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zeqian-li-resume.tex
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%-------------------------
% Based on Sourabh Bajaj's template (https://github.com/sb2nov/resume). Credit to him.
%-------------------------
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%-------------------------------------------
%%%%%% CV STARTS HERE %%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{document}
%----------HEADING-----------------
\begin{tabular*}{\textwidth}{l@{\extracolsep{\fill}}r}
\textbf{\href{https://zeqianli.me}{\Large Zeqian Li}} & [email protected] $\mid$ 217-377-7442
\vspace{-10pt}
\end{tabular*}
% & \href{https://zeqianli.me}{https://zeqianli.me}
%-----------EDUCATION-----------------
\section{Education}
\resumeSubHeadingListStart
% \resumeSubheading
% {Graduate Research Assistant}{University of Chicago}{Chicago, IL}{Expected July 2023}
% \vspace{3pt}
% \vspace{-12pt}
% \resumeSubheading
% {Graduate Research Assistant}{University of Chicago}{Chicago, IL}{Expected July 2023}
% \vspace{3pt}
% % \vspace{-12pt}
\resumeSubheading
{Ph.D in Physics}{University of Illinois at Urbana-Champaign}{Champaign, IL}{Aug 2018 - Aug 2023}
\resumeItemListStart
\item Center for Physics of Living Cells Fellow (\textit{2018 - 2020})
\resumeItemListEnd
\vspace{-2pt}
\resumeSubheading
{B.S in Green Energy Science}{Hong Kong Baptist University}{Hong Kong}{Sep 2014 -- July 2018}
\resumeItemListStart
\item Hong Kong Special Administrative Region Government Scholarship (\textit{2015 - 2018})
\item Scholastic Award (\textit{2018})
% \end{tabular*}\vspace{-5pt}
\resumeItemListEnd %\vspace{-10pt}
\vspace{-2pt}
\resumeSubHeadingListEnd
\vspace{-10pt}
%-----------EXPERIENCE-----------------
%-----------Publications----------------
\section{Research and Professional Experience}
\resumeSubHeadingListStart
\resumeSubheading
{BillionToOne}{Senior Bioinformatics Scientist, Oncology}
{CA}{Aug 2023 - Present}
\resumeItemListStart
\resumeItem{}{Joined as the first bioinformatic scientist in BillionToOne oncology and built the bioinformatics roadmap for BillionToOne liquid biopsy assays, Northstar Select and Northstar Response}
\resumeItem{}{Coordinated a 30+ people cross-functional CLIA laboratory to process 2000+ clinical samples. Regularly conducted custom NGS data analysis, performed quality control, and troubleshooted wet-lab processes}
\resumeItem{}{Launched Northstar Response V1.1, a bioinformatic enhancement that boosted performance by 5x}
\resumeItem{}{Launched Northstar Select Nextflow pipeline (3x faster) and reduced turnaround-time by 1 day}
\resumeItem{}{Launched a full-stack oncology data dashboard web-app (NiceGUI, AWS)}
\resumeItem{}{Led continuous algorithm development for the Northstar products (MSI caller, CNV caller, QC metrics)}
\resumeItem{}{Led continous software development to scale-up sample processing capacity by $>$100X}
\resumeItem{}{Grew the bioinformatics team by 6X. Facilitated hiring of 15+ full-time roles in BillionToOne.}
\resumeItem{}{Worked with executive team in decision-making, facilitated commercial growth, and delivered accurate results to 2000+ cancer patients}
\resumeItemListEnd
\resumeSubheading
{Seppe Kuehn lab (University of Chicago / UIUC)}{Research Assistant}
{IL}{July 2019 - July 2023}
\resumeItemListStart
\resumeItem{Experimental design:}{Designed and conducted end-to-end genotyping (shotgun whole-genome sequencing) and phenotyping (carbon utilization assay) experiments on $100+$ novel environmental microbes}
\resumeItem{Statistical modeling:}{Used machine learning to achieve state-of-the-art prediction of microbial carbon utilization, combining experimental data and large-scale web-scrapped datasets with over $4000$ bacterial genomes}
\resumeItem{Bioinformatics:}{Built custom bioinformatic pipelines (Snakemake) on high-performance computing clusters to analyze over $10$TBs of multi-omics NGS data spanning more than $1000$ samples}
\resumeItem{Theoretical modeling:}{Created accurate mathematical models for two systems (microbial respiration/photosynthesis and buffering capacity of complex biological media) and validated the models in experiments}
\resumeItem{Hardware:}{Constructed microcontroller-based (Raspberry Pi) experimental devices and troubleshot Python-based software to interface sensors, PID controllers, and other electronic components}
\resumeItemListEnd
\resumeSubheading
{Upward Farms}{Microbial Research Associate}{Brooklyn, NY}{May 2022 - Aug 2022}
\resumeItemListStart
\resumeItem{Research:}{Led end-to-end experiment to improve hydroponic crop yields by plant microbiome maniputation. Used statistical modeling and 16S sequencing to identify potential plant growth-promoting bacteria}
\resumeItem{Production-level software:}{Prototyped two production software in AWS: a NGS annotatation pipeline (Snakemake) and a R\&D experiment management web portal}
\resumeItem{Experiments:}{Performed Nanopore long-read sequencing with the R\&D team to profile hydroponic metagenome}
\resumeItem{Other wet lab experiments:}{Contributed to other R\&D experiments in crop phenotyping and sample collection}
