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Transcriptomic and proteomic effects of gene deletion are not evolutionarily conserved

Genome Research
2025-02-18 | Journal article
DOI: 10.1101/gr.280008.124
Contributors: Yang Li; Jianzhi Zhang
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Further Evidence for Strong Nonneutrality of Yeast Synonymous Mutations

Molecular Biology and Evolution
2024-11-01 | Journal article
DOI: 10.1093/molbev/msae224
Contributors: Xukang Shen; Siliang Song; Chuan Li; Jianzhi Zhang; Jun Gojobori
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In search of the genetic variants of human sex ratio at birth: was Fisher wrong about sex ratio evolution?

Proceedings of the Royal Society B: Biological Sciences
2024-10 | Journal article
DOI: 10.1098/rspb.2024.1876
Contributors: Siliang Song; Jianzhi Zhang
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The loci of environmental adaptation in a model eukaryote

Nature Communications
2024-07-06 | Journal article
DOI: 10.1038/s41467-024-50002-y
Contributors: Piaopiao Chen; Jianzhi Zhang
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Where Are the Formerly Y-linked Genes in the Ryukyu Spiny Rat that has Lost its Y Chromosome?

Genome Biology and Evolution
2024-03-02 | Journal article
DOI: 10.1093/gbe/evae046
Contributors: Jiachen Li; Siliang Song; Jianzhi Zhang; John Wang
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Genetic variants underlying human bisexual behavior are reproductively advantageous

Science Advances
2024-01-05 | Journal article
DOI: 10.1126/sciadv.adj6958
Contributors: Siliang Song; Jianzhi Zhang
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Ascertainment Bias in the Genomic Test of Positive Selection on Regulatory Sequences

Molecular Biology and Evolution
2024-01-03 | Journal article
DOI: 10.1093/molbev/msad284
Contributors: Daohan Jiang; Jianzhi Zhang; Katja Nowick
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Evidence for the role of selection for reproductively advantageous alleles in human aging

Science Advances
2023-12-08 | Journal article
DOI: 10.1126/sciadv.adh4990
Contributors: Erping Long; Jianzhi Zhang
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Effective fitness under fluctuating selection with genetic drift

G3: Genes, Genomes, Genetics
2023-12-06 | Journal article
DOI: 10.1093/g3journal/jkad230
Contributors: Siliang Song; Jianzhi Zhang; N Barton
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COL: a pipeline for identifying putatively functional back-splicing

2023-11-13 | Preprint
DOI: 10.1101/2023.11.08.566217
Contributors: Zheng Li; Bandhan Sarker; Fengyu Zhao; Tianjiao Zhou; Jianzhi Zhang; Chuan Xu
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Genomic estimates of mutation and substitution rates contradict the evolutionary speed hypothesis of the latitudinal diversity gradient

Proceedings of the Royal Society B: Biological Sciences
2023-10-25 | Journal article
DOI: 10.1098/rspb.2023.1787
Contributors: Haoxuan Liu; Mengyi Sun; Jianzhi Zhang
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Transcriptomic analysis reveals the rareness of genetic assimilation of gene expression in environmental adaptations

Science Advances
2023-09-29 | Journal article
DOI: 10.1126/sciadv.adi3053
Contributors: Piaopiao Chen; Jianzhi Zhang
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On the Decoupling of Evolutionary Changes in mRNA and Protein Levels

Molecular Biology and Evolution
2023-08-03 | Journal article
DOI: 10.1093/molbev/msad169
Contributors: Daohan Jiang; Alexander L Cope; Jianzhi Zhang; Matt Pennell; Julian Echave
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Masatoshi Nei (1931–2023)

Nature Ecology & Evolution
2023-06-28 | Journal article
DOI: 10.1038/s41559-023-02119-4
Contributors: Jianzhi Zhang; Sudhir Kumar
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Contraception ends the genetic maintenance of human same-sex sexual behavior

Proceedings of the National Academy of Sciences
2023-05-23 | Journal article
DOI: 10.1073/pnas.2303418120
Contributors: Siliang Song; Jianzhi Zhang
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Author Correction: The rate and molecular spectrum of mutation are selectively maintained in yeast

Nature Communications
2023-04-04 | Journal article
DOI: 10.1038/s41467-023-37354-7
Contributors: Haoxuan Liu; Jianzhi Zhang
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Chance promoter activities illuminate the origins of eukaryotic intergenic transcriptions

Nature Communications
2023-04-01 | Journal article
DOI: 10.1038/s41467-023-37610-w
Contributors: Haiqing Xu; Chuan Li; Chuan Xu; Jianzhi Zhang
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What Has Genomics Taught an Evolutionary Biologist?

