Cheng-Lin Li
Bioinformatician at SOPHiA GENETICS- Claim this Profile
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Bio
Credentials
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Machine Learning and AI Foundations: Decision Trees
LinkedInDec, 2020- Nov, 2024
Experience
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SOPHiA GENETICS
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Switzerland
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Biotechnology Research
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400 - 500 Employee
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Bioinformatician
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Apr 2021 - Present
• Design and release targeted gene panels and analysis pipelines to effectively identify clinically relevant genomic alterations. • Optimize analysis pipelines to improve analytical performance while reducing total execution time. For instance, I dissected the time-consuming steps in a pipeline for a comprehensive genomic profiling panel. Optimizing the variant calling steps reduced the total execution time by 30% to 50% (24 hours to ~12 hours) without compromising the analytical… Show more • Design and release targeted gene panels and analysis pipelines to effectively identify clinically relevant genomic alterations. • Optimize analysis pipelines to improve analytical performance while reducing total execution time. For instance, I dissected the time-consuming steps in a pipeline for a comprehensive genomic profiling panel. Optimizing the variant calling steps reduced the total execution time by 30% to 50% (24 hours to ~12 hours) without compromising the analytical performance. • Document/review pipeline design, code change, and analytical documents. • Provide support internally and externally: support internal R&D (e.g., improve the detection of Alu insertion) and investigate dry-lab/wet-lab-related issues (e.g., capture bias, off-target, cross-contamination, and hairpin artifacts). • Analyze and summarize various types of NGS data to clients (e.g., SNPs/INDELs, CNV, RNA fusion, microsatellite instability, and Alu insertion). • Help the team identify, test, and release bug fixes for analysis pipelines. (e.g., variant calling, microsatellite instability, tumor mutation burden, fusion, etc.). • Identify bottlenecks and unmet needs in bioinformatics workflows and provide solutions. Show less • Design and release targeted gene panels and analysis pipelines to effectively identify clinically relevant genomic alterations. • Optimize analysis pipelines to improve analytical performance while reducing total execution time. For instance, I dissected the time-consuming steps in a pipeline for a comprehensive genomic profiling panel. Optimizing the variant calling steps reduced the total execution time by 30% to 50% (24 hours to ~12 hours) without compromising the analytical… Show more • Design and release targeted gene panels and analysis pipelines to effectively identify clinically relevant genomic alterations. • Optimize analysis pipelines to improve analytical performance while reducing total execution time. For instance, I dissected the time-consuming steps in a pipeline for a comprehensive genomic profiling panel. Optimizing the variant calling steps reduced the total execution time by 30% to 50% (24 hours to ~12 hours) without compromising the analytical performance. • Document/review pipeline design, code change, and analytical documents. • Provide support internally and externally: support internal R&D (e.g., improve the detection of Alu insertion) and investigate dry-lab/wet-lab-related issues (e.g., capture bias, off-target, cross-contamination, and hairpin artifacts). • Analyze and summarize various types of NGS data to clients (e.g., SNPs/INDELs, CNV, RNA fusion, microsatellite instability, and Alu insertion). • Help the team identify, test, and release bug fixes for analysis pipelines. (e.g., variant calling, microsatellite instability, tumor mutation burden, fusion, etc.). • Identify bottlenecks and unmet needs in bioinformatics workflows and provide solutions. Show less
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Cornell University
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United States
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Higher Education
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700 & Above Employee
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Postdoctoral Associate
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Sep 2016 - Mar 2021
Project: epigenetic mechanisms of aging-associated disorders. • Having wet and dry lab experiences working on various NGS projects (whole-genome sequencing, RNA-seq, small RNA-seq, ATAC-seq, and CUT&RUN-seq etc.). Having dry lab experiences working on 10x Genomics' single-cell RNA-seq (scRNA-seq). • For the first time, apply and optimize the CUT&RUN technique to profile histone modifications in C. elegans somatic tissues. It improves the signal intensity by more than 100% and reduces the… Show more Project: epigenetic mechanisms of aging-associated disorders. • Having wet and dry lab experiences working on various NGS projects (whole-genome sequencing, RNA-seq, small RNA-seq, ATAC-seq, and CUT&RUN-seq etc.). Having dry lab experiences working on 10x Genomics' single-cell RNA-seq (scRNA-seq). • For the first time, apply and optimize the CUT&RUN technique to profile histone modifications in C. elegans somatic tissues. It improves the signal intensity by more than 100% and reduces the number of worms used to 10% compared to typical ChIP-seq experiments. • Investigate aging-associated changes in epigenome and their functional consequences. Discover that the landscape of histone modifications established at the juvenile stage predicts the epigenetic alterations at old age. Show less Project: epigenetic mechanisms of aging-associated disorders. • Having wet and dry lab experiences working on various NGS projects (whole-genome sequencing, RNA-seq, small RNA-seq, ATAC-seq, and CUT&RUN-seq etc.). Having dry lab experiences working on 10x Genomics' single-cell RNA-seq (scRNA-seq). • For the first time, apply and optimize the CUT&RUN technique to profile histone modifications in C. elegans somatic tissues. It improves the signal intensity by more than 100% and reduces the… Show more Project: epigenetic mechanisms of aging-associated disorders. • Having wet and dry lab experiences working on various NGS projects (whole-genome sequencing, RNA-seq, small RNA-seq, ATAC-seq, and CUT&RUN-seq etc.). Having dry lab experiences working on 10x Genomics' single-cell RNA-seq (scRNA-seq). • For the first time, apply and optimize the CUT&RUN technique to profile histone modifications in C. elegans somatic tissues. It improves the signal intensity by more than 100% and reduces the number of worms used to 10% compared to typical ChIP-seq experiments. • Investigate aging-associated changes in epigenome and their functional consequences. Discover that the landscape of histone modifications established at the juvenile stage predicts the epigenetic alterations at old age. Show less
