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您的检索式：作者名="Shanjun Deng"
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| 1 | Mutation signatures inform the natural host of SARS-CoV-2显示文摘The origin of SARS-CoV-2,the causative virus of COVID-19,has been a mystery since the beginning of the outbreak and has been heavily debated lately.One of the main reasons for this is that RaTG13,the closest relative found to date[1](in the horseshoe bat Rhinolophus affinis),has only 96.1%nucleotide similarity to SARS-CoV-2(with~1200 nucleotide differences). | Shanjun Deng Ke Xing Xionglei He | 2022 | National Science Review2022，9，2： | 2 |
| 2 | An instantaneous coalescent method insensitive to population structure显示文摘Conventional coalescent inferences of population history make the critical assumption that the population under examination is panmictic.However,most populations are structured.This complicates the prevailing coalescent analyses and sometimes leads to inaccurate estimates.To develop a coalescent method unhampered by population structure,we perform two analyses.First,we demonstrate that the coalescent probability of two randomly sampled alleles from the immediate preceding generation(one generation back)is independent of population structure.Second,motivated by this finding,we propose a new coalescent method:i-coalescent analysis.The i-coalescent analysis computes the instantaneous coalescent rate by using a phylogenetic tree of sampled alleles.Using simulated data,we broadly demonstrate the capability of i-coalescent analysis to accurately reconstruct population size dynamics of highly structured populations,although we find this method often requires larger sample sizes for structured populations than for panmictic populations.Overall,our results indicate i-coalescent analysis to be a useful tool,especially for the inference of population histories with intractable structure such as the developmental history of cell populations in the organs of complex organisms. | Zeqi Yao Kehui Liu Shanjun Deng Xionglei He | 2021 | Journal of Genetics and Genomics2021，48，3： | 0 |
| 3 | Decoupling gene functions from knockout effects by evolutionary analyses显示文摘Genic functions have long been confounded by pleiotropic mutational effects.To understand such genetic effects,we examine HAP4,a well-studied transcription factor in Saccharomyces cerevisiae that functions by forming a tetramer with HAP2,HAP3 and HAP5.Deletion of HAP4 results in highly pleiotropic gene expression responses,some of which are clustered in related cellular processes(clustered effects)while most are distributed randomly across diverse cellular processes(distributed effects).Strikingly,the distributed effects that account for much of HAP4 pleiotropy tend to be non-heritable in a population,suggesting they have few evolutionary consequences.Indeed,these effects are poorly conserved in closely related yeasts.We further show substantial overlaps of clustered effects,but not distributed effects,among the four genes encoding the HAP2/3/4/5 tetramer.This pattern holds for other biochemically characterized yeast protein complexes or metabolic pathways.Examination of a set of cell morphological traits of the deletion lines yields consistent results.Hence,only some deletion effects of a gene support related biochemical understandings with the rest being often pleiotropic and evolutionarily decoupled from the gene’s normal functions.This study suggests a new framework for reverse genetic analysis. | Li Liu Mengdi Liu Di Zhang Shanjun Deng Piaopiao Chen Jing Yang Yunhan Xie Xionglei He | 2020 | National Science Review2020，7，7： | 0 |
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