Cheng-Yu Hou

Bioinformatician

10+ years work experience in Bioinformatics.

Advantages:
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]

Education

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 (10+ years in Bioinformatics)

NGS team, Microbio Group, Taiwan, Senior assistant reseacher, Dec 2021 ~ Current

1. Microbiota analysis(Gut, Skin)

2. Server and Database management

3. Statical analysis for biology data(microbiota, new drug development)

4. Data intergration, visualization and interpretation

BioInformatics team, Sofiva Genomics, Taiwan, Bioinformatician, Jun 2016 ~ Nov 2021

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

Publications

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

Skills

NGS data analyses

Variant calling: Human
Whole exon sequencing : Human
Barcode De-multiplex
miRNA analysis : Arabidopsis, Rice
RNA Degradome analysis : Yeast, Arabidopsis, Rice, Soybean, Grape, Maize, Human
Ribo-seq analysis : Arabidopsis

Bioinformatics tools

Read aligner: Bowtie, BWA, STAR
Adaptor trimming tool: Trimmomatic, Fastx
Genome Analysis Toolkit: GATK
miRNA target prediction tool: psRNATarget, CleaveLand
Genome browser: IGV, GenomeBrowse
Powerful platform for microbiota analysis: Qiime2
Motif-based sequence analysis tool: MEME suite
RNA structure prediction tool: Vienna RNA
Protein 3D structure prediction tool: (PS)2 server

Programming skills

Perl
Python
Html, PHP
MySQL(MariaDB)
Visual Basic
VBA

Molecular Biology skills

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

Statistics / Visualization tools

Sigmaplot
R package

Computer graphics tools

CorelDRAW
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 the problem and fix it. Sometimes people would against each other, I don’t want to face the situation, which makes work harder to finish. Thus, I always am kind to communicate with my colleagues when we have different opinions on 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 though I don’t have much experience at the moment, I‘ve gained the necessary skills in a short period, such as program coding and designing customized pipelines to conduct biology research. My efforts were published on The Plant Cell and BMC Genomics.

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