photo shot in Chicago, USA (Dec. 2016; July 2023)

有女吳晗雅(霓)，

此生無憾呀(矣)！

追芬®成功®吳妻®大肚®加人

教授

See 開授課程 from 2009/02 to 2016/06

piRNA對於細胞抵禦外來核酸扮演重要角色，piRNA可以結合到這些外來核酸上並且抑制這些核酸的表現。線蟲細胞內大概有15000種piRNA。由於不知道piRNA結合到核酸的規則為何，所以對於piRNA的功能以及它會結合到什麼核酸都無法有效地進行研究。

2021年是我的產學元年 (耗損我不少的研究精力但收入增加41萬,值得?!)

¨生醫及金融數據分析實驗室簡介檔案

¨我給大學生的建議及實驗室介紹影片

• 各種資訊分析工具及資料庫開發 任何領域皆可,歡迎有興趣的民間公司找我洽談產學合作計畫

• 財經分析網頁工具開發

• 金融大數據分析Fintech

• 雲端APP應用開發

•  區塊鏈應用開發

•  

• 優良期刊(Q1)發表教練 任何領域皆可,歡迎有發表困難的研究人員找我洽談諮詢事宜

• 本人每年固定約有3篇數據分析研究Q1期刊發表,經驗十分豐富,絕對能夠輔導你成功發表數據分析Q1期刊!

•  

• 用Deep Learning解各種生物領域的分類問題 (題目多如牛毛,做也做不完,可以出到滿手論文!)

• 台大陳倩瑜老師生物資訊科普式介紹 (陳倩瑜老師Youtube頻道)

•  

• NGS資料分析

• 計算系統生物學   (簡介投影片)  此為電機最新領域!!

• 計算轉錄體學(基因調控網路建模)

• 計算蛋白體學(質譜資料分析、蛋白質晶片資料分析)

• 計算非編碼核糖核酸體學

• 計算表觀遺傳體學

• 癌症研究

• 線蟲piRNA, tRFs, rRFs研究

• circRNA研究

• tRNA研究

• 蘭花基因體研究

• 果蠅基因體研究

• 川崎症研究

• 生物資料庫及生物伺服器建立

• 提出及解答有趣的生物問題

我們實驗室就是專門培養Data Scientists來處理生醫及金融大數據資料

新聞報導:

Data scientist is the 'best job in America' for 2022

台灣人在美國當AI科學家！年薪破7百萬公開學霸經歷

本實驗室發展之網頁伺服器及網頁資料庫

http://140.116.215.235/astwastw/login/?next=%2Fastwastw%2Ffinancial_home%2Fhome%2F%3Ffbclid%3DIwAR1Abes_fFKYQ6MVfwEN4TQw8r5Vwywb3W0nHAiYT06lTlihpNDjxFToAvE&fbclid=IwAR0Ul2om09LMKl9srMJ7QGdDTbqBnz7yQnX3jXIfnGkWfFhqrM4IIKZh-Ik

本實驗室建立網頁資料庫和伺服器之程式語言組合：

Linux系統 + Perl (2011~2012)
   Linux系統 + PHP (2013~2017)
   Linux系統 + Python (2018~now)
   Linux系統 + Note.js (2023~now)

生物知識Video

■ DNA --> RNA --> Protein

■ A New Frontier: Systems Biology 

■ Lee Hood MD PhD - Institute for Systems Biology

■ DNA Science            一堆鼎鼎大名的生物學家都出現在影片中 看完你就入門了

         Part I  The Secret of Life

         Part II  Playing God

         Part III  The Human Race

         Part IV  Curing Cancer

         Part V  Pandoras Box

■ Gene regulation part I

■ Gene regulation part II

■ Programming of life

■ Creating life (Synthetic biology documentary)

■ Can we live forever?

■ How does the brain work?

■ Evolution - why sex?

■ Epigenetics - The ghost in your genes

■ James Watson: How we discovered DNA

■ RNAi

碩士班該學什麼?    (清大彭明輝教授)

引用以下彭老師文字:

  文獻回顧與分析的過程可以很紮實地培養出分析問題的能力與吸收新知識的速度，所以我一向把文獻回顧與分析的能力看成碩士班最重要的學習內容，所以寫了「學術文獻回顧與分析的程序與技巧 」這一篇文章給碩士班新生。此外，學生跟我學習的兩年期間內，從碩一一開學就要每週要報告一次論文給我聽，然後我每次都會指出學生的錯誤，投影片製作沒有重點，分析論文不夠深入，找的論文沒有價值等等。這整個過程都是在建立學生分析與批判的能力。

    但是很多學生覺得這過程很痛苦，因為很多過去的習慣都必須要改，才有辦法把論文讀得又快又透徹。學生往往看不到自己以後的需要，因而只顧眼前的開心與溫馨。其實，開心而溫馨的研究室往往只能學到皮毛（到處都可以學的coding、儀器操作、跟國內業界的需要有距離的「專業知識」），而學不到真正的分析能與批判能力（適用於各種行業，隨著產業急遽變化，這些能力可以帶著走，到處都有用）。

學術文獻回顧與分析的程序與技巧    (清大彭明輝教授)

 Institute for Systems Biology 系統生物學的發源地

Computational and Systems Biology at MIT

Systems Biology at Harvard University

•  

• (2025)  我今年發表論文數xx篇。(繼續這樣衝下去能拿傑出研究獎嗎?)

• (2025)  114年度國立成功大學電資學院彈性薪資補助xx萬元。

• ----------------------------------------------------------

• (2024)  我今年發表論文數xx篇。(繼續這樣衝下去能拿傑出研究獎嗎?)

• (2024)  第五個產學合作案xx萬元(成大敏求計算學院SOC旗艦計畫)。(有額外收入,讚啦!)

• (2024)  第四個產學合作案45萬元(幫Safer Trader公司開發權證標的篩選程式)。(有額外收入,讚啦!)

• (2024)  113年度國立成功大學電資學院彈性薪資補助xx萬元。

• (2024)  國立成功大學卓越學術研究補助xx萬元。

• (2024)  美國韋恩州立大學、西北大學、芝加哥大學訪問學者(July and August)。

• ----------------------------------------------------------

• (2023)  我今年發表論文數4篇。(繼續這樣衝下去能拿傑出研究獎嗎?)

