Cheng-Yu Hou


9+ years work experience in Bioinformatics.

Experiences of both hands on Bioinformatics analysis and molecular biology experiments, which helps me to solve biology problems and to interpret questions as a biologist.

Phone: +886972105534    Line ID: Irous    Mail: [email protected]

Profile 04 00@2x


National Taiwan Ocean University, Taiwan, Master degree, Bioscience and Biotechnology

2009 ~ 2011 | Thesis: Production of Chitooligosaccharides by Enzyme Engineering

Chinese Culture University, Taiwan, Bachelor degree, Life Science

2005 ~ 2009 | Student Association of Life Science Department

Work Experience (9+ years in Bioinformatics)

BioInformatics team, Sofiva Genomics, Taiwan, Bioinformatician, Jun 2016 ~ Current

1. To intergrade demands from different teams in the lab and design (web/stand-along) tools with Graphical User Interface to generate data for reports.
2. Development of customized programs and flexible pipe-lines (Linux, Windows)
3. Analysis of disease-related NGS data (inherited disease, tumor)
4. Consulting for software and web-tools for NGS data analysis

Agricultural Biotechnology Research Center, Academia Sinica, Taiwan, Research Assistant, Jul 2012 ~ May 2016

1. Development of customized programs for NGS data filtering, retrieval, manipulation and mining
2. RNA Degradome data analyses
3. Computer maintenance


W.C. Lee#, B.H. Hou#, C.Y. Hou#, S.M. Tsao, Ping. Kao, H.M. Chen*(2020) Widespread EJC footprints in the RNA degradome mark mRNA degradation before the steady-state translation. Plant Cell

Impact factor: 8.6, ranking: 4/453 in Plant Sciences
# These authors contributed equally to this work.

C.Y. Hou, W.C. Lee, H.C. Chou, A.P. Chen, S.J. Chou, H.M. Chen* (2016) Global Analysis of Truncated RNA Ends Reveals New Insights into Ribosome Stalling in Plants, Plant Cell.

Impact factor: 8.5, ranking: 4/209 in Plant Sciences

C.Y. Hou, M.T. Wu, S.H. Lu, H.M. Chen* (2014) Beyond cleaved small RNA targets: unraveling the complexity of plant RNA degradome data, BMC Genomics, 15(1), 15 

Impact factor: 3.8, ranking: 32/161 in Biotechnology and Applied Microbiology


NGS data analyses

  1. Variant calling: Human 
  2. Whole exon sequencing : Human 
  3. Barcode De-multiplex
  4. miRNA analysis : Arabidopsis, Rice 
  5. RNA Degradome analysis : Yeast, Arabidopsis, Rice, Soybean, Grape, Maize, Human 
  6. Ribo-seq analysis : Arabidopsis

Bioinformatics tools

  1. Read aligner: Bowtie, BWA, STAR
  2. Adaptor trimming tool: Trimmomatic, Fastx
  3. Genome Analysis Toolkit: GATK
  4. miRNA target prediction tool: psRNATarget, CleaveLand
  5. Genome browser: IGV, GenomeBrowse 
  6. Motif-based sequence analysis tool: MEME suite
  7. RNA structure prediction tool: Vienna RNA
  8. Protein 3D structure prediction tool: (PS)2 server

Programming skills

  1. Perl 
  2. Python  
  3. Html, PHP
  4. MySQL(MariaDB)
  5. Visual Basic 
  6. VBA

Molecular Biology skills

  1. Protein 3D structure prediction and functional engineering 
  2. Gene cloning and protein expression 
  3. DNA / Protein extraction, purification and gel electrophoresis 

Statistics / Visualization tools

  1. Sigmaplot 
  2. R package 

Computer graphics tools

  1. CorelDRAW 
  2. Photoshop 

International Conferences

9th AYRCOB(Asian Young Researchers Conference on Computational and Omics Biology), Biopolis, Singapore

21.Feb.2016 - 22.Feb.2016 (supported by Academia Sinica) 

Poster presentation: Footprints of ribosomes and exon junction complexes are widespread in RNA degradome  

Computational RNA Biology conference, Cambridge, England

11.Nov.2014 - 13.Nov.2014 (supported by Academia Sinica RPAS travel award) 

Poster presentation: Genome-wide analysis of truncated RNA ends reveals degradation of newly synthesized targets of nonsense-mediated mRNA decay and microRNA  

7th AYRCOB (Asian Young Researchers Conference on Computational and Omics Biology) Tokyo, Japan

08.Sep.2013 - 10.Sep.2013 (supported by AYRCOB) 

Selected oral presentation: Beyond the cleavage products of small regulatory RNAs: unraveling the complexity of plant RNA degradome data  

Mandatory Military service                             Jun. 2011 – May 2012

Service in Artillery Company

About me

I’m the eldest child in my family. Maybe it’s the reason why I like to be a pioneer, the one who always be first to face problem and to fix it. Sometimes people would against each other, I don’t want to face the situation, which make work harder to finish. Thus, I always be kind to communicate with my colleagues when we have different opinions in business.

After I finished my mandatory military service in 2012, I entered Academia Sinica as a research assistant. I’m responsible for data mining and computer maintenance. Even I don’t have much experiences at the moment, I ‘ve gained necessary skills in a short period, such as program coding and design customized pipelines to conduct biology research. My efforts was published on The Plant Cell and BMC Genomics.

After years of experiences in Bioinformatics, I found I possess an excellent ability to gain new knowledge and to apply it on my work. For instance, the SofivaPedigree in my portfolio,  it's the first time I apply python on my work, as you can see, SofivaPedigree is a python based stand-along CAD(Computer Aid Graphic Design) program, which is piece of art for the first try. The ability of Independent study must be my best gift to solve the problems. Moreover, I found I possess highly patient in data mining because I think finding what is meaningful in tons of data is very interesting and feel satisfied by doing research. You will be satisfied by hiring a person who always loves to improve one self’s ability. 



Projects 01 00@2x

A python based stand-along CAD(Computer Aid Graphic Design) program. Designed for generating consistent outputs

Functions: 1. Save/Load file 2. Load setting file 3. Image output 4. Copy/Paste 


Projects 01 00@2x
To generate figure which applied on the final report


Projects 01 00@2x

A web tool for sequence alignment.

Paragraph image 01 00@2x

Queue system

Showing queue, user can terminate their job manually.

WiseAlignment result

Projects 01 00@2x

The results of alignment, the interested sites are marked.


Projects 01 00@2x

A web tool for searching annotation from multiple database.

Paragraph image 01 00@2x

Queue system

Showing queue, user can terminate their job manually.

AnnotationPlus result

Projects 01 00@2x

The results of annotation, shown in Excel.


Below is the art work plotted by CorelDraw and Photoshop

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Plant defense mechanism

Illustrating a figure for explaining plants response differently in differ environments

Paragraph image 03 00@2x

Model of ribosome stalling

Illustrating a biological model of ribosome stalling

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Paragraph image 05 01@2x

RNA movement

Illustrating figure of project for applying for funds explaining how RNAs interfere plant system

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