 2022, v. 12, p. 1, doi. 10.3389/fimmu.2022.995886

By:

Kuang-Den Chen;
Ying-Hsien Huang;
Wei-Sheng Wu;
Ling-Sai Chang;
Chiao-Lun Chu;
Ho-Chang Kuo

Publication type:

Article

Fuzzy Logic Applications in Control Theory and Systems Biology.

Published in:

Advances in Fuzzy Systems, 2013, p. 1, doi. 10.1155/2013/504728

By:

Sendren Sheng-Dong Xu;
Hao Ying;
Carbonell, Pablo;
Ching-Hung Lee;
Wei-Sheng Wu

Publication type:

Article

Functional redundancy of transcription factors explains why most binding targets of a transcription factor are not affected when the transcription factor is knocked out.

Published in:

BMC Systems Biology, 2015, v. 9, p. 1, doi. 10.1186/1752-0509-9-S6-S2

By:

Wei-Sheng Wu;
Fu-Jou Lai

Publication type:

Article

YAGM: a web tool for mining associated genes in yeast based on diverse biological associations.

Published in:

2015

By:

Wei-Sheng Wu;
Chung-Ching Wang;
Meng-Jhun Jhou;
Yu-Cheng Wang

Publication type:

Product Review

A regulatory similarity measure using the location information of transcription factor binding sites in Saccharomyces cerevisiae.

Published in:

BMC Systems Biology, 2014, v. 8, p. 1, doi. 10.1186/1752-0509-8-S5-S9

By:

Wei-Sheng Wu;
Ming-Liang Wei;
Chia-Ming Yeh;
Darby Tien-Hao Chang

Publication type:

Article

Identifying cooperative transcription factors in yeast using multiple data sources.

Published in:

BMC Systems Biology, 2014, v. 8, p. 1, doi. 10.1186/1752-0509-8-S5-S2

By:

Fu-Jou Lai;
Mei-Huei Jhu;
Chia-Chun Chiu;
Yueh-Min Huang;
Wei-Sheng Wu

Publication type:

Article

A comprehensive performance evaluation on the prediction results of existing cooperative transcription factors identification algorithms.

Published in:

BMC Systems Biology, 2014, v. 8, p. 1, doi. 10.1186/1752-0509-8-S4-S9

By:

Fu-Jou Lai;
Hong-Tsun Chang;
Yueh-Min Huang;
Wei-Sheng Wu

Publication type:

Article

cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila.

Published in:

BMC Systems Biology, 2014, v. 8, p. 1, doi. 10.1186/1752-0509-8-S4-S8

By:

Tzu-Hsien Yang;
Chung-Ching Wang;
Po-Cheng Hung;
Wei-Sheng Wu

Publication type:

Article

Inferring functional transcription factor-gene binding pairs by integrating transcription factor binding data with transcription factor knockout data.

Published in:

BMC Systems Biology, 2013, v. 7, p. 1, doi. 10.1186/1752-0509-7-S6-S13

By:

Tzu-Hsien Yang;
Wei-Sheng Wu

Publication type:

Article

Missing value imputation for microarray data: a comprehensive comparison study and a web tool.

Published in:

BMC Systems Biology, 2013, v. 7, p. 1, doi. 10.1186/1752-0509-7-S6-S12

By:

Chia-Chun Chiu;
Shih-Yao Chan;
Chung-Ching Wang;
Wei-Sheng Wu

Publication type:

Article

Shrinkage regression-based methods for microarray missing value imputation.

Published in:

BMC Systems Biology, 2013, v. 7, p. 1, doi. 10.1186/1752-0509-7-S6-S11

By:

Hsiuying Wang;
Chia-Chun Chiu;
Yi-Ching Wu;
Wei-Sheng Wu

Publication type:

Article

Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data.

Published in:

BMC Systems Biology, 2012, v. 6, n. 1, p. 102, doi. 10.1186/1752-0509-6-102

By:

Tzu-Hsien Yang;
Wei-Sheng Wu

Publication type:

Article

OrchidBase 4.0: a database for orchid genomics and molecular biology.

Published in:

BMC Plant Biology, 2021, v. 21, n. 1, p. 1, doi. 10.1186/s12870-021-03140-0

By:

Hsiao, Yu-Yun;
Fu, Chih-Hsiung;
Ho, Sau-Yee;
Li, Chung-I;
Chen, You-Yi;
Wu, Wan-Lin;
Wang, Jeen-Shing;
Zhang, Di-Yang;
Hu, Wen-Qi;
Yu, Xia;
Sun, Wei-Hong;
Zhou, Zhuang;
Liu, Ke-Wei;
Huang, Laiqiang;
Lan, Si-Ren;
Chen, Hong-Hwa;
Wu, Wei-Sheng;
Liu, Zhong-Jian;
Tsai, Wen-Chieh

Publication type:

Article

Investigation of microRNAs in mouse macrophage responses to lipopolysaccharide-stimulation by combining gene expression with microRNA-target information.

