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  1. CIMP (CpG island methylator phenotype) is an epigenetic molecular subtype, observed in multiple malignancies and associated with the epigenetic silencing of tumor suppressors. Currently, for most cancers inclu...

    Authors: Nisha Padmanabhan, Huang Kie Kyon, Arnoud Boot, Kevin Lim, Supriya Srivastava, Shuwen Chen, Zhiyuan Wu, Hyung-Ok Lee, Vineeth T. Mukundan, Charlene Chan, Yarn Kit Chan, Ong Xuewen, Jason J. Pitt, Zul Fazreen Adam Isa, Manjie Xing, Ming Hui Lee…

    Citation: Genome Biology 2021 22:167

    Content type: Research

    Published on:

    The Author Correction to this article has been published in Genome Biology 2021 22:181

  2. Despite the prevalence and recurrence of polyploidization in the speciation of flowering plants, its impacts on crop intraspecific genome diversification are largely unknown. Brassica rapa is a mesopolyploid spec...

    Authors: Xu Cai, Lichun Chang, Tingting Zhang, Haixu Chen, Lei Zhang, Runmao Lin, Jianli Liang, Jian Wu, Michael Freeling and Xiaowu Wang

    Citation: Genome Biology 2021 22:166

    Content type: Research

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  3. Advancing RNA structural probing techniques with next-generation sequencing has generated demands for complementary computational tools to robustly extract RNA structural information amidst sampling noise and ...

    Authors: Paolo Marangio, Ka Ying Toby Law, Guido Sanguinetti and Sander Granneman

    Citation: Genome Biology 2021 22:165

    Content type: Method

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  4. High-throughput chromosome conformation capture assays, such as Hi-C, have shown that the genome is organized into organizational units such as topologically associating domains (TADs), which can impact gene r...

    Authors: Da-Inn Lee and Sushmita Roy

    Citation: Genome Biology 2021 22:164

    Content type: Method

    Published on:

  5. A pressing challenge in single-cell transcriptomics is to benchmark experimental protocols and computational methods. A solution is to use computational simulators, but existing simulators cannot simultaneousl...

    Authors: Tianyi Sun, Dongyuan Song, Wei Vivian Li and Jingyi Jessica Li

    Citation: Genome Biology 2021 22:163

    Content type: Method

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    The Publisher Correction to this article has been published in Genome Biology 2021 22:177

  6. Visual validation is an important step to minimize false-positive predictions from structural variant (SV) detection. We present Samplot, a tool for creating images that display the read depth and sequence ali...

    Authors: Jonathan R. Belyeu, Murad Chowdhury, Joseph Brown, Brent S. Pedersen, Michael J. Cormier, Aaron R. Quinlan and Ryan M. Layer

    Citation: Genome Biology 2021 22:161

    Content type: Method

    Published on:

  7. Elevated temperatures can cause physiological, biochemical, and molecular responses in plants that can greatly affect their growth and development. Mutations are the most fundamental force driving biological e...

    Authors: Zhaogeng Lu, Jiawen Cui, Li Wang, Nianjun Teng, Shoudong Zhang, Hon-Ming Lam, Yingfang Zhu, Siwei Xiao, Wensi Ke, Jinxing Lin, Chenwu Xu and Biao Jin

    Citation: Genome Biology 2021 22:160

    Content type: Research

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  8. Structural variation (SV) acts as an essential mutational force shaping the evolution and function of the human genome. However, few studies have examined the role of SVs in high-altitude adaptation and little...

    Authors: Cheng Quan, Yuanfeng Li, Xinyi Liu, Yahui Wang, Jie Ping, Yiming Lu and Gangqiao Zhou

    Citation: Genome Biology 2021 22:159

    Content type: Research

    Published on:

  9. treeclimbR is for analyzing hierarchical trees of entities, such as phylogenies or cell types, at different resolutions. It proposes multiple candidates that capture the latent signal and pinpoints branches or le...

    Authors: Ruizhu Huang, Charlotte Soneson, Pierre-Luc Germain, Thomas S.B. Schmidt, Christian Von Mering and Mark D. Robinson

    Citation: Genome Biology 2021 22:157

    Content type: Method

    Published on:

  10. Lung adenocarcinoma (LUAD) is a highly malignant and heterogeneous tumor that involves various oncogenic genetic alterations. Epigenetic processes play important roles in lung cancer development. However, the ...

