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  1. Lamina-associated domains (LADs) are large genomic regions that are positioned at the nuclear lamina. It has remained largely unclear what drives the positioning and demarcation of LADs. Because the insulator ...

    Authors: Tom van Schaik, Ning Qing Liu, Stefano G. Manzo, Daan Peric-Hupkes, Elzo de Wit and Bas van Steensel
    Citation: Genome Biology 2022 23:185
  2. Out of the thousands of metabolites in a given specimen, most metabolomics experiments measure only hundreds, with poor overlap across experimental platforms. Here, we describe Metabolite Imputation via Rank-T...

    Authors: Benjamin A. Freeman, Sophie Jaro, Tricia Park, Sam Keene, Wesley Tansey and Ed Reznik
    Citation: Genome Biology 2022 23:184
  3. With the arrival of telomere-to-telomere (T2T) assemblies of the human genome comes the computational challenge of efficiently and accurately constructing multiple genome alignments at an unprecedented scale. ...

    Authors: Bryce Kille, Advait Balaji, Fritz J. Sedlazeck, Michael Nute and Todd J. Treangen
    Citation: Genome Biology 2022 23:182
  4. RNA-DNA hybrid (R-loop)-associated long noncoding RNAs (lncRNAs), including the Arabidopsis lncRNA AUXIN-REGULATED PROMOTER LOOP (APOLO), are emerging as important regulators of three-dimensional chromatin confor...

    Authors: Camille Fonouni-Farde, Aurélie Christ, Thomas Blein, María Florencia Legascue, Lucía Ferrero, Michaël Moison, Leandro Lucero, Juan Sebastián Ramírez-Prado, David Latrasse, Daniel Gonzalez, Moussa Benhamed, Leandro Quadrana, Martin Crespi and Federico Ariel
    Citation: Genome Biology 2022 23:181
  5. Maize (Zea mays L.) is at the vanguard facing the upcoming breeding challenges. However, both a super pan-genome for the Zea genus and a comprehensive genetic variation map for maize breeding are still lacking.

    Authors: Songtao Gui, Wenjie Wei, Chenglin Jiang, Jingyun Luo, Lu Chen, Shenshen Wu, Wenqiang Li, Yuebin Wang, Shuyan Li, Ning Yang, Qing Li, Alisdair R. Fernie and Jianbing Yan
    Citation: Genome Biology 2022 23:178
  6. Dyskerin is a nuclear protein involved in H/ACA box snoRNA-guided uridine modification of RNA. In humans, its defective function is associated with cancer development and induces specific post-transcriptional ...

    Authors: Federico Zacchini, Giulia Venturi, Veronica De Sanctis, Roberto Bertorelli, Claudio Ceccarelli, Donatella Santini, Mario Taffurelli, Marianna Penzo, Davide Treré, Alberto Inga, Erik Dassi and Lorenzo Montanaro
    Citation: Genome Biology 2022 23:177
  7. Cross-species comparison of transcriptomes is important for elucidating evolutionary molecular mechanisms underpinning phenotypic variation between and within species, yet to date it has been essentially limit...

    Authors: Yuelin Yao, Shuli Liu, Charley Xia, Yahui Gao, Zhangyuan Pan, Oriol Canela-Xandri, Ava Khamseh, Konrad Rawlik, Sheng Wang, Bingjie Li, Yi Zhang, Erola Pairo-Castineira, Kenton D’Mellow, Xiujin Li, Ze Yan, Cong-jun Li…
    Citation: Genome Biology 2022 23:176
  8. We present a novel unsupervised deep learning approach called BindVAE, based on Dirichlet variational autoencoders, for jointly decoding multiple TF binding signals from open chromatin regions. BindVAE can dis...

    Authors: Meghana Kshirsagar, Han Yuan, Juan Lavista Ferres and Christina Leslie
    Citation: Genome Biology 2022 23:174
  9. Simple translocations and complex rearrangements are formed through illegitimate ligations of double-strand breaks of fusion partners and lead to generation of oncogenic fusion genes that affect cellular funct...

    Authors: Zhihao Xing, Huirong Mai, Xiaorong Liu, Xiaoying Fu, Xingliang Zhang, Lichun Xie, Yunsheng Chen, Adam Shlien and Feiqiu Wen
    Citation: Genome Biology 2022 23:173
  10. Recombination maps are  important resources for epidemiological and evolutionary analyses; however, there are currently no recombination maps representing any African population outside of those with West Afri...