Published in:

BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/1471-2164-16-S12-S13

By:

Chia-Chun Chiu;
Wei-Sheng Wu

Publication type:

Article

Properly defining the targets of a transcription factor significantly improves the computational identification of cooperative transcription factor pairs in yeast.

Published in:

BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/1471-2164-16-S12-S10

By:

Wei-Sheng Wu;
Fu-Jou Lai

Publication type:

Article

The Yeast Nucleosome Atlas (YNA) database: an integrative gene mining platform for studying chromatin structure and its regulation in yeast.

Published in:

BMC Genomics, 2014, v. 15, p. 1, doi. 10.1186/1471-2164-15-S9-S5

By:

Po-Cheng Hung;
Tzu-Hsien Yang;
Hung-Jiun Liaw;
Wei-Sheng Wu

Publication type:

Article

Detecting Cooperativity between Transcription Factors Based on Functional Coherence and Similarity of Their Target Gene Sets.

Published in:

PLoS ONE, 2016, v. 11, n. 9, p. 1, doi. 10.1371/journal.pone.0162931

By:

Wu, Wei-Sheng;
Lai, Fu-Jou

Publication type:

Article

YCRD: Yeast Combinatorial Regulation Database.

Published in:

PLoS ONE, 2016, v. 11, n. 7, p. 1, doi. 10.1371/journal.pone.0159213

By:

Wu, Wei-Sheng;
Hsieh, Yen-Chen;
Lai, Fu-Jou

Publication type:

Article

Combined Interactions of Plant Homeodomain and Chromodomain Regulate NuA4 Activity at DNA Double-Strand Breaks.

Published in:

Genetics, 2016, v. 202, n. 1, p. 77, doi. 10.1534/genetics.115.184432

By:

Wen-Pin Su;
Sen-Huei Hsu;
Li-Chiao Chia;
Jui-Yang Lin;
Song-Bin Chang;
Zong-da Jiang;
Yi-Ju Lin;
Min-Yu Shih;
Yi-Cheng Chen;
Mau-Sun Chang;
Wen-Bin Yang;
Jan-Jong Hung;
Po-Cheng Hung;
Wei-Sheng Wu;
Kyungjae Myung;
Hungjiun Liaw

Publication type:

Article

YARG: A repository for arsenic-related genes in yeast.

Published in:

PLoS ONE, 2018, v. 13, n. 7, p. 1, doi. 10.1371/journal.pone.0201204

By:

Rathod, Jagat;
Tu, Hao-Ping;
Chang, Yung-I;
Chu, Yu-Han;
Tseng, Yan-Yuan;
Jean, Jiin-Shuh;
Wu, Wei-Sheng

Publication type:

Article

Identifying piRNA targets on mRNAs in C. elegans using a deep multi-head attention network.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04428-6

By:

Yang, Tzu-Hsien;
Shiue, Sheng-Cian;
Chen, Kuan-Yu;
Tseng, Yan-Yuan;
Wu, Wei-Sheng

Publication type:

Article

A tool for analyzing and visualizing ribo-seq data at the isoform level.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04192-7

By:

Wu, Wei-Sheng;
Tsao, Yi-Hong;
Shiue, Sheng-Cian;
Chen, Ting-Yu;
Tseng, Yan-Yuan;
Tseng, Joseph T.

Publication type:

Article

Wolfberry genome database: integrated genomic datasets for studying molecular biology.

Published in:

Frontiers in Plant Science, 2024, p. 1, doi. 10.3389/fpls.2024.1310346

By:

You-Long Cao;
You-Yi Chen;
Yan-Long Li;
Chung-I Li;
Shao-Ting Lin;
Bing-Ru Lee;
Chun-Lin Hsieh;
Yu-Yun Hsiao;
Yun-Fang Fan;
Qing Luo;
Jian-Hua Zhao;
Yue Yin;
Wei An;
Zhi-Gang Shi;
Chi-Nga Chow;
Wen-Chi Chang;
Chun-Lin Huang;
Wei-Hung Chang;
Zhong-Jian Liu;
Wei-Sheng Wu

Publication type:

Article

Taxonomic and Functional Dysregulation in Salivary Microbiomes During Oral Carcinogenesis.