• (2023)  112年度國立成功大學電資學院彈性薪資補助60萬元。(出頭天了!)

• (2023)  111學年度第二學期國立成功大學電資學院深耕重點課程補助5萬元。

• (2023)  112年度國立成功大學理學院模組化課程補助6萬元。

• (2023)  跟中研院莊樹諄老師合作的研究榮登NAR database

• (2023)  美國韋恩州立大學、西北大學、芝加哥大學訪問學者(July and August)。

• (2023) 2篇Multiomics and Precision Medicine Joint Conference The Best Poster Award 。

• ----------------------------------------------------------

• (2022)  我今年發表論文數6篇。(繼續這樣衝下去能拿傑出研究獎嗎?)

• (2022)  111年度國立成功大學電資學院彈性薪資補助48萬元。(出頭天了!)

• (2022)  111年度創惟論文潛力獎12萬元。

• (2022)  111年度國立成功大學電資學院深耕國際面向經費補助12萬元。

• (2022)  第一個顧問案20萬元(昶裕公司)+捐款系上10萬元。(有額外收入,讚啦!)

• (2022)  111年度國科會工程司控制學門專題研究計畫申覆案複審委員。

• ----------------------------------------------------------

• (2021)  我今年發表論文數10篇創歷史新高。(繼續這樣衝下去能拿傑出研究獎嗎?)

• (2021)  第三個產學合作案100萬元(幫凱納公司開發解決里程焦慮演算法)。(有額外收入,讚啦!)

• (2021)  第二個產學合作案30萬元(幫昶裕公司開發虛擬貨幣程式交易程式)。(有額外收入,讚啦!)

• (2021)  第一個產學合作案100萬元(幫凱納公司開發APP)。(有額外收入,讚啦!)

• (2021)  110年度國立成功大學電資學院彈性薪資補助24萬元。(這是我的天花板? 連續三年都只有這樣,大概上不去了?)

• (2021)  我們的兩篇研究被APBC2021接受口頭報告並轉投到BMC系列期刊(其中一篇轉投的期刊太爛,故放棄刊登)。

• ----------------------------------------------------------

• (2020)  109年度科技部工程司控制學門專題研究計畫複審委員。

• (2020)  109年度科技部工程司智慧計算學門發展重點規劃委員。

• (2020)  109年度國立成功大學電資學院彈性薪資補助24萬元。(每年出一堆papers的我跟每年出1篇paper而已的人,彈薪每個月只差1萬元,看來寫papers的CP值真的是有夠低,我應該把精力放在找產學計畫來做,對收入而言才比較有感!)

• -----------------------------------------------------------------

• (2019) 台灣蛋白體學會年會，壁報論文競賽特優(陳健生老師之碩班學生研究成果)。

• (2019)  美國韋恩州立大學、西北大學、芝加哥大學訪問學者(July and August)。

• (2019)  109年度補助科學與技術人員國外短期研究10個月。(因武漢肺炎故放棄不用)

• (2019)  108年度國立成功大學電資學院彈性薪資補助24萬元。

• (2019)  108年度科技部工程司控制學門專題研究計畫複審委員。

• (2019)  108年度科技部工程司智慧計算學門優秀年輕學者計畫三年期(有面子沒裡子，還得被一群外行的審核委員挑毛病，以後不申請了)。

• (2019)  108年度中國電機工程師學會高雄市分會傑出電機工程教授獎。
  
  

• -----------------------------------------------------------------

• (2018)  107年度國立成功大學電資學院彈性薪資補助12萬元。(全電資院只有排名前1/3共43位老師可以拿到此補助，因算分公式對我這種純學術研究而無產學計畫者不利，不然以我研究表現，應可拿到更高補助才對!)

• (2018)  國立成功大學卓越學術研究補助17萬元。

• (2018)  ISEGB2018 invited talk。

• (2018)  美國韋恩州立大學、西北大學、芝加哥大學訪問學者(July and August)。

• (2018)  國立成功大學鼓勵發表國際頂尖期刊獎勵7萬元。

• (2018)  國立成功大學國際頂尖期刊獎。

• 

• (2018)  參與芝加哥大學李亨啓教授的研究榮登NAR database。

• (2018)  參與芝加哥大學李亨啓教授的研究榮登NAR web server。

• (2018)  參與芝加哥大學李亨啓教授的研究榮登Science。

• (2018)  107年度科技部工程司控制學門發展重點規劃委員。

• (2018)  107年度科技部工程司控制學門專題研究計畫複審委員。

• -----------------------------------------------------------------

• (2017)  106年度科技部工程司智慧計算學門優秀年輕學者計畫兩年期(有面子沒裡子)。

• (2017)  美國韋恩州立大學、西北大學、芝加哥大學訪問學者(July and August)。

• -----------------------------------------------------------------

• (2016)  美國芝加哥大學生態與演化學系訪問學者8個月(2016/7-2017/2)。

• (2016)  105年度科技部工程司智慧計算學門優秀年輕學者計畫決選(最後沒上)。

• (2016)  國立成功大學電資學院獎勵學生參與學術競賽計畫3萬元。

• -----------------------------------------------------------------

• (2015)  105年度補助科學與技術人員國外短期研究9個月。

• (2015)  Best Paper Award of GIW/InCoB2015 (博士班學生邱家軍的論文)。

• (2015)  我們的五篇研究被GIW/InCoB2015接受口頭報告並轉投到BMC系列期刊 (本實驗室為GIW/InCoB2015中單一實驗室被接受最多文章者)。

• (2015)  國立成功大學電資學院明日之星獎助計畫25萬元。

• (2015)  德國海德堡大學跨領域科學計算中心訪問學者一個月(July)。

• -----------------------------------------------------------------

• (2014)  德國海德堡大學跨領域科學計算中心訪問學者一個月(July)。

• (2014)  我們的兩篇研究被GIW2014接受口頭報告並轉投到BMC Systems Biology 。

• (2014)  我們的四篇研究被InCoB2014接受口頭報告並轉投到BMC系列期刊 (本實驗室為InCoB2014中單一實驗室被接受最多文章者)。

• (2014)  科技部及國立成功大學補助教師出國參加研討會經費 (放棄沒用)。

• (2014)  國立成功大學電資學院研究扶植計畫6萬元。

• (2014)  國立成功大學電資學院高品質、高排名論文獎助計畫4萬元。

• (2014)  國立成功大學電資學院明日之星獎助計畫60萬元。

• ------------------------------------------------------------------

• (2013)  國立成功大學電資學院論文出版費補助18萬元。(跟院長要來的)

