About yuehe ding:
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.
Post-doctoral Researcher 07/2012-02/2016 | National Institute of Biological Sciences, Beijing, China
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.
B.S. |Biotechnology | University of Science and Technology of China (USTC), China | 09/2003– 07/2007
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