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  1. 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

  2. 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
  3. 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

  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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

  15. 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

  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. Cancer is a set of diseases characterized by unchecked cell proliferation and invasion of surrounding tissues. The many genes that have been genetically associated with cancer or shown to directly contribute t...

    Authors: Anupama Jha, Mathieu Quesnel-Vallières, David Wang, Andrei Thomas-Tikhonenko, Kristen W Lynch and Yoseph Barash
    Citation: Genome Biology 2022 23:117
  32. Pleiotropy describes the phenomenon in which a gene affects multiple phenotypes. The extent of pleiotropy is still disputed, mainly because of issues of inadequate power of analyses. A further challenge is tha...

    Authors: Eirini Christodoulaki, Viola Nolte, Wei-Yun Lai and Christian Schlötterer
    Citation: Genome Biology 2022 23:116
  33. Several high-throughput antibody-free methods for RNA modification detection from sequencing data have been developed. We present JACUSA2 as a versatile software solution and comprehensive analysis framework f...

    Authors: Michael Piechotta, Isabel S. Naarmann-de Vries, Qi Wang, Janine Altmüller and Christoph Dieterich
    Citation: Genome Biology 2022 23:115
  34. Technological development has enabled the profiling of gene expression and chromatin accessibility from the same cell. We develop scREG, a dimension reduction methodology, based on the concept of cis-regulatory p...

    Authors: Zhana Duren, Fengge Chang, Fnu Naqing, Jingxue Xin, Qiao Liu and Wing Hung Wong
    Citation: Genome Biology 2022 23:114
  35. Colorectal cancer (CRC) consensus molecular subtypes (CMS) have different immunological, stromal cell, and clinicopathological characteristics. Single-cell characterization of CMS subtype tumor microenvironmen...

    Authors: Ateeq M. Khaliq, Cihat Erdogan, Zeyneb Kurt, Sultan Sevgi Turgut, Miles W. Grunvald, Tim Rand, Sonal Khare, Jeffrey 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 23:113

    The Author Correction to this article has been published in Genome Biology 2022 23:156

  36. Integration of single-cell multiomics profiles generated by different single-cell technologies from the same biological sample is still challenging. Previous approaches based on shared features have only provi...

    Authors: Jinzhuang Dou, Shaoheng Liang, Vakul Mohanty, Qi Miao, Yuefan Huang, Qingnan Liang, Xuesen Cheng, Sangbae Kim, Jongsu Choi, Yumei Li, Li Li, May Daher, Rafet Basar, Katayoun Rezvani, Rui Chen and Ken Chen
    Citation: Genome Biology 2022 23:112
  37. Recent proteogenomic studies revealed extensive translation outside of annotated protein coding regions, such as non-coding RNAs and untranslated regions of mRNAs. This non-canonical translation is largely due...

    Authors: Dmitry E. Andreev, Gary Loughran, Alla D. Fedorova, Maria S. Mikhaylova, Ivan N. Shatsky and Pavel V. Baranov
    Citation: Genome Biology 2022 23:111

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