Mingsheng Qi, Ph.D.

Bioinformatics & NGS Solutions Scientist

  • St. Louis, MO 63132 * 217-819-6637 * tonyqms@gmail.com

PROFESSIONAL SUMMARY

Computational biologist and NGS platform expert with 11+ years of hands-on experience developing, optimizing, and implementing Next-Generation Sequencing solutions across commercial, research, and product development environments. Proven ability to bridge science and commerce through customer-centric technical support, rigorous bioinformatics analysis, and cross-functional collaboration. Deep expertise in Illumina and Complete Genomics NGS workflows, target enrichment, GBS, RNA-seq, and microbiome applications. Experienced in translating complex technical challenges into actionable insights, building scalable data pipelines on AWS cloud platforms, and creating high-impact scientific communications. Strong track record managing diverse teams, driving product adoption, and enabling customer success through technical excellence and clear communication.

CORE COMPETENCIES

NGS Applications & Workflow Development

  • End-to-end NGS workflows: library preparation (target enrichment, amplicon, RNA-seq, GBS), sequencing (Illumina and Complete Genomics platforms), and data analysis
  • Hands-on platform operation & optimization: troubleshooting, protocol development, QC validation
  • Experimental design, assay development, and high-throughput process optimization
  • Data quality metrics: coverage uniformity, off-target rates, cost-per-data-point analysis

Bioinformatics & Data Science

  • NGS data analysis pipeline development: alignment, variant calling, quality control, downstream interpretation
  • Bioinformatics toolset: R, bash, Python for data analysis and automation
  • Specialized tools: BWA, GATK, samtools, bcftools, bedtools, Picard, IGV, plink, GPU-accelerated Parabricks suite
  • Visualization & presentation: RShiny, Python Streamlit and Plotly for interactive reports and data dashboard
  • Cloud computing: AWS (EC2, S3, SageMaker, Docker) for scalable analysis and pipeline deployment
  • AI/ML analysis: Genomic Prediction, GWAS, microbiome ecology metrics, quality control frameworks

Customer-Facing Technical Support

  • Pre-sales technical engagement: requirements gathering, use case development, proof-of-concept design
  • Post-sales support: troubleshooting, technical consulting, data interpretation assistance
  • Scientific communication: explaining complex NGS/bioinformatics concepts to diverse audiences
  • Training delivery: customer workshops, hands-on training on NGS workflows and data analysis platforms

Product Development & Cross-Functional Leadership

  • Workflow design and validation for high-throughput production environments
  • Requirements translation: converting customer/business needs into technical specifications
  • Collaboration with R&D, product management, engineering, and data teams
  • Data-driven quality management systems (QMS) and LIMS integration
  • Automation platform experience: Biomek, Agilent Bravo, Tecan, Formulatrix liquid handlers

Scientific Communication & Thought Leadership

  • Author of 15+ peer-reviewed publications in high-impact journals (ISME Journal IF 10.3, PLoS Pathogens IF 9.1)
  • White paper, technical documentation, case study, and application note authoring
  • Conference presentations and scientific storytelling
  • Key Opinion Leader (KOL) engagement and emerging trend analysis

PROFESSIONAL EXPERIENCE

Bioinformatics Scientist * Solis Genomics (Sequencing Services & Analysis) * Jun 2024-Jan 2026 Customer-Facing NGS Support & Technical Consulting

  • Provided pre- and post-sales technical support for commercial NGS projects, translating customer research goals into optimized sequencing workflows
  • Designed custom NGS panels and protocols for target enrichment applications in collaboration with sales and product teams
  • Performed comprehensive troubleshooting of NGS datasets (library prep quality, alignment metrics, variant calling accuracy) and delivered technical reports and recommendations
  • Supported proof-of-concept (PoC) analyses and client presentations demonstrating real-world value of NGS solutions
  • Collaborated with customers, field application scientists, and internal teams to capture requirements and drive product improvements

