Resume/CV - Rui Guo (grui@sas.upenn.edu) pdf
Education
Ph.D., University of Pennsylvania, Jun 2023 (expected)
- Physical Chemistry - Advisor: Dr. Jeffery Saven; - GPA: 3.90/4.0
- Thesis: Computational engineering of protein features: charge variation, host-guest assembly, and structural motif.
B.S., University of Science and Technology of China, 2016
- Chemistry - Advisor: Dr. Tongwen Xu; GPA: 3.63/4.3
- Awarded Outstanding Student Scholarship for 4 years
- Grade 1 (top 3%) in 2015; Grade 2 (top 10%) in 2013 & 2014; Grade 3 (top 25%) in 2012
Skills
- Programming: intermediate C++ & python (STL data structures, object orienting programming, python libs - numpy, pandas, matplotlib) [6+years]
- Developer tools: Linux Command Line, Git, high-performance cluster maintenance [6+years]
- Computational Protein Design/Engineering
- Extensive knowledge in protein design (sequence prediction) problem. [6+years]
- Practice of implementing an entropy based statistical algorithm in C++ program to solve the protein design problem. [6+years]
- Using Molecular Dynamics Simulations (NAMD) to investigate protein interactions. [6+years]
- Protein visualization and animation with VMD & Pymol (render materials, lighting, electrostatic surfaces, RMSD & heatmap analysis, movie making). [6+years]
- Collaboration with protein experimentalists, applying theoretical models to interpret data (Mass, CD, melting temperature, PI, charge-PH relations). [5+years]
- Bioinformatics/Genomics
- Genomics concepts: blogs on NGS techniques & applications; genetics – exon, intron, splicing; epigenetics- transcription factors, promoters, histone packing, transposons; GWAS, DNM; cell biology; etc.
- Algorithms for DNA sequences: blogs and coding projects of naïve exact match, Boyer-Moore, index assisted matching, edit distance and Smith-Waterman dynamic programming algorithms.
- Common software & data processing: blogs and coding projects regarding SAM/BAM, BED, GFF/GTF, VCF/BCF, FastA/Q files; alignment and variant callings with samtools, bfctools, bedtools.
Publications & Presentations
Guo, R.; Sinha, N. J.; Misra, R..; Tang, Y.; Langenstein, M.; Kim, K.; Fagan, J. A.; Kloxin, C. J.; Jensen, G. V.; Pochan, D. J.; Saven, J. G., Biomacromolecules, 2022, 23, 4, 1652–1661
Sinha, N. J.; Guo, R.; Misra, R.; Fagan, J.; Faraone, A.; Kloxin, C. J.; Saven, J. G.; Jensen, G. V.; Pochan, D. J., J. Colloid Interface Sci. 606 (2022) 1974–1982
Bulos, J. A.; Guo, R.; Wang, Z.; Delessio, M. A.; Saven, J. G.; Dmochowski, I. J., Biochemistry, 2021, 60, 47, 3596–3609
*Yang, Z.; *Guo, R.; Malpass-Evans, R.; Carta, M.; McKeown, N. B.; Guiver, M. D.; Wu, L.; Xu, T., Angew. Chem. Int. Ed., 2016, 55, 11499 –11502 [*co-first authors]
Yang, Z.; Liu, Y.; Guo, R.; Hou, J.; Wu, L.; Xu, T., Chem. Commun., 2016, 52, 2788-2791
Guo, R.; Sinha, N. J.; Misra, R..; Tang, Y.; Langenstein, M.; Kim, K.; Fagan, J. A.; Kloxin, C. J.; Jensen, G. V.; Pochan, D. J.; Saven, J. G., ACS Sprig 2023
Research Experience
2017 - 2023: Graduate Research Associate, University of Pennsylvania
Applying a statistical model to solve the protein design problem, i.e., calculating amino acid sequences that when synthesized, fold into target 3D protein structures, to create proteins that possess desired functionalities, such as high thermal stability, enzyme activity or host-guest assemblies
- Computational Protein Design: 2 projects • 18 designed proteins • 16 confirmed to fold correctly
- Molecular dynamics (MD) simulations: Uncovering unstable interactions in problematic sequences
For details of grad research, please refer to Research page.
2014 - 2016: Undergraduate Researcher, University of Science and Technology of China
- Synthesized 3 microporous anion exchange membranes (crucial component of fuel cells) with exceptional high hydroxide conductivity and chemical stability. At the time of publication, one of the membranes demonstrated the highest conductivity at 80 °C reported in the field.
Leadership, Teaching and Outreach
Computational Lab Manager, Saven Lab - 2018 - 2023
- Mentored 4 graduate students in the knowledge and tools required for our research, including protein design principles & algorithms; the group developed C++ code base; protein visualization & MD simulation software.
- Administrator of the group’s Red Hat Linux based high-performance computing clusters and RAID arrays.
XSEDE Supercomputer Resource Proposal Manager, Saven Lab - 2019 – 2023
- Organizer and main contributor to the group’s annual proposal for the Extreme Science and Engineering Discovery Environment (XSEDE) supercomputing resource allocation.
- Proposal requests were 90% granted in 2022, 100% granted in 2021 and 2020, averaging ~70K CPU & 600K GPU node hrs each year.
Graduate Teaching Assistant, UPenn - Fall 2016 – Spring 2017 & Fall 2019 – Spring 2020
- Rewarded “Commendation for Excellence in Teaching” in 2017 (8 awarded out of 32 TA candidates).
- Teaching courses include General Chemistry I, General Chemistry Lab I & II.
Philadelphia Area Girls Enjoying Science (PAGES) Outreach - Nov 2019
- Contributed to the lecture design and instructed 60+ sixth-grade girls in the outreach, offering them hands-on experiences with science and fostering awareness of scientific career opportunities for women.
Vice Chairman of the Chemistry Student Group, School of Chemistry & Material Science, USTC - 2014 – 2015
- Leader of the group’s technical department, in charge of making posters (~20 posters/year), editing video/audio contents and managing social media accounts for the group’s publicity purposes.
