Yuehe Ding
CRISPR, Aging, RNAi, LC-MS/MS, Proteomics, NGS
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About
Biological researcher with 15 years of research experiences including four years in Aging, five years in Protein Mass spectrometry and seven years in Small RNA biology and RNAi. In total, I have 8 publications in Nature Cell Biology, Elife, Cell reports, JBC, Analytical Chemistry etc. as first or co-first author and 25 additional publications as co-authors. Experienced in project management, experiment design, data analysis, data presentation and publication.
Skilled in Biochemistry, Molecular biology, Genetics and computer science as below.
Biochemistry – HPLC ,UPLC,Proteomics, LC-MS/MS, Protein Mass spec, Protein Posttranslational Modifications (PTM) analysis, Protein Expression and Purification, Kinase Assay, Western Blot, Silver Staining, SDS-PAGE, etc.
Molecular biology – DNA/RNA Next Generation Sequencing, Genome Sequencing, Small RNA Cloning and Sequencing, NGS, RNA/DNA FISH, Confocal Microscopy, CHIP, RT-qPCR, Northern Blot, Molecular Cloning, etc.
Genetics – CRISPR Genome Editing, C. elegans, Transgenic worms, MosSCI, RNAi, Genetic Screening, Genotyping, etc.
Computer science – Data analysis, R, Perl, Image J, Microsoft office, Adobe illustrator, etc.
Experience
Instructor 02/2023-now | UMass Chan Medical School, Worcester, US
Post-doctoral Associate 02/2016-01/2023 | UMass Chan Medical School, Worcester, US
Advisor: Craig C. Mello, Laureate of Nobel Prize in 2006 for Discovering RNAi
- Developed C-BERST to define subnuclear proteomic landscapes at specific genomic loci using dCas9-APEX2.
- Identified HDA-1 and SUMO as novel regulators of the piRNA pathway through genetic screening.
- Identified HDA-1 SUMOylation sites and demonstrated that this modification is critical for its complex assembly and recruitment by the piRNA pathway.
- Demonstrated the SUMO E3 ligase-like activity of PIE-1, through quantitative SUMO proteomics.
- Developed a protein-RNA tethering system, which led to the discovery of a self-enforcing mechanism of the piRNA pathway.
- Applied next-generation sequencing strategies, including mRNA seq, genome seq, and small RNA seq, to study the silencing mechanism of the piRNA pathway.
- Mentored PhD students to achieve their academic goals.
Advisor: Meng-Qiu Dong, Postdoc of John Yates III, Pioneer of Protein Mass Spec and Proteomics
- Introduced amine-sulfhydryl and amine-carboxyl cross-linkers to increase the depth of cross-linking mass spectrometry and applied that information for modeling protein-protein interaction.
- Developed arginine-selective chemical cross-linkers to improve mass spec analysis of protein structures.
- Modeled protein excited-state structures from "over-length" chemical cross-links.
- Developed DynaXL to visualize the ensemble structures of protein complexes using spatial information obtained from cross-linking mass spectrometry.
- Developed open-pFind, an open search engine for comprehensive identification of peptides from ms2 spectra.
- Identified STIMATE as a regulator of Ca2+ influx by proteomics mapping of ER-PM junctions using proximal labeling (APEX).
- Applied cross-linking mass spectrometry to study complex assembly, including exocyst complex, ATG2B-WDR45 complex, PI3KC3 complex, etc.
- Identified phosphorylation sites of LSD1 by PLK1 and MYPT1 by Chk1 with HRAM MS and HCD fragmentation.
- Identified O-GlcNAcylation sites of Polη during translesion DNA synthesis with HRAM MS and HCD fragmentation.
Education
Advisor: Meng-Qiu Dong, Postdoc of John Yates III, Pioneer of Protein Mass Spec and Proteomics
- Studied the functions of a gene family that were highly increased in the long-lived daf-2 mutant.
- Discovered the crosstalk between CAMKII/Calcineurin and the insulin pathway in lifespan regulation.
- Identified the Actin K84me by ALKBH4 using Mass spectrometry.
- Conducted quantitative proteomics, PTM identification and developed CXMS methods to elucidate protein structures.
- Developed cross-linking mass spectrometry methods to study protein folding and protein-protein interactions.
- Developed search engine pLink to identify cross-linked peptides from complex samples after cross-linking.
- Developed high-speed cross-linking search engine pLink2 which is 40 times faster than pLink1.
