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  1. Article: Effectiveness of parent coaching on the literacy skills of Hong Kong Chinese Children with and without dyslexia.

    Ruan, Yijun / Ye, Yanyan / McBride, Catherine

    Reading and writing

    2023  , Page(s) 1–22

    Abstract: Literacy skills are important for children's development. The present study explored the effectiveness of a parent coaching approach on the reading and spelling skills and compared cognitive-linguistic skills performances between Chinese children with ... ...

    Abstract Literacy skills are important for children's development. The present study explored the effectiveness of a parent coaching approach on the reading and spelling skills and compared cognitive-linguistic skills performances between Chinese children with and without dyslexia. Participants were 33 children with dyslexia and 77 children without dyslexia, as well as their parent, in Hong Kong. Children were divided into three groups: dyslexia with training, non-dyslexia with training, and non-dyslexia without training. Parents in both training groups were instructed to facilitate children's literacy skills. A series of cognitive-linguistic skills were tested on children at pretest. Children received measures of character reading, word reading, and word spelling before and after the parent coaching. Results showed that, compared to children without dyslexia, children with dyslexia performed significantly more poorly on all cognitive-linguistic skills. Analyses of the training effect demonstrated that the dyslexia with training group significantly improved their performances on word reading and word spelling following the intervention. In addition, those without dyslexia who experienced training performed significantly better on character reading and word spelling at posttest than pretest. These results suggest that parent coaching can be one potentially effective method of promoting literacy skills among children both with and without dyslexia.
    Language English
    Publishing date 2023-01-17
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1478082-3
    ISSN 1573-0905 ; 0922-4777
    ISSN (online) 1573-0905
    ISSN 0922-4777
    DOI 10.1007/s11145-022-10408-w
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  2. Article ; Online: Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions.

    Chiliński, Mateusz / Lipiński, Jakub / Agarwal, Abhishek / Ruan, Yijun / Plewczynski, Dariusz

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 11693

    Abstract: There have been multiple attempts to predict the expression of the genes based on the sequence, epigenetics, and various other factors. To improve those predictions, we have decided to investigate adding protein-specific 3D interactions that play a ... ...

    Abstract There have been multiple attempts to predict the expression of the genes based on the sequence, epigenetics, and various other factors. To improve those predictions, we have decided to investigate adding protein-specific 3D interactions that play a significant role in the condensation of the chromatin structure in the cell nucleus. To achieve this, we have used the architecture of one of the state-of-the-art algorithms, ExPecto, and investigated the changes in the model metrics upon adding the spatially relevant data. We have used ChIA-PET interactions that are mediated by cohesin (24 cell lines), CTCF (4 cell lines), and RNAPOL2 (4 cell lines). As the output of the study, we have developed the Spatial Gene Expression (SpEx) algorithm that shows statistically significant improvements in most cell lines. We have compared ourselves to the baseline ExPecto model, which obtained a 0.82 Spearman's rank correlation coefficient (SCC) score, and 0.85, which is reported by newer Enformer were able to obtain the average correlation score of 0.83. However, in some cases (e.g. RNAPOL2 on GM12878), our improvement reached 0.04, and in some cases (e.g. RNAPOL2 on H1), we reached an SCC of 0.86.
    MeSH term(s) Chromatin/genetics ; CCCTC-Binding Factor/genetics ; Chromosomes/metabolism ; Cell Nucleus/metabolism ; Cell Cycle Proteins/metabolism ; Gene Expression
    Chemical Substances Chromatin ; CCCTC-Binding Factor ; Cell Cycle Proteins
    Language English
    Publishing date 2023-07-20
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-38865-5
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  3. Article: Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions.

    Chiliński, Mateusz / Lipiński, Jakub / Agarwal, Abhishek / Ruan, Yijun / Plewczynski, Dariusz

    bioRxiv : the preprint server for biology

    2023  

    Abstract: There have been multiple attempts to predict the expression of the genes based on the sequence, epigenetics, and various other factors. To improve those predictions, we have decided to investigate adding protein-specific 3D interactions that play a major ...