    Authors: Chongze Yuan, Haojie Chen, Shiqi Tu, Hsin-Yi Huang, Yunjian Pan, Xiuqi Gui, Muyu Kuang, Xuxia Shen, Qiang Zheng, Yang Zhang, Chao Cheng, Hui Hong, Xiaoting Tao, Yizhou Peng, Xingxin Yao, Feilong Meng…

    Citation: Genome Biology 2021 22:156

    Content type: Research

    Published on:

  11. Nascent RNA profiling is growing in popularity; however, there is no standard analysis pipeline to uniformly process the data and assess quality. Here, we introduce PEPPRO, a comprehensive, scalable workflow f...

    Authors: Jason P. Smith, Arun B. Dutta, Kizhakke Mattada Sathyan, Michael J. Guertin and Nathan C. Sheffield

    Citation: Genome Biology 2021 22:155

    Content type: Software

    Published on:

  12. The majority of pancreatic ductal adenocarcinomas (PDAC) are diagnosed at the metastatic stage, and standard therapies have limited activity with a dismal 5-year survival rate of only 8%. The liver and lung ar...

    Authors: Won Jin Ho, Rossin Erbe, Ludmila Danilova, Zaw Phyo, Emma Bigelow, Genevieve Stein-O’Brien, Dwayne L. Thomas II, Soren Charmsaz, Nicole Gross, Skylar Woolman, Kayla Cruz, Rebecca M. Munday, Neeha Zaidi, Todd D. Armstrong, Marcelo B. Sztein, Mark Yarchoan…

    Citation: Genome Biology 2021 22:154

    Content type: Research

    Published on:

  13. Most research articles presenting new data analysis methods claim that “the new method performs better than existing methods,” but the veracity of such statements is questionable. Our manuscript discusses and ...

    Authors: Stefan Buchka, Alexander Hapfelmeier, Paul P. Gardner, Rory Wilson and Anne-Laure Boulesteix

    Citation: Genome Biology 2021 22:152

    Content type: Short Report

    Published on:

  14. The developmental gradient in monocot leaves has been exploited to uncover leaf developmental gene expression programs and chloroplast biogenesis processes. However, the relationship between the two is barely ...

    Authors: Naresh Loudya, Priyanka Mishra, Kotaro Takahagi, Yukiko Uehara-Yamaguchi, Komaki Inoue, Laszlo Bogre, Keiichi Mochida and Enrique López-Juez

    Citation: Genome Biology 2021 22:151

    Content type: Research

    Published on:

  15. The 3D organization of the chromatin fiber in cell nuclei plays a key role in the regulation of gene expression. Genome-wide techniques to score DNA-DNA contacts, such as Hi-C, reveal the partitioning of chrom...

    Authors: Xian Hao, Jyotsana J. Parmar, Benoît Lelandais, Andrey Aristov, Wei Ouyang, Christian Weber and Christophe Zimmer

    Citation: Genome Biology 2021 22:150

    Content type: Research

    Published on:

  16. Androgen receptor (AR) is critical to the initiation, growth, and progression of prostate cancer. Once activated, the AR binds to cis-regulatory enhancer elements on DNA that drive gene expression. Yet, there ...

    Authors: Chia-Chi Flora Huang, Shreyas Lingadahalli, Tunc Morova, Dogancan Ozturan, Eugene Hu, Ivan Pak Lok Yu, Simon Linder, Marlous Hoogstraat, Suzan Stelloo, Funda Sar, Henk van der Poel, Umut Berkay Altintas, Mohammadali Saffarzadeh, Stephane Le Bihan, Brian McConeghy, Bengul Gokbayrak…

    Citation: Genome Biology 2021 22:149

    Content type: Research

    Published on:

  17. In maize hybrid breeding, complementary pools of parental lines with reshuffled genetic variants are established for superior hybrid performance. To comprehensively decipher the genetics of heterosis, we prese...

    Authors: Yingjie Xiao, Shuqin Jiang, Qian Cheng, Xiaqing Wang, Jun Yan, Ruyang Zhang, Feng Qiao, Chuang Ma, Jingyun Luo, Wenqiang Li, Haijun Liu, Wenyu Yang, Wenhao Song, Yijiang Meng, Marilyn L. Warburton, Jiuran Zhao…

    Citation: Genome Biology 2021 22:148

    Content type: Research

    Published on:

  18. Pseudogenes are gene copies presumed to mainly be functionless relics of evolution due to acquired deleterious mutations or transcriptional silencing. Using deep full-length PacBio cDNA sequencing of normal hu...

