Haibo Liu, PhD²
Senior Bioinformatician | UMass Chan Medical School
Summary
Highly self-motivated and results-driven bioinformatics scientist with over 10 years of experience in developing software, analyzing and interpreting diverse complex biological data. Proven expertise in programming with R, Python, SQL, and other languages, with version control (Git/GitHub). Proven ability to work independently and as a reliable team player. A self-driven quick learner eager to learn and grow.
Skills
Sequencing Data Analysis
Proficient in managing, analyzing, integrating, and interpreting diverse sequencing data, including:
- Single-cell: scRNA-seq, scATAC-seq
- Bulk: RNA-seq, ATAC-seq, ChIP-seq
- Genomics: WGS/WES, RRBS/WGBS
- Long-read: PacBio Iso-seq, Nanopore sequencing
Programming Languages
R, Python, Perl, Awk, Bash, SQL, Java
Pipeline Development & Infrastructure
- Workflow Management: Nextflow
- Version Control: Git/GitHub
- Containerization: Docker, Singularity
- Environment Management: Conda/mamba
- HPC & Cloud: Institutional clusters, Amazon Web Services (AWS)
Data Science & Analysis
- Machine Learning (including Deep Learning)
- Statistical Analysis
- Data Visualization
- Experimental Design
- Data Wrangling
Multi-omics Expertise
Spatial transcriptomics, Microbiomics, Metabolomics, Proteomics
Biology Background
Molecular biology, Genetics, Epigenetics, Genomics, Transcriptomics
Professional Experience
June 2022 – Present
- Provide bioinformatics analysis and consultation to 10+ research labs, contributing to high-profile publications.
- Developed CleanUpRNAseq, an R package for detecting and correcting gDNA contamination in RNA-seq data.
- Co-maintainer of DoubletFinder (scRNA-seq doublet detection), a widely used R package.
- Published first-authored book chapter: Best practices for the ATAC-seq assay and its data analysis.
April 2020 – June 2022
- Provided bioinformatics analysis and consultation to 10+ research labs.
- Designed OneStopRNAseq, a Snakemake pipeline for comprehensive bulk RNA-seq analysis.
- Developed scATACpipe, a Nextflow pipeline for integrative scATAC-seq analysis.
Associate Scientist | Iowa State University, Ames, IA
August 2018 – March 2020
- Led bioinformatics analysis for the pig FAANG project, including the first scRNA-seq analysis in domestic animals.
- Secured over $1.65M in USDA grants as PI/Co-PI.
July 2017 – June 2018
- Provided bioinformatics analysis and consultation to 10+ research labs.
- Enhanced ATACseqQC, a widely used R package for ATAC-seq quality control (highly cited).
Postdoctoral Fellow | DuPont Pioneer (now Corteva), Johnston, IA
March 2017 – July 2017
- Established MapReduce algorithm for calculating correlation coefficients from large gene expression matrices.
- Constructed gene co-expression networks in maize using hundreds of RNA-seq datasets.
April 2016 – August 2016
- Accomplished bioinformatics projects generating $80K in revenue within 3 months.
- Developed a patented SNP marker panel for maize genotyping.
Graduate Research Assistant | Iowa State University, Ames, IA
August 2012 – March 2017
- Saved over $100K in sequencing costs by rescuing RNA-seq projects through proper library construction recommendations.
- Led integrative analysis of Illumina RNA-seq and PacBio Iso-Seq data to improve structural annotation of pig reference genome (Sscrofa11.1).
Education
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Ph.D. in Bioinformatics & Computational Biology
Iowa State University, Ames, IA (August 2012 – March 2017)
Honor: Research Excellence Award
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Master of Science (M.S) in Biochemistry & Molecular Biology
Huazhong Agricultural University, Wuhan, CN (September 1998 – June 2001)
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Bachelor of Science (B.S) in Biotechnology
Huazhong Agricultural University, Wuhan, CN (September 1995 – June 1999)
Certifications
- Machine Learning (Coursera, Stanford University, by Andrew Ng)
- Data Science with Python (Coursera, IBM)
- Data Science in Python (Coursera, University of Michigan)
Key Publications & Presentations
Notable Achievements
- Rescued multiple RNA-seq projects, saving over $100K in sequencing costs
- Secured over $1.65M in USDA grants as PI/Co-PI
- Developed and maintained widely-used R packages (DoubletFinder, CleanUpRNAseq, ATACseqQC)
- Led first scRNA-seq analysis in domestic animals (pig FAANG project)
- Contributed to pig reference genome annotation (Sscrofa11.1)
- Published first-authored book chapter on ATAC-seq best practices
- Most viewed presentation at BioC2020 conference
Feel free to reach out if you’d like to collaborate, discuss bioinformatics challenges, or have questions about any of my work!