Lifeng Lin, PhD's Resume

Highlights

14+ years of experience delivering robust point-of-care assays across multiple disciplines: infectious diseases, cancer early-detection and immune repertoire
Experienced with various technology platforms: NGS, qPCR, single-cell, microarray
Built successful bioinformatics functions to support efficient assay development
Led a team to work cross-functionally in fast-paced projects

Experience

Principal Scientist - Bioinformatics - Cepheid inc. (A Danaher Company)

Duration: 2020.10 - present

Managed Bioinformatics Engineering team, overseeing server setup, code repository organization, and workflow automation
Built bioinformatics libraries for assay development (Python, AWS)
Created a company-wide bioinformatics web portal for assay storage and evaluation (Flask, MySQL, Docker, nginx)
Set up a Galaxy server for automated workflows
Advised company leadership on bioinformatics aspects for decision-making
Developed thermodynamic predictive models for special nucleotides

Reason for termination: None - still working here.

Data Scientist III - Bio-Rad Laboratories

Duration: 2019.04 - 2020.10

Maintained the performance of the Digital Assay Design Engine
Led design engine updates for the Digital Assays customer portal
Designed in-house infectious disease assays

Reason for termination: Resigned for a better career opportunity at Cepheid.

Panel Design Lead / System Admin - Paragon Genomics

Duration: 2017.12 - 2019.04

Built ParagonDesigner, an online portal to track custom design requests (WordPress + PHP + Python)
Created a pipeline that removed bottlenecks in RNA expression assay design (Bash + Python + R)
Set up and maintained AWS clusters for data analysis
Administered company website, FTP, and data analysis servers
Repackaged NGS data processing pipeline for inexperienced customers (Snakemake + Anaconda + Python)

Reason for termination: Relocated for family reasons.

Staff Scientist (Promoted from Scientist III) - Thermo Fisher Scientific

Duration: 2015.04 - 2017.12

Led the design of non-standard panels, including Immune Repertoire (patent pending) and plant barcoding
Improved design of custom human NGS panels for FDA submissions
Wrote design pipelines for bacterial and viral target analysis

Reason for termination: Joined Paragon to help a colleague with a startup.

Senior Bioinformatics Scientist - Nanosphere inc (A Luminex Company)

Duration: 2010.6 - 2015.4

Performed genome analysis for target pathogens
Developed sequence databases for over 500 organisms
Led the design of Verigene Enteric Pathogen panels (Virus, bacteria, and parasites)
Co-designed Verigene Respiratory Pathogen assays and Blood Sepsis assays
Built automated pipelines and portals

Reason for termination: Relocated to California from Illinois.

PhD Student / Research Assistant - University of Georgia, Plant Genome Mapping Lab (PGML)

Duration: 2003.8 - 2010.5

Reason for termination:

Patents

Compositions and Methods for Immune Repertoire Sequencing

Date: Filed Jan 17th, 2018 | ID: WO2020018836

Inventors: Timothy Looney, Geoffrey Lowman, Lifeng Lin

Publications

Research Gate Profile: http://www.researchgate.net/profile/Lifeng_Lin/publications

Journal Publications

Paterson, A. H., J. F. Wendell, et al. (2012). “Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.”
Nature 492 : 423-427.
Lin, L., A. H. Paterson (2009). “Physical composition and organization of the Gossypium genomes.”
Genetics and Genomics of Cotton .
Lin, L., A. H. Paterson (2011). “Size variation in homologous segments across divergent plant genomes.”
Mob Genet Elements 1 : 92-96.
Lin, L., G. J. Pierce, et al. (2010). “A draft physical map of a D-genome cotton species (Gossypium raimondii).”
BMC Genomics 11 : 395.
Lin, L., H. Tang, et al. (2011). “Comparative analysis of Gossypium and Vitis genomes indicates genome duplication specific to the Gossypium lineage.”
Genomics 97 : 313-320.
He, S., Y. Zheng, et al. (2013). “Converting restriction fragment length polymorphism to single-strand conformation polymorphism markers and its application in the fine mapping of a trichome gene in cotton.”
Plant Breeding 132 : 337-343.
Paterson, A. H., J. E. Bowers, et al. (2009). “Comparative genomics of grasses promises a bountiful harvest.”
Plant Physiol 149 : 125-131.
Paterson, A. H., B. K. Mashope, L. Lin (2009). “The Comparative Genomics of Orphan Crops.”
ATDF Journal 6 : 16-23.
Rong, J., F. A. Feltus, L. Lin, et al. (2010). “Gene copy number evolution during tetraploid cotton radiation.”
Heredity (Edinb) 105 : 463-472.
Wang, X., M. J. Torres, et al. (2011). “A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations.”
BMC Genomics 12 : 470.
Ding, M., J. Chen, et al. (2014). “Genome-wide investigation and transcriptome analysis of the WRKY gene family in Gossypium.”
Molecular Genetics and Genomics .
Ding, M, Y. Jiang, et al. (2013). “Gene expression profile analysis of Ligon lintless (Li1) mutant reveals important insights.”
Unknown .

