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  1. Untranslated regions (UTRs) are important mediators of post-transcriptional regulation. The length of UTRs and the composition of regulatory elements within them are known to vary substantially across genes, b...

    Authors: Nechama Wieder, Elston N. D’Souza, Alexandra C. Martin-Geary, Frederik H. Lassen, Jonathan Talbot-Martin, Maria Fernandes, Sonia P. Chothani, Owen J. L. Rackham, Sebastian Schafer, Julie L. Aspden, Daniel G. MacArthur, Robert W. Davies and Nicola Whiffin
    Citation: Genome Biology 2024 25:111
  2. Single-cell multiplexing techniques (cell hashing and genetic multiplexing) combine multiple samples, optimizing sample processing and reducing costs. Cell hashing conjugates antibody-tags or chemical-oligonuc...

    Authors: Fabiola Curion, Xichen Wu, Lukas Heumos, Mylene Mariana Gonzales André, Lennard Halle, Matiss Ozols, Melissa Grant-Peters, Charlotte Rich-Griffin, Hing-Yuen Yeung, Calliope A. Dendrou, Herbert B. Schiller and Fabian J. Theis
    Citation: Genome Biology 2024 25:109
  3. Prime editing enables precise base substitutions, insertions, and deletions at targeted sites without the involvement of double-strand DNA breaks or exogenous donor DNA templates. However, the large size of pr...

    Authors: Shuangshuang Mu, Huangyao Chen, Qianru Li, Shixue Gou, Xiaoyi Liu, Junwei Wang, Wei Zheng, Menglong Chen, Qin Jin, Liangxue Lai, Kepin Wang and Hui Shi
    Citation: Genome Biology 2024 25:108
  4. Long-read sequencing data, particularly those derived from the Oxford Nanopore sequencing platform, tend to exhibit high error rates. Here, we present NextDenovo, an efficient error correction and assembly too...

    Authors: Jiang Hu, Zhuo Wang, Zongyi Sun, Benxia Hu, Adeola Oluwakemi Ayoola, Fan Liang, Jingjing Li, José R. Sandoval, David N. Cooper, Kai Ye, Jue Ruan, Chuan-Le Xiao, Depeng Wang, Dong-Dong Wu and Sheng Wang
    Citation: Genome Biology 2024 25:107
  5. The proliferation antigen Ki-67 has been widely used in clinical settings for cancer staging for many years, but investigations on its biological functions have lagged. Recently, Ki-67 has been shown to regula...

    Authors: Konstantinos Stamatiou, Florentin Huguet, Lukas V. Serapinas, Christos Spanos, Juri Rappsilber and Paola Vagnarelli
    Citation: Genome Biology 2024 25:105
  6. Single-cell sequencing datasets are key in biology and medicine for unraveling insights into heterogeneous cell populations with unprecedented resolution. Here, we construct a single-cell multi-omics map of hu...

    Authors: Lu Pan, Paolo Parini, Roman Tremmel, Joseph Loscalzo, Volker M. Lauschke, Bradley A. Maron, Paola Paci, Ingemar Ernberg, Nguan Soon Tan, Zehuan Liao, Weiyao Yin, Sundararaman Rengarajan and Xuexin Li
    Citation: Genome Biology 2024 25:104
  7. Splicing factors are vital for the regulation of RNA splicing, but some have also been implicated in regulating transcription. The underlying molecular mechanisms of their involvement in transcriptional proces...

    Authors: Xian Du, Wenying Qin, Chunyu Yang, Lin Dai, Mingkui San, Yingdan Xia, Siyu Zhou, Mengyang Wang, Shuang Wu, Shaorui Zhang, Huiting Zhou, Fangshu Li, Fang He, Jingfeng Tang, Jia-Yu Chen, Yu Zhou…
    Citation: Genome Biology 2024 25:102
  8. Multiplexed assays of variant effect (MAVEs) have emerged as a powerful approach for interrogating thousands of genetic variants in a single experiment. The flexibility and widespread adoption of these techniq...

    Authors: Melina Claussnitzer, Victoria N. Parikh, Alex H. Wagner, Jeremy A. Arbesfeld, Carol J. Bult, Helen V. Firth, Lara A. Muffley, Alex N. Nguyen Ba, Kevin Riehle, Frederick P. Roth, Daniel Tabet, Benedetta Bolognesi, Andrew M. Glazer and Alan F. Rubin
    Citation: Genome Biology 2024 25:100
  9. Spatial molecular data has transformed the study of disease microenvironments, though, larger datasets pose an analytics challenge prompting the direct adoption of single-cell RNA-sequencing tools including no...

