Enhancing Single-Cell and Bulk Hi-C Data Using a Generative Transformer Model by Ruoying Gao, Thomas N. Ferraro, Liang Chen, Shaoqiang Zhang, Yong Chen

Subjects: “…Hi-C…”
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RobusTAD: reference panel based annotation of nested topologically associating domains by Yanlin Zhang, Rola Dali, Mathieu Blanchette

Subjects: “…Hi-C…”
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Comparison of normalization methods for Hi-C data by Hongqiang Lyu, Erhu Liu, Zhifang Wu

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Unveiling Multi‐Scale Architectural Features in Single‐Cell Hi‐C Data Using scCAFE by Fuzhou Wang, Jiecong Lin, Hamid Alinejad‐Rokny, Wenjing Ma, Lingkuan Meng, Lei Huang, Jixiang Yu, Nanjun Chen, Yuchen Wang, Zhongyu Yao, Weidun Xie, Ka‐Chun Wong, Xiangtao Li

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A mini-review of single-cell Hi-C embedding methods by Rui Ma, Jingong Huang, Tao Jiang, Wenxiu Ma

Subjects: “…Single-cell Hi-C…”
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The hierarchical folding dynamics of topologically associating domains during early embryo development by Xuemei Bai, Xiaohan Tang, Yuyang Wang, Shutong Yue, Xiang Xu, Pengzhen Hu, Jingxuan Xu, Yaru Li, Junting Wang, Huan Tao, Yang Zheng, Bijia Chen, Mengge Tian, Lin Lin, Ruiqing Wang, Yu Sun, Chao Ren, Xiaochen Bo, Hao Li, Hebing Chen, Meisong Lu

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Single‐Cell Hi‐C Technologies and Computational Data Analysis by Madison A Dautle, Yong Chen

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Differential genome organization revealed by comparative topological analysis of Mycobacterium tuberculosis strains H37Rv and H37Ra by Mohit Mishra, Ajay Arya, Md. Zubbair Malik, Akanksha Mishra, Seyed E. Hasnain, Rakesh Bhatnagar, Shandar Ahmad, Rupesh Chaturvedi

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ProbC: joint modeling of epigenome and transcriptome effects in 3D genome by Emre Sefer

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A 3D Genome Atlas of Genetic Variants and Their Pathological Effects in Cancer by Li Tang, Matthew C. Hill, Mingxing He, Junhao Chen, Zirui Wang, Patrick T. Ellinor, Min Li

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HiCDiffusion - diffusion-enhanced, transformer-based prediction of chromatin interactions from DNA sequences by Mateusz Chiliński, Dariusz Plewczynski

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TADBD: a sensitive and fast method for detection of typologically associated domain boundaries by Hongqiang Lyu, Lin Li, Zhifang Wu, Tian Wang, Jiguang Zheng, Hongda Wang

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Chromosome‐Level Genome Assembly for the Chinese Serow (Capricornis milneedwardsii) Provides Insights Into Its Taxonomic Status and Evolution by Anning Li, Qimeng Yang, Rongrong Li, Keli Cai, Li Zhu, Xiaoyu Wang, Gong Cheng, Xihong Wang, Yinghu Lei, Yu Jiang, Linsen Zan

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A chromosome-scale genome assembly of mungbean (Vigna radiata) by Supaporn Khanbo, Poompat Phadphon, Chaiwat Naktang, Duangjai Sangsrakru, Pitchaporn Waiyamitra, Nattapol Narong, Chutintorn Yundaeng, Sithichoke Tangphatsornruang, Kularb Laosatit, Prakit Somta, Wirulda Pootakham

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Using genomics to explore the epidemiology of vancomycin resistance in a sewage system by Emilie Egholm Bruun Jensen, Saria Otani, Ivan Liachko, Benjamin Auch, Frank M. Aarestrup

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Linear dicentric chromosomes in bacterial natural isolates reveal common constraints for replicon fusion by Ram Sanath-Kumar, Arafat Rahman, Zhongqing Ren, Ian P. Reynolds, Lauren Augusta, Clay Fuqua, Alexandra J. Weisberg, Xindan Wang

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Multi-omics analysis in primary T cells elucidates mechanisms behind disease-associated genetic loci by Chenfu Shi, Danyun Zhao, Jake Butler, Antonios Frantzeskos, Stefano Rossi, James Ding, Carlo Ferrazzano, Charlotte Wynn, Ryan Malcolm Hum, Ellie Richards, Muskan Gupta, Khadijah Patel, Chuan Fu Yap, Darren Plant, Richard Grencis, Paul Martin, Antony Adamson, Stephen Eyre, John Bowes, Anne Barton, Pauline Ho, Magnus Rattray, Gisela Orozco

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Editorial: Precision exploration of plant germplasm resources: breakthroughs and applications in telomere-to-telomere (T2T) genomics by Longxin Wang, Kai-Hua Jia

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SEE: A Method for Predicting the Dynamics of Chromatin Conformation Based on Single‐Cell Gene Expression by Minghong Li, Yurong Yang, Rucheng Wu, Haiyan Gong, Zan Yuan, Jixin Wang, Erping Long, Xiaotong Zhang, Yang Chen

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Hidden origami in Trypanosoma cruzi nuclei highlights its non-random 3D genomic organization by Natália Karla Bellini, Pedro Leonardo Carvalho de Lima, David da Silva Pires, Julia Pinheiro Chagas da Cunha

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