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Yi-Kuo Yu, PhD


Research Interests

As a theoretical physicist working in biology, I have always been fascinated by the functional and organizational complexity achievable in a myriad of diverse organisms, all of which share a universal set of building blocks (water, ions, saccharides, fatty acids, amino acids, nucleotides and other small molecules). Despite vast amounts of effort invested, our current understanding of biology, ranging from a microscopic level to a more macroscopic level, is far from complete. For example, in terms of molecular interactions, phenomenological treatments at the intra- and inter-protein level have not yet fostered an effective theory capable of predicting how proteins fold and how a protein complex organizes itself. Namely, a proper coarse-graining procedure to bring out only the relevant degrees of freedom is lacking. This may be due to our insufficient understanding of biology in terms of relevant physics and chemistry, or it may be because the search for higher organizing principles is hindered by our inability to bring out information buried in noise and/or by conflicting interpretations of data. Developing methods to improve information extraction and establishing a firm foundation at the microscopic level are essential. Our approach to mitigate the issue of noise (or conflicting information) is to devise data analysis methods that can assign accurate statistical significance to signals identified; our take on building a firm foundation at the microscopic level is via development of calculation methods whose accuracy can be controlled. All our research efforts center about these two main emphases.


Alves G, Yu Y. Robust Accurate Identification and Biomass Estimates of Microorganisms via Tandem Mass Spectrometry. J Am Soc Mass Spec. 2020 January; 31(1):85-102. doi: 10.1021/jasms.9b00035.

Hamaneh MB, Yu YK. Exploring induced pluripotency in human fibroblasts via construction, validation, and application of a gene regulatory network. PLoS One. 2019;14(8):e0220742. doi: 10.1371/journal.pone.0220742. eCollection 2019. PubMed PMID: 31374103; PubMed Central PMCID: PMC6677386.

Yu YK. Electrostatics of charged dielectric spheres with application to biological systems. II. A formalism bypassing Wigner rotation matrices. Phys Rev E. 2019 Jul;100(1-1):012401. doi: 10.1103/PhysRevE.100.012401. PubMed PMID: 31499794.

Ogurtsov AY, Alves G, Yu YK. RAId: Knowledge-Integrated Proteomics Web Service with Accurate Statistical Significance Assignment. Proteomics. 2019 Jul;19(14):e1800367. doi: 10.1002/pmic.201800367. PubMed PMID: 30908818; PubMed Central PMCID: PMC6635056.