Chen Yang Email & Phone Number

Vancouver, British Columbia, Canada

Vancouver, British Columbia, Canada

Project 1 NANOSIM: NANOPORE SEQUENCE READ SIMULATOR BASED ON STATISTICAL CHARACTERIZATION (github.com/bcgsc/NanoSim)Employed multiple statistical techniques to analyze, quantify, and simulate nucleotide sequencing data, including kernel density estimation, mixed statistical models, Markov Chain and hidden Markov model, and EM algorithmDeveloped the first Oxford Nanopore sequencing read simulator, maintained the Github repository, actively responded to user’s feature requests, made 16 releases with 3 major version upgrades, and achieved over 20k Conda downloads and 106 citationsMentored and trained co-op student to work on a sub-project, which was invited for an oral presentation in the largest bioinformatics conference ISMB and received ISMB travel award (10% acceptance)Project 2 TERMINITOR: THE FIRST TRANSCRIPT COMPLETENESS ASSESSMENT PIPELINE (github.com/bcgsc/Terminitor)Explored various deep learning models for nucleotide sequence classification task, including MLP, RNN, CNN, and ResNETDesigned novel sequence representation using embedding method for improved prediction accuracyDeveloped prediction models for transcript terminus, out performed state-of-the-art algorithmsIntroduced the first transcript completeness assessment pipeline built on top of the prediction models for RNA sequencing data, and applied on the annotation of non-model organisms

Vancouver, Canada Area

Vancouver, British Columbia, Canada

Courses: DSCI511 Programming, DSCI551 Exploratoary Data Analysis, DSCI552 Statistical Inference, CPSC320 Intermediate Algorithm Design and Analysis, STAT 545/547 Exploratory Data Analysis and Topics in StatisticsPrepared course material including laboratory experiments, lectures, exams, homework, and practice problems. Designed grading rubrics, and graded assignments and exams for over 200 students in totalLed weekly laboratory sessions and office hours to classes of > 30 graduate students and >100 sophomores

Optimization of novel marine actinobacteria culture methods.Species identification via 16S DNA sequencing and antibiotic activity screening.

Responsible for routine test of pharmaceutical ingredients and manufactured products.Help to draft and monitor Standard Operating Procedure, study and evaluate quality specificationsand auditing programs.

Investigate stress related genes of mangrove.Use molecular and computational methods to study oxidation genes including SOD and POD.Evaluate enzymatic activity of gene products.

Doctor Of Philosophy (Ph.D.), Bioinformatics

Master'S Degree, Bioscience

Master thesis titled "Isolation, Phylogenetic analysis and bioactive screening of Red Sea sponge associated actinomycetes".

Bachelor'S Degree, Life Science And Biotechnology

Bachelor thesis titled "The establishment and preliminary application of Alzheimer’s disease model caused by factors related to diabetes".