Conference Appearances

Lucie Li, Lily Liu, Jacey Zhang, Jeffery Liu, Lifeng Lin, Guoying Liu, Zhitong Liu (2018). “Detecting low allele frequency somatic mutations using targeted amplicon sequencing and a novel double strand molecular barcoding scheme.”
AACR Annual Meeting 2018 .
Timothy Looney, Geoffrey Lowman, Elizabeth Linch, Denise Topacio, Lauren Miller, Lifeng Lin, Aleksandr Pankov, Janice Au-Young, Mark Andersen, Ann Mongan, Fiona Hyland (2017). “Tracking the interplay between circulating and tumor-infiltrating T cells using AmpliSeq-based Ion Torrent TCRβ immune repertoire sequencing.”
, Journal of Clinical Oncology 35 : e14518.
Ann Mongan, Geoffrey Lowman, Yuan-Chieh Ku, Timothy Looney, Lifeng Lin, Xinzhan Peng, Fiona Hyland (2017). “Using NGS to characterize 40 NSCLC tumor with gene expression and tumor infiltrating T cell repertoire profiling from FFPE and matched Fresh Frozen samples.”
Proceedings of the American Association for Cancer Research Annual Meeting 2017 .
Denise S. Topacio-Hall, Tim Looney, Yongming Sun, Lauren Miller, Elizabeth Linch, Geoffrey Lowman, Lifeng Lin, Mark Andersen, Fiona Hyland, Ann Mongan (2017). “Sequencing the human TCRβ repertoire on the Ion S5™ System.”
, Cancer Research 77 .
S. Marla, M. Dado, C. Gerstein, et al. (2013). “Development of Nanosphere’s Verigene BC-GN Test for rapid detection of Gram-negative bacteria and resistance determinants directly from positive blood cultures.”
23rd European Congress of Clinical Microbiology and Infectious Diseases .
Lin, L., Rong, J., Paterson, A.H. (2009). “Progress toward cloning a gene involved in cotton fiber development (Ligon lintless-2, Li2) with the assistance of genetically anchored BAC libraries.”
Large Insert DNA Libraries and Their Applications Workshop at Plant & Animal Genome XVII .
Lifeng Lin, Gary Pierce, John E. Bowers, et al. (2010). “A Draft Physical Map of a D-genome Cotton Species (G. ramondii).”
Plant & Animal Genome XVIII .
Tang, H., Lin, L., Bowers, J.E., Rong, J., Paterson A.H. (2006). “Large Scale EST Resource Compilation and Applications for Phylogenomics of Major Crop Plants.”
Annual SMBE Meeting 2006 .
Lin, L., Pierce, G., Bowers, J.E., et al. (2007). “Progress toward a fingerprinted physical map of D genome cotton G. raimondii.”
Plant & Animal Genome XV .

Public Profiles

Education

PhD - University of Georgia (2010)

B.S. - Fudan University (2003)

Certifications

HarvardX: PH525.2x Linear Models and Matrix Algebra (2016)
HKUSTx: COMP102.1x Introduction to Java Programming (2016)
The Data Scientist's Toolbox (2015)
R Programming (2015)
Design Control Concepts and Implementation Workshop (2014)
MITx: 6.00.2x Introduction to Computational Thinking and Data Science (2014)
MITx: 6.00.1x Introduction to Computer Science and Programming Using Python (2014)
UC-Davis Bioinformatics Training Program (2014)
Excellence in Documentation of Teaching Proficiency (2010)