Bioinformatics Pipeline & Data Analysis

  • Developed and optimized bioinformatics pipelines for production NGS analysis inlcuding genomic alignment, variant calling, de novo genome assembly, imputation reference panel building, skim sequencing imputation
  • Achieved 95%+ first-pass QC success across 100,000+ commercial sequencing samples
  • Performed data visualization and quality assessment (coverage uniformity, alignment rates, variant annotation)
  • Generated technical documentation and standard operating procedures (SOPs) for NGS data analysis workflows

Scientist II & Scientific Manager * Benson Hill Inc. (Agribiotech Product Development) * July 2021–June 2024

Genotyping Platform Development & Product Commercialization

  • Led cross-functional initiatives to design, validate, and deploy three NGS-based genotyping platforms: amplicon sequencing, Genotyping-By-Sequencing (GBS), and probe-based target enrichment sequencing
  • Instrument integration & optimization: Onboarded and established standard operating procedures for Illumina MiSeq and NextSeq systems; optimized protocols for maximum data quality, throughput, and cost-efficiency
  • Data strategy & KPI development: Established comprehensive quality control framework with actionable metrics (coverage uniformity, off-target reads, cost per genotype); enabled data-driven decision-making
  • Scalable data infrastructure: Directed development of automated bioinformatics pipelines in collaboration with software and data engineers (AWS EC2, Docker containerization, R/Python/bash workflows, SageMaker)
  • High-volume production: Managed NGS workflow processing 100,000+ samples/year from library preparation through quality assurance and data delivery; identified and resolved technical bottlenecks
  • Cross-functional collaboration: Partnered with breeding, gene editing, and product teams to translate NGS outputs into actionable insights; presented findings to internal stakeholders and external partners
  • Team leadership: Managed two individuals; established personalized development plans; elevated team bioinformatics competency through hands-on mentoring and training

Commercial Impact

  • Enabled successful gene editing and breeding pipeline deployment through reliable, scalable NGS genotyping
  • Reduced data turnaround time from 18 days to 10 days while maintaining 93%+ data quality

Research Scientist * Donald Danforth Plant Science Center * August 2018–July 2021

Microbiome Analysis & NGS Application Development

  • Led multi-scale microbiome project identifying beneficial and detrimental bacteria impacting sorghum stress responses using amplicon sequencing, advanced statistical ecology metrics, and bioinformatics analysis
  • Performed comprehensive NGS data analysis (16S rRNA amplicon processing, comparative genomics, ecological analysis)
  • Integrated high-throughput plant phenotyping data with microbiome datasets to identify correlations and biomarkers
  • Published in The ISME Journal (IF 10.3): “Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons” (2022)
  • Collaborated with plant scientists, phenotyping teams, and field researchers to inform experimental design and interpretation

Postdoctoral Associate & Assistant Scientist I * Iowa State University * August 2011–August 2018

Molecular Plant-Pathogen Genomics & Bioinformatics

  • Established innovative bacterial screening systems for phenotypic characterization of fungal proteins; discovered novel secreted effector proteins related to fungal virulence
  • Conducted genome sequencing projects and comparative genomics analysis to identify molecular mechanisms of pathogenesis
  • Developed bioinformatics workflows for NGS data processing and interpretation
  • Published 4 peer-reviewed articles on plant-microbe interactions and genomics in high-impact journals
  • Mentored and managed 10+ individuals including PhD students, undergraduate researchers, high school educators, and international visiting scholars; established training protocols and career development plans

Postdoctoral Associate * University of Illinois at Urbana-Champaign * February 2009–August 2011

Genome Sequencing & Comparative Genomics

  • Coordinated whole genome sequencing projects and performed comparative genomics analysis
  • Developed bioinformatics pipelines for large-scale sequence data processing and interpretation
  • Contributed to peer-reviewed publications and scientific collaboration

EDUCATION

Ph.D. in Genetics Chinese Academy of Sciences, Institute of Genetics and Developmental Biology, Beijing, China 2008
B.S. in Microbiology Nanjing Normal University, China 2003

