Data Scientist Machine Learning Bioinformatics Data Mining Statistics

Jianjiao Chen, Ph.D.

**** ***** ***, ********** ** Pittsburgh, Pittsburgh, PA 15261

Email: ********@*****.***

Career Objective

My background is in Computer Science with extensive experience in Bioinformatics, Biostatistics, and Data Science. I have over five years of postdoctoral training in Bioinformatics from top universities including Yale University, Georgia Institute of Technology, University of Miami, and University of Pittsburgh. My career goal is to be an excellent data scientist specializing in data science and big data, covering bioinformatics, machine learning, deep learning, and big data analysis, and to tackle challenges across various fields using my comprehensive data analysis skills and experience. Currently, I am a Senior Data Scientist at the Center of Neurobiology, University of Pittsburgh.

Professional Experience

Senior Data Scientist 2022-Present

Center of Neurobiology, University of Pittsburgh, Pittsburgh, PA Analyze large-scale genetic and genomic datasets, including single-cell sequencing (scRNA-Seq, scATAC- Seq) and bulk RNA-Seq data.

Develop analytical pipelines and methodologies to interpret complex biological data. Collaborate with cross-functional teams to deliver insights into disease mechanisms. Data Scientist 2020-2022

Center of Neurobiology, University of Pittsburgh, Pittsburgh, PA Conducted multimodal data integration and analysis for cancer research projects. Utilized machine learning techniques to identify biomarkers and therapeutic targets. Bioinformatics Postdoctoral Researcher 2018-2019

Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA Bioinformatics Postdoctoral Researcher 2016-2018

Department of Statistics, Sylvester Miller Cancer Center, University of Miami, Miami, FL Bioinformatics Postdoctoral Researcher 2015-2016

School of Biology, Georgia Institute of Technology, Atlanta, GA Bioinformatics Postdoctoral Researcher 2014-2015

School of Medicine, Yale University, New Haven, CT Instructor—Data Mining and Machine Learning 2012-2013 Institute of Information Science and Engineering, Xinjiang University, Xinjiang, China Exchange Scholar 2009-2012

Center for Bioinformatics Technology, Chinese Academy of Sciences, Shanghai, China Instructor—Photoshop; Multimedia Technology; 3DMax; Computer Foundation Shanghai Zhendan College, Shanghai, China

Instructor—Introduction to Computer Foundation 2009-2010 Shanghai Business College, Shanghai, China

Exchange Scholar 2008-2009

Department of Computer Science, Fudan University, Shanghai, China Instructor— Object-Oriented Programming C++; SQL Server; C; Data Structure and Algorithm; Database Principles; Computer Maintenance; Software Engineering; Compiler Principle; Concrete Mathematics and Application; Probability and Statistics

2001-2007

Institute of Information Science and Engineering, Xinjiang University, Xinjiang, China Project Experience

Single-Cell Sequencing Analysis: Analyzed scRNA-Seq, scATAC-Seq, and CyTOF data to identify cell- specific gene expression profiles and regulatory elements. University of Pittsburgh, USA TCGA Data Analysis: Conducted integrative analysis of TCGA omics data to uncover molecular profiles of Triple Negative Breast Cancer subtypes. University of Miami, USA AI/ML Applications: Applied machine learning algorithms to predict cancer drug targets and explore genetic variants. Georgia Institute of Technology, USA

Molecular Profile Differences in TNBC Subtypes: Designed algorithms and analyzed TCGA Omics data to compare race disparities within TNBC subtypes. University of Miami, USA Role of miRNA in Ovarian Cancer: Analyzed microarray data of microRNA, mRNA, LS-MS protein mass spectrometry, and RPPA protein microarray. Georgia Institute of Technology, USA Skills

Programming: R, Python, Shell scripting, C++, Java Data Analysis: Single-cell sequencing (scRNA-Seq, scATAC-Seq), RNA-Seq, DNA-Seq, ChIP-Seq, GWAS Tools: Git, Slurm, Hadoop, Spark, Seurat, Scanpy

AI/ML: Deep learning (Keras, PyTorch), topic modeling, large language models Education

Ph.D., Computer Technology and Application

Shanghai University, China, 2012

M.S., Computer Application Technology

Xinjiang University, China, 2006

B.S., Computer Science and Software

Xinjiang University, China, 2001

Selected Publications

SYK-mediated epithelial cell state is associated with response to c-Met inhibitors in c-Met- overexpressing lung cancer, Nature Communications, 2023, doi: https://www.nature.com/articles/s41392- 023-01403-w

