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  1. Computational biology provides software tools for testing and making inferences about biological data. In the face of increasing volumes of data, heuristic methods that trade software speed for accuracy may be...

    Authors: Paul P. Gardner, James M. Paterson, Stephanie McGimpsey, Fatemeh Ashari-Ghomi, Sinan U. Umu, Aleksandra Pawlik, Alex Gavryushkin and Michael A. Black
    Citation: Genome Biology 2022 23:56
  2. Multiplexing of samples in single-cell RNA-seq studies allows a significant reduction of the experimental costs, straightforward identification of doublets, increased cell throughput, and reduction of sample-s...

    Authors: Viacheslav Mylka, Irina Matetovici, Suresh Poovathingal, Jeroen Aerts, Niels Vandamme, Ruth Seurinck, Kevin Verstaen, Gert Hulselmans, Silvie Van den Hoecke, Isabelle Scheyltjens, Kiavash Movahedi, Hans Wils, Joke Reumers, Jeroen Van Houdt, Stein Aerts and Yvan Saeys
    Citation: Genome Biology 2022 23:55
  3. Ribosomal DNA (rDNA) displays substantial inter-individual genetic variation in human and mouse. A systematic analysis of how this variation impacts epigenetic states and expression of the rDNA has thus far no...

    Authors: Francisco Rodriguez-Algarra, Robert A. E. Seaborne, Amy F. Danson, Selin Yildizoglu, Harunori Yoshikawa, Pui Pik Law, Zakaryya Ahmad, Victoria A. Maudsley, Ama Brew, Nadine Holmes, Mateus Ochôa, Alan Hodgkinson, Sarah J. Marzi, Madapura M. Pradeepa, Matthew Loose, Michelle L. Holland…
    Citation: Genome Biology 2022 23:54
  4. Hybridization and backcrossing are commonly used in animal and plant breeding to induce heritable variation including epigenetic changes such as paramutation. However, the molecular basis for hybrid-induced ep...

    Authors: Shuai Cao, Longfei Wang, Tongwen Han, Wenxue Ye, Yang Liu, Yi Sun, Stephen P. Moose, Qingxin Song and Z. Jeffrey Chen
    Citation: Genome Biology 2022 23:53
  5. The high-activity adenine base editors (ABEs), engineered with the recently-developed tRNA adenosine deaminases (TadA8e and TadA9), show robust base editing activity but raise concerns about off-target effects.

    Authors: Shaofang Li, Lang Liu, Wenxian Sun, Xueping Zhou and Huanbin Zhou
    Citation: Genome Biology 2022 23:51
  6. Circular RNAs (circRNAs), a novel class of poorly conserved non-coding RNAs that regulate gene expression, are highly enriched in the human brain. Despite increasing discoveries of circRNA function in human ne...

    Authors: Yangping Li, Feng Wang, Peng Teng, Li Ku, Li Chen, Yue Feng and Bing Yao
    Citation: Genome Biology 2022 23:48
  7. High-throughput single-cell analysis today is facilitated by protocols like the 10X Genomics platform or Drop-Seq which generate cDNA pools in which the origin of a transcript is encoded at its 5′ or 3′ end. H...

    Authors: Roger Volden and Christopher Vollmers
    Citation: Genome Biology 2022 23:47
  8. Despite remarkable advances in our knowledge of epigenetically mediated transcriptional programming of cell differentiation in plants, little is known about chromatin topology and its functional implications i...

    Authors: Liuling Pei, Xianhui Huang, Zhenping Liu, Xuehan Tian, Jiaqi You, Jianying Li, David D. Fang, Keith Lindsey, Longfu Zhu, Xianlong Zhang and Maojun Wang
    Citation: Genome Biology 2022 23:45
  9. The human pathogen Haemophilus influenzae was the main cause of bacterial meningitis in children and a major cause of worldwide infant mortality before the introduction of a vaccine in the 1980s. Although the occ...

    Authors: Meriam Guellil, Marcel Keller, Jenna M. Dittmar, Sarah A. Inskip, Craig Cessford, Anu Solnik, Toomas Kivisild, Mait Metspalu, John E. Robb and Christiana L. Scheib
    Citation: Genome Biology 2022 23:22
  10. Clonal analysis of tumour sequencing data enables the evaluation of the relationship of histologically distinct synchronous lesions, such as co-existing benign areas, and temporally distinct tumours, such as p...

