Journal Club

Plant Genetics Lab

Journal Club



2022

Sep 16, 2022

Presenter: Zelin Niu
Paper: van der Wijst, M.G.P., de Vries, D.H., Brugge, H. et al. An integrative approach for building personalized gene regulatory networks for precision medicine[J]. Genome Med, 2018, 10:96.
https://doi.org/10.1186/s13073-018-0608-4

Sep 9, 2022

Presenter: Xuebing Qiu
Paper: Heyduk, K., Moreno-Villena, J.J., Gilman, I. et al. The genetics of convergent evolution: insights from plant photosynthesis[J]. Nat Rev Genet, 2019, 20:485–493.
https://doi.org/10.1038/s41576-019-0107-5

Aug 19, 2022

Presenter: Hua Zhang
Paper: Wang S, Teng D, Li X, et al. The evolution and diversification of oakleaf butterflies[J]. Cell, 2022, 185(17):3138-3152.
https://doi.org/10.1016/j.cell.2022.06.042

Aug 12, 2022

Presenter: Bingjie Zhu
Paper: Ganna A, Verweij K J H, Nivard M G, et al. Large-scale GWAS reveals insights into the genetic architecture of same-sex sexual behavior[J]. Science, 2019, 365(6456).
DOI: 10.1126/science.aat7693

Aug 5, 2022

Presenter: Luyan Tian
Paper: Morrill K, Hekman J, Li X, et al. Ancestry-inclusive dog genomics challenges popular breed stereotypes[J]. Science, 2022, 376(6592).
DOI: 10.1126/science.abk063

Jul 22, 2022

Presenter: Xueting Hu
Paper: Hu, G., Feng, J., Xiang, X. et al. Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars. Nature Genetics, 2022, 54:73–83.
https://doi.org/10.1038/s41588-021-00971-3

Jul 22, 2022

Presenter: Jiayu Dong
Paper: Hsieh P, Vollger M R, Dang V, et al. Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes[J]. Science, 2019, 366(6463).
DOI: 10.1126/science.aax208

Jul 8, 2022

Presenter: Xuebo Zhao
Paper: Shen, X., Song, S., Li, C. et al. Synonymous mutations in representative yeast genes are mostly strongly non-neutral[J]. Nature, 2022, 606:725–731.
https://doi.org/10.1038/s41586-022-04823-w

May 13, 2022

Presenter: Xiaohan Yang
Paper: Abell N S, DeGorter M K, Gloudemans M J, et al. Multiple causal variants underlie genetic associations in humans[J]. Science, 2022, 375(6586): 1247-1254.
DOI: 10.1126/science.abj5117

May 6, 2022

Presenter: Liping Jiang
Paper: Bradley L, M. D M, Alexandre M, et al. The pan-genome effector-triggered immunity landscape of a host-pathogen interaction[J]. Science, 2020, 367(6479): 763-768.
https://doi.org/10.1038/s41586-022-04549-9

Apr 30, 2022

Presenter: Daxing Xu
Paper: Gardner, E.J., Neville, M.D.C., Samocha, K.E. et al. Reduced reproductive success is associated with selective constraint on human genes. Nature, 2022, 603: 858–863.
DOI: 10.1126/science.aa

Apr 15, 2022

Presenter: Aoyue Bi
Paper: Chen, S. et al. A genome-wide mutational constraint map quantified from variation in 76,156 human genomes. bioRxiv 2022.03.20.485034
https://doi.org/10.1101/2022.03.20.485034

Apr 08, 2022

Presenter: Yafei Guo
Paper: Sohail M, Vakhrusheva O A, Sul J H, et al. Negative selection in humans and fruit flies involves synergistic epistasis. Science, 2017, 356(6337): 539-542.
https://www.science.org/doi/10.1126/science.aah5238

Apr 01, 2022

Presenter: Xinyue Song
Paper: Santangelo J S, Ness R W, Cohan B, et al. Global urban environmental change drives adaptation in white clover. Science, 2022, 375(6586): 1275-1281.
https://www.science.org/doi/10.1126/science.abk0989

Mar 25, 2022

Presenter: Jun Xu
Paper: Vaishnav E D, De Boer C G, Molinet J, et al. The evolution, evolvability and engineering of gene regulatory DNA. Nature, 2022, 603(7901): 455-463.
https://doi.org/10.1038/s41586-022-04506-6