    Authors: Robin-Lee Troskie, Yohaann Jafrani, Tim R. Mercer, Adam D. Ewing, Geoffrey J. Faulkner and Seth W. Cheetham

    Citation: Genome Biology 2021 22:146

    Content type: Short Report

    Published on:

  19. Cellular senescence is a permanent state of replicative arrest defined by a specific pattern of gene expression. The epigenome in senescent cells is sculptured in order to sustain the new transcriptional requi...

    Authors: Eros Di Giorgio, Harikrishnareddy Paluvai, Emiliano Dalla, Liliana Ranzino, Alessandra Renzini, Viviana Moresi, Martina Minisini, Raffaella Picco and Claudio Brancolini

    Citation: Genome Biology 2021 22:129

    Content type: Research

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  20. Four-stranded G-quadruplexes (G4s) are DNA secondary structures in the human genome that are primarily found in active promoters associated with elevated transcription. Here, we explore the relationship betwee...

    Authors: Jiazhen Shen, Dhaval Varshney, Angela Simeone, Xiaoyun Zhang, Santosh Adhikari, David Tannahill and Shankar Balasubramanian

    Citation: Genome Biology 2021 22:143

    Content type: Research

    Published on:

  21. Trans-acting expression quantitative trait loci (trans-eQTLs) account for ≥70% expression heritability and could therefore facilitate uncovering mechanisms underlying the origination of complex diseases. Identify...

    Authors: Saikat Banerjee, Franco L. Simonetti, Kira E. Detrois, Anubhav Kaphle, Raktim Mitra, Rahul Nagial and Johannes Söding

    Citation: Genome Biology 2021 22:142

    Content type: Method

    Published on:

  22. Hybridization of plants that differ in number of chromosome sets (ploidy) frequently causes endosperm failure and seed arrest, a phenomenon referred to as triploid block. In Arabidopsis, loss of function of NRPD1

    Authors: Zhenxing Wang, Nicolas Butel, Juan Santos-González, Lauriane Simon, Cecilia Wärdig and Claudia Köhler

    Citation: Genome Biology 2021 22:141

    Content type: Research

    Published on:

  23. How species can adapt to abrupt environmental changes, particularly in the absence of standing genetic variation, is poorly understood and a pressing question in the face of ongoing climate change. Here we lev...

    Authors: Pierre Baduel, Basile Leduque, Amandine Ignace, Isabelle Gy, José Gil Jr, Olivier Loudet, Vincent Colot and Leandro Quadrana

    Citation: Genome Biology 2021 22:138

    Content type: Research

    Published on:

  24. Selection has dramatically shaped genetic and phenotypic variation in bread wheat. We can assess the genomic basis of historical phenotypic changes, and the potential for future improvement, using experimental...

    Authors: Michael F. Scott, Nick Fradgley, Alison R. Bentley, Thomas Brabbs, Fiona Corke, Keith A. Gardner, Richard Horsnell, Phil Howell, Olufunmilayo Ladejobi, Ian J. Mackay, Richard Mott and James Cockram

    Citation: Genome Biology 2021 22:137

    Content type: Research

    Published on:

  25. Eukaryotic genomes undergo pervasive transcription, leading to the production of many types of stable and unstable RNAs. Transcription is not restricted to regions with annotated gene features but includes alm...

    Authors: Federico Agostini, Julian Zagalak, Jan Attig, Jernej Ule and Nicholas M. Luscombe

    Citation: Genome Biology 2021 22:136

    Content type: Research

    Published on:

  26. Researchers must be able to generate experimentally testable hypotheses from sequencing-based observational microbiome experiments to discover the mechanisms underlying the influence of gut microbes on human h...

    Authors: Samuel S. Minot, Kevin C. Barry, Caroline Kasman, Jonathan L. Golob and Amy D. Willis

    Citation: Genome Biology 2021 22:135

    Content type: Method

    Published on:

  27. The evolution of multicellularity is a critical event that remains incompletely understood. We use the social amoeba, Dictyostelium discoideum, one of the rare organisms that readily transits back and forth betwe...

