Relevant bibliographies by topics / Chia-PET

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers

Academic literature on the topic 'Chia-PET'

Author: Grafiati
Published: 9 March 2023
Last updated: 31 July 2025

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Journal articles on the topic "Chia-PET"

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Liu, Tong, and Zheng Wang. "DeepChIA-PET: Accurately predicting ChIA-PET from Hi-C and ChIP-seq with deep dilated networks." PLOS Computational Biology 19, no. 7 (2023): e1011307. http://dx.doi.org/10.1371/journal.pcbi.1011307.

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Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) can capture genome-wide chromatin interactions mediated by a specific DNA-associated protein. The ChIA-PET experiments have been applied to explore the key roles of different protein factors in chromatin folding and transcription regulation. However, compared with widely available Hi-C and ChIP-seq data, there are not many ChIA-PET datasets available in the literature. A computational method for accurately predicting ChIA-PET interactions from Hi-C and ChIP-seq data is needed that can save the efforts of performing wet-lab
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Li, Sun, Chang, Cai, Hong, and Zhou. "Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3)." Genes 10, no. 7 (2019): 554. http://dx.doi.org/10.3390/genes10070554.

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Understanding chromatin interactions is important because they create chromosome conformation and link the cis- and trans- regulatory elements to their target genes for transcriptional regulation. Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing is a genome-wide high-throughput technology that detects chromatin interactions associated with a specific protein of interest. We developed ChIA-PET Tool for ChIA-PET data analysis in 2010. Here, we present the updated version of ChIA-PET Tool (V3) as a computational package to process the next-generation sequence data generate
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Lee, Byoungkoo, Jiahui Wang, Liuyang Cai, et al. "ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization." Science Advances 6, no. 28 (2020): eaay2078. http://dx.doi.org/10.1126/sciadv.aay2078.

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ChIA-PET (chromatin interaction analysis with paired-end tags) enables genome-wide discovery of chromatin interactions involving specific protein factors, with base pair resolution. Interpretation of ChIA-PET data requires a robust analytic pipeline. Here, we introduce ChIA-PIPE, a fully automated pipeline for ChIA-PET data processing, quality assessment, visualization, and analysis. ChIA-PIPE performs linker filtering, read mapping, peak calling, and loop calling and automates quality control assessment for each dataset. To enable visualization, ChIA-PIPE generates input files for two-dimensi
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Hershey, David. "Don't Just Pet Your Chia." Science Activities: Classroom Projects and Curriculum Ideas 32, no. 2 (1995): 8–12. http://dx.doi.org/10.1080/00368121.1995.10113179.

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Vardaxis, Ioannis, Finn Drabløs, Morten B. Rye, and Bo Henry Lindqvist. "MACPET: model-based analysis for ChIA-PET." Biostatistics 21, no. 3 (2019): 625–39. http://dx.doi.org/10.1093/biostatistics/kxy084.

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Summary We present model-based analysis for ChIA-PET (MACPET), which analyzes paired-end read sequences provided by ChIA-PET for finding binding sites of a protein of interest. MACPET uses information from both tags of each PET and searches for binding sites in a two-dimensional space, while taking into account different noise levels in different genomic regions. MACPET shows favorable results compared with MACS in terms of motif occurrence and spatial resolution. Furthermore, significant binding sites discovered by MACPET are involved in a higher number of significant three-dimensional intera
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Small, Ernest. "34. Chia – not just a pet." Biodiversity 12, no. 1 (2011): 49–56. http://dx.doi.org/10.1080/14888386.2011.575104.

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Li, Guipeng, Yang Chen, Michael P. Snyder, and Michael Q. Zhang. "ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis." Nucleic Acids Research 45, no. 1 (2016): e4-e4. http://dx.doi.org/10.1093/nar/gkw809.

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Zhang, Jingyao, Huay Mei Poh, Su Qin Peh, et al. "ChIA-PET analysis of transcriptional chromatin interactions." Methods 58, no. 3 (2012): 289–99. http://dx.doi.org/10.1016/j.ymeth.2012.08.009.

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He, Chao, Guipeng Li, Diekidel M. Nadhir, Yang Chen, Xiaowo Wang, and Michael Q. Zhang. "Advances in computational ChIA-PET data analysis." Quantitative Biology 4, no. 3 (2016): 217–25. http://dx.doi.org/10.1007/s40484-016-0080-3.

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Phanstiel, Douglas H., Alan P. Boyle, Nastaran Heidari, and Michael P. Snyder. "Mango: a bias-correcting ChIA-PET analysis pipeline." Bioinformatics 31, no. 19 (2015): 3092–98. http://dx.doi.org/10.1093/bioinformatics/btv336.

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Dissertations / Theses on the topic "Chia-PET"

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PAGIN, MIRIAM. "Identification and functional characterization of Sox2-target genes involved in brain disease and abnormal brain development." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2017. http://hdl.handle.net/10281/170795.

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Il gene Sox2 codifica per un fattore di trascrizione attivo nelle cellule staminali durante lo sviluppo del SNC nei vertebrati. Mutazioni eterozigoti di Sox2 nell'uomo causano uno spettro caratteristico di anomalie del SNC, che coinvolgono l'ippocampo e l'occhio, e che causano epilessia, disabilità di apprendimento e difettivo controllo motorio. Per comprendere il ruolo di Sox2 nello sviluppo neuronale, il nostro laboratorio ha generato KO condizionali di Sox2 nel topo. Le conseguenze della delezione di Sox2 in diversi momenti dello sviluppo producono importanti difetti cerebrali. Il KO condiz
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Book chapters on the topic "Chia-PET"

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Ruan, Xiaoan, and Yijun Ruan. "Chromatin Interaction Analysis Using Paired-End Tag Sequencing (ChIA-PET)." In Tag-Based Next Generation Sequencing. Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527644582.ch12.

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Ouyang, Weizhi, and Xingwang Li. "Mapping Active Gene-Associated Chromatin Loops by ChIA-PET in Rice." In Methods in Molecular Biology. Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-3354-0_12.

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Chabasiński, Rafał, Kaustav Sengupta, and Dariusz Plewczynski. "The Identification of Chromatin Contact Domains (CCD) in Human Genomes from ChIA-PET Data Using Graph Methods." In Proceedings of International Conference on Data, Electronics and Computing. Springer Nature Singapore, 2023. http://dx.doi.org/10.1007/978-981-99-1509-5_23.

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Buisine, Nicolas, Patrice Bilesimo, Gladys Alfama, et al. "Thyroid Hormone Receptor Mapping onXenopus tropicalisGenome by ChIA-PET Analysis." In BASIC - The Expanding Universe of Thyroid Biology. The Endocrine Society, 2011. http://dx.doi.org/10.1210/endo-meetings.2011.part4.or2.or30-1.

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Conference papers on the topic "Chia-PET"

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Sun, Jialiang, Zhihan Ruan, Chaoyang Yan, and Jian Liu. "AREDCI: Assessing Reproducibility and Differential Chromatin Interactions for ChIA-PET Sequencing Data." In 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2024. https://doi.org/10.1109/bibm62325.2024.10822709.

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"Computer tools for spatial chromosome contacts analysis by ChIA-PET and Hi-C data." In SYSTEMS BIOLOGY AND BIOINFORMATICS. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 2019. http://dx.doi.org/10.18699/sbb-2019-07.

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You might also be interested in the extended bibliographies on the topic 'Chia-PET' for particular source types:
Journal articles
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