• (2013)  我們的三篇研究被GIW2013接受口頭報告並轉投到BMC Systems Biology (本實驗室為GIW2013中單一實驗室被接受最多文章者)。

• -------------------------------------------------------------------

• (2012)  ISEGB2012 invited talk。

• ---------------------------------------------------------------------------------

• (2011)  我們的研究被ICSB2011從733篇投稿摘要中選為103位演講者之一，在三百多位聽眾面前發表我們的研究。

• (2011)  我們的酵母菌啟動子資料庫(http://ypa.ee.ncku.edu.tw)被選為Nucleic Acids Research期刊的featured article。

• --------------------------------------------------------------------

• (2010)  SiPS2010 invited talk。

• (2010) 國科會傑出學者養成計畫(個別型)三年期。

• --------------------------------------------------------------------

• (2009) 台灣生物資訊與系統生物學研討會，壁報論文競賽優等獎。

• (2007) 國科會菁英留學獎學金130萬元(Postdoctoral Research Abroad Program Fellowship)

• (2001) 美國 UC Berkeley, UCSB, UCLA, Purdue, U of Michigan 等知名學府之 EECS博士班入學資格。

• (2000) 斐陶斐榮譽會員(Phi Tau Phi Scholastic Honor Society)---碩二成績優良

• (2000) 潘文淵獎學金(Pan Wen-yuan Memorial Scholarship)---碩一下成績優良

• (1999) 台灣國際航電獎學金(GARMIN Corporation’s Scholarship)---碩一上成績優良

• (1997) 嚴慶齡獎學金(Yen Tjing Ling Industrial Development Foundation’s Scholarship)---大三下成績優良

• (1995) 周桐甫先生與周林冰若夫人紀念獎學金---大一下成績優良

• (1995) 周桐甫先生與周林冰若夫人紀念獎學金---大一上成績優良

   

  　

  為下列期刊或研討會的Reviewer

  Journal or Conference	Year
  GIW/ICSB Asia 2022: International Conference on Genome Informatics	2022
  Briefings in Bioinformatics	2022, 2023
  BMC Bioinformatics	2021
  PLoS One	2016
  BBA General Subjects	2016
  Knowledge and Information Systems	2016
  Computers in Biology and Medicine	2016
  BMC Genomics	2015
  Microarrays	2015
  DNA Research	2015
  PeerJ	2015, 2018
  APBC 2015: Asia Pacific Bioinformatics Conference	2015
  ICCA 2014: International Conference of Control and Automation	2014
  Genetica	2013
  ICSB-Asia/SCCG 2012	2012
  GIW 2012: International Conference on Genome Informatics	2012
  BMC Systems Biology	2009, 2011, 2012, 2013, 2015
  IJCIC: International Journal of Computational Intelligence in Control	2011
  ISCAS: IEEE International Symposium on Circuits and Systems	2010
  IJDMB: International Journal of Data Mining and Bioinformatics	2009, 2015
  AJC: Asian Journal of Control	2008
  EURASIP: Journal on Advances in Signal Processing	2002

Citation statistics of my papers by Google Scholar 

Citation statistics of my papers by ResearchGate 

Citation statistics of my papers by ResearchNCKU

My h-index (since 2018)=13 vs. 傑出研究獎得主Dr. Tseng=45    還差好多，真的慘不忍睹!

我都笑稱自己是King of BMC (10 BMC Systems Biology, 8 BMC Bioinformatics,  5 BMC Genomics,  2 BMC Plant Biology)，希望有一天我的研究能攻入生物主流期刊(IF>5)，不必再受困於BMC等級的期刊(曾幾何時BMC排名已經變差，不能再往那投了)。

我的58篇論文登在下列Q1內的期刊:

A. Journal Papers

(2001/09~2007/06) PhD Student (6 papers) 2 BMC Bioinformatics, 1 Bioinformatics

-------------------2005 (1 paper)

1. Chen BS*, Wang YC, Wu WS, Li WH (2005 June): A new measure of robustness of biochemical networks. Bioinformatics, 21(11):2698-2705. 
SCI, impact factor=5.04, Ranking 1% (1/92) in Computer Science & Interdisciplinary Application

-------------------2006 (1 paper)

2. Wu WS*, Li WH, Chen BS (2006 Sept.): Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics, 7:421.
SCI, impact factor=3.49, Ranking 11% (3/27) in Mathematical & Computational Biology

-------------------2007 (4 papers)

3. Chen BS*, Wu WS, Wu WS, Li WH (2007 Feb.): On the adaptive design rules of biochemical networks in evolution. Evolutionary Bioinformatics, 2:1-13.
SCI, impact factor=1.23, Ranking 70% (33/47) in Mathematical & Computational Biology

4. Wu WS*, Li WH, Chen BS (2007 June): Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data. BMC Bioinformatics, 8:188.
SCI, impact factor=3.49, Ranking 11% (3/27) in Mathematical & Computational Biology

5. Chen BS*, Wu WS (2007 Sept.) Underlying principles of natural selection in network evolution: systems biology approach. Evolutionary Bioinformatics, 3:245-262.
SCI, impact factor=1,23, Ranking 70% (33/47) in Mathematical & Computational Biology

6. Wu WS*, Chen BS (2007 Oct.): Identifying stress transcription factors using gene expression and TF-gene association data. Bioinformatics and Biology Insights, 1:137-145.

 (2007/10~2009/01) Postdoctoral Fellow (4 papers)  1 BMC Genomics, 1 BMC Bioinformatics

-------------------2008 (4 papers)

7. Chen BS*, Wu WS (2008 Feb.): Robust filtering circuit design for gene networks under intrinsic and extrinsic molecular noises. Mathematical Biosciences, 211:342-355.
SCI, impact factor=1.19, Ranking 54% (38/71) in Biology

8. Wu WS*, Li WH, Chen BS (2008 Feb.): Reconstructing a network of stress-response regulators via dynamic system modeling of gene regulation. Gene Regulation and Systems Biology, 2:53-62.

