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  1. Article ; Online: Structure-Kinetic Relationship for Drug Design Revealed by a PLS Model with Retrosynthesis-Based Pre-Trained Molecular Representation and Molecular Dynamics Simulation.

    Zhou, Feng / Yin, Shiqiu / Xiao, Yi / Lin, Zaiyun / Fu, Weiqiang / Zhang, Yingsheng J

    ACS omega

    2023  Volume 8, Issue 20, Page(s) 18312–18322

    Abstract: Drug design based on kinetic properties is growing in application. Here, we applied retrosynthesis-based pre-trained molecular representation (RPM) in machine learning (ML) to train 501 inhibitors of 55 proteins and successfully predicted the ... ...

    Abstract Drug design based on kinetic properties is growing in application. Here, we applied retrosynthesis-based pre-trained molecular representation (RPM) in machine learning (ML) to train 501 inhibitors of 55 proteins and successfully predicted the dissociation rate constant (
    Language English
    Publishing date 2023-05-12
    Publishing country United States
    Document type Journal Article
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.3c02294
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  2. Article ; Online: G2GT: Retrosynthesis Prediction with Graph-to-Graph Attention Neural Network and Self-Training.

    Lin, Zaiyun / Yin, Shiqiu / Shi, Lei / Zhou, Wenbiao / Zhang, Yingsheng John

    Journal of chemical information and modeling

    2023  Volume 63, Issue 7, Page(s) 1894–1905

    Abstract: Retrosynthesis prediction, the task of identifying reactant molecules that can be used to synthesize product molecules, is a fundamental challenge in organic chemistry and related fields. To address this challenge, we propose a novel graph-to-graph ... ...

    Abstract Retrosynthesis prediction, the task of identifying reactant molecules that can be used to synthesize product molecules, is a fundamental challenge in organic chemistry and related fields. To address this challenge, we propose a novel graph-to-graph transformation model, G2GT. The model is built on the standard transformer structure and utilizes graph encoders and decoders. Additionally, we demonstrate the effectiveness of self-training, a data augmentation technique that utilizes unlabeled molecular data, in improving the performance of the model. To further enhance diversity, we propose a weak ensemble method, inspired by reaction-type labels and ensemble learning. This method incorporates beam search, nucleus sampling, and top-
    MeSH term(s) Neural Networks, Computer ; Learning ; Algorithms ; Electric Power Supplies
    Language English
    Publishing date 2023-03-22
    Publishing country United States
    Document type Journal Article
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.2c01302
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1230: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  3. Article ; Online: Global gene expression perturbations in rapeseed due to the introduction of alien radish chromosomes.

    Shao, Yujiao / Pan, Qi / Zhang, Dawei / Kang, Lei / Li, Zaiyun

    Journal of genetics

    2021  Volume 100

    Abstract: The aneuploidy chromosome addition lines with individual chromosomes of one species into the whole genome of another species developed from interspecific or intergeneric crosses are ideal for studying the gene expression regulation under asymmetrical ... ...

    Abstract The aneuploidy chromosome addition lines with individual chromosomes of one species into the whole genome of another species developed from interspecific or intergeneric crosses are ideal for studying the gene expression regulation under asymmetrical genome interactions. Here, we chose two rapeseed-radish addition lines (2
    MeSH term(s) Brassica napus/genetics ; Brassica rapa/genetics ; Chromosomes, Plant/genetics ; Gene Expression Regulation, Plant/genetics ; Genome, Plant/genetics ; Hybridization, Genetic/genetics ; Raphanus/genetics ; Transcriptome/genetics
    Language English
    Publishing date 2021-06-29
    Publishing country India
    Document type Journal Article
    ZDB-ID 3039-9
    ISSN 0973-7731 ; 0958-8361 ; 0022-1333
    ISSN (online) 0973-7731
    ISSN 0958-8361 ; 0022-1333
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    In stock of ZB MED Cologne/Königswinter

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    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)
    Zs.MA 8: Show issues

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  4. Article: Global gene expression perturbations in rapeseed due to the introduction of alien radish chromosomes

    Shao, Yujiao / Pan, Qi / Zhang, Dawei / Kang, Lei / Li, Zaiyun

    Journal of genetics. 2021 Oct., v. 100, no. 2

    2021  

    Abstract: The aneuploidy chromosome addition lines with individual chromosomes of one species into the whole genome of another species developed from interspecific or intergeneric crosses are ideal for studying the gene expression regulation under asymmetrical ... ...

