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  1. Genomic structural variations (SV) are important determinants of genotypic and phenotypic changes in many organisms. However, the detection of SV from next-generation sequencing data remains challenging.

    Authors: Michael M. Khayat, Sayed Mohammad Ebrahim Sahraeian, Samantha Zarate, Andrew Carroll, Huixiao Hong, Bohu Pan, Leming Shi, Richard A. Gibbs, Marghoob Mohiyuddin, Yuanting Zheng and Fritz J. Sedlazeck
    Citation: Genome Biology 2021 22:347
  2. Multimodal data is rapidly growing in many fields of science and engineering, including single-cell biology. We introduce MultiMAP, a novel algorithm for dimensionality reduction and integration. MultiMAP can ...

    Authors: Mika Sarkin Jain, Krzysztof Polanski, Cecilia Dominguez Conde, Xi Chen, Jongeun Park, Lira Mamanova, Andrew Knights, Rachel A. Botting, Emily Stephenson, Muzlifah Haniffa, Austen Lamacraft, Mirjana Efremova and Sarah A. Teichmann
    Citation: Genome Biology 2021 22:346
  3. CRISPR loss of function screens are powerful tools to interrogate biology but exhibit a number of biases and artifacts that can confound the results. Here, we introduce Chronos, an algorithm for inferring gene...

    Authors: Joshua M. Dempster, Isabella Boyle, Francisca Vazquez, David E. Root, Jesse S. Boehm, William C. Hahn, Aviad Tsherniak and James M. McFarland
    Citation: Genome Biology 2021 22:343
  4. Population-scale single-cell RNA sequencing (scRNA-seq) is now viable, enabling finer resolution functional genomics studies and leading to a rush to adapt bulk methods and develop new single-cell-specific met...

    Authors: Christina B. Azodi, Luke Zappia, Alicia Oshlack and Davis J. McCarthy
    Citation: Genome Biology 2021 22:341
  5. Congenital heart diseases are the major cause of death in newborns, but the genetic etiology of this developmental disorder is not fully known. The conventional approach to identify the disease-causing genes f...

    Authors: Hieu T. Nim, Louis Dang, Harshini Thiyagarajah, Daniel Bakopoulos, Michael See, Natalie Charitakis, Tennille Sibbritt, Michael P. Eichenlaub, Stuart K. Archer, Nicolas Fossat, Richard E. Burke, Patrick P. L. Tam, Coral G. Warr, Travis K. Johnson and Mirana Ramialison
    Citation: Genome Biology 2021 22:335
  6. Single-cell RNA-sequencing (scRNA-seq) technologies and associated analysis methods have rapidly developed in recent years. This includes preprocessing methods, which assign sequencing reads to genes to create...

    Authors: Yue You, Luyi Tian, Shian Su, Xueyi Dong, Jafar S. Jabbari, Peter F. Hickey and Matthew E. Ritchie
    Citation: Genome Biology 2021 22:339
  7. Aggregating transcriptomics data across hospitals can increase sensitivity and robustness of differential expression analyses, yielding deeper clinical insights. As data exchange is often restricted by privacy...

    Authors: Olga Zolotareva, Reza Nasirigerdeh, Julian Matschinske, Reihaneh Torkzadehmahani, Mohammad Bakhtiari, Tobias Frisch, Julian Späth, David B. Blumenthal, Amir Abbasinejad, Paolo Tieri, Georgios Kaissis, Daniel Rückert, Nina K. Wenke, Markus List and Jan Baumbach
    Citation: Genome Biology 2021 22:338
  8. Obesity and related comorbidities are major health concerns among many US immigrant populations. Emerging evidence suggests a potential involvement of the gut microbiome. Here, we evaluated gut microbiome feat...

    Authors: Zheng Wang, Mykhaylo Usyk, Yoshiki Vázquez-Baeza, Guo-Chong Chen, Carmen R. Isasi, Jessica S. Williams-Nguyen, Simin Hua, Daniel McDonald, Bharat Thyagarajan, Martha L. Daviglus, Jianwen Cai, Kari E. North, Tao Wang, Rob Knight, Robert D. Burk, Robert C. Kaplan…
    Citation: Genome Biology 2021 22:336
  9. Transdifferentiation describes transformation in vivo of specialized cells from one lineage into another. While there is extensive literature on forced induction of lineage reprogramming in vitro, endogenous m...