    Authors: Gerald van Eeden, Caitlin Uren, Evlyn Pless, Mira Mastoras, Gian D. van der Spuy, Gerard Tromp, Brenna M. Henn and Marlo Möller
    Citation: Genome Biology 2022 23:172
  11. A fused method using a combination of multi-omics data enables a comprehensive study of complex biological processes and highlights the interrelationship of relevant biomolecules and their functions. Driven by...

    Authors: Dongjin Leng, Linyi Zheng, Yuqi Wen, Yunhao Zhang, Lianlian Wu, Jing Wang, Meihong Wang, Zhongnan Zhang, Song He and Xiaochen Bo
    Citation: Genome Biology 2022 23:171
  12. Oxidative phosphorylation (OXPHOS) complexes consist of nuclear and mitochondrial DNA-encoded subunits. Their biogenesis requires cross-compartment gene regulation to mitigate the accumulation of disproportion...

    Authors: Iliana Soto, Mary Couvillion, Katja G. Hansen, Erik McShane, J. Conor Moran, Antoni Barrientos and L. Stirling Churchman
    Citation: Genome Biology 2022 23:170
  13. Spatial transcriptomic studies are reaching single-cell spatial resolution, with data often collected from multiple tissue sections. Here, we present a computational method, BASS, that enables multi-scale and ...

    Authors: Zheng Li and Xiang Zhou
    Citation: Genome Biology 2022 23:168
  14. Plants undergo programmed chromatin changes in response to environment, influencing heritable phenotypic plasticity. The RNA-directed DNA methylation (RdDM) pathway is an essential component of this reprogramm...

    Authors: Hardik Kundariya, Robersy Sanchez, Xiaodong Yang, Alenka Hafner and Sally A. Mackenzie
    Citation: Genome Biology 2022 23:167
  15. Individual and environmental health outcomes are frequently linked to changes in the diversity of associated microbial communities. Thus, deriving health indicators based on microbiome diversity measures is es...

    Authors: M. Senthil Kumar, Eric V. Slud, Christine Hehnly, Lijun Zhang, James Broach, Rafael A. Irizarry, Steven J. Schiff and Joseph N. Paulson
    Citation: Genome Biology 2022 23:166
  16. Due to post-cleavage residence of the Cas9-sgRNA complex at its target, Cas9-induced DNA double-strand breaks (DSBs) have to be exposed to engage DSB repair pathways. Target interaction of Cas9-sgRNA determine...

    Authors: Si-Cheng Liu, Yi-Li Feng, Xiu-Na Sun, Ruo-Dan Chen, Qian Liu, Jing-Jing Xiao, Jin-Na Zhang, Zhi-Cheng Huang, Ji-Feng Xiang, Guo-Qiao Chen, Yi Yang, Chao Lou, Hao-Dan Li, Zhen Cai, Shi-Ming Xu, Hui Lin…
    Citation: Genome Biology 2022 23:165
  17. Cytosine DNA methylation is widely described as a transcriptional repressive mark with the capacity to silence promoters. Epigenome engineering techniques enable direct testing of the effect of induced DNA met...

    Authors: Alex de Mendoza, Trung Viet Nguyen, Ethan Ford, Daniel Poppe, Sam Buckberry, Jahnvi Pflueger, Matthew R. Grimmer, Sabine Stolzenburg, Ozren Bogdanovic, Alicia Oshlack, Peggy J. Farnham, Pilar Blancafort and Ryan Lister
    Citation: Genome Biology 2022 23:163
  18. Two-dimensional high-throughput data have become increasingly common in functional genomics studies, which raises new challenges in data analysis. Here, we introduce a new statistic called Zeta, initially deve...

    Authors: Yajing Hao, Shuyang Zhang, Changwei Shao, Junhui Li, Guofeng Zhao, Dong-Er Zhang and Xiang-Dong Fu
    Citation: Genome Biology 2022 23:162
  19. Low efficiency has seriously restricted the application of prime editing (PE) systems in plants. In this study, we develop an enhanced plant prime editor 2 system, enpPE2, by stacking various optimization stra...

    Authors: Juan Li, Like Chen, Jing Liang, Rongfang Xu, Yingli Jiang, Yizhen Li, Jian Ding, Min Li, Ruiying Qin and Pengcheng Wei
    Citation: Genome Biology 2022 23:161
  20. The most stable structure of DNA is the canonical right-handed double helix termed B DNA. However, certain environments and sequence motifs favor alternative conformations, termed non-canonical secondary struc...

