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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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

  9. 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
  10. 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

  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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

  22. 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

  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. The COVID-19 pandemic has emphasized the importance of accurate detection of known and emerging pathogens. However, robust characterization of pathogenic sequences remains an open challenge. To address this ne...

    Authors: Advait Balaji, Bryce Kille, Anthony D. Kappell, Gene D. Godbold, Madeline Diep, R. A. Leo Elworth, Zhiqin Qian, Dreycey Albin, Daniel J. Nasko, Nidhi Shah, Mihai Pop, Santiago Segarra, Krista L. Ternus and Todd J. Treangen
    Citation: Genome Biology 2022 23:133
  29. Proteogenomics aims to identify variant or unknown proteins in bottom-up proteomics, by searching transcriptome- or genome-derived custom protein databases. However, empirical observations reveal that these la...

    Authors: Laura Fancello and Thomas Burger
    Citation: Genome Biology 2022 23:132
  30. Genetic studies of human traits have revolutionized our understanding of the variation between individuals, and yet, the genetics of most traits is still poorly understood. In this review, we highlight the maj...

    Authors: Nadav Brandes, Omer Weissbrod and Michal Linial
    Citation: Genome Biology 2022 23:131
  31. A challenge in bulk gene differential expression analysis is to differentiate changes due to cell type-specific gene expression and cell type proportions. SCADIE is an iterative algorithm that simultaneously e...

    Authors: Daiwei Tang, Seyoung Park and Hongyu Zhao
    Citation: Genome Biology 2022 23:129
  32. Copy number alterations constitute important phenomena in tumor evolution. Whole genome single-cell sequencing gives insight into copy number profiles of individual cells, but is highly noisy. Here, we propose...

    Authors: Magda Markowska, Tomasz Cąkała, BłaŻej Miasojedow, Bogac Aybey, Dilafruz Juraeva, Johanna Mazur, Edith Ross, Eike Staub and Ewa Szczurek
    Citation: Genome Biology 2022 23:128
  33. Multiple sclerosis (MS) is an autoimmune condition of the central nervous system with a well-characterized genetic background. Prior analyses of MS genetics have identified broad enrichments across peripheral ...

    Authors: Michael H. Guo, Prashanth Sama, Brenna A. LaBarre, Hrishikesh Lokhande, John Balibalos, Ci Chu, Xiaomi Du, Pouya Kheradpour, Charles C. Kim, Taylor Oniskey, Thomas Snyder, Damien Z. Soghoian, Howard L. Weiner, Tanuja Chitnis and Nikolaos A. Patsopoulos
    Citation: Genome Biology 2022 23:127
  34. SARS-CoV-2 infection results in a broad spectrum of COVID-19 disease, from mild or no symptoms to hospitalization and death. COVID-19 disease severity has been associated with some pre-existing conditions and ...

    Authors: Matthew C. Pahl, Carole Le Coz, Chun Su, Prabhat Sharma, Rajan M. Thomas, James A. Pippin, Emylette Cruz Cabrera, Matthew E. Johnson, Michelle E. Leonard, Sumei Lu, Alessandra Chesi, Kathleen E. Sullivan, Neil Romberg, Struan F. A. Grant and Andrew D. Wells
    Citation: Genome Biology 2022 23:125
  35. Tumors are complex tissues of cancerous cells surrounded by a heterogeneous cellular microenvironment with which they interact. Single-cell sequencing enables molecular characterization of single cells within ...

    Authors: Jan Dohmen, Artem Baranovskii, Jonathan Ronen, Bora Uyar, Vedran Franke and Altuna Akalin
    Citation: Genome Biology 2022 23:123
  36. DNA methylation plays vital roles in both prokaryotes and eukaryotes. There are three forms of DNA methylation in prokaryotes: N6-methyladenine (6mA), N4-methylcytosine (4mC), and 5-methylcytosine (5mC). Although...

    Authors: Xuwen Li, Shiyuan Guo, Yan Cui, Zijian Zhang, Xinlong Luo, Margarita T. Angelova, Laura F. Landweber, Yinsheng Wang and Tao P. Wu
    Citation: Genome Biology 2022 23:122
  37. The plasticity along the epithelial-mesenchymal transition (EMT) spectrum has been shown to be regulated by various epigenetic repertoires. Emerging evidence of local chromatin conformation changes suggests th...

    Authors: Qing You Pang, Tuan Zea Tan, Vignesh Sundararajan, Yi-Chia Chiu, Edward Yu Wing Chee, Vin Yee Chung, Mahesh A. Choolani and Ruby Yun-Ju Huang
    Citation: Genome Biology 2022 23:121

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