Sarah Huang - Research Associate

Sarah Huang

Research Associate

Boston, Massachusetts, United States

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Summary

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Rockstar

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Top School

Sarah Huang is a research associate based in Boston with a decade of hands-on experience across molecular neuroscience and computational genomics. She studies prefrontal cortex development and the role of human complement factor C4A in schizophrenia risk using single-nucleus RNA-seq, murine models, and gene-editing approaches. Her background spans labs in Boston and Taipei, with deep technical expertise in cell culture, DNA/RNA/protein quantification, and transcriptomic analysis. Beyond wet lab work, she has contributed backend code and architecture to major open-source genomics tools (notably GATK and htsjdk), improving structural variant detection and VCF handling for high-throughput sequencing pipelines. This blend of experimental neuroscience and production-quality bioinformatics gives her a rare ability to translate complex biological questions into robust computational workflows. Colleagues describe her as a pragmatic problem-solver who bridges cross-disciplinary teams to move reproducible science forward.

10 years of coding experience

3 years of employment as a software developer

High School Diploma, High School Diploma at Taipei American School

Bachelor of Science - BS, Human Physiology, Bachelor of Science - BS, Human Physiology at Boston University

Chinese

Github Skills (19)

variants10

architecture10

testing10

vcf-files10

java10

javas10

bioinformatics10

genomics10

architectures10

data-structure9

spark9

biom9

algorithm9

unit-testing9

algorithms9

Programming languages (24)

JavaC++CRustDTeXMakefileScala

Github contributions (5)

broadinstitute/gatk

Feb 2016 - Aug 2020

Official code repository for GATK versions 4 and up

Role in this project:

Back-end Developer & Software Architect

Contributions:160 commits, 217 PRs, 1141 pushes in 4 years 6 months

Contributions summary:Sarah's primary contribution focuses on implementing and integrating various functionalities related to structural variant (SV) calling within the GATK framework. They developed and maintained tools for local assembly, breakpoint detection, and variant calling, including modifications to the alignment and variant interpretation steps. The user also added new features, improved annotation, and refactored existing code, suggesting a strong understanding of the software architecture and its internal workings. Their work impacted the processing of contigs, identifying potential SVs, and ensuring the accuracy and reliability of the variant calling pipeline.

genomesciencednaspark-mlngs

samtools/htsjdk

Jun 2016 - Jul 2019

A Java API for high-throughput sequencing data (HTS) formats.

Role in this project:

Back-end Developer & QA Engineer

Contributions:8 commits, 9 PRs, 51 comments in 3 years

Contributions summary:Sarah primarily contributed to the back-end aspects of the project, focusing on the Java API. They fixed a bug in the VCFStandardHeaderLines related to a header line count and updated unit tests for the same class. They also implemented new methods within the SAMRecord class and fixed a copy-paste error in VCFHeader. Further, they fixed a NullPointerException in GenotypeJEXLContext and added tests for JEXL contexts. Finally, they implemented a check for negative lengths in the CigarElement constructor and added associated tests.

sequencednabamcramsequencing-data

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