Yuping Li
Stanford University
9 Papers
4 Citations
Yuping Li is an academic researcher from Stanford University. The author has contributed to research in topics: Adaptation & Evolutionary dynamics. The author has an hindex of 6, co-authored 9 publications. Previous affiliations of Yuping Li include Chinese Academy of Sciences & University of California, San Francisco.
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Papers
Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast
Sandeep Venkataram,Barbara Dunn,Yuping Li,Atish Agarwala,Jessica Chang,Emily R. Ebel,Kerry Geiler-Samerotte,Lucas Hérissant,Jamie R. Blundell,Jamie R. Blundell,Sasha F. Levy,Daniel S. Fisher,Gavin Sherlock,Dmitri A. Petrov +13 more
TL;DR: A DNA barcoding approach was used to generate the genotype-to-fitness map for adaptation-driving mutations from a Saccharomyces cerevisiae population experimentally evolved by serial transfer under limiting glucose to determine that there are significant differences in fitness between mutations in different genes, between different paralogs, and even between different classes of mutations within the same gene.
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Single nucleotide mapping of trait space reveals Pareto fronts that constrain adaptation
TL;DR: Dense sampling and precise measuring of performance of adaptive mutations in evolving yeast shows that while many such mutations result in modest improvements in multiple traits, the totality of the data reveals the existence of trade-offs even during initial adaptation.
101
Hidden Complexity of Yeast Adaptation under Simple Evolutionary Conditions
Yuping Li,Sandeep Venkataram,Atish Agarwala,Barbara Dunn,Dmitri A. Petrov,Gavin Sherlock,Daniel S. Fisher +6 more
TL;DR: The results reveal hidden complexities of the adaptive process even under ostensibly simple evolutionary conditions, in which fitness gains can accrue during time spent in a growth phase with little cell division, and reveal that the memory of those gains can be realized in the subsequent growth cycle.
84
Anti-CRISPRs go viral: The infection biology of CRISPR-Cas inhibitors
TL;DR: In this paper, a framework of phage autonomy was proposed to evaluate CRISPR-immune evasion strategies, where a community of acr-carrying phages cooperated to suppress bacterial immunity.
55
Changes in the distribution of fitness effects and adaptive mutational spectra following a single first step towards adaptation
TL;DR: In this article, the authors study the extent of diminishing returns and the changes in the adaptive mutational spectra following a single first adaptive step and show that adaptive loss-of-function mutations such as nonsense and frameshift mutations are less common in the second step of adaptation than in the first step.