\resumeItemListEnd
\resumeSubheading
{Hong Kong Baptist University}{Research Assistant}
{Hong Kong}{July 2015 - June 2018}
\resumeItemListStart
\resumeItem{Computational modeling:}{Built novel machine learning models based on biological neural networks and non-equilibrium statistical physics to conduct signal computation}
\resumeItem{}{Implemented novel optimization algorithms in C\texttt{++} and Python to model \textit{C. elegans} neurons}
\resumeItem{Data-driven research:}{Collaborated in three data-driven projects with interdisciplinary teams spanning four research labs}
\resumeItemListEnd
\resumeSubHeadingListEnd
\vspace{-10pt}
%--------PROGRAMMING SKILLS------------
\section{Skills}
\resumeSubHeadingListStart
\resumeSubItem{Full-stack bioinformatics:}{Nextflow, NGS (amplicon, target enrichment,whole-genome sequencing, UMI); extraction, library prep, common wet lab; microcontrollers (Arduino, Raspberry Pi)}
\resumeSubItem{Full-stack data science:}{machine learning, statistics, high-dimensional data analysis; data engineering, dashboards (NiceGUI/Dash), databases (Postgresql); AWS, Django, REST APIs, CI/CD, Git; Python, Rust, SQL, R, Bash, Java, Groovy, JavaScript, C/C++, \LaTeX; project management}
\resumeSubItem{Computational biology:}{cancer biology, liquid biopsy, statistical physics}
\resumeSubHeadingListEnd
\section{Other Experience}
\resumeSubHeadingListStart
\vspace{-1pt}\item[]
\begin{tabular*}{0.97\textwidth}[t]{l@{\extracolsep{\fill}}r}
\textbf{The Abdus Salam International Centre for Theoretical Physics} & {\textit{Mar 2018}} \\ Spring College on the Physics of Complex Systems (Trieste, Italy) &
\end{tabular*}\vspace{-5pt}
\resumeItemListStart
\resumeItem{Coursework:}{Completed graduate-level courses with the highest grade in reinforcement learning, statistical physics, protein biophysics, and computational neuroscience}
\resumeItemListEnd
\resumeSubheading
{Iowa State University}{Exchange Student}
{Ames, Iowa, United States}{August 2016 - December 2016}
% \resumeItemListStart
% \resumeItem{}{Completed coursework in physics, mathematics, and computer science.}
% \resumeItemListEnd
\resumeSubheading
{Hong Kong Baptist University}{Teaching Assistant}
{Hong Kong}{July 2016 - June 2018}
% \resumeItemListStart
% \resumeItem{}{Taught discussion sessions of Introduction to Physics for two semesters}
% \resumeItemListEnd
\resumeSubHeadingListEnd
\section{Publications}
\resumeSubHeadingListStart
\item[] Xavier Bower, Jan Wignall, Joyce Zhu, Michael O’Sullivan, Naomi E. Searle, Lenny K. Hong, Matthew G. Varga, Tiffany E. Farmer, Emilio Rosas-Linhard, \textbf{Zeqian Li}, Jason Luong, Esther Lin, Marie Erica Simon, David S. Tsao, John R. ten Bosch, Gary Palmer MD, Ajeet Gajra MD, Chanh Huynh MD, Wen Zhou ``Validation of a liquid biopsy assay with increased sensitivity for clinical comprehensive genomic profiling.'' \textit{Manuscript submitted for publication.} (2024)
\item[] Hsiao, Angela, Brian Woodward, Patrick Ye, Matthew G. Varga, Ghaith Altaie, Kevin Lu, Naomi Searle, Robb Viens, Sydne Langpap, \textbf{Zeqian Li}, Gary Palmer, Hatim Husain ``Brief Report: Methylation-Based ctDNA Serial Monitoring Correlates with Immunotherapy Response in NSCLC.'' \textit{Clinical Lung Cancer} (2024).
\item[] \textbf{Zeqian Li}, Ahmed Selim, Seppe Kuehn. ``Statistical prediction of microbial metabolic traits from genomes.'' \textit{PLOS Computational Biology} 19.12 (2023): e1011705.
\item[] Kyle Crocker, Milena Chakraverti-Wuerthwein, \textbf{Zeqian Li}, Madhav Mani, Karna Gowda, Seppe Kuehn. ``Genomics patterns in the global soil microbiome emerge from microbial interactions.'' \textit{Nature Microbiology} (2024): 838-853.
\item[] Chandana Gopalakrishnappa, \textbf{Zeqian Li}, Seppe Kuehn. ``Environmental modulators of algae-bacteria interactions at scale.'' \textit{Cell Systems} 15.9 (2024): 838-853.
\item[] \textbf{Zeqian Li}, Vaibhhav Sinha, and Seppe Kuehn. "Constraints on microbial metabolic complexity." \textit{Nature Microbiology} 8.10 (2023): 1756-1757.
\item[] Luis Miguel de Jesús Astacio$^*$, Kaumudi H. Prabhakara$^*$, \textbf{Zeqian Li}, Harry Mickalide, Seppe Kuehn. ``Closed microbial communities self-organize to persistently cycle carbon.'' \textit{Proceedings of the National Academy of Sciences} 118, no. 45 (2021): e2013564118.
\resumeSubHeadingListEnd
\section{Selected conference presentations}
\resumeSubHeadingListStart
\item[] \textbf{Speaker:} Microbiome Research Symposium, The University of Chicago, ``Machine learning predicts microbial metabolic traits from genomes.'' (2023)
\item[] \textbf{Speaker:} The American Physical Society March Meeting, ``Unique functional structure of the Yellowstone hot spring microbial mats revealed by multi-omics studies.'' (2022)
\item[] \textbf{Speaker:} The Yellowstone Hot Spring Microbial Mats Symposium, Carnegie Institution for Science, ``Co-expression constrains genome organization in an extensively recombined microbial population.'' (2022)
\resumeSubHeadingListEnd
%-------------------------------------------
\end{document}