9. Wu WS, Li WH* (2008 Sept.): Identifying gene regulatory modules of heat shock response in yeast. BMC Genomics, 9:439.  (Highly accessed)
SCI, impact factor=4.18, Ranking 15% (21/138) in Biotechnology & Applied Microbiology

10.Wu WS, Li WH* (2008 Dec.): Systematic identification of yeast cell cycle transcription factors using multiple data sources. BMC Bioinformatics, 9:522.
SCI, impact factor=3.49, Ranking 11% (3/27) in Mathematical & Computational Biology

 (2009/02~2013/07) Assistant Professor (10 papers) 1 NAR, 1 BMC Systems Biology

-------------------2009 (0 paper) 太混了!

-------------------2010 (3 papers)

11.Lin Z^, Wu WS^, Liang H, Yoo Y, Li WH* (2010 Oct.): The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcription regulation. BMC Genomics, 11:581.   (^co-first author)
SCI, impact factor=3.76, Ranking 18% (28/152) in Biotechnology & Applied Microbiology

12.Wu WS* (2010 June): Identifying highly confident TF-gene regulatory relationships in yeast. International Journal of Systems and Synthetic Biology, 1(1):121-133. (Invited paper)

13.Lai F, Chang JS, Wu WS* (2010 Dec.): Identifying a transcription factor's regulatory targets from its binding targets. Gene Regulation and Systems Biology, 4:125-133.  

-------------------2011 (4 papers)

14.Wu WS* (2011 Jan.): Different functional gene clusters in yeast have different spatial distribution of the transcription factor binding sites. Bioinformatics and Biology Insights, 5:1-11.  

15.Chang DTH, Huang CY, Wu CY, Wu WS* (2011 Jan.): YPA: an integrated repository of promoter features in Saccharomyces cerevisiae. Nucl. Acids Res., 39(1):D647-D652.
Featured article in NAR (represents the top 5% of NAR papers in terms of originality, significance and scientific excellence!)
SCI, impact factor=7.48, Ranking 10% (27/283) in Biochemistry & Molecular Biology

16.Wu WS* (2011 June): A quantitative robustness measure for gene regulatory networks. International Journal of Computational Intelligence in Control, 3(1):1-8.  (Invited paper)

17.Wang H, Wang YH, Wu WS* (2011 Oct.): Yeast cell cycle transcription factors identification by variable selection criteria. Gene, 485:172-176.
SCI, impact factor=2.416, Ranking 53% (78/146) in Genetics & Heredity

-------------------2012 (2 papers)

18.Yang TH, Wu WS* (2012 Aug.): Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data. BMC Systems Biology, 6:102.
SCI, impact factor=3.15, Ranking 9% (4/47) in Mathematical & Computational Biology

19.Chang DTH, Li WS, Bai YH, Wu WS* (2012 Dec.): YGA: identifying distinct biological features between yeast gene sets. Gene, 518:26-34.
SCI, impact factor=2.341, Ranking 53% (78/146) in Genetics & Heredity

-------------------2013 (6 papers)

20.Xu SSD, Ying H, Carbonell P, Lee CH, Wu WS (2013 May): Fuzzy logic application in control theory and systems biology. Advances in Fuzzy Systems, vol. 2013, Article ID 504728, 1 page, 2013.

(2013/08~2017/07) Associate Professor (24 papers) 9 BMC Systems Biology, 4 Plos One, 3 BMC Bioinformatics, 3 BMC Genomics, 2 Database, 1 Genetics, 1 Sci Rep

出這麼多Papers又有什麼用呢? 指導碩士班所做的研究都好像是在做科展，太膚淺了，都是雞肋研究!我應該少收碩士生，好好靜下心來搞比較大的研究課題!

21.Wang H, Chiu CC, Wu YC, Wu WS* (2013 Dec.): Shrinkage regression-based methods for microarray missing value imputation. BMC Systems Biology, 7(Suppl 6):S11. 
SCI, 2012impact factor=2.982, Ranking 15% (7/47) in Mathematical & Computational Biology

22.Chiu CC, Chan SY, Wang CC,  Wu WS* (2013 Dec.): Missing value imputation for microarray data: a comprehensive comparison study and a web tool. BMC Systems Biology, 7(Suppl 6):S12.
SCI, 2012impact factor=2.982, Ranking 15% (7/47) in Mathematical & Computational Biology　

23.Yang TH, Wu WS* (2013 Dec.): Inferring functional transcription factor-gene binding pairs by integrating transcription factor binding data with transcription factor knockout data. BMC Systems Biology, 7(Suppl 6):S13.
SCI, 2012impact factor=2.982, Ranking 15% (7/47) in Mathematical & Computational Biology　

25.Juang JN*, Shiau JH, Wu WS (2013 Dec.): A hybrid parameter estimation algorithm for S-system model of gene regulatory networks. Journal of the Astronautical Sciences, 60(3):559-576.
SCI, 2012impact factor=0.697, Ranking 36% (10/28) in Engineering, Aerospace

-------------------2014 (7 papers)

26.Yang TH, Wang CC, Wang YC, Wu WS* (2014 Mar.): YTRP: a repository for yeast transcriptional regulatory pathways. Database, vol. 2014, Article ID bau014.
SCI, 2013impact factor=4.457, Ranking 10% (5/52) in Mathematical & Computational Biology

27.Yang TH, Chang HT, Hsiao ESL, Sun JL, Wang CC, Wu HY, Liao PC*, Wu WS* (2014 Dec.): iPhos: toolkit to streamline the alkaline phosphatase assisted comprehensive LC-MS phosphorproteome investigation. BMC Bioinformatics, 15(Suppl 16):S10.
SCI, 2013impact factor=2.672, Ranking 15% (8/52) in Mathematical & Computational Biology

28.Yang TH, Wang CC, Hung PC, Wu WS* (2014 Dec.): cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila. BMC Systems Biology, 8(Suppl 4):S8.
SCI, 2013impact factor=2.853, Ranking 13% (7/52) in Mathematical & Computational Biology

29.Hung PC, Yang TH, Liaw HJ*, Wu WS* (2014 Dec.): YNA: an integrative gene mining platform for studying chromatin structure and its regulation in Yeast. BMC Genomics, 15(Suppl 9):S5.
SCI, 2013impact factor=4.041, Ranking 18% (29/165) in Biotechnology & Applied Microbiology