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Baylor College of Medicine
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United States
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Higher Education
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700 & Above Employee
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PhD candidate
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Aug 2010 - Jul 2016
• 2 publications and 4 awards. • Designed and developed the first forward genetic screen and bioinformatics pipeline in Dictyostelium that allow me to both identify and experimentally confirm four novel causative mutations in a year3 compared to only one novel causative mutation in 2 years by the traditional method. The new pipeline improves the gene discovery productivity by eight-fold (8X). • Discovered the roles of protein glycosylation in mediating cell-cell recognition and cell… Show more • 2 publications and 4 awards. • Designed and developed the first forward genetic screen and bioinformatics pipeline in Dictyostelium that allow me to both identify and experimentally confirm four novel causative mutations in a year3 compared to only one novel causative mutation in 2 years by the traditional method. The new pipeline improves the gene discovery productivity by eight-fold (8X). • Discovered the roles of protein glycosylation in mediating cell-cell recognition and cell differentiation. Show less • 2 publications and 4 awards. • Designed and developed the first forward genetic screen and bioinformatics pipeline in Dictyostelium that allow me to both identify and experimentally confirm four novel causative mutations in a year3 compared to only one novel causative mutation in 2 years by the traditional method. The new pipeline improves the gene discovery productivity by eight-fold (8X). • Discovered the roles of protein glycosylation in mediating cell-cell recognition and cell… Show more • 2 publications and 4 awards. • Designed and developed the first forward genetic screen and bioinformatics pipeline in Dictyostelium that allow me to both identify and experimentally confirm four novel causative mutations in a year3 compared to only one novel causative mutation in 2 years by the traditional method. The new pipeline improves the gene discovery productivity by eight-fold (8X). • Discovered the roles of protein glycosylation in mediating cell-cell recognition and cell differentiation. Show less
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Research Assistant
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Feb 2008 - May 2010
Advisor: Dr. Chau-Ti Ting • Performed Quantitative Loci (QTL) mapping for genes that regulate sexual conflict and cryptic female choice across several sister species of Drosophila. I had identified three candidate genetic loci for further investigation. Advisor: Dr. Chau-Ti Ting • Performed Quantitative Loci (QTL) mapping for genes that regulate sexual conflict and cryptic female choice across several sister species of Drosophila. I had identified three candidate genetic loci for further investigation.
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Republic of China Army
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Mental and Physical Health Consulting Center
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Assistant Consultant
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Jan 2007 - Dec 2007
• Helped resolve cases of conflicts and bullying in army. Organized and coordinated the “Spread the Love” campaigns with the international humanitarian organization, Tzu Chi foundation. Our center was awarded "The Best Mental and Physical Health Consulting Center of the Year". Our center was filmed and interviewed by The Ministry of National Defense in Taiwan to share our success. • Helped resolve cases of conflicts and bullying in army. Organized and coordinated the “Spread the Love” campaigns with the international humanitarian organization, Tzu Chi foundation. Our center was awarded "The Best Mental and Physical Health Consulting Center of the Year". Our center was filmed and interviewed by The Ministry of National Defense in Taiwan to share our success.
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Institute of Molecular and Cellular Biology, National Tsing Hua University
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Hsinchu City, Taiwan
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Master's Student
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Sep 2004 - Jul 2006
Advisor: Dr. Chau-Ti Ting • Performed the first Quantitative Loci (QTL) mapping to identify genes that are implicated in cryptic female choice across several sister species of Drosophila. The project had been awarded a three-year research grant (>$100,000) by the Ministry of Science and Technology in Taiwan (2007~2010). Advisor: Dr. Chau-Ti Ting • Performed the first Quantitative Loci (QTL) mapping to identify genes that are implicated in cryptic female choice across several sister species of Drosophila. The project had been awarded a three-year research grant (>$100,000) by the Ministry of Science and Technology in Taiwan (2007~2010).
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Institute of Molecular and Cellular Biology, National Tsing Hua University
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Hsinchu County, Taiwan
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Undergraduate intern
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Jul 2002 - Feb 2003
• Analyzed prevalence of the primary resistance to metronidazole, clarithromycin, and amoxicillin of Helicobacter pylori clinical isolates in Taiwan. • Analyzed prevalence of the primary resistance to metronidazole, clarithromycin, and amoxicillin of Helicobacter pylori clinical isolates in Taiwan.
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Education
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2010 - 2016
Baylor College of Medicine
Doctor of Philosophy (PhD), Molecular and Human Genetics -
2004 - 2006
National Tsing Hua University
Master of Science (MS), Molecular and cellular biology -
2000 - 2004
National Tsing Hua University
Bachelor of Science (BS), Biology, General
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