    Authors: Tanjina Kader, Magnus Zethoven and Kylie L. Gorringe
    Citation: Genome Biology 2022 23:43
  11. Advances in multi-omics have led to an explosion of multimodal datasets to address questions from basic biology to translation. While these data provide novel opportunities for discovery, they also pose manage...

    Authors: Danila Bredikhin, Ilia Kats and Oliver Stegle
    Citation: Genome Biology 2022 23:42
  12. The cell cycle is a highly conserved, continuous process which controls faithful replication and division of cells. Single-cell technologies have enabled increasingly precise measurements of the cell cycle bot...

    Authors: Shijie C. Zheng, Genevieve Stein-O’Brien, Jonathan J. Augustin, Jared Slosberg, Giovanni A. Carosso, Briana Winer, Gloria Shin, Hans T. Bjornsson, Loyal A. Goff and Kasper D. Hansen
    Citation: Genome Biology 2022 23:41
  13. N6-methyladenosine (m6A) mRNA modification is essential for mammalian and plant viability. The U6 m6A methyltransferases in other species regulate S-adenosylmethionine (SAM) homeostasis through installing m6A in ...

    Authors: Chunling Wang, Junbo Yang, Peizhe Song, Wei Zhang, Qiang Lu, Qiong Yu and Guifang Jia
    Citation: Genome Biology 2022 23:40
  14. We introduce AGAMEMNON (https://​github.​com/​ivlachos/​agamemnon) for the acquisition of microbial abundances from shotgun metagenomics and metatranscriptomic samples...

    Authors: Giorgos Skoufos, Fatemeh Almodaresi, Mohsen Zakeri, Joseph N. Paulson, Rob Patro, Artemis G. Hatzigeorgiou and Ioannis S. Vlachos
    Citation: Genome Biology 2022 23:39
  15. Viruses change constantly during replication, leading to high intra-species diversity. Although many changes are neutral or deleterious, some can confer on the virus different biological properties such as bet...

    Authors: Herui Liao, Dehan Cai and Yanni Sun
    Citation: Genome Biology 2022 23:38
  16. We introduce CellPhy, a maximum likelihood framework for inferring phylogenetic trees from somatic single-cell single-nucleotide variants. CellPhy leverages a finite-site Markov genotype model with 16 diploid ...

    Authors: Alexey Kozlov, Joao M. Alves, Alexandros Stamatakis and David Posada
    Citation: Genome Biology 2022 23:37
  17. Microbiome samples with low microbial biomass or severe DNA degradation remain challenging for amplicon-based or whole-metagenome sequencing approaches. Here, we introduce 2bRAD-M, a highly reduced and cost-ef...

    Authors: Zheng Sun, Shi Huang, Pengfei Zhu, Lam Tzehau, Helen Zhao, Jia Lv, Rongchao Zhang, Lisha Zhou, Qianya Niu, Xiuping Wang, Meng Zhang, Gongchao Jing, Zhenmin Bao, Jiquan Liu, Shi Wang and Jian Xu
    Citation: Genome Biology 2022 23:36
  18. Genetic alterations of somatic cells can drive non-malignant clone formation and promote cancer initiation. However, the link between these processes remains unclear and hampers our understanding of tissue hom...

    Authors: Lisa Dressler, Michele Bortolomeazzi, Mohamed Reda Keddar, Hrvoje Misetic, Giulia Sartini, Amelia Acha-Sagredo, Lucia Montorsi, Neshika Wijewardhane, Dimitra Repana, Joel Nulsen, Jacki Goldman, Marc Pollitt, Patrick Davis, Amy Strange, Karen Ambrose and Francesca D. Ciccarelli
    Citation: Genome Biology 2022 23:35
  19. Bread wheat (Triticum aestivum) is an allohexaploid that is generated by two subsequent allopolyploidization events. The large genome size (16 Gb) and polyploid complexity impede our understanding of how regulato...

    Authors: Jingya Yuan, Haojie Sun, Yijin Wang, Lulu Li, Shiting Chen, Wu Jiao, Guanghong Jia, Longfei Wang, Junrong Mao, Zhongfu Ni, Xiue Wang and Qingxin Song
    Citation: Genome Biology 2022 23:34
  20. Meta-analysis has been established as an effective approach to combining summary statistics of several genome-wide association studies (GWAS). However, the accuracy of meta-analysis can be attenuated in the pr...