30.Lai FJ, Chang HT, Huang YM, Wu WS* (2014 Dec.): A comprehensive performance evaluation on the prediction results of existing cooperative transcription factors identification algorithms. BMC Systems Biology, 8(Suppl 4):S9.
SCI, 2013impact factor=2.853, Ranking 13% (7/52) in Mathematical & Computational Biology

31.Lai FJ, Jhu MH, Chiu CC, Huang YM, Wu WS* (2014 Dec.): Identifying cooperative transcription factors in yeast using multiple data sources. BMC Systems Biology, 8(Suppl 5):S2.
SCI, 2013impact factor=2.853, Ranking 13% (7/52) in Mathematical & Computational Biology

32.Wu WS, Wei ML, Yeh CM, DTH Chang* (2014 Dec.): A regulatory similarity measure using the location information of transcription factor binding sites in Saccharomyces cerevisiae. BMC Systems Biology, 8(Suppl 5):S9.
SCI, 2013impact factor=2.853, Ranking 13% (7/52) in Mathematical & Computational Biology

-------------------2015 (6 papers)

33.Su WP, Hsu SH, Chia LC, Lin JY, Chang SB, Jiang ZD, Lin YJ, Shih MY, Chen YC, Chang MS, Yang WB, Hung JJ, Hung PC, Wu WS, Myung K, Liaw HG* (2015 Nov.): Combined interactions of plant homeodomain and chromodomain regulate NuA4 activity at DNA double-strand breaks. Genetics, 115:184432.
SCI, 2014impact factor=5.963, Ranking 13% (21/167) in Genetics & Heredity

34.Chiu CC, Wu WS* (2015 Dec.): Investigation of microRNAs in mouse macrophage responses to lipoposaccharide-stimulation by combining gene expression with microRNA-target information. BMC Genomics, 16(Suppl 12):S13.
SCI, 2014impact factor=3.986, Ranking 16% (26/163) in Biotechnology & Applied Microbiology
Best Paper Award of GIW/InCoB 2015

35.Wu WS*, Lai FJ (2015 Dec.): Properly defining the targets of a transcription factor significantly improves the computational identification of cooperative transcription factor pairs in yeast. BMC Genomics, 16(Suppl 12):S10.
SCI, 2014impact factor=3.986, Ranking 16% (26/163) in Biotechnology & Applied Microbiology

36.Lai FJ, Chang HT, Wu WS* (2015 Dec.): PCTFPeval: a web tool for benchmarking newly developed algorithms for predicting cooperative transcription factor pairs in yeast. BMC Bioinformatics, 16(Suppl 18):S2.
SCI, 2014impact factor=2.576, Ranking 19% (11/57) in Mathematical & Computational Biology

37.Wu WS*, Lai FJ (2015 Dec.): Functional redundancy of transcription factors explains why most binding targets of a transcription factor are not affected when the transcription factor is knocked out. BMC Systems Biology, 9(Suppl 6):S2.
SCI, 2014impact factor=2.435, Ranking 23% (13/57) in Mathematical & Computational Biology

38.Wu WS*, Wang CC, Jhou MJ, Wang YC (2015 Dec.): YAGM: a web tool for mining associated genes in yeast based on diverse biological associations. BMC Systems Biology, 9(Suppl 6):S1.
SCI, 2014impact factor=2.435, Ranking 23% (13/57) in Mathematical & Computational Biology

-------------------2016 (3 papers)

39.Wu WS*, Lai FJ, Tu BW (2016 May): CoopTFD: a repository for predicted yeast cooperative transcription factor pairs. Database, vol. 2016, Article ID baw092.
SCI, 2015impact factor=2.627, Ranking 14% (8/56) in Mathematical & Computational Biology

40.Wu WS*, Hsieh YC, Lai FJ (2016 July): YCRD: Yeast Combinatorial Regulation Database. PLoS ONE, 11(7): e0159213.
SCI, 2015impact factor=3.057, Ranking 17% (11/63) in Multidisciplinary Sciences　

41.Wu WS*, Lai FJ (2016 Sept): Detecting Cooperativity between Transcription Factors Based on Functional Coherence and Similarity of Their Target Gene Sets. PLoS ONE, 11(9):e0162931.
SCI, 2015impact factor=3.057, Ranking 17% (11/63) in Multidisciplinary Sciences

-------------------2017 (4 papers)

42.Wu WS*, Jhou MJ (2017 Jan.): MVIAeval: a web tool for comprehensively evaluating the performance of a new missing value imputation algorithm. BMC Bioinformatics, 18:31. 
SCI, 2017impact factor=2.213, Ranking 23.72% (14/59) in Mathematical & Computational Biology

43.Su WP, Ho YC, Wu CK, Hsu SH, Shiu JL, Huang JC, Chang SB, Chiu WT, Hung JJ, Liu TL, Wu WS, Wu PY, Su WC, Chang JY, Liaw HG* (2017 June): Chronic treatment with cisplatin induces chemoresistance through the TIP60-mediated Fanconi anemia and homologous recombination repair pathways. Sci Rep, 7(1):3879.
SCI, 2016impact factor=4.259, Ranking 16% (10/64) in in Multidisciplinary Sciences

44.Wu WS*, Tu BW, Chen TT, Hou SW, Tseng JT (2017 July): CSmiRTar: condition-specific microRNA targets database. PLoS ONE, 12(7):e0181231.
SCI, 2017impact factor=2.766, Ranking 23.4% (15/64) in Multidisciplinary Sciences

(2017/08~now) Professor (34 papers) 3 NAR, 1 Science, 4 Database,

期許自己以後只發有impact的論文，不要浪費生命去發一堆雞肋論文了!

可是我只有碩士生可用，要他們做做網站還行，要他們和我一起做有insight的研究，有可能嗎?

