Weichen Huang
Chelsea,MA
Summary
Expert in bioinformatics, RNA Chemistry & LC-MS Analytics | Postdoc at Tufts University
Overview
8
8
years of professional experience
Work History
Postdoctoral Research Associate
Tufts University
07.2024 - Current
- Spearheading LC-MS/MS–based mapping of tRNA modifications, with emphasis on anticodon loop structures critical for translational regulation in neurons.
- Isolated individual tRNAs from Aplysia neurons using DNA-probe capture, followed by enzymatic digestion and mass spectrometry to pinpoint modified nucleosides and map their positions.
- Developed innovative RNA labeling strategies (e.g., DNA oligo ligation) to enhance MS sensitivity and enable multiplexing of low-abundance targets.
- Produced and purified large RNA species (e.g., 18S rRNA) via in vitro transcription and size-exclusion chromatography, supporting reference standards and control assays for RNA-based analytics.
- Advanced platform methods applicable to functional and structural characterization of therapeutic RNAs in neurobiology and precision medicine.
Postdoctoral Research Associate
New York Institute of Technology - NY New York
06.2023 - 05.2024
- Developed a novel direct RNA sequencing method using Orbitrap high-resolution LC-MS and acid hydrolysis laddering to read RNA sequences and locate chemical modifications.
- Optimized ion-pairing reversed-phase HPLC workflows to enhance separation and spectral resolution for fragments of up to 100 nt.
- Pushed detection limit to 10 pmol for RNAs ~160 nt in length—advancing utility for therapeutic RNA analytics and epi-transcriptomics.
- Conducted monoisotopic mass deconvolution, enabling modification profiling across RNA ladders in a 2D LC-MS dataset (mass vs. elution time).
- Contributed to extending sequencing read length and reducing analytical noise, positioning the platform for applications in RNA drug QC and structural characterization.
Graduate Research Assistant
Pennsylvania State University State College
08.2017 - 05.2023
- Led a large-scale phylogenomic analysis of the Poaceae (grass) family, assembling and mining over 300 transcriptomic and genomic datasets to resolve evolutionary relationships and reconstruct the history of C₄ photosynthesis.
- Built custom pipelines for de novo transcriptome assembly, orthologous gene identification, and gene tree generation, integrating tools for supermatrix and coalescent phylogeny reconstruction.
- Applied extensive bioinformatics workflows across NGS datasets, combining scripting, high-performance computing, and large-scale data automation.
- Developed strong expertise in gene family analysis, RNA data extraction, sequence alignment, and comparative genomics.
Education
Ph.D. - Biology
The Pennsylvania State University
State College, PA05.2023
Bachelor of Science - Biotechnology
Zhejiang University
Hangzhou, China06.2017
Skills
- Analytical methods for oligonucleotide quality assessment
- HPLC and LC-MS expertise
- Bioinformatics analysis on NGS data, including transcriptomics and genomics Automation of large-scale data analysis on Linux system or using web-based applications
- Oligonucleotide purification from various samples
- PCR/RT-PCR, in vitro transcription of RNA
Publications
- A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C4 photosynthesis. Weichen Huang, L. Zhang, J. Columbus, Y. Hu, Y. Zhao, L. Tang, Z. Guo, W. Chen, M. McKain, M. Bartlett, C. Huang, D. Li, S. Ge, H. Ma. 2022, Molecular plant.
- Phylotranscriptomics Resolves the Phylogeny of Pooideae and Uncovers Factors for Their Adaptive Evolution. L. Zhang, X. Zhu, Y. Zhao, J. Guo, T. Zhang, Weichen Huang, J. Huang, Y. Hu, C. Huang, H. Ma. 2022, Molecular biology and evolution.
- Isolation, Identification and Characteristics of a Salt-Tolerant Autotrophic Ferrous-Dependent Denitrifying Bacterium. Wang, R., Ye, Z., Huang, Weichen., Xu, S. Y., Dai, C. L., Liang, L. Y., and Zheng, P. 2017, Gao Xiao Hua Xue Gong Cheng Xue Bao/Journal Chem. Eng. Chinese Univ. 31:456–462.
- Phylogenomic Profiles of Whole-Genome Duplications in Poaceae and Landscape of Differential Duplicate Retention and Losses among Major Poaceae Lineages. Taikui Zhang, Weichen Huang, Lin Zhang, De-Zhu Li, Ji Qi, Hong Ma. 2024, Nat Communications.
Languages
English
Full Professional
Chinese (Mandarin)
Native or Bilingual
Timeline
Postdoctoral Research Associate
Tufts University
07.2024 - Current
Postdoctoral Research Associate
New York Institute of Technology - NY New York
06.2023 - 05.2024
Graduate Research Assistant
Pennsylvania State University State College
08.2017 - 05.2023
Ph.D. - Biology
The Pennsylvania State University
Bachelor of Science - Biotechnology
Zhejiang University
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