Mar 18, 2022

Presenter: Lipeng Kang
Paper: Powell D L, García-Olazábal M, Keegan M, et al. Natural hybridization reveals incompatible alleles that cause melanoma in swordtail fish. Science, 2020, 368(6492): 731-736.
https://www.science.org/doi/abs/10.1126/science.aba5216

Mar 04, 2022

Presenter: Beirui Niu
Paper:He F, Wang W, Rutter W B, et al. Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat. Nature Communications, 2022, 13(1): 826.
https://doi.org/10.1038/s41467-022-28453-y

Feb 25, 2022

Presenter: Zelin Niu
Paper: Monroe J G, Srikant T, Carbonell-Bejerano P, et al. Mutation bias reflects natural selection in Arabidopsis thaliana. Nature, 2022, 602(7895): 101-105.
https://doi.org/10.1038/s41586-021-04269-6

Jan 14, 2022

Presenter: Xuebing Qiu
Paper: Laricchia KM, Lake NJ, Watts NA, et al. Mitochondrial DNA variation across 56,434 individuals in gnomAD. Genome Res. 2022, 32(3): 569-582.
https://doi.org/10.1101/2021.07.23.453510



2021

Dec 31, 2021

Presenter: Hangyuan Cheng
Paper: Zheng J, Guo N, Wagner A. Selection enhances protein evolvability by increasing mutational robustness and foldability. Science, 2020, 370(6521).
https://www.science.org/doi/10.1126/science.abb5962

Dec 24, 2021

Presenter: Hua Zhang
Paper: Yonova-Doing E, Calabrese C, Gomez-Duran A, et al. An atlas of mitochondrial DNA genotype–phenotype associations in the UK Biobank. Nature Genetics, 2021, 53(7): 982-993.
https://doi.org/10.1038/s41588-021-00868-1

Dec 10, 2021

Presenter: Xuebo Zhao
Paper: Bergström A, Stringer C, Hajdinjak M, et al. Origins of modern human ancestry. Nature, 2021, 590(7845): 229-237.
https://doi.org/10.1038/s41586-021-03244-5

Dec 03, 2021

Presenter: Jiayu Dong
Paper: Peter B M. Admixture, Population Structure, and F-Statistics. Genetics, 2016, 202(4): 1485-1501.
https://doi.org/10.1534/genetics.115.183913

Nov 26, 2021

Presenter: Liping Jiang
Paper: Avsec Ž, Agarwal V, Visentin D, et al. Effective gene expression prediction from sequence by integrating long-range interactions. Nature Methods, 2021, 18(10): 1196-1203.
https://doi.org/10.1038/s41592-021-01252-x

Nov 19, 2021

Presenter: Xiaohan Yang
Paper: Bonder M J, Smail C, Gloudemans M J, et al. Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics. Nature Genetics, 2021, 53(3): 313-321.
https://doi.org/10.1038/s41588-021-00800-7

Nov 12, 2021

Presenter: Song Xu
Paper: Wong A K, Sealfon R S G, Theesfeld C L, et al. Decoding disease: from genomes to networks to phenotypes. Nature Reviews Genetics, 2021, 22(12): 774-790.
https://doi.org/10.1038/s41576-021-00389-x

Nov 05, 2021

Presenter: Daxing Xu
Paper: Frazer J, Notin P, Dias M, et al. Disease variant prediction with deep generative models of evolutionary data. Nature, 2021, 599(7883): 91-95.
https://doi.org/10.1038/s41586-021-04043-8

Oct 28, 2021

Presenter: Aoyue Bi
Paper: Li J T, Wang Q, Huang Yang M D, et al. Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish. Nature Genetics, 2021, 53(10): 1493-1503.
https://doi.org/10.1038/s41588-021-00933-9

Sep 30,2021

Presenter: Ming Zhang
Paper: Harvey M G, Bravo G A, Claramunt S, et al. The evolution of a tropical biodiversity hotspot. Science, 2020, 370(6522): 1343-1348.
https://www.science.org/doi/10.1126/science.aaz6970

Sep 24, 2021

Presenter: Yafei Guo
Paper: Fuller Z L, Mocellin V J L, Morris L A, et al. Population genetics of the coral Acropora millepora: Toward genomic prediction of bleaching. Science, 2020, 369(6501): 4674.
https://www.science.org/doi/10.1126/science.aba4674