    Authors: Dharmesh D. Bhuva, Chin Wee Tan, Agus Salim, Claire Marceaux, Marie A. Pickering, Jinjin Chen, Malvika Kharbanda, Xinyi Jin, Ning Liu, Kristen Feher, Givanna Putri, Wayne D. Tilley, Theresa E. Hickey, Marie-Liesse Asselin-Labat, Belinda Phipson and Melissa J. Davis
    Citation: Genome Biology 2024 25:99
  10. Amino acid substitutions can perturb protein activity in multiple ways. Understanding their mechanistic basis may pinpoint how residues contribute to protein function. Here, we characterize the mechanisms unde...

    Authors: Sarah Gersing, Thea K. Schulze, Matteo Cagiada, Amelie Stein, Frederick P. Roth, Kresten Lindorff-Larsen and Rasmus Hartmann-Petersen
    Citation: Genome Biology 2024 25:98
  11. As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinformatic virus identif...

    Authors: Ling-Yi Wu, Yasas Wijesekara, Gonçalo J. Piedade, Nikolaos Pappas, Corina P. D. Brussaard and Bas E. Dutilh
    Citation: Genome Biology 2024 25:97
  12. We present a non-parametric statistical method called TDEseq that takes full advantage of smoothing splines basis functions to account for the dependence of multiple time points in scRNA-seq studies, and uses ...

    Authors: Yue Fan, Lei Li and Shiquan Sun
    Citation: Genome Biology 2024 25:96
  13. Aneuploidy, an abnormal number of chromosomes within a cell, is a hallmark of cancer. Patterns of aneuploidy differ across cancers, yet are similar in cancers affecting closely related tissues. The selection p...

    Authors: Juman Jubran, Rachel Slutsky, Nir Rozenblum, Lior Rokach, Uri Ben-David and Esti Yeger-Lotem
    Citation: Genome Biology 2024 25:95
  14. Recent innovations in single-cell RNA-sequencing (scRNA-seq) provide the technology to investigate biological questions at cellular resolution. Pooling cells from multiple individuals has become a common strat...

    Authors: Drew Neavin, Anne Senabouth, Himanshi Arora, Jimmy Tsz Hang Lee, Aida Ripoll-Cladellas, Lude Franke, Shyam Prabhakar, Chun Jimmie Ye, Davis J. McCarthy, Marta Melé, Martin Hemberg and Joseph E. Powell
    Citation: Genome Biology 2024 25:94
  15. Unraveling bacterial gene function drives progress in various areas, such as food production, pharmacology, and ecology. While omics technologies capture high-dimensional phenotypic data, linking them to genom...

    Authors: Thomas Roder, Grégory Pimentel, Pascal Fuchsmann, Mireille Tena Stern, Ueli von Ah, Guy Vergères, Stephan Peischl, Ola Brynildsrud, Rémy Bruggmann and Cornelia Bär
    Citation: Genome Biology 2024 25:93
  16. Although sequencing technologies have boosted the measurement of the genomic diversity of plant crops, it remains challenging to accurately genotype millions of genetic variants, especially structural variatio...

    Authors: Ze-Zhen Du, Jia-Bao He and Wen-Biao Jiao
    Citation: Genome Biology 2024 25:91
  17. Single-cell ATAC-seq has emerged as a powerful approach for revealing candidate cis-regulatory elements genome-wide at cell-type resolution. However, current single-cell methods suffer from limited throughput ...

    Authors: Xuan Zhang, Alexandre P. Marand, Haidong Yan and Robert J. Schmitz
    Citation: Genome Biology 2024 25:90
  18. Advancements in cytometry technologies have enabled quantification of up to 50 proteins across millions of cells at single cell resolution. Analysis of cytometry data routinely involves tasks such as data inte...

    Authors: Givanna H. Putri, George Howitt, Felix Marsh-Wakefield, Thomas M. Ashhurst and Belinda Phipson
    Citation: Genome Biology 2024 25:89
  19. Inferring gene regulatory networks (GRNs) from single-cell data is challenging due to heuristic limitations. Existing methods also lack estimates of uncertainty. Here we present Probabilistic Matrix Factorizat...