    Abstract The aneuploidy chromosome addition lines with individual chromosomes of one species into the whole genome of another species developed from interspecific or intergeneric crosses are ideal for studying the gene expression regulation under asymmetrical genome interactions. Here, we chose two rapeseed-radish addition lines (2n=40, AACC+2R) with all chromosomes of rapeseed and one pair of radish chromosomes carrying 25S rDNA loci and both 5S and 25S rDNA loci, respectively. Transcriptome sequencing of these two rapeseed-radish addition lines, together with two parents (Brassica napus, 2n=38, AACC; Raphanus sativus, 2n=18, RR), was performed to assess gene expression changes due to the aneuploidy effect. Our results showed that the global gene expression perturbations in two addition lines showed asymmetric distributions between A and C subgenomes, for more downregulated genes located in the C subgenome. Moreover, several dysregulated domains occurred in the addition lines and majority of them were clustered in C subgenome, further revealing that C subgenome was more inclined to be repressed by the aneuploidy. Homoeolog expression was slightly biased toward C subgenome in the parent B. napus, but had no preference to either of A or C subgenome in the addition lines. The total number of biased genes increased sharply and most of them were shared only by two addition lines, indicating that aneuploidy could change the extent and direction of homoeolog expression. The triplicated subgenomes which were orthologs to the chromosomes of Arabidopsis thaliana also exhibited dramatic alternations in two additions. Together, our results revealed that the addition of individual radish chromosomes could induce dramatically transcriptomic disturbances and those expression changes gave asymmetric distributions between two subgenomes in B. napus. The possible mechanisms including the uniparental expression of rRNA genes in the allopolyploids and additions for the findings are discussed.
    Keywords Arabidopsis thaliana ; Brassica napus ; Raphanus sativus ; allopolyploidy ; aneuploidy ; chromosome addition ; gene expression ; gene expression regulation ; radishes ; rapeseed ; transcriptome ; transcriptomics
    Language English
    Dates of publication 2021-10
    Size p. 25.
    Publishing place Springer India
    Document type Article
    ZDB-ID 3039-9
    ISSN 0973-7731 ; 0958-8361 ; 0022-1333
    ISSN (online) 0973-7731
    ISSN 0958-8361 ; 0022-1333
    DOI 10.1007/s12041-021-01276-4
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    In stock of ZB MED Bonn / Germany

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  5. Book ; Online: G2GT

    Lin, Zaiyun / Yin, Shiqiu / Shi, Lei / Zhou, Wenbiao / Zhang, YingSheng

    Retrosynthesis Prediction with Graph to Graph Attention Neural Network and Self-Training

    2022  

    Abstract: Retrosynthesis prediction is one of the fundamental challenges in organic chemistry and related fields. The goal is to find reactants molecules that can synthesize product molecules. To solve this task, we propose a new graph-to-graph transformation ... ...

    Abstract Retrosynthesis prediction is one of the fundamental challenges in organic chemistry and related fields. The goal is to find reactants molecules that can synthesize product molecules. To solve this task, we propose a new graph-to-graph transformation model, G2GT, in which the graph encoder and graph decoder are built upon the standard transformer structure. We also show that self-training, a powerful data augmentation method that utilizes unlabeled molecule data, can significantly improve the model's performance. Inspired by the reaction type label and ensemble learning, we proposed a novel weak ensemble method to enhance diversity. We combined beam search, nucleus, and top-k sampling methods to further improve inference diversity and proposed a simple ranking algorithm to retrieve the final top-10 results. We achieved new state-of-the-art results on both the USPTO-50K dataset, with top1 accuracy of 54%, and the larger data set USPTO-full, with top1 accuracy of 50%, and competitive top-10 results.

    Comment: number of pages:12 and number of figures:5
    Keywords Quantitative Biology - Quantitative Methods ; Computer Science - Machine Learning
    Subject code 006
    Publishing date 2022-04-18
    Publishing country us
    Document type Book ; Online
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  6. Article: Gene Expression Changes During the Allo-/Deallopolyploidization Process of

    Pan, Qi / Zhu, Bin / Zhang, Dawei / Tong, Chaobo / Ge, Xianhong / Liu, Shengyi / Li, Zaiyun

    Frontiers in genetics

    2019  Volume 10, Page(s) 1279

    Abstract: Gene expression changes due to allopolyploidization have been extensively studied in plants over the past few decades. Nearly all these studies focused on comparing the changes before and after genome merger. In this study, we used the uniquely ... ...