    Abstract There have been multiple attempts to predict the expression of the genes based on the sequence, epigenetics, and various other factors. To improve those predictions, we have decided to investigate adding protein-specific 3D interactions that play a major role in the compensation of the chromatin structure in the cell nucleus. To achieve this, we have used the architecture of one of the state-of-the-art algorithms, ExPecto (J. Zhou et al., 2018), and investigated the changes in the model metrics upon adding the spatially relevant data. We have used ChIA-PET interactions that are mediated by cohesin (24 cell lines), CTCF (4 cell lines), and RNAPOL2 (4 cell lines). As the output of the study, we have developed the Spatial Gene Expression (SpEx) algorithm that shows statistically significant improvements in most cell lines.
    Language English
    Publishing date 2023-04-06
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.04.06.535849
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  4. Article: Methods for comparative ChIA-PET and Hi-C data analysis

    Capurso, Dan / Tang, Zhonghui / Ruan, Yijun

    Methods. 2020 Jan. 01, v. 170

    2020  

    Abstract: The three-dimensional architecture of chromatin in the nucleus is important for genome regulation and function. Advanced high-throughput sequencing-based methods have been developed for capturing chromatin interactions (Hi-C, genome-wide chromosome ... ...

    Abstract The three-dimensional architecture of chromatin in the nucleus is important for genome regulation and function. Advanced high-throughput sequencing-based methods have been developed for capturing chromatin interactions (Hi-C, genome-wide chromosome conformation capture) or enriching for those involving a specific protein (ChIA-PET, chromatin interaction analysis with paired-end tag sequencing). There is widespread interest in utilizing and interpreting ChIA-PET and Hi-C. We review methods for comparative ChIA-PET and Hi-C data analysis and visualization. The topics reviewed include: downloading ChIA-PET and Hi-C data from the ENCODE and 4DN portals; processing ChIA-PET data using ChIA-PIPE; processing Hi-C data using Juicer or distiller and cooler; viewing 2D contact maps using Juicebox or Higlass; viewing peaks, loops, and domains using BASIC Browser; annotating convergent and tandem CTCF loops.
    Keywords chromatin ; genome ; high-throughput nucleotide sequencing
    Language English
    Dates of publication 2020-0101
    Size p. 69-74.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 1066584-5
    ISSN 1095-9130 ; 1046-2023
    ISSN (online) 1095-9130
    ISSN 1046-2023
    DOI 10.1016/j.ymeth.2019.09.019
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  5. Article ; Online: Genome-sequencing anniversary. Presenting the human genome: now in 3D!

    Ruan, Yijun

    Science (New York, N.Y.)

    2011  Volume 331, Issue 6020, Page(s) 1025–1026

    MeSH term(s) Chromatin/ultrastructure ; Chromosomes, Human/ultrastructure ; Genome, Human ; Human Genome Project ; Humans
    Chemical Substances Chromatin
    Language English
    Publishing date 2011-02-25
    Publishing country United States
    Document type Journal Article
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.1203602
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  6. Article: Identification of pharmacokinetic markers for safflower injection using a combination of system pharmacology, multicomponent pharmacokinetics, and quantitative proteomics study.

    Shi, Peiying / Ruan, Yijun / Zhong, Chenhui / Teng, Linglin / Ke, Liyuan / Yao, Hong

    Frontiers in pharmacology

    2022  Volume 13, Page(s) 1062026

    Abstract: Safflower injection (SI), a water-extract preparation from safflower ( ...

    Abstract Safflower injection (SI), a water-extract preparation from safflower (
    Language English
    Publishing date 2022-11-23
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587355-6
    ISSN 1663-9812
    ISSN 1663-9812
    DOI 10.3389/fphar.2022.1062026
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  7. Article ; Online: Kdm1a safeguards the topological boundaries of PRC2-repressed genes and prevents aging-related euchromatinization in neurons.

    Del Blanco, Beatriz / Niñerola, Sergio / Martín-González, Ana M / Paraíso-Luna, Juan / Kim, Minji / Muñoz-Viana, Rafael / Racovac, Carina / Sanchez-Mut, Jose V / Ruan, Yijun / Barco, Ángel

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 1781

    Abstract: Kdm1a is a histone demethylase linked to intellectual disability with essential roles during gastrulation and the terminal differentiation of specialized cell types, including neurons, that remains highly expressed in the adult brain. To explore Kdm1a's ... ...

    Abstract Kdm1a is a histone demethylase linked to intellectual disability with essential roles during gastrulation and the terminal differentiation of specialized cell types, including neurons, that remains highly expressed in the adult brain. To explore Kdm1a's function in adult neurons, we develop inducible and forebrain-restricted Kdm1a knockouts. By applying multi-omic transcriptome, epigenome and chromatin conformation data, combined with super-resolution microscopy, we find that Kdm1a elimination causes the neuronal activation of nonneuronal genes that are silenced by the polycomb repressor complex and interspersed with active genes. Functional assays demonstrate that the N-terminus of Kdm1a contains an intrinsically disordered region that is essential to segregate Kdm1a-repressed genes from the neighboring active chromatin environment. Finally, we show that the segregation of Kdm1a-target genes is weakened in neurons during natural aging, underscoring the role of Kdm1a safeguarding neuronal genome organization and gene silencing throughout life.
    MeSH term(s) Histone Demethylases/genetics ; Histone Demethylases/metabolism ; Chromatin/genetics ; Neurons/metabolism
    Chemical Substances Histone Demethylases (EC 1.14.11.-) ; Chromatin
    Language English
    Publishing date 2024-03-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-45773-3
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  8. Article ; Online: The 5th International 3D Genomics Workshop 2018: conference report.