    Authors: Saba Rezaei-Lotfi, Filip Vujovic, Mary Simonian, Neil Hunter and Ramin M. Farahani
    Citation: Genome Biology 2021 22:334
  10. scRNA-seq datasets are increasingly used to identify gene panels that can be probed using alternative technologies, such as spatial transcriptomics, where choosing the best subset of genes is vital. Existing m...

    Authors: Alsu Missarova, Jaison Jain, Andrew Butler, Shila Ghazanfar, Tim Stuart, Maigan Brusko, Clive Wasserfall, Harry Nick, Todd Brusko, Mark Atkinson, Rahul Satija and John C. Marioni
    Citation: Genome Biology 2021 22:333
  11. Cytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other dis...

    Authors: Jonathan Foox, Jessica Nordlund, Claudia Lalancette, Ting Gong, Michelle Lacey, Samantha Lent, Bradley W. Langhorst, V. K. Chaithanya Ponnaluri, Louise Williams, Karthik Ramaswamy Padmanabhan, Raymond Cavalcante, Anders Lundmark, Daniel Butler, Christopher Mozsary, Justin Gurvitch, John M. Greally…
    Citation: Genome Biology 2021 22:332

    The Author Correction to this article has been published in Genome Biology 2022 23:76

    The Author Correction to this article has been published in Genome Biology 2021 22:350

  12. We developed a single-cell approach to detect CRISPR-modified mRNA transcript structures. This method assesses how genetic variants at splicing sites and splicing factors contribute to alternative mRNA isoform...

    Authors: Heon Seok Kim, Susan M. Grimes, Anna C. Hooker, Billy T. Lau and Hanlee P. Ji
    Citation: Genome Biology 2021 22:331
  13. Pseudouridine (Ψ) is an abundant mRNA modification in mammalian transcriptome, but its functions have remained elusive due to the difficulty of transcriptome-wide mapping. We develop a nanopore native RNA sequ...

    Authors: Sihao Huang, Wen Zhang, Christopher D. Katanski, Devin Dersh, Qing Dai, Karen Lolans, Jonathan Yewdell, A. Murat Eren and Tao Pan
    Citation: Genome Biology 2021 22:330
  14. Mitochondria are ancient endosymbiotic organelles crucial to eukaryotic growth and metabolism. The mammalian mitochondrial genome encodes for 13 mitochondrial proteins, and the remaining mitochondrial proteins...

    Authors: Marcos Francisco Perez and Peter Sarkies
    Citation: Genome Biology 2021 22:328
  15. Alternative splicing (AS) is an important aspect of gene regulation. Nevertheless, its role in molecular processes and pathobiology is far from understood. A roadblock is that tools for the functional analysis...

    Authors: Zakaria Louadi, Maria L. Elkjaer, Melissa Klug, Chit Tong Lio, Amit Fenn, Zsolt Illes, Dario Bongiovanni, Jan Baumbach, Tim Kacprowski, Markus List and Olga Tsoy
    Citation: Genome Biology 2021 22:327
  16. Recent advances in single-cell biotechnologies have resulted in high-dimensional datasets with increased complexity, making feature selection an essential technique for single-cell data analysis. Here, we revi...

    Authors: Pengyi Yang, Hao Huang and Chunlei Liu
    Citation: Genome Biology 2021 22:321
  17. Polyploidy, especially allopolyploidy, which entails merging divergent genomes via hybridization and whole-genome duplication (WGD), is a major route to speciation in plants. The duplication among the parental...

    Authors: Xiaofei Yang, Haopeng Yu, Wenqing Sun, Ling Ding, Ji Li, Jitender Cheema, Ricardo Ramirez-Gonzalez, Xuebo Zhao, Azahara C. Martín, Fei Lu, Bao Liu, Cristobal Uauy, Yiliang Ding and Huakun Zhang
    Citation: Genome Biology 2021 22:326
  18. High-throughput single-cell technologies hold the promise of discovering novel cellular relationships with disease. However, analytical workflows constructed for these technologies to associate cell proportion...

    Authors: Adam Chan, Wei Jiang, Emily Blyth, Jean Yang and Ellis Patrick
    Citation: Genome Biology 2021 22:324
  19. We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly processed by our new Monorail analysis pipeline. To facilitate access to th...

    Authors: Christopher Wilks, Shijie C. Zheng, Feng Yong Chen, Rone Charles, Brad Solomon, Jonathan P. Ling, Eddie Luidy Imada, David Zhang, Lance Joseph, Jeffrey T. Leek, Andrew E. Jaffe, Abhinav Nellore, Leonardo Collado-Torres, Kasper D. Hansen and Ben Langmead
    Citation: Genome Biology 2021 22:323
  20. The dynamic process of transcription termination produces transient RNA intermediates that are difficult to distinguish from each other via short-read sequencing methods.