    Authors: Ilias Georgakopoulos-Soares, Candace S. Y. Chan, Nadav Ahituv and Martin Hemberg
    Citation: Genome Biology 2022 23:159

    The Author Correction to this article has been published in Genome Biology 2022 23:164

  21. The Oxford Nanopore (ONT) platform provides portable and rapid genome sequencing, and its ability to natively profile DNA methylation without complex sample processing is attractive for point-of-care real-time...

    Authors: Efrat Katsman, Shari Orlanski, Filippo Martignano, Ilana Fox-Fisher, Ruth Shemer, Yuval Dor, Aviad Zick, Amir Eden, Iacopo Petrini, Silvestro G. Conticello and Benjamin P. Berman
    Citation: Genome Biology 2022 23:158
  22. Authors: Ateeq M. Khaliq, Cihat Erdogan, Zeyneb Kurt, Sultan Sevgi Turgut, Miles W. Grunvald, Tim Rand, Sonal Khare, Jefrey A. Borgia, Dana M. Hayden, Sam G. Pappas, Henry R. Govekar, Audrey E. Kam, Jochen Reiser, Kiran Turaga, Milan Radovich, Yong Zang…
    Citation: Genome Biology 2022 23:156

    The original article was published in Genome Biology 2022 23:113

  23. Speciation genes contribute disproportionately to species divergence, but few examples exist, especially in vertebrates. Here we test whether Zan, which encodes the sperm acrosomal protein zonadhesin that mediate...

    Authors: Emma K. Roberts, Steve Tardif, Emily A. Wright, Roy N. Platt II, Robert D. Bradley and Daniel M. Hardy
    Citation: Genome Biology 2022 23:155
  24. Ubiquitination is essential for many cellular processes in eukaryotes, including 26S proteasome-dependent protein degradation, cell cycle progression, transcriptional regulation, and signal transduction. Altho...

    Authors: Ruyi Wang, Xiaoman You, Chongyang Zhang, Hong Fang, Min Wang, Fan Zhang, Houxiang Kang, Xiao Xu, Zheng Liu, Jiyang Wang, Qingzhen Zhao, Xuli Wang, Zeyun Hao, Feng He, Hui Tao, Debao Wang…
    Citation: Genome Biology 2022 23:154
  25. Nanopore sequencing enables the efficient and unbiased measurement of transcriptomes. Current methods for transcript identification and quantification rely on mapping reads to a reference genome, which preclud...

    Authors: Ivan de la Rubia, Akanksha Srivastava, Wenjing Xue, Joel A. Indi, Silvia Carbonell-Sala, Julien Lagarde, M. Mar Albà and Eduardo Eyras
    Citation: Genome Biology 2022 23:153
  26. We develop scSTEM, single-cell STEM, a method for clustering dynamic profiles of genes in trajectories inferred from pseudotime ordering of single-cell RNA-seq (scRNA-seq) data. scSTEM uses one of several metr...

    Authors: Qi Song, Jingtao Wang and Ziv Bar-Joseph
    Citation: Genome Biology 2022 23:150
  27. Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technolog...

    Authors: Runxuan Zhang, Richard Kuo, Max Coulter, Cristiane P. G. Calixto, Juan Carlos Entizne, Wenbin Guo, Yamile Marquez, Linda Milne, Stefan Riegler, Akihiro Matsui, Maho Tanaka, Sarah Harvey, Yubang Gao, Theresa Wießner-Kroh, Alejandro Paniagua, Martin Crespi…
    Citation: Genome Biology 2022 23:149
  28. Sensing and responding to stresses determine the tolerance of plants to adverse environments. The triploid Chinese white poplar is widely cultivated in North China because of its adaptation to a wide range of ...

    Authors: Shaofei Tong, Yubo Wang, Ningning Chen, Deyan Wang, Bao Liu, Weiwei Wang, Yang Chen, Jianquan Liu, Tao Ma and Yuanzhong Jiang
    Citation: Genome Biology 2022 23:148
  29. There are many short-read variant-calling tools, with different strengths and weaknesses. We present a tool, Minos, which combines outputs from arbitrary variant callers, increasing recall without loss of prec...

    Authors: Martin Hunt, Brice Letcher, Kerri M. Malone, Giang Nguyen, Michael B. Hall, Rachel M. Colquhoun, Leandro Lima, Michael C. Schatz, Srividya Ramakrishnan and Zamin Iqbal
    Citation: Genome Biology 2022 23:147
  30. Plant metabolites reshaped by nature and human beings are crucial for both their lives and human health. However, which metabolites respond most strongly to selection pressure at different evolutionary stages ...