PEER-REVIEWED PUBLICATIONS & SCIENTIFIC IMPACT

Published Works (15+ publications, 1,200+ citations)
Full publication list and impact metrics: https://scholar.google.com/citations?user=qEQPHFwAAAAJ

Selected High-Impact Publications:

  • Qi, M. et al. (2022). Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons. The ISME Journal, 16: 2197-2210. IF: 10.3. DOI: 10.1038/s41396-022-01245-4

  • Qi, M. et al. (2019). Candidate effectors from Uromyces appendiculatus can be discriminated based on suppression of immune responses. Frontiers in Plant Science, 10: 1182. IF: 4.298. DOI: 10.3389/fpls.2019.01182

  • Qi, M. et al. (2018). Suppression or activation of immune responses by predicted secreted proteins of Phakopsora pachyrhizi. Molecular Plant-Microbe Interactions, 31: 163–174. IF: 4.455. DOI: 10.1094/MPMI-08-17-0201-R

  • Qi, M. et al. (2018). QQS orphan gene and its interactor NF-YC4 reduce susceptibility to pathogens and pests. Plant Biotechnology Journal, 16: 1612-1624. IF: 7.443. DOI: 10.1111/pbi.12961

  • Qi, M. et al. (2016). A small cysteine-rich protein from Phakopsora pachyrhizi suppresses plant immunity. PLoS Pathogens, 12(9): e1005827. IF: 9.127. DOI: 10.1371/journal.ppat.1005827

TECHNICAL SKILLS & PROFICIENCIES

Programming & Bioinformatics

  • Languages: R, bash scripting, Python
  • NGS Analysis & Genomics Tools: BWA, GATK, samtools, bedtools, Picard, IGV, UCSC Genome Browser
  • Data Visualization & Reporting: ggplot2, matplotlib, Jupyter notebooks, MultiQC, interactive dashboards
  • Cloud & Automation: AWS (EC2, S3, SageMaker), Docker containerization, workflow automation
  • IDEs & Development Tools: RStudio, Visual Studio Code, Git version control

Laboratory & Instrumentation

  • NGS Platforms: Illumina, Complete Genomics sequencers, full operational proficiency, troubleshooting, protocol optimization
  • Sample Preparation: Library construction (target enrichment, amplicon, GBS, RNA-seq), DNA purification (SPRI), quantification (Qubit), quality assessment (BioAnalyzer)
  • Automation: Biomek i7, Agilent Bravo, Tecan Freedom Evo, Formulatrix Tempest liquid handling robots
  • Molecular Biology: PCR/qPCR optimization, DNA/RNA extraction, gel electrophoresis, fragment analysis
  • High-Throughput Techniques: Liquid handling protocols, multi-well plate optimization, assay validation

Data Management & Compliance

  • LIMS (Laboratory Information Management Systems) integration and data workflows
  • Quality Management Systems (QMS) and Standard Operating Procedure (SOP) documentation
  • Data quality frameworks and regulatory compliance familiarity
  • Project tracking, timeline management, and resource allocation

Software & Platforms

  • Microsoft Office Suite (Word, Excel, PowerPoint), Google Workspace
  • Scientific communication and visualization tools
  • Remote collaboration platforms and tools

PROFESSIONAL ATTRIBUTES & ADDITIONAL INFORMATION

  • U.S. Citizen: no visa sponsorship required
  • Location: St. Louis, Missouri, remote-friendly, flexible to travel (up to 15%) for customer meetings and conferences
  • Work Style: Entrepreneurial mindset with bias for action and clarity; collaborative across cross-functional and geographically distributed teams; self-motivated and detail-oriented
  • Continuous Learning: Committed to staying current with NGS advancements, bioinformatics tools, and industry best practices; active participant in scientific and professional associations
  • Global Collaboration: Proven track record working with diverse, international teams across academia, biotech, and commercial environments