    Authors: Claudia Skok Gibbs, Omar Mahmood, Richard Bonneau and Kyunghyun Cho
    Citation: Genome Biology 2024 25:88
  20. DNA methylation is an essential epigenetic modification. However, its contribution to trait changes and diversity in the domestication of perennial fruit trees remains unknown.

    Authors: Bobo Song, Jinshan Yu, Xiaolong Li, Jiaming Li, Jing Fan, Hainan Liu, Weilin Wei, Lingchao Zhang, Kaidi Gu, Dongliang Liu, Kejiao Zhao and Jun Wu
    Citation: Genome Biology 2024 25:87
  21. Cell type annotation and lineage construction are two of the most critical tasks conducted in the analyses of single-cell RNA sequencing (scRNA-seq). Four recent scRNA-seq studies of differentiating xylem prop...

    Authors: Ying-Lan Chen, Jo-Wei Allison Hsieh, Shang-Che Kuo, Chung-Ting Kao, Chia-Chun Tung, Jhong-He Yu, Tien-Hsien Chang, Chuan Ku, Jianbo Xie, Deqiang Zhang, Quanzi Li and Ying-Chung Jimmy Lin
    Citation: Genome Biology 2024 25:85

    The original article was published in Genome Biology 2023 24:3

    The original article was published in Genome Biology 2021 22:319

    The Correspondence to this article has been published in Genome Biology 2024 25:86

  22. Epigenetic marks are reprogrammed during sexual reproduction. In flowering plants, DNA methylation is only partially remodeled in the gametes and the zygote. However, the timing and functional significance of ...

    Authors: Xue Li, Bo Zhu, Yue Lu, Feng Zhao, Qian Liu, Jiahao Wang, Miaomiao Ye, Siyuan Chen, Junwei Nie, Lizhong Xiong, Yu Zhao, Changyin Wu and Dao-Xiu Zhou
    Citation: Genome Biology 2024 25:84
  23. The rise of large-scale multi-species genome sequencing projects promises to shed new light on how genomes encode gene regulatory instructions. To this end, new algorithms are needed that can leverage conserva...

    Authors: Alexander Karollus, Johannes Hingerl, Dennis Gankin, Martin Grosshauser, Kristian Klemon and Julien Gagneur
    Citation: Genome Biology 2024 25:83
  24. The spatial organization of molecules in a cell is essential for their functions. While current methods focus on discerning tissue architecture, cell–cell interactions, and spatial expression patterns, they ar...

    Authors: Clarence K. Mah, Noorsher Ahmed, Nicole A. Lopez, Dylan C. Lam, Avery Pong, Alexander Monell, Colin Kern, Yuanyuan Han, Gino Prasad, Anthony J. Cesnik, Emma Lundberg, Quan Zhu, Hannah Carter and Gene W. Yeo
    Citation: Genome Biology 2024 25:82
  25. The use of single-cell technologies for clinical applications requires disconnecting sampling from downstream processing steps. Early sample preservation can further increase robustness and reproducibility by ...

    Authors: Laura Jiménez-Gracia, Domenica Marchese, Juan C. Nieto, Ginevra Caratù, Elisa Melón-Ardanaz, Victoria Gudiño, Sara Roth, Kellie Wise, Natalie K. Ryan, Kirk B. Jensen, Xavier Hernando-Momblona, Joana P. Bernardes, Florian Tran, Laura Katharina Sievers, Stefan Schreiber, Maarten van den Berge…
    Citation: Genome Biology 2024 25:81
  26. Small RNAs are essential for germ cell development and fertilization. However, fundamental questions remain, such as the level of conservation in small RNA composition between species and whether small RNAs co...

    Authors: Li Hou, Wei Liu, Hongdao Zhang, Ronghong Li, Miao Liu, Huijuan Shi and Ligang Wu
    Citation: Genome Biology 2024 25:80
  27. Further advancement of genome editing highly depends on the development of tools with higher compatibility with eukaryotes. A multitude of described Cas9s have great potential but require optimization for geno...

    Authors: Giulia Vittoria Ruta, Matteo Ciciani, Eyemen Kheir, Michele Domenico Gentile, Simone Amistadi, Antonio Casini and Anna Cereseto
    Citation: Genome Biology 2024 25:79
  28. The problem of missing heritability requires the consideration of genetic interactions among different loci, called epistasis. Current GWAS statistical models require years to assess the entire combinatorial e...