    Authors: Reza Nasirigerdeh, Reihaneh Torkzadehmahani, Julian Matschinske, Tobias Frisch, Markus List, Julian Späth, Stefan Weiss, Uwe Völker, Esa Pitkänen, Dominik Heider, Nina Kerstin Wenke, Georgios Kaissis, Daniel Rueckert, Tim Kacprowski and Jan Baumbach
    Citation: Genome Biology 2022 23:32
  21. Adaptive sampling is a method of software-controlled enrichment unique to nanopore sequencing platforms. To test its potential for enrichment of rarer species within metagenomic samples, we create a synthetic ...

    Authors: Samuel Martin, Darren Heavens, Yuxuan Lan, Samuel Horsfield, Matthew D. Clark and Richard M. Leggett
    Citation: Genome Biology 2022 23:11
  22. Chromatin conformation capture (3C)-based technologies have enabled the accurate detection of topological genomic interactions, and the adoption of ChIP techniques to 3C-based protocols makes it possible to id...

    Authors: Li Tang, Matthew C. Hill, Patrick T. Ellinor and Min Li
    Citation: Genome Biology 2022 23:30
  23. Plants have the remarkable ability to generate callus, a pluripotent cell mass that acquires competence for subsequent tissue regeneration. Global chromatin remodeling is required for this cell fate transition...

    Authors: Yu-Chan Zhang, Yan-Fei Zhou, Yu Cheng, Jia-Hui Huang, Jian-Ping Lian, Lu Yang, Rui-Rui He, Meng-Qi Lei, Yu-Wei Liu, Chao Yuan, Wen-Long Zhao, Shi Xiao and Yue-Qin Chen
    Citation: Genome Biology 2022 23:28
  24. Blood-based markers of cognitive functioning might provide an accessible way to track neurodegeneration years prior to clinical manifestation of cognitive impairment and dementia.

    Authors: Daniel L. McCartney, Robert F. Hillary, Eleanor L. S. Conole, Daniel Trejo Banos, Danni A. Gadd, Rosie M. Walker, Cliff Nangle, Robin Flaig, Archie Campbell, Alison D. Murray, Susana Muñoz Maniega, María del C. Valdés-Hernández, Mathew A. Harris, Mark E. Bastin, Joanna M. Wardlaw, Sarah E. Harris…
    Citation: Genome Biology 2022 23:26
  25. Models developed using Nanopore direct RNA sequencing data from in vitro synthetic RNA with all adenosine replaced by N6-methyladenosine (m6A) are likely distorted due to superimposed signals from saturated m6A r...

    Authors: Hang Qin, Liang Ou, Jian Gao, Longxian Chen, Jia-Wei Wang, Pei Hao and Xuan Li
    Citation: Genome Biology 2022 23:25
  26. Epigenetic clocks use DNA methylation (DNAm) levels of specific sets of CpG dinucleotides to accurately predict individual chronological age. A popular application of these clocks is to explore whether the dev...

    Authors: Thomas H. Jonkman, Koen F. Dekkers, Roderick C. Slieker, Crystal D. Grant, M. Arfan Ikram, Marleen M. J. van Greevenbroek, Lude Franke, Jan H. Veldink, Dorret I. Boomsma, P. Eline Slagboom, B. I. O. S. Consortium and Bastiaan T. Heijmans
    Citation: Genome Biology 2022 23:24
  27. Polygenic risk scores (PRS) are valuable to translate the results of genome-wide association studies (GWAS) into clinical practice. To date, most GWAS have been based on individuals of European-ancestry leadin...

    Authors: Yanyu Liang, Milton Pividori, Ani Manichaikul, Abraham A. Palmer, Nancy J. Cox, Heather E. Wheeler and Hae Kyung Im
    Citation: Genome Biology 2022 23:23
  28. Here, we present a multi-modal deep generative model, the single-cell Multi-View Profiler (scMVP), which is designed for handling sequencing data that simultaneously measure gene expression and chromatin acces...

    Authors: Gaoyang Li, Shaliu Fu, Shuguang Wang, Chenyu Zhu, Bin Duan, Chen Tang, Xiaohan Chen, Guohui Chuai, Ping Wang and Qi Liu
    Citation: Genome Biology 2022 23:20
  29. Next-generation sequencing (NGS) can identify mutations in the human genome that cause disease and has been widely adopted in clinical diagnosis. However, the human genome contains many polymorphic, low-comple...

    Authors: Andre L. M. Reis, Ira W. Deveson, Bindu Swapna Madala, Ted Wong, Chris Barker, Joshua Xu, Niall Lennon, Weida Tong and Tim R. Mercer
    Citation: Genome Biology 2022 23:19
  30. The ability to discover new cell phenotypes by unsupervised clustering of single-cell transcriptomes has revolutionized biology. Currently, there is no principled way to decide whether a cluster of cells conta...

