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  1. 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

    Content type: Method

    Published on:

  2. 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

    Content type: Method

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  3. 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

    Content type: Research

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  4. 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

    Content type: Research

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  5. 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

    Content type: Method

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  6. 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

    Content type: Method

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  7. 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

    Content type: Method

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  8. 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

    Content type: Research

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  9. 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

    Content type: Research

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  10. 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

    Content type: Method

    Published on:

  11. 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

    Content type: Research

    Published on:

  12. 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

    Content type: Research

    Published on:

  13. 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

    Content type: Method

    Published on:

  14. 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

    Content type: Research

    Published on:

  15. 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

    Content type: Method

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  16. 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

    Content type: Research

    Published on:

  17. 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

    Content type: Method

    Published on:

  18. 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

    Content type: Research

    Published on:

  19. 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

    Content type: Research

    Published on:

  20. 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

    Content type: Research

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  21. 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

    Content type: Research

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  22. 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

    Content type: Method

    Published on:

  23. 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

    Content type: Method

    Published on:

  24. 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

    Content type: Research

    Published on:

  25. RNA-targeting CRISPR-Cas can provide potential advantages over DNA editing, such as avoiding pleiotropic effects of genome editing, providing precise spatiotemporal regulation, and expanded function including ...

    Authors: Veerendra Kumar Sharma, Sandeep Marla, Wenguang Zheng, Divya Mishra, Jun Huang, Wei Zhang, Geoffrey Preston Morris and David Edward Cook

    Citation: Genome Biology 2022 23:6

    Content type: Research

    Published on:

  26. Direct analogs of chemically modified bases that carry important epigenetic information, such as 5-methylcytosine (m5C)/5-methyldeoxycytosine (5mC), 5-hydroxymethylcytosine (hm5C)/5-hydroxymethyldeoxycytosine ...

    Authors: Shuai Wang, Hairong Xie, Fei Mao, Haiyan Wang, Shu Wang, Zhenglin Chen, Yuxia Zhang, Zhihui Xu, Jinming Xing, Zhaokang Cui, Xiquan Gao, Hongmei Jin, Jian Hua, Bo Xiong and Yufeng Wu

    Citation: Genome Biology 2022 23:5

    Content type: Research

    Published on:

  27. Reproducible detection of inherited variants with whole genome sequencing (WGS) is vital for the implementation of precision medicine and is a complicated process in which each step affects variant call qualit...

    Authors: Bohu Pan, Luyao Ren, Vitor Onuchic, Meijian Guan, Rebecca Kusko, Steve Bruinsma, Len Trigg, Andreas Scherer, Baitang Ning, Chaoyang Zhang, Christine Glidewell-Kenney, Chunlin Xiao, Eric Donaldson, Fritz J. Sedlazeck, Gary Schroth, Gokhan Yavas…

    Citation: Genome Biology 2022 23:2

    Content type: Research

    Published on:

  28. 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 22:350

    Content type: Author Correction

    Published on:

    The original article was published in Genome Biology 2021 22:332

  29. We have developed an efficient and inexpensive pipeline for streamlining large-scale collection and genome sequencing of bacterial isolates. Evaluation of this method involved a worldwide research collaboratio...

    Authors: Blanca M. Perez-Sepulveda, Darren Heavens, Caisey V. Pulford, Alexander V. Predeus, Ross Low, Hermione Webster, Gregory F. Dykes, Christian Schudoma, Will Rowe, James Lipscombe, Chris Watkins, Benjamin Kumwenda, Neil Shearer, Karl Costigan, Kate S. Baker, Nicholas A. Feasey…

    Citation: Genome Biology 2021 22:349

    Content type: Method

    Published on:

  30. Understanding the contributions of transcription factor DNA binding sites to transcriptional enhancers is a significant challenge. We developed Quantitative enhancer-FACS-Seq for highly parallel quantification...

    Authors: Colin T. Waters, Stephen S. Gisselbrecht, Yuliya A. Sytnikova, Tiziana M. Cafarelli, David E. Hill and Martha L. Bulyk

    Citation: Genome Biology 2021 22:348

    Content type: Method

    Published on:

  31. 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

    Content type: Research

    Published on:

  32. 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

    Content type: Method

    Published on:

  33. 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

    Content type: Method

    Published on:

  34. 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

    Content type: Method

    Published on:

  35. 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

    Content type: Research

    Published on:

  36. 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

    Content type: Method

    Published on:

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