    Authors: Clément Carré, Jean Baptiste Carluer, Christian Chaux, Chad Estoup-Streiff, Nicolas Roche, Eric Hosy, André Mas and Gabriel Krouk
    Citation: Genome Biology 2024 25:76
  29. We develop a large-scale single-cell ATAC-seq method by combining Tn5-based pre-indexing with 10× Genomics barcoding, enabling the indexing of up to 200,000 nuclei across multiple samples in a single reaction....

    Authors: Hao Zhang, Ryan M. Mulqueen, Natalie Iannuzo, Dominique O. Farrera, Francesca Polverino, James J. Galligan, Julie G. Ledford, Andrew C. Adey and Darren A. Cusanovich
    Citation: Genome Biology 2024 25:78
  30. B-type lamins are critical nuclear envelope proteins that interact with the three-dimensional genomic architecture. However, identifying the direct roles of B-lamins on dynamic genome organization has been cha...

    Authors: Emily M. Pujadas Liwag, Xiaolong Wei, Nicolas Acosta, Lucas M. Carter, Jiekun Yang, Luay M. Almassalha, Surbhi Jain, Ali Daneshkhah, Suhas S. P. Rao, Fidan Seker-Polat, Kyle L. MacQuarrie, Joe Ibarra, Vasundhara Agrawal, Erez Lieberman Aiden, Masato T. Kanemaki, Vadim Backman…
    Citation: Genome Biology 2024 25:77
  31. Although the human bladder is reported to harbor unique microbiota, our understanding of how these microbial communities interact with their human hosts is limited, mostly owing to the lack of isolates to test...

    Authors: Jingjie Du, Mark Khemmani, Thomas Halverson, Adriana Ene, Roberto Limeira, Lana Tinawi, Baylie R. Hochstedler-Kramer, Melline Fontes Noronha, Catherine Putonti and Alan J. Wolfe
    Citation: Genome Biology 2024 25:75
  32. Early embryonic developmental programs are guided by the coordinated interplay between maternally inherited and zygotically manufactured RNAs and proteins. Although these processes happen concomitantly and aff...

    Authors: Danielson Baia Amaral, Rhonda Egidy, Anoja Perera and Ariel A Bazzini
    Citation: Genome Biology 2024 25:74
  33. With the rapid advancements in spatial transcriptome sequencing, multiple tissue slices are now available, enabling the integration and interpretation of spatial cellular landscapes. Herein, we introduce SpaDo...

    Authors: Bin Duan, Shaoqi Chen, Xiaojie Cheng and Qi Liu
    Citation: Genome Biology 2024 25:73
  34. DANCE is the first standard, generic, and extensible benchmark platform for accessing and evaluating computational methods across the spectrum of benchmark datasets for numerous single-cell analysis tasks. Cur...

    Authors: Jiayuan Ding, Renming Liu, Hongzhi Wen, Wenzhuo Tang, Zhaoheng Li, Julian Venegas, Runze Su, Dylan Molho, Wei Jin, Yixin Wang, Qiaolin Lu, Lingxiao Li, Wangyang Zuo, Yi Chang, Yuying Xie and Jiliang Tang
    Citation: Genome Biology 2024 25:72
  35. Recent advances in microscopy have enabled studying chromosome organization at the single-molecule level, yet little is known about inherited chromosome organization. Here we adapt single-molecule chromosome t...

    Authors: Silvia Gutnik, Jia Emil You, Ahilya N. Sawh, Aude Andriollo and Susan E. Mango
    Citation: Genome Biology 2024 25:71
  36. Extensive research has been conducted on fruit development in crops, but the metabolic regulatory networks underlying perennial fruit trees remain poorly understood. To address this knowledge gap, we conduct a...

    Authors: Chao Gu, Mao-Song Pei, Zhi-Hua Guo, Lei Wu, Kai-Jie Qi, Xue-Ping Wang, Hong Liu, Zhongchi Liu, Zhaobo Lang and Shaoling Zhang
    Citation: Genome Biology 2024 25:70
  37. Long-read sequencing can enable the detection of base modifications, such as CpG methylation, in single molecules of DNA. The most commonly used methods for long-read sequencing are nanopore developed by Oxfor...