Controlling Batch Effect in Epigenome-Wide Association Study, Springer Protocols, 2022, doi: https://link.springer.com/protocol/10.1007/978-1-0716-1994-0_6 Transcriptional and anatomical diversity of medium spiny neurons in the primate striatum, Current Biology, 2021, doi: https://www.cell.com/current-biology/pdf/S0960-9822(21)01369-5.pdf Multi-omics analysis identifies therapeutic vulnerabilities in triple-negative breast cancer subtypes, Nature Communications, 2021, doi: https://www.nature.com/articles/s41467-021-26502-6 Transcriptional Diversity of Medium Spiny Neurons in the Primate Striatum, bioRxiv, 2020, doi: https://doi.org/10.1101/2020.10.25.354159

Paired Immunoglobulin-like Receptors Mediate Monocyte and Macrophage Memory to Non-self MHC Molecules, Science, 2020, doi: 10.1126/science.aax4040 Integrative Genomic Analysis Identifies Distinct Mutational, Epigenetic and Immunological Patterns Among Triple-Negative Breast Cancer Subtypes, Cancer Research, 2019, doi: 10.1158/1538- 7445

Multi-Objective Optimization Approaches in Biological Learning System on Microarray Data: Evolutionary to Hybrid Framework, Multi-Objective Optimization, Springer, 2018 Utilizing Bat Algorithm to Optimize Membership Functions for Fuzzy Association Rules Mining, 28th International Conference on Database and Expert Systems Applications, 2017 A Novel BAT Algorithm for Learning Membership Functions in Light of Fuzzy Association Rules, Scientific Computing, 2017

Multi-Objective Association Rule Mining with Binary Bat Algorithm, Intelligent Data Analysis, 2016, 20(1):105-128

Hybrid Clustering Methods Based on Adaptive K-Harmonic Means, International Journal of Advancements in Computing Technology, 2012, 4(6):10-23 Hybrid K-Harmonic Clustering Approach for High Dimensional Gene Expression Data, Journal of Convergence Information Technology, 2012, 7(3):39-49 A Novel Hybrid Gene Selection Approach Based on ReliefF and FCBF, International Journal of Digital Content Technology and Its Applications, 2011, 5(10):404-411 Clustering High Dimensional Gene Expression Data via Two Step Feature Filtering, International Conference on Communications and Information Technology, 2011, pp.299-303 Selected Presentations

Deep Diversification of an AAV Capsid Protein by Machine Learning, 2024 Machine Learning Driven Cell Type-Specific Enhancer Discovery, 2024 Comparing the Workflow System—Nextflow, Airflow & Snakemake, University of Pittsburgh, 2023 Identify Cell-type Specific MSNs and RShiny, University of Pittsburgh, 2022 Defining Discrete and Continuous Cell Types in the NHP Brain Striatum, University of Pittsburgh, 2021

Single Cell Sequencing Discovery Cell-specific Enhancers and Promoters in NHP Brain Striatum, University of Pittsburgh, 2020

Exploring the Mechanism of Innate Allorecognition of Monocytes Memory by scRNA-Seq, University of Pittsburgh, 2019

Introduction to Single Cell Sequencing and CyTOF, University of Pittsburgh, 2018 Molecular Profile Difference of TNBC Subtypes Based on TCGA Omics Data, University of Miami, 2017

Integrating RNA-Seq and Methylation450k for TNBC Subtype Analysis, University of Miami, 2016 Research of Regulation Relationship Among miRNA, mRNA and Protein in Transfected miR-429 Ovarian Cancer HEY Cell Line at Variable Time Points, Georgia Institute of Technology, 2015 Tissue-based Human Protein Map, Georgia Institute of Technology, 2015 GERV: A Statistical Method for Generative Evaluation of Regulation Variants for Transcription Factor Binding, Georgia Institute of Technology, 2015 The Pipeline Optimization for PIWI Epigenetic Functions Modeling, Yale University, 2014 Dynamic Adaptive K-harmonic Clustering Algorithms and Application to Cancer Classification, Chinese Academy of Science, 2014

Two Steps Feature Selection Algorithms and Application to Biomarker Discovery, Chinese Academy of Science, 2013

Clustering Methods and Applications for High-Dimensional Data Based on K-harmonic Means, Thesis Defense Seminar, Shanghai University, 2012

Novel Hybrid Gene Selection Algorithm Based on ReliefF and FCBF for MOPSO Heterogeneous Clustering Ensemble, Shanghai University, 2011

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