    Authors: Maria Mircea, Mazène Hochane, Xueying Fan, Susana M. Chuva de Sousa Lopes, Diego Garlaschelli and Stefan Semrau
    Citation: Genome Biology 2022 23:18
  31. Circadian (daily) timekeeping is essential to the survival of many organisms. An integral part of all circadian timekeeping systems is negative feedback between an activator and repressor. However, the role of...

    Authors: Jonathan Tyler, Yining Lu, Jay Dunlap and Daniel B. Forger
    Citation: Genome Biology 2022 23:17
  32. Many circular RNAs (circRNAs) are produced from back-splicing of exons of precursor mRNAs and are generally co-expressed with cognate linear RNAs. Methods for circRNA-specific knockout are lacking, largely due...

    Authors: Xiang Gao, Xu-Kai Ma, Xiang Li, Guo-Wei Li, Chu-Xiao Liu, Jun Zhang, Ying Wang, Jia Wei, Jia Chen, Ling-Ling Chen and Li Yang
    Citation: Genome Biology 2022 23:16
  33. Angiotensin-converting enzyme 2 (ACE2) is the cell-entry receptor for SARS-CoV-2. It plays critical roles in both the transmission and the pathogenesis of COVID-19. Comprehensive profiling of ACE2 expression p...

    Authors: Navchetan Kaur, Boris Oskotsky, Atul J. Butte and Zicheng Hu
    Citation: Genome Biology 2022 23:15
  34. As a perennial crop, oil-Camellia possesses a long domestication history and produces high-quality seed oil that is beneficial to human health. Camellia oleifera Abel. is a sister species to the tea plant, which ...

    Authors: Ping Lin, Kailiang Wang, Yupeng Wang, Zhikang Hu, Chao Yan, Hu Huang, Xianjin Ma, Yongqing Cao, Wei Long, Weixin Liu, Xinlei Li, Zhengqi Fan, Jiyuan Li, Ning Ye, Huadong Ren, Xiaohua Yao…
    Citation: Genome Biology 2022 23:14
  35. Genome-wide association study (GWAS) single nucleotide polymorphisms (SNPs) are known to preferentially co-locate to active regulatory elements in tissues and cell types relevant to disease aetiology. Further ...

    Authors: Charles E. Breeze, Eric Haugen, Alex Reynolds, Andrew Teschendorff, Jenny van Dongen, Qing Lan, Nathaniel Rothman, Guillaume Bourque, Ian Dunham, Stephan Beck, John Stamatoyannopoulos, Nora Franceschini and Sonja I. Berndt
    Citation: Genome Biology 2022 23:13
  36. Accurate detection of somatic mutations is challenging but critical in understanding cancer formation, progression, and treatment. We recently proposed NeuSomatic, the first deep convolutional neural network-b...

    Authors: Sayed Mohammad Ebrahim Sahraeian, Li Tai Fang, Konstantinos Karagiannis, Malcolm Moos, Sean Smith, Luis Santana-Quintero, Chunlin Xiao, Michael Colgan, Huixiao Hong, Marghoob Mohiyuddin and Wenming Xiao
    Citation: Genome Biology 2022 23:12
  37. In cancer, fusions are important diagnostic markers and targets for therapy. Long-read transcriptome sequencing allows the discovery of fusions with their full-length isoform structure. However, due to higher ...

    Authors: Nadia M. Davidson, Ying Chen, Teresa Sadras, Georgina L. Ryland, Piers Blombery, Paul G. Ekert, Jonathan Göke and Alicia Oshlack
    Citation: Genome Biology 2022 23:10
  38. While it is established that the functional impact of genetic variation can vary across cell types and states, capturing this diversity remains challenging. Current studies using bulk sequencing either ignore ...

    Authors: Tobias Heinen, Stefano Secchia, James P. Reddington, Bingqing Zhao, Eileen E. M. Furlong and Oliver Stegle
    Citation: Genome Biology 2022 23:8
  39. The daily cycling of plant physiological processes is speculated to arise from the coordinated rhythms of gene expression. However, the dynamics of diurnal 3D genome architecture and their potential functions ...

    Authors: Li Deng, Baibai Gao, Lun Zhao, Ying Zhang, Qing Zhang, Minrong Guo, Yongqing Yang, Shuangqi Wang, Liang Xie, Hao Lou, Meng Ma, Wei Zhang, Zhilin Cao, Qinghua Zhang, C. Robertson McClung, Guoliang Li…
    Citation: Genome Biology 2022 23:7

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