Haipeng Li
Chinese Academy of Sciences
Genek-nearest neighbors algorithmMachine learningGenomeFeature selectionArtificial intelligenceNeutral theory of molecular evolutionPopulation sizeChemistryBiological systemCoalescent theoryPopulationPositive selectionComputer scienceDNA sequencingGeneticsBioinformaticsGenetic variationComputational biologyNatural selectionEvolutionary biologySelection (genetic algorithm)Genetic diversityPopulation geneticsBiology
Publications 70
#1Guopeng Liu (CAS: Chinese Academy of Sciences)H-Index: 1
#2Chunxiao Zhang (CAS: Chinese Academy of Sciences)
Last. Haipeng Li (CAS: Chinese Academy of Sciences)H-Index: 24
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Abstract null null Introduction null The chorioallantoic placenta is a specific organ for placental mammals. However, the adaptive events during its emergence are still poorly investigated. null null null Methods null We scanned the chromosome X to detect the accelerated evolution in the ancestral lineage of placental mammals, and constructed 3D protein structure models of a candidate by homology modeling. null null null Results null Eight branch-specific accelerated regions were identified. Fiv...
#1Zi-Qian HaoH-Index: 4
#2Pengyuan DuH-Index: 2
Last. Haipeng LiH-Index: 24
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Recombination is a major force that shapes genetic diversity. Determination of recombination rate is important and can theoretically be improved by increasing the sample size. However, it is challenging to estimate recombination rates when the sample size is extraordinarily large because of computational burden. In this study, we used a refined artificial intelligence approach to estimate the recombination rate of the human genome using the UK10K human genomic dataset with 7,562 genomic sequence...
#1Wangjie Hu (CAS: Chinese Academy of Sciences)H-Index: 2
#2Zi-Qian Hao (CAS: Chinese Academy of Sciences)H-Index: 4
Last. Haipeng Li (CAS: Chinese Academy of Sciences)H-Index: 24
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The demographic history is a foundation of human evolutionary studies. We developed the fast infinitesimal time coalescent (FitCoal) process, which allows the accurate calculation of the composite likelihood of a site frequency spectrum and provides the precise inference of demographic history. Genomic analysis showed that African populations have passed through a population super bottleneck, a small effective size of approximately 1,280 breeding individuals between 930 and 813 thousand years ag...
1 CitationsSource
#1Jianing Yang (CAS: Chinese Academy of Sciences)H-Index: 1
#1Jianing Yang (CAS-MPG Partner Institute for Computational Biology)
Last. Haipeng LiH-Index: 24
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The SARS-CoV-2 variant of concern B.1.1.7 has quickly spread. To identify its crucial mutations, we explored the B.1.1.7 associated mutations on an evolutionary tree by the Coronavirus GenBrowser and VENAS. We found that a non-coding deletion g.a28271-, at upstream of the nucleocapsid (N) gene, has triggered the high transmissibility of B.1.1.7. The deletion changes the core Kozak site of the N gene and may reduce the expression of N protein and increase that of ORF9b. The expression of ORF9b is...
#1Yanni Ma (Peking Union Medical College)H-Index: 22
#2Siqi Liu (Peking Union Medical College)H-Index: 3
Last. Jia Yu (Peking Union Medical College)H-Index: 32
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The human genome harbors 14,000 duplicated or retroposed pseudogenes. Given their functionality as regulatory RNAs and low conservation, we hypothesized that pseudogenes could shape human-specific phenotypes. To test this, we performed co-expression analyses and found that pseudogene exhibited tissue-specific expression, especially in the bone marrow. By incorporating genetic data, we identified a bone-marrow-specific duplicated pseudogene, HBBP1 (η-globin), which has been implicated in β-thalas...
2 CitationsSource
#1Dalang YuH-Index: 2
#2Xiao Yang (CAS: Chinese Academy of Sciences)H-Index: 2
Last. Haipeng Li (CAS: Chinese Academy of Sciences)H-Index: 24
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COVID-19 has widely spread across the world, and much research is being conducted on the causative virus SARS-CoV-2. To help control the infection, we developed the Coronavirus GenBrowser (CGB) to monitor the pandemic. CGB allows visualization and analysis of the latest viral genomic data. Distributed genome alignments and an evolutionary tree built on the existing subtree are implemented for easy and frequent updates. The tree-based data are compressed at a ratio of 2,760:1, enabling fast acces...
2 CitationsSource
#1Zhong-Yin Zhou (KIZ: Kunming Institute of Zoology)H-Index: 7
#2Hang Liu (KIZ: Kunming Institute of Zoology)H-Index: 1
Last. Ya-Ping Zhang (KIZ: Kunming Institute of Zoology)H-Index: 90
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Understanding the mutational and evolutionary dynamics of SARS-CoV-2 is essential for treating COVID-19 and the development of a vaccine. Here, we analyzed publicly available 15,818 assembled SARS-CoV-2 genome sequences, along with 2,350 raw sequence datasets sampled worldwide. We investigated the distribution of inter-host single nucleotide polymorphisms (inter-host SNPs) and intra-host single nucleotide variations (iSNVs). Mutations have been observed at 35.6% (10,649/29,903) of the bases in t...
2 CitationsSource
#1Dong-Dong Wu (KIZ: Kunming Institute of Zoology)H-Index: 22
#2Cui-Ping Yang (KIZ: Kunming Institute of Zoology)H-Index: 15
Last. Ya-Ping Zhang (KIZ: Kunming Institute of Zoology)H-Index: 3
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Abundant and diverse domestic mammals living on the Tibetan Plateau provide useful materials for investigating adaptive evolution and genetic convergence. Here, we utilized 327 genomes from horses, sheep, goats, cattle, pigs and dogs living at both high and low altitudes, including 73 genomes generated for this study, to disentangle the genetic mechanisms underlying local adaptation of domestic mammals. Although molecular convergence is comparatively rare at the DNA sequence level, we found conv...
16 CitationsSource
#1Jingyang Hu (KIZ: Kunming Institute of Zoology)H-Index: 2
#1Jing-Yang Hu (KIZ: Kunming Institute of Zoology)H-Index: 1
Last. Li Yu (Yunnan University)H-Index: 18
view all 11 authors...
8 CitationsSource
#1Yuting Wang (CAS: Chinese Academy of Sciences)H-Index: 1
#2Guangyi Dai (CAS-MPG Partner Institute for Computational Biology)H-Index: 2
Last. Haipeng Li (CAS: Chinese Academy of Sciences)H-Index: 24
view all 26 authors...
Social hierarchies emerged during evolution, and social rank influences behavior and health of individuals. However, the evolutionary mechanisms of social hierarchy are still unknown in amniotes. Here we developed a new method and performed a genome-wide screening for identifying regions with accelerated evolution in the ancestral lineage of placental mammals, where mammalian social hierarchies might have initially evolved. Then functional analyses were conducted for the most accelerated region ...
3 CitationsSource