Python Assistant

Pei-Chen Wu

**** * ***** **, *****, AZ, *****

626-***-****;******@*****.***

SUMMARY

Bioinformatics and life Science Master with strong oncological molecular biology research background(7 years) focus on oncology and immunology, analytical and programming skills and understanding of lab experimental and clinical procedure. Familiar with analyzing big genomic data sets and developed to the crucial decisions. Excellent team worked communication skills.

WORK EXPERIENCE

Caris Life Science Phoenix, AZ

Bioinformatics Analyst 02/2018 - present

Skills: MySQL, Linux, Python, R, Django(html/css), hpc, SGE, GUI, NGS data analysis, clinical data analysis.

● Accomplished Project:

1. WTS(Whole transcriptome sequencing) and WES(Whole Exome sequencing) analysis Batch QC pipeline construct.(Levey QC and WestGard Rule application, and InterOp automation) 2. establish database and app for lab experiment data(DNA Conc, RNA Conc, Hyb mass, etc.) map- ping to sequencing data for NGS performance improvement, QC, and RUO, and interactive visual- ization for the data correlation analysis.

3. WTS Fusion variant detection concordance analysis pipeline construct. 4. C.O.D.E. Vision 3 clinical and genomic data curation. Create R code to test all the statistics cor- related function in C.O.D.E. for all cohort. Including grade or lineage stratification, Hazard ratio, survival curve and p value modeling.

5. 8000+ tiles in 592 RNA genes underperforming baits reads depth data analyzing, QC for the baits performence.

6. Construct app for WES performance tracking.

7. P.O.A. clinical and genomic data QC and import. 8. Advance data pull and compute for investigating the biomarkers pattern correlate to clinical treatment and outcome.

9. pathogenetic mutational variants merging in cis. RUCDR Infinite Biologics Piscataway, NJ

Researcher IV in Bioinformatics 09/2017 - 02/2018

Skills: Linux, Python, Scripting, Affymetrix Axiom Genotyping Analysis, NextSeq NGS data analysis.

● Project: Optimize the pipeline and create python script for GeneReg File creation and demulti- plex and QC from reading of Manifest for customized request. NEW YORK UNIVERSITY (NYU) New York, USA

Graduate Teaching Assistant for Bioinformatics I & II 01/2016 - 12/2016 MEMORIAL SLOAN KETTERING CANCER CENTER New York, USA Immunotherapy Research Technician(CAR-T cell) in Michel Sadelain’s Lab 07/2014 - 07/2015 Skills: T-cells purification,T cell modification(virus transduction, CAR-T cell), CTL assay, orthotopic injection, BLI, cancer cell primary culture, Multi-color Flow Cytometry(FACS), MS Excel, SPSS, NGS

● Accomplished Project:

1. Analyzing and gathering infiltrated CAR-T cells markers(CD3/CD4/CD8/CD25/CD28/ CD45/CD137) data by FlowJo(flow cytometry) in clinical sample from mesothelioma patients before and after immunotherapy and construct the protocol for work flow, and visualized by excel and python.

2. Construct pipeline for gene differential expression from mesothelioma tumor specimens after CART-Cell therapy in GNU/Linux platform.

3. Collaborated with PI’s and pathologists to execute CAR-T cell clinical trial and trained staffs on protocols, also present all projects progression in the lab meeting weekly. WEILL MEDICAL COLLEGE OF CORNELL UNIVERSITY New York, USA Staff Associate in Nancy Du’s Lab 07/2013 - 07 /2014 Skills: BLAST, PCR, Q-PCR, Molecular cloning(E. coli), sequence analysis, mouse model, shRNA sys- tem,genotyping

● Accomplished Project:

1.Screening metastasis related gene by pSUPER RNAi system in pancreatic cancer and identified the candidate metastasis related gene in knockout mice model. 2.Construct the molecular cloning system for the lab. NATIONAL TAIWAN UNIVERSITY, CENTER OF GENOMIC MEDICINE Taipei, Taiwan Senior Research Assistant in Dr. Chao-Chi Ho and Pan-Chyr Yang’s Lab 09/2009 – 06/2013 Skills: NGS, Microarray, BLAST, CLUSTAL, SWISSPROT, primary culture, Q-PCR, confocal microscopy(high-content imaging), luminescence-based assays, cytotoxicity assay(IC50), cell prolifera- tion assay

• Accomplished Project:

1.Detection of EGFR mutation in malignant pleural effusion of lung cancer patients by RNA-Seq, track specimen information pathologically and diagnose clinically, and built cancer cell lines es- tablishment method from clinical samples in hypoxia, also present all projects progression in the lab meeting weekly.

