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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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

  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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
  37. Assembled genome sequences are being generated at an exponential rate. Here we present FCS-GX, part of NCBI’s Foreign Contamination Screen (FCS) tool suite, optimized to identify and remove contaminant sequenc...

    Authors: Alexander Astashyn, Eric S. Tvedte, Deacon Sweeney, Victor Sapojnikov, Nathan Bouk, Victor Joukov, Eyal Mozes, Pooja K. Strope, Pape M. Sylla, Lukas Wagner, Shelby L. Bidwell, Larissa C. Brown, Karen Clark, Emily W. Davis, Brian Smith-White, Wratko Hlavina…
    Citation: Genome Biology 2024 25:60
  38. CRISPR/Cas-derived base editor enables precise editing of target sites and has been widely used for basic research and crop genetic improvement. However, the editing efficiency of base editors at different tar...

    Authors: Guanying Wang, Fuqiu Wang, Zhongping Xu, Ying Wang, Can Zhang, Yi Zhou, Fengjiao Hui, Xiyan Yang, Xinhui Nie, Xianlong Zhang and Shuangxia Jin
    Citation: Genome Biology 2024 25:59
  39. Recent developments in auxin-inducible degron (AID) technology have increased its popularity for chemogenetic control of proteolysis. However, generation of human AID cell lines is challenging, especially in h...

    Authors: Shiqian Li, Yafei Wang, Miesje van der Stoel, Xin Zhou, Shrinidhi Madhusudan, Kristiina Kanerva, Van Dien Nguyen, Nazli Eskici, Vesa M. Olkkonen, You Zhou, Taneli Raivio and Elina Ikonen
    Citation: Genome Biology 2024 25:58
  40. A critical challenge of single-cell spatial transcriptomics (sc-ST) technologies is their panel size. Being based on fluorescence in situ hybridization, they are typically limited to panels of about a thousand...

    Authors: Mashrur Ahmed Yafi, Md. Hasibul Husain Hisham, Francisco Grisanti, James F. Martin, Atif Rahman and Md. Abul Hassan Samee
    Citation: Genome Biology 2024 25:57
  41. RNA secondary structure (RSS) can influence the regulation of transcription, RNA processing, and protein synthesis, among other processes. 3′ untranslated regions (3′ UTRs) of mRNA also hold the key for many a...

    Authors: Tianru Zhang, Changhao Li, Jiaying Zhu, Yanjun Li, Zhiye Wang, Chun-Yip Tong, Yu Xi, Yi Han, Hisashi Koiwa, Xu Peng and Xiuren Zhang
    Citation: Genome Biology 2024 25:54
  42. The FokI catalytic domain can be fused to various DNA binding architectures to improve the precision of genome editing tools. However, evaluation of off-target effects is essential for developing these tools. ...

    Authors: Long Xie, Hu Feng, Zhifang Li, Di Li, Xiali Yang, Tanglong Yuan, Nana Yan, Chenfei He, Jitan Zheng, Zhenrui Zuo, Yaxuan Zheng, Yaqi Cao, Yangqing Lu, Xing Yao Xiong and Erwei Zuo
    Citation: Genome Biology 2024 25:51
  43. Nanopore sequencing generates noisy electrical signals that need to be converted into a standard string of DNA nucleotide bases using a computational step called basecalling. The performance of basecalling has...

    Authors: Gagandeep Singh, Mohammed Alser, Kristof Denolf, Can Firtina, Alireza Khodamoradi, Meryem Banu Cavlak, Henk Corporaal and Onur Mutlu
    Citation: Genome Biology 2024 25:49

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