    Authors: Ke Cao, Bin Wang, Weichao Fang, Gengrui Zhu, Changwen Chen, Xinwei Wang, Yong Li, Jinlong Wu, Tang Tang, Zhangjun Fei, Jie Luo and Lirong Wang
    Citation: Genome Biology 2022 23:146
  31. Persian walnut, Juglans regia, occurs naturally from Greece to western China, while its closest relative, the iron walnut, Juglans sigillata, is endemic in southwest China; both species are cultivated for their n...

    Authors: Ya-Mei Ding, Yu Cao, Wei-Ping Zhang, Jun Chen, Jie Liu, Pan Li, Susanne S. Renner, Da-Yong Zhang and Wei-Ning Bai
    Citation: Genome Biology 2022 23:145
  32. Genome-wide mapping of histone modifications is critical to understanding transcriptional regulation. CUT&Tag is a new method for profiling histone modifications, offering improved sensitivity and decreased co...

    Authors: William M. Yashar, Garth Kong, Jake VanCampen, Brittany M. Curtiss, Daniel J. Coleman, Lucia Carbone, Galip Gürkan Yardimci, Julia E. Maxson and Theodore P. Braun
    Citation: Genome Biology 2022 23:144
  33. We developed Bookend, a package for transcript assembly that incorporates data from different RNA-seq techniques, with a focus on identifying and utilizing RNA 5′ and 3′ ends. We demonstrate that correct ident...

    Authors: Michael A. Schon, Stefan Lutzmayer, Falko Hofmann and Michael D. Nodine
    Citation: Genome Biology 2022 23:143

    The Publisher Correction to this article has been published in Genome Biology 2022 23:157

  34. Authors: J. James E. Barrett, Chiara Herzog, Yoo-Na Kim, Thomas E. Bartlett, Allison Jones, Iona Evans, David Cibula, Michal Zikan, Line Bjørge, Nadia Harbeck, Nicoletta Colombo, Sacha J. Howell, Angelique Flöter Rådestad, Kristina Gemzell-Danielsson and Martin Widschwendter
    Citation: Genome Biology 2022 23:142

    The original article was published in Genome Biology 2022 23:52

  35. Clinical laboratories routinely use formalin-fixed paraffin-embedded (FFPE) tissue or cell block cytology samples in oncology panel sequencing to identify mutations that can predict patient response to targete...

    Authors: Yifan Zhang, Thomas M. Blomquist, Rebecca Kusko, Daniel Stetson, Zhihong Zhang, Lihui Yin, Robert Sebra, Binsheng Gong, Jennifer S. Lococo, Vinay K. Mittal, Natalia Novoradovskaya, Ji-Youn Yeo, Nicole Dominiak, Jennifer Hipp, Amelia Raymond, Fujun Qiu…
    Citation: Genome Biology 2022 23:141
  36. Coessentiality networks derived from CRISPR screens in cell lines provide a powerful framework for identifying functional modules in the cell and for inferring the roles of uncharacterized genes. However, thes...

    Authors: Eiru Kim, Lance C. Novak, Chenchu Lin, Medina Colic, Lori L. Bertolet, Veronica Gheorghe, Christopher A. Bristow and Traver Hart
    Citation: Genome Biology 2022 23:140
  37. There are major efforts underway to make genome sequencing a routine part of clinical practice. A critical barrier to these is achieving practical solutions for data ownership and integrity. Blockchain provide...

    Authors: Gamze Gürsoy, Charlotte M. Brannon, Eric Ni, Sarah Wagner, Amol Khanna and Mark Gerstein
    Citation: Genome Biology 2022 23:134
  38. In studies of cellular function in cancer, researchers are increasingly able to choose from many -omics assays as functional readouts. Choosing the correct readout for a given study can be difficult, and which...

    Authors: Jake Crawford, Brock C. Christensen, Maria Chikina and Casey S. Greene
    Citation: Genome Biology 2022 23:137
  39. Chromatin states and enhancers associate gene expression, cell identity and disease. Here, we systematically delineate the acute innate immune response to endotoxin in terms of human macrophage enhancer activi...

    Authors: Ping Zhang, Harindra E. Amarasinghe, Justin P. Whalley, Chwen Tay, Hai Fang, Gabriele Migliorini, Andrew C. Brown, Alice Allcock, Giuseppe Scozzafava, Phalguni Rath, Benjamin Davies and Julian C. Knight
    Citation: Genome Biology 2022 23:136

Annual Journal Metrics

  • 2022 Citation Impact
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    17.4 - 5-year Impact Factor
    3.476 - SNIP (Source Normalized Impact per Paper)
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    97 days submission to first editorial decision for all manuscripts (Median)
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