Published in:

Frontiers in Cellular & Infection Microbiology, 2021, v. 11, p. 1, doi. 10.3389/fcimb.2021.663068

By:

Chen, Jiung-Wen;
Wu, Jer-Horng;
Chiang, Wei-Fan;
Chen, Yuh-Ling;
Wu, Wei-Sheng;
Wu, Li-Wha

Publication type:

Article

CSmiRTar: Condition-Specific microRNA targets database.

Published in:

PLoS ONE, 2017, v. 12, n. 7, p. 1, doi. 10.1371/journal.pone.0181231

By:

Wu, Wei-Sheng;
Tu, Bor-Wen;
Chen, Tsung-Te;
Hou, Shang-Wei;
Tseng, Joseph T.

Publication type:

Article

Identifying a Transcription Factor's Regulatory Targets from its Binding Targets.

Published in:

Gene Regulation & Systems Biology, 2010, n. 4, p. 125, doi. 10.4137/GRSB.S6458

By:

Fred Lai;
Chang, Julie S.;
Wei-Sheng Wu

Publication type:

Article

Reconstructing a Network of Stress-Response Regulators via Dynamic System Modeling of Gene Regulation.

Published in:

Gene Regulation & Systems Biology, 2008, n. 2, p. 53, doi. 10.4137/GRSB.S558

By:

Wei-Sheng Wu;
Wen-Hsiung Li;
Bor-Sen Chen

Publication type:

Article

A new measure of the robustness of biochemical networks.

Published in:

Bioinformatics, 2005, v. 21, n. 11, p. 2698, doi. 10.1093/bioinformatics/bti348

By:

Bor-Sen Chen;
Yu-Chao Wang;
Wei-Sheng Wu;
Wen-Hsiung Li

Publication type:

Article

Systematical Analysis of the Protein Targets of Lactoferricin B and Histatin-5 Using Yeast Proteome Microarrays.

Published in:

International Journal of Molecular Sciences, 2019, v. 20, n. 17, p. 4218, doi. 10.3390/ijms20174218

By:

Shah, Pramod;
Wu, Wei-Sheng;
Chen, Chien-Sheng

Publication type:

Article

PCTFPeval: a web tool for benchmarking newly developed algorithms for predicting cooperative transcription factor pairs in yeast.

Published in:

BMC Bioinformatics, 2015, v. 16, p. 1, doi. 10.1186/1471-2105-16-S18-S2

By:

Fu-Jou Lai;
Hong-Tsun Chang;
Wei-Sheng Wu

Publication type:

Article

iPhos: a toolkit to streamline the alkaline phosphatase-assisted comprehensive LC-MS phosphoproteome investigation.

Published in:

BMC Bioinformatics, 2014, v. 15, n. Suppl 16, p. 1, doi. 10.1186/1471-2105-15-S16-S10

By:

Tzu-Hsien Yang;
Hong-Tsun Chang;
Hsiao, Eric S. L.;
Juo-Ling Sun;
Chung-Ching Wang;
Hsin-Yi Wu;
Pao-Chi Liao;
Wei-Sheng Wu

Publication type:

Article

piRTarBase: a database of piRNA targeting sites and their roles in gene regulation.

Published in:

Nucleic Acids Research, 2019, v. 47, n. D1, p. D181, doi. 10.1093/nar/gky956

By:

Wu, Wei-Sheng;
Brown, Jordan S;
Chen, Tsung-Te;
Chu, Yu-Han;
Huang, Wei-Che;
Tu, Shikui;
Lee, Heng-Chi

Publication type:

Article

pirScan: a webserver to predict piRNA targeting sites and to avoid transgene silencing in C. elegans.

Published in:

Nucleic Acids Research, 2018, v. 46, n. W1, p. W43, doi. 10.1093/nar/gky277

By:

Wu, Wei-Sheng;
Huang, Wei-Che;
Brown, Jordan S;
Zhang, Donglei;
Song, Xiaoyan;
Chen, Hao;
Tu, Shikui;
Weng, Zhiping;
Lee, Heng-Chi

Publication type:

Article

YPA: an integrated repository of promoter features in Saccharomyces cerevisiae.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_1, p. D647, doi. 10.1093/nar/gkq1086

By:

Chang, Darby Tien-Hao;
Huang, Cheng-Yi;
Wu, Chi-Yeh;
Wu, Wei-Sheng

Publication type:

Article

YQFC: a web tool to compare quantitative biological features between two yeast gene lists.

Published in:

Database: The Journal of Biological Databases & Curation, 2020, v. 2020, p. 1, doi. 10.1093/database/baaa076

By:

Wu, Wei-Sheng;
Wang, Lai-Ji;
Yen, Han-Chen;
Tseng, Yan-Yuan

Publication type:

Article

YHMI: a web tool to identify histone modifications and histone/chromatin regulators from a gene list in yeast.