Genomics, Proteomics & Bioinformatics
2023-02-01 | Journal article
DOI: 10.1016/j.gpb.2023.01.005
Contributors: Jianzhi Zhang
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Is the Mutation Rate Lower in Genomic Regions of Stronger Selective Constraints?

Molecular Biology and Evolution
2022-08-03 | Journal article
DOI: 10.1093/molbev/msac169
Contributors: Haoxuan Liu; Jianzhi Zhang; Weiwei Zhai
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Preferred synonymous codons are translated more accurately: Proteomic evidence, among-species variation, and mechanistic basis

Science Advances
2022-07-08 | Journal article
DOI: 10.1126/sciadv.abl9812
Contributors: Mengyi Sun; Jianzhi Zhang
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Synonymous mutations in representative yeast genes are mostly strongly non-neutral

Nature
2022-06-23 | Journal article
DOI: 10.1038/s41586-022-04823-w
Contributors: Xukang Shen; Siliang Song; Chuan Li; Jianzhi Zhang
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Testing the adaptive hypothesis of lagging-strand encoding in bacterial genomes

Nature Communications
2022-05-12 | Journal article
DOI: 10.1038/s41467-022-30000-8
Contributors: Haoxuan Liu; Jianzhi Zhang
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Transposon insertional mutagenesis of diverse yeast strains suggests coordinated gene essentiality polymorphisms

Nature Communications
2022-03-21 | Journal article
DOI: 10.1038/s41467-022-29228-1
Contributors: Piaopiao Chen; Agnès H. Michel; Jianzhi Zhang
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Unbiased inference of the fitness landscape ruggedness from imprecise fitness estimates

Evolution
2021-11 | Journal article
DOI: 10.1111/evo.14363
Contributors: Siliang Song; Jianzhi Zhang
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Is the Genetic Code Optimized for Resource Conservation?

Molecular Biology and Evolution
2021-10-27 | Journal article
DOI: 10.1093/molbev/msab239
Contributors: Haiqing Xu; Jianzhi Zhang; Xuhua Xia
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On the Origin of Frameshift-Robustness of the Standard Genetic Code

Molecular Biology and Evolution
2021-09-27 | Journal article
DOI: 10.1093/molbev/msab164
Contributors: Haiqing Xu; Jianzhi Zhang; Meredith Yeager
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Author Correction: The preponderance of nonsynonymous A-to-I RNA editing in coleoids is nonadaptive

Nature Communications
2021-07-01 | Journal article
DOI: 10.1038/s41467-021-23830-5
Contributors: Daohan Jiang; Jianzhi Zhang
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The rate and molecular spectrum of mutation are selectively maintained in yeast

Nature Communications
2021-06-30 | Journal article
DOI: 10.1038/s41467-021-24364-6
Contributors: Haoxuan Liu; Jianzhi Zhang
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Codon usage bias and nuclear mRNA concentration: Correlation vs. causation

Proceedings of the National Academy of Sciences
2021-05-18 | Journal article
DOI: 10.1073/pnas.2104714118
Contributors: Wenfeng Qian; Jianzhi Zhang
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Detecting natural selection in trait-trait coevolution

2021-05-05 | Preprint
DOI: 10.1101/2021.05.05.442737
Contributors: Daohan Jiang; Jianzhi Zhang
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Caution in testing phenotypic selection

Proceedings of the National Academy of Sciences
2021-03-02 | Journal article
DOI: 10.1073/pnas.2022180118
Contributors: Jianzhi Zhang; Haiqing Xu
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Fly wing evolution explained by a neutral model with mutational pleiotropy

Evolution
2020-09-18 | Journal article
DOI: 10.1111/evo.14076
Contributors: Daohan Jiang; Jianzhi Zhang
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Idiosyncratic epistasis creates universals in mutational effects and evolutionary trajectories

Nature Ecology & Evolution
2020-09-07 | Journal article
DOI: 10.1038/s41559-020-01286-y
Contributors: Daniel M. Lyons; Zhengting Zou; Haiqing Xu; Jianzhi Zhang
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Phenotypic plasticity as a long-term memory easing readaptations to ancestral environments