2.Research for the epigenetic event for EGFR mutant in NSCLC transformed into SCLCs after TKI

(tyrosine kinase inhibitor) treatment with identical EGFR(L858R) mutant type. NATIONAL TAIWAN UNIVERSITY, DEPARTMENT OF DENTISTRY Taipei, Taiwan Research Assistant in Dr. Min-Huey Chen’s Lab 09/2008 – 08/2009 Skills: SDS-PAGE, ELISA, gremlin construction, gene knock-out.

• Accomplished Project:

1.Construct the germline of hBMSCs-E6E7-transfected hBMSCs inserted phTERT-IRES2-EGFP. 2.Research for reversion of pluripotency and blockage of spontaneous differentiation by ectopic ex- pression of Telomerase.

EDUCATION

NEW YORK UNIVERSITY (NYU) New York, USA

Master of Science in Bioinformatics (GPA: 3.33) 09/2015 – 05/2017 Skills: Python, R(Bioconductor, DESeq2, Sigclust2, gglpots), Linux (*.pbs, scripts, BASH), MySQL, Next-Gen- eration Sequencing(NGS), CNV, RNASeq, WGS, Variant-Calling(identify sequencing variants), High-perfor- mance computing( fastQC, BWA, Samtools, Picard, GATK, Bedtools, Trimmonatic, bowtie2, STAR, etc.), De Novo Assembly(Trinity), Bioinformatics databases(UCSC, NCBI, TCGA, Ensembl, BioGRID, etc.), Git/Github

● Project1: Using Next generation sequencing (RNASeq) to subtyping breast cancer by tumor sam- ple genomic data by K-means clustering for 1208 samples from TCGA guiding to treatment deci- sions by R.(In Github: pcw271/NGS_Fianl_Project/ NGS_Project/)

● Project2: HappyOur website constructed by Django(Python), database system using MySQL.(In Github: pcw271/HappyOur-Django-)

● Project3: De Novo Transcriptome Assembly for breast cancer specimen for subtype phylogeny(Trinity).

● Project4: Design model for categorizing musical style from midi file collection and 2D- 3D-plot- ting for visualization by Python.(In Github: pcw271/final_project/sl4964)

● Graduate Scholarship is the Highest Tier.

Related classes:

● Data Structure and Algorithms.(Graduate class in Computer Science Department

● Programming in Python. (Stern Business School in NYU)

● Principe of database system(MySQL)(Graduate class in Computer Science Department)

● Programming for Data Science.(Python: pandas, numpy, matplotlib. Github)

● NGS(HPC system)

● Bioinformatics I & II

NATIONAL TAIWAN NORMAL UNIVERSITY (NTNU) Taipei, Taiwan Master of Science in Life Science (GPA: 3.77) 09/2003 - 06/2006 Thesis: “The co-evolution relation by 16s rRNA phylogenic analysis, 3D simulation(Amira) and ultra-struc- ture of bacteriocytes (Transmission Electronic Microscopy)formed by primary symbiont resides in the Be- misia argentifolii.” Published in National Taiwan Congress of Entomology. 2005 NATIONAL CHUNG-HSING UNIVERSITY (NCHU) Taipei, Taiwan Bachelor of Science in Entomology 09/1999 - 06/2003 Internship in the ACADEMIA SINICA

PUBLICATIONS

● “Endobronchial ultrasound-guided transbronchial biopsy: How many specimens are necessary?” Res- piration 2012; 84:128-34

● “The co-evolution relation by 16s rRNA phylogenic analysis and ultra-structure of bacteriocytes formed by primary symbiont resides in the Bemisia argentifolii.” National Taiwan Congress of Ento- mology. 2005

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