Published in:

Database: The Journal of Biological Databases & Curation, 2018, v. 2018, p. 1, doi. 10.1093/database/bay116

By:

Wu, Wei-Sheng;
Tu, Hao-Ping;
Chu, Yu-Han;
Nordling, Torbjörn E M;
Tseng, Yan-Yuan;
Liaw, Hung-Jiun

Publication type:

Article

HRPDviewer: human ribosome profiling data viewer.

Published in:

Database: The Journal of Biological Databases & Curation, 2018, v. 2018, p. 1, doi. 10.1093/database/bay074

By:

Wu, Wei-Sheng;
Jiang, Yu-Xuan;
Chang, Jer-Wei;
Chu, Yu-Han;
Chiu, Yi-Hao;
Tsao, Yi-Hong;
Nordling, Torbjörn E M;
Tseng, Yan-Yuan;
Tseng, Joseph T

Publication type:

Article

YGMD: a repository for yeast cooperative transcription factor sets and their target gene modules.

Published in:

Database: The Journal of Biological Databases & Curation, 2017, v. 2017, n. 1, p. 1, doi. 10.1093/database/bax085

By:

Wei-Sheng Wu;
Pin-Han Chen;
Tsung-Te Chen;
Yan-Yuan Tseng

Publication type:

Article

CoopTFD: a repository for predicted yeast cooperative transcription factor pairs.

Published in:

Database: The Journal of Biological Databases & Curation, 2016, v. 2016, p. 1, doi. 10.1093/database/baw092

By:

Wei-Sheng Wu;
Fu-Jou Lai;
Bor-Wen Tu;
Darby Tien-Hao Chang

Publication type:

Article

YTRP: a repository for yeast transcriptional regulatory pathways.

Published in:

Database: The Journal of Biological Databases & Curation, 2014, v. 2014, p. 1, doi. 10.1093/database/bau014

By:

Tzu-Hsien Yang;
Chung-Ching Wang;
Yu-Chao Wang;
Wei-Sheng Wu

Publication type:

Article

Identifying Functional Transcription Factor Binding Sites in Yeast by Considering Their Positional Preference in the Promoters.

Published in:

PLoS ONE, 2013, v. 8, n. 12, p. 1, doi. 10.1371/journal.pone.0083791

By:

Lai, Fu-Jou;
Chiu, Chia-Chun;
Yang, Tzu-Hsien;
Huang, Yueh-Min;
Wu, Wei-Sheng

Publication type:

Article

MVIAeval: a web tool for comprehensively evaluating the performance of a new missing value imputation algorithm.

Published in:

BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-016-1429-3

By:

Wei-Sheng Wu;
Meng-Jhun Jhou

Publication type:

Article

FL-circAS: an integrative resource and analysis for full-length sequences and alternative splicing of circular RNAs with nanopore sequencing.

Published in:

Nucleic Acids Research, 2024, v. 52, n. D1, p. D115, doi. 10.1093/nar/gkad829

By:

Chiang, Tai-Wei;
Jhong, Song-En;
Chen, Yu-Chen;
Chen, Chia-Ying;
Wu, Wei-Sheng;
Chuang, Trees-Juen

Publication type:

Article

GLH/VASA helicases promote germ granule formation to ensure the fidelity of piRNA-mediated transcriptome surveillance.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-32880-2

By:

Chen, Wenjun;
Brown, Jordan S.;
He, Tao;
Wu, Wei-Sheng;
Tu, Shikui;
Weng, Zhiping;
Zhang, Donglei;
Lee, Heng-Chi

Publication type:

Article

The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation.

Published in:

BMC Genomics, 2010, v. 11, n. 1, p. 1, doi. 10.1186/1471-2164-11-581

By:

Lin, Zhenguo;
Wu, Wei-Sheng;
Liang, Han;
Woo, Yong;
Li, Wen-Hsiung

Publication type:

Article

The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation.

Published in:

BMC Genomics, 2010, v. 11, p. 581, doi. 10.1186/1471-2164-11-581

By:

Zhenguo Lin;
Wei-Sheng Wu;
Han Liang;
Yong Woo;
Wen-Hsiung Li

Publication type:

Article

Interventional chemoembolization for the treatment of severe ulcerative bleeding caused by advanced breast cancer: A report of two cases.

Published in:

Experimental & Therapeutic Medicine, 2024, v. 27, n. 1, p. N.PAG, doi. 10.3892/etm.2023.12324

By:

Wei, Xing;
Zhang, Hong-Chao;
Tu, Yue-He;
Li, Xiang;
Wu, Wei-Sheng

Publication type:

Article