Biography

Shang-Hung Shih has worked as a software engineer at the genomics team in Taiwan AILabs for two years. Prior to this, He graduated from National Taiwan University (NTU) and Academia Sinica with master degree in Bioinformatics, and worked with Prof. Chien-Yu Chen.

Timeline

Jan. 2020 -

Software Engineer @ Taiwan AI Labs

TAIGenomics, PubmedKB, QCheck web app development

Mar. 2019 - Dec. 2019

Software Engineer Intern @ Taiwan AI Labs

Variant Annotator

Supervisor and Mentor: Stefan Hong

Jul. 2018 - Dec. 2020

M.S. @ NTU c4Lab

Mentor: Prof. Chien-Yu Chen

2018 - 2021

M.S. degree @ NTU and Academia Sinica

Genome and Systems Biology Degree Program

Jan. 2015 - Aug. 2018

Research Assistant @ CSMU bio608

Dockerized Next-Generation-Sequencing Analysis

Mentor: Prof. Yu-Fan Liu

2014 - 2018

B.Sc. degree @ CSMU

Biomedical Science

Selected Projects

Moneyfire Landing Page and Mobile App

Develop a mobile application to help users track and manage asset growth.

Typescript(React Native, Next.js) / Firebase / AWS(Amplify)

PubmedKB Web App

Working on a PubmedKB web app for entities relation visualization of NLP.

Typescript(ReactJS) / Node.js / Neo4j / Docker / Kubernetes

QCheck Web App

Built proteomics data visualization for QCheck web app.

Javascript(Vue.js) / php(laravel) / MySQL / AWS

TAIGenomics Web App

Developed signup system, variant table, IGV viewer, and pedigree editor for TAIGenomics web app to help genetic analysis and diagnosis.

Typescript(ReactJS) / Node.js / MongoDB / Docker / Kubernetes

V-score: Pathogenic Score Prediction

Developed rule-based ACMG, ML-based v-score and inheritance pattern interpretation system for variant prioritization.

Python(ML) / Docker

Variant Annotator

Designed and built a variant annotator with multi-processing and MySQL to solve the inefficiency of traditional annotation tools for matching 4 million variants to databases with 9 billion data, reduced the annotation time by 58%, and shortened the time for a whole genome sample from 2 hours to 50 minutes.

Python / MySQL / Docker

1st place in PIXNET 6th Hackathon Final: Travel Tech (Travel Charger)

Used Pixnet articles for correlation analysis and IG post data for sentiment analysis to provide personalized attraction recommendation and trip planning. I was mainly responsible for building relation graph for attraction recommendation.

Python / Neo4j / MySQL / Docker

Constructed Transcription Factor Binding Profiles using Deep Learning

Predicting the sequence specificities of DNA-binding proteins by convolutional neural network.

Python(DL) / MySQL / Docker

ngs-main-wes: Dockerized Multi-threads Somatic Paired WES Analysis Pipeline

For general varaints calling (GATK3 Mutect2 & GATK4 Mutect2 with PONs) and annotation (Phial based on Oncotator, paraSNP based on Annovar).

Python / Docker