Unravelling single-cell DNA replication timing dynamics using machine learning reveals heterogeneity in cancer progression

Authors: Joseph M. Josephides, Chun-Long Chen

Source: Nature Communications, Vol 16, Iss 1, Pp 1-15 (2025)

Subject Terms: Science

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Relation: https://doaj.org/toc/2041-1723

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Editorial: Epigenetic regulation of genome integrity and its implications in human diseases

Authors: Zhiming Li, Xiao Chen, Chun-Long Chen

Source: Frontiers in Cell and Developmental Biology, Vol 12 (2024)

Subject Terms: epigenetic regulation, histone modification, DNA methylation, RNA modification, genome integrity, cancer epigenetics, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fcell.2024.1535839/full; https://doaj.org/toc/2296-634X

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Assembly of short amphiphilic peptoids into nanohelices with controllable supramolecular chirality

Authors: Renyu Zheng, Mingfei Zhao, Jingshan S. Du, Tarunya Rao Sudarshan, Yicheng Zhou, Anant K. Paravastu, James J. De Yoreo, Andrew L. Ferguson, Chun-Long Chen

Source: Nature Communications, Vol 15, Iss 1, Pp 1-9 (2024)

Subject Terms: Science

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Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/521fcd784d1d4b9bb5700b22d8befa07

Directing polymorph specific calcium carbonate formation with de novo protein templates

Authors: Fatima A. Davila-Hernandez, Biao Jin, Harley Pyles, Shuai Zhang, Zheming Wang, Timothy F. Huddy, Asim K. Bera, Alex Kang, Chun-Long Chen, James J. De Yoreo, David Baker

Source: Nature Communications, Vol 14, Iss 1, Pp 1-11 (2023)

Subject Terms: Science

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Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/6cacd6f254a84ca6bc2400ddc3231925

Pan-cancer surveys indicate cell cycle-related roles of primate-specific genes in tumors and embryonic cerebrum

Authors: Chenyu Ma, Chunyan Li, Huijing Ma, Daqi Yu, Yufei Zhang, Dan Zhang, Tianhan Su, Jianmin Wu, Xiaoyue Wang, Li Zhang, Chun-Long Chen, Yong E. Zhang

Source: Genome Biology, Vol 23, Iss 1, Pp 1-29 (2022)

Subject Terms: Molecular atavism, Antagonistic pleiotropy, Primate-specific genes, Cancer evolution, Brain evolution, Cell cycle, Biology (General), QH301-705.5, Genetics, QH426-470

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Relation: https://doaj.org/toc/1474-760X

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Highly stable and tunable peptoid/hemin enzymatic mimetics with natural peroxidase-like activities

Authors: Tengyue Jian, Yicheng Zhou, Peipei Wang, Wenchao Yang, Peng Mu, Xin Zhang, Xiao Zhang, Chun-Long Chen

Source: Nature Communications, Vol 13, Iss 1, Pp 1-13 (2022)

Subject Terms: Science

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Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/e024b5609e6f4c23b5482ca6b3ce4487

Kronos scRT: a uniform framework for single-cell replication timing analysis

Authors: Stefano Gnan, Joseph M. Josephides, Xia Wu, Manuela Spagnuolo, Dalila Saulebekova, Mylène Bohec, Marie Dumont, Laura G. Baudrin, Daniele Fachinetti, Sylvain Baulande, Chun-Long Chen

Source: Nature Communications, Vol 13, Iss 1, Pp 1-15 (2022)

Subject Terms: Science

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Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/fd1aed25b9a042d2a333d9c51e20f10b

Editorial: Chromosomal fragile sites, genome instability and human diseases

Authors: Qing Hu, Advaitha Madireddy, Stefano Gnan, Chun-Long Chen

Source: Frontiers in Genetics, Vol 13 (2023)

Subject Terms: fragile sites, replication stress, genome instability, human disease, DNA damage repair, Genetics, QH426-470

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fgene.2022.1119532/full; https://doaj.org/toc/1664-8021

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DNA transposons mediate duplications via transposition-independent and -dependent mechanisms in metazoans

Authors: Shengjun Tan, Huijing Ma, Jinbo Wang, Man Wang, Mengxia Wang, Haodong Yin, Yaqiong Zhang, Xinying Zhang, Jieyu Shen, Danyang Wang, Graham L. Banes, Zhihua Zhang, Jianmin Wu, Xun Huang, Hua Chen, Siqin Ge, Chun-Long Chen, Yong E. Zhang

Source: Nature Communications, Vol 12, Iss 1, Pp 1-14 (2021)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

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Identification of new driver and passenger mutations within APOBEC-induced hotspot mutations in bladder cancer

Authors: Ming-Jun Shi, Xiang-Yu Meng, Jacqueline Fontugne, Chun-Long Chen, François Radvanyi, Isabelle Bernard-Pierrot

Source: Genome Medicine, Vol 12, Iss 1, Pp 1-20 (2020)

Subject Terms: Bladder cancer, APOBEC, Mutagenesis, Stem-loop, Driver mutation, Passenger mutation, Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s13073-020-00781-y; https://doaj.org/toc/1756-994X

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Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites

Authors: Alexy Promonet, Ismaël Padioleau, Yaqun Liu, Lionel Sanz, Anna Biernacka, Anne-Lyne Schmitz, Magdalena Skrzypczak, Amélie Sarrazin, Clément Mettling, Maga Rowicka, Krzysztof Ginalski, Frédéric Chedin, Chun-Long Chen, Yea-Lih Lin, Philippe Pasero