    Authors: Weipeng Mo, Bo Liu, Hong Zhang, Xianhao Jin, Dongdong Lu, Yiming Yu, Yuelin Liu, Jinbu Jia, Yanping Long, Xian Deng, Xiaofeng Cao, Hongwei Guo and Jixian Zhai
    Citation: Genome Biology 2021 22:322
  21. Plant secondary growth depends on the activity of the vascular cambium, which produces xylem and phloem. Wood derived from xylem is the most abundant form of biomass globally and has played key socio-economic ...

    Authors: Yang Chen, Shaofei Tong, Yuanzhong Jiang, Fandi Ai, Yanlin Feng, Junlin Zhang, Jue Gong, Jiajia Qin, Yuanyuan Zhang, Yingying Zhu, Jianquan Liu and Tao Ma
    Citation: Genome Biology 2021 22:319
  22. Promoters are genomic regions where the transcription machinery binds to initiate the transcription of specific genes. Computational tools for identifying bacterial promoters have been around for decades. Howe...

    Authors: Ruben Chevez-Guardado and Lourdes Peña-Castillo
    Citation: Genome Biology 2021 22:318
  23. Fragile X syndrome (FXS) is an intellectual disability attributable to loss of fragile X protein (FMRP). We previously demonstrated that FMRP binds mRNAs targeted for nonsense-mediated mRNA decay (NMD) and tha...

    Authors: Tatsuaki Kurosaki, Hitomi Sakano, Christoph Pröschel, Jason Wheeler, Alexander Hewko and Lynne E. Maquat
    Citation: Genome Biology 2021 22:317
  24. Heterozygous genomes are widespread in outcrossing and clonally propagated crops. However, the variation in heterozygosity underlying key agronomic traits and crop domestication remains largely unknown. Cassav...

    Authors: Wei Hu, Changmian Ji, Zhe Liang, Jianqiu Ye, Wenjun Ou, Zehong Ding, Gang Zhou, Weiwei Tie, Yan Yan, Jinghao Yang, Liming Ma, Xiaoying Yang, Yunxie Wei, Zhiqiang Jin, Jianghui Xie, Ming Peng…
    Citation: Genome Biology 2021 22:316
  25. Three-dimensional (3D) chromatin organization provides a critical foundation to investigate gene expression regulation and cellular homeostasis.

    Authors: Xingguo Zhang, Manish K. Pandey, Jianping Wang, Kunkun Zhao, Xingli Ma, Zhongfeng Li, Kai Zhao, Fangping Gong, Baozhu Guo, Rajeev K. Varshney and Dongmei Yin
    Citation: Genome Biology 2021 22:315
  26. The dynamic 3D organization of the genome is central to gene regulation and development. The nuclear lamina influences genome organization through the tethering of lamina-associated domains (LADs) to the nucle...

    Authors: Xianrong Wong, Victoria E. Hoskins, Ashley J. Melendez-Perez, Jennifer C. Harr, Molly Gordon and Karen L. Reddy
    Citation: Genome Biology 2021 22:305
  27. Stone cells in fruits of pear (Pyrus pyrifolia) negatively influence fruit quality because their lignified cell walls impart a coarse and granular texture to the fruit flesh.

    Authors: Runze Wang, Yongsong Xue, Jing Fan, Jia-Long Yao, Mengfan Qin, Tao Lin, Qun Lian, Mingyue Zhang, Xiaolong Li, Jiaming Li, Manyi Sun, Bobo Song, Jiaying Zhang, Kejiao Zhao, Xu Chen, Hongju Hu…
    Citation: Genome Biology 2021 22:313
  28. Long-read de novo genome assembly continues to advance rapidly. However, there is a lack of effective tools to accurately evaluate the assembly results, especially for structural errors. We present Inspector, ...

    Authors: Yu Chen, Yixin Zhang, Amy Y. Wang, Min Gao and Zechen Chong
    Citation: Genome Biology 2021 22:312
  29. Recent single-cell transcriptomic studies report that IDH-mutant gliomas share a common hierarchy of cellular phenotypes, independent of genetic subtype. However, the genetic differences between IDH-mutant gli...