Sep 17, 2021

Presenter: Beirui Niu
Paper: Stitzer M C, Anderson S N, Springer N M, et al. The genomic ecosystem of transposable elements in maize. PLOS Genetics, 2021, 17(10): e1009768.
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1009768

Sep 03, 2021

Presenter: Xinyue Song
Paper: Elena K, Benjamin V, N. N B A, et al. Exploring whole-genome duplicate gene retention with complex genetic interaction analysis. Science, 2020, 368(6498): eaaz5667.
DOI: 10.1126/science.aaz5667

Aug 27, 2021

Presenter: Xuebing Qiu
Paper: Wang S, Ore M J, Mikkelsen E K, et al. Signatures of mitonuclear coevolution in a warbler species complex. Nature Communications, 2021, 12(1): 4279.
DOI: https://doi.org/10.1038/s41467-021-24586-8

Aug 20, 2021

Presenter: Jun Xu
Paper: Sheng X, Guan Y, Ma Z, et al. Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments. Nature Genetics, 2021, 53(9): 1322-1333.
DOI: https://doi.org/10.1038/s41588-021-00909-9

Aug 13, 2021

Presenter: Yuqi Bai
Paper: Wang M, Li Z, Zhang Y, et al. An atlas of wheat epigenetic regulatory elements reveals subgenome divergence in the regulation of development and stress responses. Plant Cell. 2021, 33(4): 865-881.
DOI: 10.1093/plcell/koab028

Aug 06, 2021

Presenter: Kaibiao Zhang
Paper: Julca I, Ferrari C, Flores-Tornero M, et al. Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants. Nature Plants, 2021, 7(8): 1143-1159.
DOI: https://doi.org/10.1038/s41477-021-00958-2

Jul 29, 2021

Presenter: Zhengyue Sha
Paper: Corces MR, Granja JM, Shams S, et al. The chromatin accessibility landscape of primary human cancers. Science. 2018, 362(6413): 1898.
DOI: 10.1126/science.aav1898

Jul 16, 2021

Presenter: Lipeng Kang
Paper: Yang H, Luan Y, Liu T, et al. A map of cis-regulatory elements and 3D genome structures in zebrafish. Nature, 2020, 588(7837): 337-343.
DOI: https://doi.org/10.1038/s41586-020-2962-9

Apr 23, 2021

Presenter: Jijin Zhang
Paper: Jay P, Chouteau M, Whibley A, et al. Mutation load at a mimicry supergene sheds new light on the evolution of inversion polymorphisms. Nature Genetics, 2021, 53(3): 288-293.
DOI: https://doi.org/10.1038/s41588-020-00771-1

Apr 09, 2021

Presenter: Zelin Niu
Paper: Groen S C, Ćalić I, Joly-Lopez Z, et al. The strength and pattern of natural selection on gene expression in rice. Nature, 2020, 578(7796): 572-576.
DOI: https://doi.org/10.1038/s41586-020-1997-2

Apr 02, 2021

Presenter: Zhiliang Zhang
Paper: Peter E, A. A P, Qihui Z, et al. Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science, 2021, 372(6537): eabf7117.
DOI: 10.1126/science.abf7117

Mar 12, 2021

Presenter: Hua Zhang
Paper: Lovell J T, MacQueen A H, Mamidi S, et al. Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass. Nature, 2021, 590(7846): 438-444.
DOI: https://doi.org/10.1038/s41586-020-03127-1

Mar 05, 2021

Presenter: Xuebo Zhao
Paper: Anders B, Laurent F, Ryan S, et al. Origins and genetic legacy of prehistoric dogs. Science, 2020, 370(6516): 557-564.
DOI: 10.1126/science.aba9572

Jan 22, 2021

Presenter: Liping Jiang
Paper: Vuckovic D, Bao EL, Akbari P, et al. The Polygenic and Monogenic Basis of Blood Traits and Diseases. Cell. 2020, 182(5): 1214-1231.e11.
DOI: 10.1016/j.cell.2020.08.008

Jan 15, 2021

Presenter: Jiayu Dong
Paper: Skov L, Coll Macià M, Sveinbjörnsson G, et al. The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes. Nature, 2020, 582(7810): 78-83.
DOI: https://doi.org/10.1038/s41586-020-2225-9

Jan 08, 2021

Presenter: Song Xu
Paper: Fachal L, Aschard H, Beesley J, et al. Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes. Nature Genetics, 2020, 52(1): 56-73.
DOI: https://doi.org/10.1038/s41588-019-0537-1