45.Wu WS*, Chen PH, Chen TT, YY Tseng* (2017 Oct.): YGMD: a repository for yeast cooperative transcription factor sets and their target gene modules. Database, vol. 2017, Article ID bax085.
SCI, 2017impact factor=3.978, Ranking 6.78% (4/59) in Mathematical & Computational Biology

-------------------2018 (5 papers)

46.Zhang D, Tu S, Stubua M, Wu WS, Huang WC, Weng Z, Lee HC* (2018 Jan.): The piRNA targeting rules and the resistance to piRNA silencing in endogenous genes. Science, 359(6375):587-592.
SCI, 2018 impact factor=41.063, Ranking 3% (2/69) in Multidisciplinary Sciences  

47.Wu WS*, Jiang YX, Chang JW, Chu YH, Chiu YH, Tsao YH, Nordling TEM, Tseng YY, Tseng JT* (2018 June): HRPDviewer: human ribosome profiling data viewer. Database, vol. 2018, Article ID bay074.
SCI, 2017 impact factor=3.978, Ranking 6.78% (4/59) in Mathematical & Computational Biology

48.Wu WS, Huang WC, Brown J, Zhang D, Song X, Chen H, Tu S, Weng Z, Lee HC* (2018 July): pirScan: a webserver to predict piRNA targeting sites and to avoid transgene silencing in C. elegans. Nucleic Acids Res., 46(W1):W43-W48.
SCI, 2017 impact factor=11.561, Ranking 3.4% (10/292) in Biochemistry & Molecular Biology
 2018IF=11.147, Ranking 4.68% (14/299) in Biochemistry & Molecular Biology

49.Rathod J, Tu HP, Chang YI, Chu YH, Tseng YY, Jean JS, Wu WS* (2018 July): YARG: a repository for arsenic-related genes in yeast. PLoS ONE, 13(7):e0201204.
SCI, 2017 impact factor=2.766, Ranking 23.4% (15/64) in Multidisciplinary Sciences

50.Wu WS*, Tu HP, Chu YH, Nordling TEM, Tseng YY, Liaw HJ*(2018 Oct): YHMI: a web tool to identify histone modifications and histone/chromatin regulators for a gene list in yeast. Database, vol. 2018, Article ID bay116.
SCI, 2020 impact factor=3.451, Ranking 24.14% (14/58) in Mathematical & Computational Biology

-------------------2019 (3 papers  這一年我太混了,得重拾寫paper的熱情!)

51.Wu WS^, Brown J^, Chen TT, Chu YH, Huang WC, Tu S, Lee HC* (2019 Jan): piRTarBase: a database of piRNA targeting sites and their roles in gene regulation. Nucleic Acids Res.,47(D1):D181-D187.     (^co-first author)
SCI, 2020 impact factor=16.971, Ranking 2.68% (8/298) in Biochemistry & Molecular Biology

52.Wu WS*, Jiang YX, Chang JW, Chu YH, Liaw HJ* (2019 July): p53 binding loci database (p53BLD): a repository for the genome-wide binding loci of human TP53. Clinical Microbiology and Research, doi:10.31487/j.CMR.2018.01.01.    

53.Shah P, Wu WS, Chen CS* (2019 Aug.): Systematical analysis of the protein targets of Lactoferricin B and Histatin-5 using yeast proteome microarrays. Int. J. Mol. Sci.,20:E4218.    
SCI, 2020 impact factor=5.923, Ranking 22.48% (67/298) in Biochemistry & Molecular Biology

-------------------2020 (3 papers  這一年我不混了,可是成果還看不出來)

54.Wu WS*, Wang LJ, Yen HC, Tseng YY (2020 Nov.): YQFC: Yeast quantitative feature comparator. Database, 2020:baaa076.
SCI, 2020 impact factor=3.451, Ranking 24.14% (14/58) in Mathematical & Computational Biology

55.Du Z, Regan J, Bartom E, Wu WS, Zhang L, Goncharoff DK, Li L* (2020 Dec.): Elucidating the regulatory mechanism of Swi1 prion in global transcription and and stress responses. Sci Rep, 10(1):21838.
SCI, 2020 impact factor=4.379, Ranking 23.29% (17/73) in Multidisciplinary Sciences

56.Lin YH*, Gu S, Wu WS, Wang R, Wu F (2020 Dec.): Analysis and prediction of overloaded extra-heavy vehicles for highway safety using machine learning. Mobile Information Systems, Vol. 2020, Article ID 6667897.
SCI, 2020 impact factor=1.802, Ranking 76.54% (124/162) in Computer Science, Information Systems

-------------------2021 (10 papers  這一年我要專心做產學計畫, papers兼著寫就好,結果今年papers數量創歷史新高,其實是收割去年的付出)

57.Herianto S, Rathod J, Shah P, Chen YZ,  Wu WS, Liang B, Chen CS* (2021 Jan.): Systematic analysis of phosphatidylinositol-5-phosphate-interacting proteins using yeast proteome microarrays. Anal. Chemistry, 93(2):868-877.    
SCI, 2020 impact factor=6.986, Ranking 9.6% (8/83) in Chemistry, Analytical

58.Chiu SF, Ho CH, Chen YC, Wu LW, Chen YL, Wu JH, Wu WS, Hung HK, Chiang WF* (2021 Mar.): Malignant transformation of oral potentially malignant disorders in Taiwan: An observational nationwide population database study. Medicine, 100(9):e24934.
SCI, 2020impact factor=1.889, Ranking 58.58% (99/169) in Medicine, General & Internal

59.Chen MY, Chen JW, Wu LW, Huang KC, Chen JY, Wu WS, Chiang WF, Shih CJ, Tsai KN, Hsieh WT, Ho YH, Wong TY, Wu JH*, Chen YL* (2021 Apr.): Carcinogenesis of male oral submucous fibrosis alters salivary microbiomes. J Dent Res, 100(4):397-405.
SCI, 2020 impact factor=6.116, Ranking 5.49% (5/91) in Dentistry, Oral Surgery & Medicine

60.Wu WS*, Tsao YH, Shiue SC, Chen TY, Tseng YY, Tseng JT* (2021 May): A tool for analyzing and visualizing ribosome profiling data at the isoform level. BMC Bioinformatics, 22(Suppl 10):271. 
SCI, 2020impact factor=3.169, Ranking 27.59% (16/58) in Mathematical & Computational Biology

61.Rathod J, Yen HC, Liang B, Tseng YY, Chen CS*, Wu WS*  (2021 June): YPIBP: A repository for phosphoinositide-binding proteins in yeast. Comput Struct Biotechnol J, 19:3692-3707. 
SCI, 2020impact factor=7.271, Ranking 15% (45/298) in Biochemistry & Molecular Biology