    Authors: Husam Babikir, Lin Wang, Karin Shamardani, Francisca Catalan, Sweta Sudhir, Manish K. Aghi, David R. Raleigh, Joanna J. Phillips and Aaron A. Diaz
    Citation: Genome Biology 2021 22:311
  30. A modified Chromium 10x droplet-based protocol that subsamples cells for both short-read and long-read (nanopore) sequencing together with a new computational pipeline (FLAMES) is developed to enable isoform disc...

    Authors: Luyi Tian, Jafar S. Jabbari, Rachel Thijssen, Quentin Gouil, Shanika L. Amarasinghe, Oliver Voogd, Hasaru Kariyawasam, Mei R. M. Du, Jakob Schuster, Changqing Wang, Shian Su, Xueyi Dong, Charity W. Law, Alexis Lucattini, Yair David Joseph Prawer, Coralina Collar-Fernández…
    Citation: Genome Biology 2021 22:310
  31. Topologically associating domains (TADs) are important building blocks of three-dimensional genome architectures. The formation of TADs has been shown to depend on cohesin in a loop-extrusion mechanism. Recent...

    Authors: Yubao Cheng, Miao Liu, Mengwei Hu and Siyuan Wang
    Citation: Genome Biology 2021 22:309
  32. Enhancers are non-coding regions of the genome that control the activity of target genes. Recent efforts to identify active enhancers experimentally and in silico have proven effective. While these tools can p...

    Authors: Jareth C. Wolfe, Liudmila A. Mikheeva, Hani Hagras and Nicolae Radu Zabet
    Citation: Genome Biology 2021 22:308
  33. Accurate quantification and detection of intron retention levels require specialized software. Building on our previous software, we create a suite of tools called IRFinder-S, to analyze and explore intron ret...

    Authors: Claudio Lorenzi, Sylvain Barriere, Katharina Arnold, Reini F. Luco, Andrew J. Oldfield and William Ritchie
    Citation: Genome Biology 2021 22:307
  34. Coconut is an important tropical oil and fruit crop whose evolutionary position renders it a fantastic species for the investigation of the evolution of monocot chromosomes and the subsequent differentiation o...

    Authors: Shouchuang Wang, Yong Xiao, Zhi-Wei Zhou, Jiaqing Yuan, Hao Guo, Zhuang Yang, Jun Yang, Pengchuan Sun, Lisong Sun, Yuan Deng, Wen-Zhao Xie, Jia-Ming Song, Muhammad Tahir ul Qamar, Wei Xia, Rui Liu, Shufang Gong…
    Citation: Genome Biology 2021 22:304
  35. Intermixing of genomes through meiotic reassortment and recombination of homologous chromosomes is a unifying theme of sexual reproduction in eukaryotic organisms and is considered crucial for their adaptive e...

    Authors: Ioannis A. Papaioannou, Fabien Dutreux, France A. Peltier, Hiromi Maekawa, Nicolas Delhomme, Amit Bardhan, Anne Friedrich, Joseph Schacherer and Michael Knop
    Citation: Genome Biology 2021 22:303
  36. Precise gene dosage of the X chromosomes is critical for normal development and cellular function. In mice, XX female somatic cells show transcriptional X chromosome upregulation of their single active X chrom...

    Authors: Irene Talon, Adrian Janiszewski, Bart Theeuwes, Thomas Lefevre, Juan Song, Greet Bervoets, Lotte Vanheer, Natalie De Geest, Suresh Poovathingal, Ryan Allsop, Jean-Christophe Marine, Florian Rambow, Thierry Voet and Vincent Pasque
    Citation: Genome Biology 2021 22:302
  37. Common walnut (Juglans regia L.) is one of the top four most consumed nuts in the world due to its health benefits and pleasant taste. Despite its economic importance, the evolutionary history and genetic control...

    Authors: Feiyang Ji, Qingguo Ma, Wenting Zhang, Jie Liu, Yu Feng, Peng Zhao, Xiaobo Song, Jiaxin Chen, Junpei Zhang, Xin Wei, Ye Zhou, Yingying Chang, Pu Zhang, Xuehui Huang, Jie Qiu and Dong Pei
    Citation: Genome Biology 2021 22:300
  38. We present SquiggleNet, the first deep-learning model that can classify nanopore reads directly from their electrical signals. SquiggleNet operates faster than DNA passes through the pore, allowing real-time c...

    Authors: Yuwei Bao, Jack Wadden, John R. Erb-Downward, Piyush Ranjan, Weichen Zhou, Torrin L. McDonald, Ryan E. Mills, Alan P. Boyle, Robert P. Dickson, David Blaauw and Joshua D. Welch
    Citation: Genome Biology 2021 22:298

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