Source: Nature Communications, Vol 11, Iss 1, Pp 1-12 (2020)

Subject Terms: Science

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Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/bd1932962b864455ac3b032015f1a0ac

Prospectively defined patterns of APOBEC3A mutagenesis are prevalent in human cancers

Authors: Rachel A. DeWeerd, Eszter Németh, Ádám Póti, Nataliya Petryk, Chun-Long Chen, Olivier Hyrien, Dávid Szüts, Abby M. Green

Source: Cell Reports, Vol 38, Iss 12, Pp 110555- (2022)

Subject Terms: CP:Cancer, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124722002996; https://doaj.org/toc/2211-1247

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Transcription-mediated organization of the replication initiation program across large genes sets common fragile sites genome-wide

Authors: Olivier Brison, Sami El-Hilali, Dana Azar, Stéphane Koundrioukoff, Mélanie Schmidt, Viola Nähse, Yan Jaszczyszyn, Anne-Marie Lachages, Bernard Dutrillaux, Claude Thermes, Michelle Debatisse, Chun-Long Chen

Source: Nature Communications, Vol 10, Iss 1, Pp 1-12 (2019)

Subject Terms: Science

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Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/faa892657e9143c2a1486f882b9f0db1

Editorial: DNA Replication Stress and Cell Fate

Authors: Lin Deng, Chun-Long Chen, Yuanliang Zhai, Yunzhou Dong, Huiqiang Lou

Source: Frontiers in Cell and Developmental Biology, Vol 9 (2021)

Subject Terms: DNA replication, replication stress, fork reversal, DNA damage repair, genome instability, cell fate, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fcell.2021.778486/full; https://doaj.org/toc/2296-634X

Access URL: https://doaj.org/article/93476f9a1a334fe0a79aa1fefec6a297

Replication stress induces global chromosome breakage in the fragile X genome

Authors: Arijita Chakraborty, Piroon Jenjaroenpun, Jing Li, Sami El Hilali, Andrew McCulley, Brian Haarer, Elizabeth A. Hoffman, Aimee Belak, Audrey Thorland, Heidi Hehnly, Carl L. Schildkraut, Chun-long Chen, Vladimir A. Kuznetsov, Wenyi Feng

Source: Cell Reports, Vol 34, Iss 12, Pp 108838- (2021)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124721001522; https://doaj.org/toc/2211-1247

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Topoisomerase I prevents transcription-replication conflicts at transcription termination sites

Authors: Yaqun Liu, Yea-Lih Lin, Philippe Pasero, Chun-Long Chen

Source: Molecular & Cellular Oncology, Vol 8, Iss 1 (2021)

Subject Terms: transcription-replication conflict, r-loops, topoisomerase i, chromosome breaks, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://doaj.org/toc/2372-3556

Access URL: https://doaj.org/article/35e4cba44cab42719755eb47f371e731

Sequence-Defined Nanotubes Assembled from IR780-Conjugated Peptoids for Chemophototherapy of Malignant Glioma

Authors: Xiaoli Cai, Mingming Wang, Peng Mu, Tengyue Jian, Dong Liu, Shichao Ding, Yanan Luo, Dan Du, Yang Song, Chun-Long Chen, Yuehe Lin

Source: Research, Vol 2021 (2021)

Subject Terms: Science

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Relation: https://doaj.org/toc/2639-5274

Access URL: https://doaj.org/article/4ce2d729fe3846f9b457f27477aa8ac9

Sequence‐Defined Peptoids with OH and COOH Groups As Binders to Reduce Cracks of Si Nanoparticles of Lithium‐Ion Batteries

Authors: Qianyu Zhang, Chaofeng Zhang, Wenwei Luo, Lifeng Cui, Yan‐Jie Wang, Tengyue Jian, Xiaolin Li, Qizhang Yan, Haodong Liu, Chuying Ouyang, Yulin Chen, Chun‐Long Chen, Jiujun Zhang

Source: Advanced Science, Vol 7, Iss 18, Pp n/a-n/a (2020)

Subject Terms: capacity, lithium‐ion batteries, peptoids, polymeric binders, Si anodes, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2198-3844

Access URL: https://doaj.org/article/5d737492cf5f4e99add83b08a62ffe25

Replication Stress Induces Global Chromosome Breakage in the Fragile X Genome

Authors: Arijita Chakraborty, Piroon Jenjaroenpun, Jing Li, Sami El Hilali, Andrew McCulley, Brian Haarer, Elizabeth A. Hoffman, Aimee Belak, Audrey Thorland, Heidi Hehnly, Carl Schildkraut, Chun-long Chen, Vladimir A. Kuznetsov, Wenyi Feng

Source: Cell Reports, Vol 32, Iss 12, Pp 108179- (2020)

Subject Terms: fragile X syndrome, FXS, FMRP, I304N, DNA double-strand breaks, DSB, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124720311682; https://doaj.org/toc/2211-1247

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Controlled synthesis of highly-branched plasmonic gold nanoparticles through peptoid engineering

Authors: Feng Yan, Lili Liu, Tiffany R. Walsh, Yu Gong, Patrick Z. El-Khoury, Yanyan Zhang, Zihua Zhu, James J. De Yoreo, Mark H. Engelhard, Xin Zhang, Chun-Long Chen

Source: Nature Communications, Vol 9, Iss 1, Pp 1-8 (2018)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/9f8410bf5326487b8b1d7ed007a6271c