62.Hsiao YY, Fu CH, Ho SY, Li CI, Chen YY, Wu WL, Wang JS, Zhang DY, Hu WQ, Yu X, Sun WH, Zhou Z, Liu KW, Huang L, Lan SR, Chen HH. Wu WS*, Liu ZJ*, Tsai WC* (2021 Aug.): OrchidBase 4.0: a database for orchid genomics and molecular biology. BMC Plant Biology, 21:371. 
SCI, 2020impact factor=4.215, Ranking 14.5% (34/235) in Plant Sciences

63.Yang TH, Chiang YH, Shiue SC, Lin PH, Yang YC, Tu KC, Tseng YY, Tseng JT*, Wu WS*  (2021 Sept.): Cancer DEIso: an integrative analysis platform for investigating differentially expressed gene-level and isoform-level human cancer markers. Comput Struct Biotechnol J, 19:5149-5159. 
SCI, 2020impact factor=7.271, Ranking 15% (45/298) in Biochemistry & Molecular Biology

64.Chen JW, Wu JH, Chiang WF, Chen YL, Wu WS, Wu LW (2021 Sept.): Taxonomic and functional dysregulation in salivary microbiomes during oral carcinogenesis. Front Cell Infect Microbiol, 11:663068.
SCI, 2020impact factor=5.293, Ranking 24.3% (33/136) in Microbiology

65.Yang TH, Shiue SC, Chen KY, Tseng YY, Wu WS*  (2021 Oct.): Identifying piRNA targets on mRNAs in C. elegans using a deep multi-head attention network. BMC Bioinformatics, 22:503. 
SCI, 2020impact factor=3.169, Ranking 27.59% (16/58) in Mathematical & Computational Biology

66.Wu WS^, Wu HY^, Wang PH, Chen TY, Chen KR, Chang CW, Lee DE, Lin BH,  Chang CW, Liao PC* (2021 Dec.): LCMD: Lung Cancer Metabolome Database. Comput Struct Biotechnol J, 20:65-78.  (^co-first author)
SCI, 2020impact factor=7.271, Ranking 15% (45/298) in Biochemistry & Molecular Biology

-------------------2022 (6 papers  這一年我要專心做產學計畫, papers兼著寫就好, 還是要繼續衝研究拚傑出研究獎?)

67.Wu WS^, Brown J^, Chen PH, Shiue SC, Lee DN, Lee HC* (2022 Jan.): CLASH Analyst: a webserver to identify in vivo RNA-RNA interactions from CLASH data. Noncoding RNA, 8(1):6. (^co-first author)

68.Wu WS^, Yang TH^, Chen KD, Lin PH, Chen GR, Kuo HC* (2022 Mar.): KDmarkers: A biomarker database for investigating epigenetic methylation and gene expression levels in Kawasaki disease. Comput Struct Biotechnol J, 20:1295-1305. (^co-first author)
SCI, 2020impact factor=7.271, Ranking 15% (45/298) in Biochemistry & Molecular Biology

69.Chen KD, Huang YH, Wu WS, Chang LS, Chu CL, Kuo HC* (2022 Sept.): Comparable bidirectional neutrophil immune dysregulation between Kawasaki disease and severe COVID-19. Front Immunol, 13:995886.
SCI, 2021impact factor=8.786, Ranking 20% (33/161) in Immunology

70.Chen W, Brown J, He T, Wu WS, Tu S, Weng Z, Zhang D, Lee HC* (2022 Sept.): GLH/VASA helicases promote germ granule formation to ensure the fidelity of piRNA-mediated transcriptome surveillance. Nature Communications, 13(1):5306.
SCI, 2021impact factor=17.694, Ranking 8% (6/73) in Multidisciplinary Sciences

71.Yang TH, Hsu CW, Wang YX, Yu CH, Rathod J, Tseng YY,  Wu WS* (20222 Nov.): YMLA: a comparative platform to carry out functional enrichment analysis for multiple yeast gene lists Comput Biol Med, 151:106314.
SCI, 2021impact factor=6.698, Ranking 10.5% (6/57) in Mathematical & Computational Biology

72.Chen YY, Li CI, Hsiao YY, Ho SY, Zhang ZB, Liao CC, Lee BR, Lin ST, Wu WL, Wang JS, Zhang D, Liu KW, Liu DK, Zhao XW, Li YY, Ke SJ, Zhou Z, Huang MZ, Wu YS, Peng DH, Lan SR, Chen HH, Liu ZJ*, Wu WS*, Tsai WC* (2022 Dec.): OrchidBase 5.0: updates of the orchid genome knowledgebase. BMC Plant Biology, 22:557.
SCI, 2021impact factor=5.26, Ranking 12.6% (30/239) in Plant Sciences

-------------------2023 (4 papers  這一年沒產學計畫可做了,那就繼續衝研究拚傑出研究獎吧)

73.Wu WS^, Brown J^, Shiue SC, Chung CJ, Lee DE, Zhang D, Li HC* (2023 Feb.): Transcriptome-wide analyses of piRNA binding sites suggest distinct mechanisms regulate piRNA binding and silencing in C. elegans. RNA, 29(5):557-569. (^co-first author)
SCI, 2022impact factor=4.5, Ranking 35% (101/285) in Biochemistry & Molecular Biology

74.Du Z, Shi K, Brown JS, He T, Wu WS, Zhang Y, Li HC, Zhang D* (2023 July): Condensate cooperativity underlies transgenerational gene silencing. Cell Rep, 42(8):112859.
SCI, 2022impact factor=8.8, Ranking 17% (32/191) in Cell Biology

75.Chen YC, Wu HY, Wu WS, Hsu JY, Chang CW, Lee YH, Liao PC* (2023 Sept.): Identification of Xenobiotic biotransformation products using mss spectrometry-based metabolomics integrated with a structural elucidation strategy by assembling fragment signatures. Anal Chem, 95(38):14279-14287.
SCI, 20221impact factor=7.4, Ranking 8% (7/86) in Chemistry, Analytical

76.Yang TH, Chen JC, Lee YH, Lu SY, Wu SH, Chang FY, Huang YC, Lee MH, Tseng YY,  Wu WS*  (2023 Oct.) Identifying human miRNA target sites via learning the interaction patterns between miRNA and mRNA segments. J Chem Inf Model, xxxx.
SCI, 2022impact factor=5.6, Ranking 18% (11/60) in Chemistry, Medicinal

-------------------2024 (xx papers  這一年沒產學計畫可做了,那就繼續衝研究拚傑出研究獎吧)