    Authors: Simon Yuan Wang, Elizabeth Ann Pollina, I-Hao Wang, Lindsay Kristina Pino, Henry L. Bushnell, Ken Takashima, Colette Fritsche, George Sabin, Benjamin Aaron Garcia, Paul Lieberman Greer and Eric Lieberman Greer

    Citation: Genome Biology 2021 22:134

    Content type: Research

    Published on:

  28. Alternative splicing, which generates multiple mRNA isoforms from single genes, is crucial for the regulation of eukaryotic gene expression. The flux through competing splicing pathways cannot be determined by...

    Authors: Carrie Kovalak, Scott Donovan, Alicia A. Bicknell, Mihir Metkar and Melissa J. Moore

    Citation: Genome Biology 2021 22:132

    Content type: Research

    Published on:

  29. While genome sequencing and assembly are now routine, we do not have a full, precise picture of polyploid genomes. No existing polyploid phasing method provides accurate and contiguous haplotype predictions. W...

    Authors: Omar Abou Saada, Andreas Tsouris, Chris Eberlein, Anne Friedrich and Joseph Schacherer

    Citation: Genome Biology 2021 22:126

    Content type: Method

    Published on:

  30. Medulloblastoma (MB) is the most common malignant pediatric brain tumor that originates in the cerebellum and brainstem. Frequent somatic mutations and deregulated expression of epigenetic regulators in MB hig...

    Authors: Hyerim Kim, Yunhee Kang, Yujing Li, Li Chen, Li Lin, Nicholas D. Johnson, Dan Zhu, M. Hope Robinson, Leon McSwain, Benjamin G. Barwick, Xianrui Yuan, Xinbin Liao, Jie Zhao, Zhiping Zhang, Qiang Shu, Jianjun Chen…

    Citation: Genome Biology 2021 22:125

    Content type: Research

    Published on:

  31. To investigate molecular mechanisms underlying cell state changes, a crucial analysis is to identify differentially expressed (DE) genes along the pseudotime inferred from single-cell RNA-sequencing data. Howe...

    Authors: Dongyuan Song and Jingyi Jessica Li

    Citation: Genome Biology 2021 22:124

    Content type: Method

    Published on:

  32. Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptom...

    Authors: Matthew Chung, Vincent M. Bruno, David A. Rasko, Christina A. Cuomo, José F. Muñoz, Jonathan Livny, Amol C. Shetty, Anup Mahurkar and Julie C. Dunning Hotopp

    Citation: Genome Biology 2021 22:121

    Content type: Review

    Published on:

  33. Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly.

    Authors: Giulio Formenti, Arang Rhie, Jennifer Balacco, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, Samara Brown, Marco Rosario Capodiferro, Farooq O. Al-Ajli, Roberto Ambrosini, Peter Houde, Sergey Koren, Karen Oliver, Michelle Smith, Jason Skelton, Emma Betteridge…

    Citation: Genome Biology 2021 22:120

    Content type: Research

    Published on:

  34. Millennia of directional human selection has reshaped the genomic architecture of cultivated cotton relative to wild counterparts, but we have limited understanding of the selective retention and fractionation...

    Authors: Jianying Li, Daojun Yuan, Pengcheng Wang, Qiongqiong Wang, Mengling Sun, Zhenping Liu, Huan Si, Zhongping Xu, Yizan Ma, Boyang Zhang, Liuling Pei, Lili Tu, Longfu Zhu, Ling-Ling Chen, Keith Lindsey, Xianlong Zhang…

    Citation: Genome Biology 2021 22:119

    Content type: Research

    Published on:

  35. Recent genome-wide studies of many species reveal the existence of a myriad of RNAs differing in size, coding potential and function. Among these are the long non-coding RNAs, some of them producing functional...

    Authors: Audrey Montigny, Patrizia Tavormina, Carine Duboe, Hélène San Clémente, Marielle Aguilar, Philippe Valenti, Dominique Lauressergues, Jean-Philippe Combier and Serge Plaza

    Citation: Genome Biology 2021 22:118

    Content type: Research

    Published on:

  36. The binding of transcription factors (TF) to genomic targets is critical in the regulation of gene expression. Short, double-stranded DNA sequence motifs are routinely implicated in TF recruitment, but many qu...

    Authors: Jochen Spiegel, Sergio Martínez Cuesta, Santosh Adhikari, Robert Hänsel-Hertsch, David Tannahill and Shankar Balasubramanian

    Citation: Genome Biology 2021 22:117

    Content type: Research

    Published on:

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