Bioinformatics / Data Scientist

Ya-Ting Yang

***********@*****.***

SKILLS

Programming Languages: Python, R, Bash, SQL, MySQL

Machine Learning: Supervised & unsupervised learning, Random Forest, Support Vector Machines, feature selection, model validation, scikit learn, tidymodels Bioinformatics Tools: BLAST, BEDTools, SAMtools, Bowtie, DESeq2, Bioconductor, ggplot2, RDKit, pandas, scikit-learn, matplotlib, MATLAB, Merlin, Hail, Haploview, Plink, Jalview, PyMOL, Smina, Docking, Singularity Data: Genome-Wide Association Study (GWAS), Next-Generation Sequencing (NGS), Transcriptomics (RNA-seq, scRNA-seq), Flow Cytometry Data, Mass Spectrometry data, high-throughput (HT) cell-based assays PROJECT EXPERIENCE

1. Kidney Renal Clear Cell Carcinoma Classification Using TCGA RNA-Seq Data in R. Link

Built an end-to-end bioinformatics pipeline using R for RNA-seq–based cancer classification.

Processed >200 TCGA samples, normalized expression data, and performed differential gene analysis.

Developed and evaluated machine learning models; visualized feature contributions and key biomarkers.

2. Drug Repositioning Strategy for Novel Therapeutic Indications. Link

Built an in silico drug repositioning workflow integrating cheminformatics and virtual screening of top 500 FDA-approved drugs targeting ASK1 kinase for DKD treatment.

Performed molecular docking using smina docking and machine learning model with molecular descriptors. Visualized binding interactions in PyMOL to evaluate potential repurposing candidates. 3. Design an informatics workflow to analyze and report on the expressed genes in Python. Link

Developed a Python-based workflow for FASTQ quality control, alignment (BWA), and BAM processing

(samtools) in human tumor samples.

Automated NGS data analysis pipeline integrating Biopython for sequence metrics and Integrated Genome Viewer (IGV) for gene expression visualization. EDUCATION

Apr 2024-Aug 2025 Master of Science (M.S.) in Bioinformatics, Brandeis University Waltham, MA, USA

Aug 2010-Dec 2012 PhD student in Life Science, National Defense Medical Center Academia Sinica, Taipei, Taiwan

Sep 2007-Jun 2009 Master of Science (M.S.) in Biotechnology, HungKuang University Taichung, Taiwan

Sep 2003-Jun 2007 Bachelor of Science (B.S) in Medical Technology, Chung Hwa University of Medical Technology, Tainan, Taiwan

WORK EXPERIENCE

Apr 2019-Apr 2023

Retail consultant, MKO retail consultant, USA

Established a logistics system for purchasing products and selling to overseas customers while maintaining and expanding the client network. Wrote product copy for new items, livestreamed with clients, packaged products for international shipping, and provided friendly customer service and after-sales support.

Mar 2016-Feb 2017

Research assistant, Boston University Medical Center, USA

Treated LOX-PP knock-in mice with a specific chemical to induce oral tumor.

Detected metastasis for oral cancer in nude mice by In Vivo Imaged system (IVIS).

Used specific antibodies for human and mouse tissues by immunohistochemistry and immune-fluorescence.

Prepared Mass Spectrometry samples and managed the laboratory by maintaining reagents and other equipment.

Apr 2013-Aug 2014

Shop assistant, Teapatea, Taiwan

Responsible for brewing various types of tea, warmly greeting customers, providing introductions to specialty drinks, and simultaneously handling orders at the counter and over the phone.

Aug 2009-Jul 2010

Research assistant, Tri-Service General Hospital, Taipei, Taiwan

Cross-bred different strains of mice, including knock-out/in mouse.

Created animal and cell models for several renal diseases and discovered gene and herbal therapies and detected the associated proteins in chronic renal disease, researched the mechanism, and defined numerous biomarkers.

Produced UUO (unilateral ureteral obstruction) model and autoimmune model.

Performed hydrodynamic method to inject pDNR-CMV-mKlotho into DBA/2J mouse tail vein for induction of acute renal disease.

Used double immunofluorescence staining of murine cells to observe specific immune targets, such as CD3, CD4, CD8, CD39, and macrophage by flow-cytometry. PUBLICATIONS

1. LSD1 inhibition regulates key mediator of OSCC growth and metastasis. Oncotarget. 2017 Sep 26; 8(43): 73372–73386.

AWARDS

National Science Council Scholarship (2009) / HungKuang University Scholarships (2008)

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