    Authors: Brynja D. Sigurpalsdottir, Olafur A. Stefansson, Guillaume Holley, Doruk Beyter, Florian Zink, Marteinn Þ. Hardarson, Sverrir Þ. Sverrisson, Nina Kristinsdottir, Droplaug N. Magnusdottir, Olafur Þ. Magnusson, Daniel F. Gudbjartsson, Bjarni V. Halldorsson and Kari Stefansson
    Citation: Genome Biology 2024 25:69
  38. In rheumatoid arthritis (RA), the activation of T and B cell clones specific for self-antigens leads to the chronic inflammation of the synovium. Here, we perform an in-depth quantitative analysis of the seven...

    Authors: Adrià Aterido, María López-Lasanta, Francisco Blanco, Antonio Juan-Mas, María Luz García-Vivar, Alba Erra, Carolina Pérez-García, Simón Ángel Sánchez-Fernández, Raimon Sanmartí, Antonio Fernández-Nebro, Mercedes Alperi-López, Jesús Tornero, Ana María Ortiz, Carlos Marras Fernández-Cid, Núria Palau, Wenjing Pan…
    Citation: Genome Biology 2024 25:68
  39. Bromo-adjacent homology-plant homeodomain domain containing protein 1 (BP1) is a reader of histone post-translational modifications in fungi. BP1 recognizes trimethylation of lysine 27 in histone H3 (H3K27me3)...

    Authors: Guangfei Tang, Haoxue Xia, Yufei Huang, Yuanwen Guo, Yun Chen, Zhonghua Ma and Wende Liu
    Citation: Genome Biology 2024 25:67
  40. Oncometabolites, often generated as a result of a gene mutation, show pro-oncogenic function when abnormally accumulated in cancer cells. Identification of such mutation-associated metabolites will facilitate ...

    Authors: GaRyoung Lee, Sang Mi Lee, Sungyoung Lee, Chang Wook Jeong, Hyojin Song, Sang Yup Lee, Hongseok Yun, Youngil Koh and Hyun Uk Kim
    Citation: Genome Biology 2024 25:66
  41. Tumors are able to acquire new capabilities, including traits such as drug resistance and metastasis that are associated with unfavorable clinical outcomes. Single-cell technologies have made it possible to st...

    Authors: Jae-Won Cho, Jingyi Cao and Martin Hemberg
    Citation: Genome Biology 2024 25:65
  42. The function of diverse ruminal microbes is tightly linked to rumen development and host physiology. The system of ruminal microbes is an excellent model to clarify the fundamental ecological relationships amo...

    Authors: Daming Sun, Gaorui Bian, Kai Zhang, Ning Liu, Yuyang Yin, Yuanlong Hou, Fei Xie, Weiyun Zhu, Shengyong Mao and Junhua Liu
    Citation: Genome Biology 2024 25:64
  43. Centromeres are critical for maintaining genomic stability in eukaryotes, and their turnover shapes genome architectures and drives karyotype evolution. However, the co-evolution of centromeres from different ...

    Authors: Chuanye Chen, Siying Wu, Yishuang Sun, Jingwei Zhou, Yiqian Chen, Jing Zhang, James A. Birchler, Fangpu Han, Ning Yang and Handong Su
    Citation: Genome Biology 2024 25:63
  44. Cancer cells often exhibit DNA copy number aberrations and can vary widely in their ploidy. Correct estimation of the ploidy of single-cell genomes is paramount for downstream analysis. Based only on single-ce...

    Authors: Michael P. Schneider, Amy E. Cullen, Justina Pangonyte, Jason Skelton, Harvey Major, Elke Van Oudenhove, Maria J. Garcia, Blas Chaves Urbano, Anna M. Piskorz, James D. Brenton, Geoff Macintyre and Florian Markowetz
    Citation: Genome Biology 2024 25:62
  45. Tartary buckwheat, Fagopyrum tataricum, is a pseudocereal crop with worldwide distribution and high nutritional value. However, the origin and domestication history of this crop remain to be elucidated.

    Authors: Yuqi He, Kaixuan Zhang, Yaliang Shi, Hao Lin, Xu Huang, Xiang Lu, Zhirong Wang, Wei Li, Xibo Feng, Taoxiong Shi, Qingfu Chen, Junzhen Wang, Yu Tang, Mark A. Chapman, Mateja Germ, Zlata Luthar…
    Citation: Genome Biology 2024 25:61

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