Science Advances
2020-05-22 | Journal article
DOI: 10.1126/sciadv.aba3388
Contributors: Wei-Chin Ho; Diyan Li; Qing Zhu; Jianzhi Zhang
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Dissimilation of synonymous codon usage bias in virus–host coevolution due to translational selection

Nature Ecology & Evolution
2020-03-02 | Journal article
DOI: 10.1038/s41559-020-1124-7
Contributors: Feng Chen; Peng Wu; Shuyun Deng; Heng Zhang; Yutong Hou; Zheng Hu; Jianzhi Zhang; Xiaoshu Chen; Jian-Rong Yang
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Publisher Correction: Antagonistic pleiotropy conceals molecular adaptations in changing environments

Nature Ecology & Evolution
2020-02-19 | Journal article
DOI: 10.1038/s41559-020-1149-y
Contributors: Piaopiao Chen; Jianzhi Zhang
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Antagonistic pleiotropy conceals molecular adaptations in changing environments

Nature Ecology & Evolution
2020-02-10 | Journal article
DOI: 10.1038/s41559-020-1107-8
Contributors: Piaopiao Chen; Jianzhi Zhang
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A different perspective on alternative cleavage and polyadenylation

Nature Reviews Genetics
2020-01-19 | Journal article
DOI: 10.1038/s41576-019-0198-z
Contributors: Chuan Xu; Jianzhi Zhang
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Amino acid exchangeabilities vary across the tree of life

Science Advances
2019-12-06 | Journal article
DOI: 10.1126/sciadv.aax3124
Contributors: Zhengting Zou; Jianzhi Zhang
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The preponderance of nonsynonymous A-to-I RNA editing in coleoids is nonadaptive

Nature Communications
2019-11-27 | Journal article
DOI: 10.1038/s41467-019-13275-2
Contributors: Daohan Jiang; Jianzhi Zhang
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Synchronization of stochastic expressions drives the clustering of functionally related genes

Science Advances
2019-10-11 | Journal article
DOI: 10.1126/sciadv.aax6525
Contributors: Haiqing Xu; Jing-Jing Liu; Zhen Liu; Ying Li; Yong-Su Jin; Jianzhi Zhang
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Chromosome-wide co-fluctuation of stochastic gene expression in mammalian cells

PLOS Genetics
2019-09-16 | Journal article
DOI: 10.1371/journal.pgen.1008389
Contributors: Mengyi Sun; Lu Bai; Jianzhi Zhang
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Parallel transcriptomic changes in the origins of divergent monogamous vertebrates?

Proceedings of the National Academy of Sciences
2019-09-03 | Journal article
DOI: 10.1073/pnas.1910749116
Contributors: Daohan Jiang; Jianzhi Zhang
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Retesting the influences of mutation accumulation and antagonistic pleiotropy on human senescence and disease

Nature Ecology & Evolution
2019-06-24 | Journal article
DOI: 10.1038/s41559-019-0925-z
Contributors: Erping Long; Jianzhi Zhang
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Allele-specific single-cell RNA sequencing reveals different architectures of intrinsic and extrinsic gene expression noises

2019-06-11 | Other
DOI: 10.1101/667840
Contributors: Mengyi Sun; Jianzhi Zhang
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Stop-codon read-through arises largely from molecular errors and is generally nonadaptive

PLOS Genetics
2019-05-23 | Journal article
DOI: 10.1371/journal.pgen.1008141
Contributors: Chuan Li; Laurent Duret; Jianzhi Zhang
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Evidence that alternative transcriptional initiation is largely nonadaptive

PLOS Biology
2019-03-18 | Journal article
DOI: 10.1371/journal.pbio.3000197
Contributors: Chuan Xu; Laurence D. Hurst; Joong-Ki Park; Jianzhi Zhang
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Environment-dependent pleiotropic effects of mutations on the maximum growth rate r and carrying capacity K of population growth

PLOS Biology
2019-01-25 | Journal article
DOI: 10.1371/journal.pbio.3000121
Contributors: Xinzhu Wei; Csaba Pál; Jianzhi Zhang
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The optimal mating distance resulting from heterosis and genetic incompatibility

Science Advances
2018-11-02 | Journal article
DOI: 10.1126/sciadv.aau5518
Contributors: Xinzhu Wei; Jianzhi Zhang
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Multi-environment fitness landscapes of a tRNA gene

Nature Ecology & Evolution
2018-04-23 | Journal article
DOI: 10.1038/s41559-018-0549-8
Contributors: Chuan Li; Jianzhi Zhang
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