77.Chiang TW, Jhong SE, Chen YC, Chen CY, Wu WS*, Chuang TJ* (2024 Jan.) FL-circAS: an integrative resource and analysis for full-length sequences and alternative splicing of circular RNAs with annopore sequencing. Nucleic Acids Res.,52(D1):D115-D123.
SCI, 2022impact factor=14.9, Ranking 3.5% (10/285) in Biochemistry & Molecular Biology

78.Cao YL, Chen YY, Li YL, Li CI, Lin ST, Lee BR, Hsieh CL, Hsiao YY, Fan YF, Luo Q, Zhao JH, Yin Y, An W, Shi ZG, Chow CN, Chang WC, Huang CL, Chang WH, Liu ZJ*, Wu WS*, Tsai WC* (2024 Feb.) Wolfberry genome database: integrated genomic datasets for studying molecular biology. Front Plant Sci,15:1310346.
SCI, 2022impact factor=5.6, Ranking 11% (27/239) in Plant Sciences

74.NMOkb

75.Review

76.miRNA

77.Fly?

78.OrchidBase 6.0?

pirtarbase2

mirnaclash

crosslink

KD

B. Conference talks, posters, and papers

See會議論文列表 from 2002/07 to 2021/12

a. 國際會議

24.Wu WS*, Lai FJ (2015 Sept.): Functional redundancy of transcription factors explains why most binding targets of a transcription factors are not affected when the transcription factor is knocked out.  In GIW/InCoB 2015: Tokyo, Japan.  (Oral)　

25.Lai FJ, Chang HT, Wu WS* (2015 Sept.): PCTFPeval: a web tool for benchmarking newly developed algorithms for predicting cooperative transcription factor pairs in yeast. In GIW/InCoB 2015: Tokyo, Japan.  (Oral)　　

26.Wu WS*, Wang CC, Jhou MJ, Wang YC (2015 Sept.): YAGM: a web tool for mining associated genes in yeast based on diverse biological associations. In GIW/InCoB 2015: Tokyo, Japan.  (Oral)　　

27.Chiu CC, Wu WS* (2015 Sept.): Investigation of microRNAs in mouse macrophage responses to lipoposaccharide-stimulation by combining gene expression with microRNA-target information. In GIW/InCoB 2015: Tokyo, Japan.  (Oral)　

28.Wu WS*, Lai FJ (2015 Sept.): Properly defining the targets of a transcription factor significantly improves the computational identification of cooperative transcription factor pairs in yeast. In GIW/InCoB 2015: Tokyo, Japan.  (Oral)　

29.Chiu CC, Jhou MJ, Wu WS* (2015 Sept.): EMVA: an R package for comparing and testing missing value imputation algorithms. In GIW/InCoB 2015: Tokyo, Japan.  (Poster)　

-------------------

30.Wu WS*, Jiang YX (2019 Sept.): DEIso: a database of differentially expressed isoforms/genes in human cancer. In The 78th Annual Meeting of the Japanese Cancer Association 2019: Kyoto, Japan.  (Poster)

31.Wu WS*, Jiang YX (2019 Nov.): DEIso: a database of differentially expressed isoforms/genes in human cancer. In The 20th International Conference on Systems Biology (ICSB) 2019: Okinawa, Japan.  (Poster)

32.Wu WS, Lee HC* (2019 Nov.): pirScan: a webserver to predict piRNA targeting sites and to avoid transgene silencing in C. elegans. In The 20th International Conference on Systems Biology (ICSB) 2019: Okinawa, Japan.  (Poster)

-------------------

 

==========================================================

b. 國內會議

50. Wu WS* (2022 Nov.): Developing orchid omics data analyzing platform and constructing orchid omics knowledgebase. In 控制學門成果發表會: KaoHsiung, Taiwan. (Poster)

51. Lee BR, Chang SY, Ting CT, Wu WS* (2022 Nov.): A new Drosophila genome database for evolutionary researches. In 多體學及精準醫學聯合會議: Taipei, Taiwan. (Poster)

-----------------

52. Wu WS* (2023 Oct.): Developing orchid omics data analyzing platform and constructing orchid omics knowledgebase. In 控制學門成果發表會: PengHu, Taiwan. (Poster)

53. Chen YC, Chen CY, Chiang TW, Chan MH, Hsiao M, Ke HM, Tsai IS, Jhong SE, Wu WS, Chuang TJ* (2023 Nov.): The charm of long-read sequencing: Distinguishing between trans-spliced and circular RNAs. In Multiomics and Precision Medicine Joint Conference: Taipei, Taiwan. (Best Poster Award)

54. Lee XW, Lee YH, Lee HC, Wu WS* (2023 Nov.): miRTarCLASH: a repository of miRNA-mRNA interactions identified by experimental CLASH data. In Multiomics and Precision Medicine Joint Conference: Taipei, Taiwan. (Best Poster Award)

55. Wang YT, Lu SY, Lee HC, Wu WS* (2023 Nov.): Establishing a comprehensive database for piRNA-regulated RNA targets in C. elegans. In Multiomics and Precision Medicine Joint Conference: Taipei, Taiwan. (Poster)

-----------------

56. Lee XW, Lee YH, Lee HC, Wu WS* (2024 Mar.): miRxx. In SMBE Regional Meeting in Taiwan: Taipei, Taiwan. (Poster)

57. Lee XW, Lee YH, Lee HC, Wu WS* (2024 Mar.): miRxx. In SMBE Regional Meeting in Taiwan: Taipei, Taiwan. (Poster)

 

C. Book Chapters

1.  Wu WS, Wang CH, Chiu MC, Chao CC* (2002): Stability analysis of the Turbo decoding algorithm using Max-Log-MAP. In Information, Coding and Mathematics. Edited by Farrell P, van Tilborg H, Blaum M. Boston: Kluwer; 257-278.

2.  Wu WS*, Li WH, Chen BS (2008): Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. In Analysis of Microarray Data: Network based Approaches. Edited by Emmert-Streib F, Dehmer M. NJ: Wiley; 331-354.

3.  Wu WS* (2015): A computational method for identifying yeast cell cycle transcription factors. In Cell Cycle Oscillators. Methods in Molecular Biology Volume 1342. Edited by Coutts AS, Weston L. NY: Springer; 209-219.

D. 演講

E. 研究合作對象