    Abstract Gene expression changes due to allopolyploidization have been extensively studied in plants over the past few decades. Nearly all these studies focused on comparing the changes before and after genome merger. In this study, we used the uniquely restituted
    Language English
    Publishing date 2019-12-19
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2019.01279
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  7. Article: Association of Clubroot Resistance Locus

    Zhan, Zongxiang / Jiang, Yingfen / Shah, Nadil / Hou, Zhaoke / Zhou, Yuanwei / Dun, Bicheng / Li, Shisheng / Zhu, Li / Li, Zaiyun / Piao, Zhongyun / Zhang, Chunyu

    Frontiers in plant science

    2020  Volume 11, Page(s) 810

    Abstract: Clubroot caused ... ...

    Abstract Clubroot caused by
    Language English
    Publishing date 2020-06-11
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2020.00810
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  8. Article: Effects of miR-126 on the STAT3 signaling pathway and the regulation of malignant behavior in lung cancer cells.

    Zhang, Zaiyun / Wang, Jihua / Cheng, Jian / Yu, Xiaoming

    Oncology letters

    2018  Volume 15, Issue 6, Page(s) 8412–8416

    Abstract: The functions of miR-126-mediated signal transducers and activators of the transcription 3 (STAT3) signal pathway were investigated in regulating the behavior of cells in non-small cell lung cancer (NSCLC). Cultured NSCLC A549 cells were transfected with ...

    Abstract The functions of miR-126-mediated signal transducers and activators of the transcription 3 (STAT3) signal pathway were investigated in regulating the behavior of cells in non-small cell lung cancer (NSCLC). Cultured NSCLC A549 cells were transfected with empty, miR-126 overexpression or miR-126 knocked-down expression plasmids. After transfection efficiency verification by reverse transcription polymerase chain reaction (RT-PCR) and culture for 24 h, methyl thiazolyl tetrazolium (MTT) was applied to detect cell proliferation rate, migration distance was measured in scratch assays, cell cycle was determined through flow cytometry, the mRNA expression level of caspase-3 in cells was detected using RT-PCR and protein expression levels of STAT3 were detected using western blotting. Our results showed the cell proliferation rate was significantly higher in cells of the overexpression group than that in those of the control group (p<0.05) and the rate in the cells of the low-expression group was the lowest among the three groups (p<0.05). The migration distance of the overexpression group cells was significantly longer than that in the control group cells and the shortest migration distance was found in the low-expression group cells (p<0.05). The amount of cells in mitotic phase in the overexpression group was significantly higher than that in the control group and the same amount in the low-expression group was the lowest (p<0.05). The mRNA expression level of caspase-3 of cells in the overexpression group was significantly lower than that of cells in the control group and the highest expression level was found in the low-expression group (p<0.05). Finally, the protein expression levels of STAT3 in cells in the overexpression group were significantly lower than those in the control group and the highest expression levels were identified in the low-expression group (p<0.05). Based on our findings, the cancer-promoting miR-126 can mediate the activation of the STAT3 signal pathway to regulate the malignant biological behavior of NSCLC cells affecting their proliferation, migration, cycle and apoptosis susceptibility.
    Language English
    Publishing date 2018-03-28
    Publishing country Greece
    Document type Journal Article
    ZDB-ID 2573196-8
    ISSN 1792-1082 ; 1792-1074
    ISSN (online) 1792-1082
    ISSN 1792-1074
    DOI 10.3892/ol.2018.8360
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  9. Article: Genome-Wide Gene Expressions Respond Differently to A-subgenome Origins in

    Zhang, Dawei / Pan, Qi / Tan, Chen / Zhu, Bin / Ge, Xianhong / Shao, Yujiao / Li, Zaiyun

    Frontiers in plant science

    2016  Volume 7, Page(s) 1508

    Abstract: The young ... ...

    Abstract The young allotetraploid
    Language English
    Publishing date 2016-10-13
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2711035-7
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2016.01508
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  10. Article ; Online: Boundary Stabilization of a Nonlinear Viscoelastic Equation with Interior Time-Varying Delay and Nonlinear Dissipative Boundary Feedback

    Zaiyun Zhang / Jianhua Huang / Zhenhai Liu / Mingbao Sun

    Abstract and Applied Analysis, Vol

    2014  Volume 2014

    Keywords Mathematics ; QA1-939 ; Science ; Q
    Language English
    Publishing date 2014-01-01T00:00:00Z
    Publisher Hindawi Publishing Corporation
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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