    Zhang, Yan / Ruan, Yijun / Li, Guoliang

    Epigenomics

    2019  Volume 11, Issue 12, Page(s) 1353–1357

    Abstract: The International 3D Genomics Workshop is an annual international scientific conference focused on the research of the 3D structure of the genome in the nucleus. The 5th International 3D Genomics Workshop 2018 was held at the International Academic ... ...

    Abstract The International 3D Genomics Workshop is an annual international scientific conference focused on the research of the 3D structure of the genome in the nucleus. The 5th International 3D Genomics Workshop 2018 was held at the International Academic Center of Huazhong Agricultural University on the 13th-14th of October 2018. It attracted >150 international and local participants, including leading researchers in the field of the 3D genomics and editors from top journals. The main topic of the conference was the research achievements newly published or unpublished on the 3D genome area. The invited speakers shared their works on the topic of the new detection technologies on the 3D genome, the advanced computational analysis algorithms or suites, the nucleus microimaging technique, the simulation modeling method, the application on the biological research in different species (human, animals, plants, microorganisms, etc.) and the applications of 3D genome on medicine and agriculture. The workshop provided a forum to discuss the latest scientific news and ideas from the field of 3D genome research on various aspects of interesting topics.
    MeSH term(s) Algorithms ; Cell Nucleus/genetics ; Computational Biology/methods ; DNA/chemistry ; Nucleic Acid Conformation
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2019-10-01
    Publishing country England
    Document type Congress ; Research Support, Non-U.S. Gov't
    ISSN 1750-192X
    ISSN (online) 1750-192X
    DOI 10.2217/epi-2019-0185
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  9. Article ; Online: Methods for comparative ChIA-PET and Hi-C data analysis.

    Capurso, Dan / Tang, Zhonghui / Ruan, Yijun

    Methods (San Diego, Calif.)

    2019  Volume 170, Page(s) 69–74

    Abstract: The three-dimensional architecture of chromatin in the nucleus is important for genome regulation and function. Advanced high-throughput sequencing-based methods have been developed for capturing chromatin interactions (Hi-C, genome-wide chromosome ... ...

    Abstract The three-dimensional architecture of chromatin in the nucleus is important for genome regulation and function. Advanced high-throughput sequencing-based methods have been developed for capturing chromatin interactions (Hi-C, genome-wide chromosome conformation capture) or enriching for those involving a specific protein (ChIA-PET, chromatin interaction analysis with paired-end tag sequencing). There is widespread interest in utilizing and interpreting ChIA-PET and Hi-C. We review methods for comparative ChIA-PET and Hi-C data analysis and visualization. The topics reviewed include: downloading ChIA-PET and Hi-C data from the ENCODE and 4DN portals; processing ChIA-PET data using ChIA-PIPE; processing Hi-C data using Juicer or distiller and cooler; viewing 2D contact maps using Juicebox or Higlass; viewing peaks, loops, and domains using BASIC Browser; annotating convergent and tandem CTCF loops.
    MeSH term(s) Cell Line ; Chromatin/genetics ; Chromatin/isolation & purification ; Chromatin Immunoprecipitation/methods ; Data Analysis ; Datasets as Topic ; Genomics/methods ; Humans ; Sequence Analysis, DNA ; Software
    Chemical Substances Chromatin
    Language English
    Publishing date 2019-10-16
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1066584-5
    ISSN 1095-9130 ; 1046-2023
    ISSN (online) 1095-9130
    ISSN 1046-2023
    DOI 10.1016/j.ymeth.2019.09.019
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  10. Article ; Online: Corrigendum: Chromatin Immunoprecipitation for Chromatin Interaction Analysis Using Paired-End-Tag (ChIA-PET) Sequencing in Tadpole Tissues.

    Buisine, Nicolas / Ruan, Xiaoan / Ruan, Yijun / Sachs, Laurent M

    Cold Spring Harbor protocols

    2020  Volume 2020, Issue 1, Page(s) pdb.corr106765

    Language English
    Publishing date 2020-01-02
    Publishing country United States
    Document type Journal Article ; Published Erratum
    ISSN 1559-6095
    ISSN (online) 1559-6095
    DOI 10.1101/pdb.corr106765
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