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  1. 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:

  2. 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

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  3. 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

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  4. 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

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  5. 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

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  6. 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

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  7. 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

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  8. 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

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  9. DNA methylation dynamics in the brain are associated with normal development and neuropsychiatric disease and differ across functionally distinct brain regions. Previous studies of genome-wide methylation diff...

    Authors: Lindsay F. Rizzardi, Peter F. Hickey, Adrian Idrizi, Rakel Tryggvadóttir, Colin M. Callahan, Kimberly E. Stephens, Sean D. Taverna, Hao Zhang, Sinan Ramazanoglu, Kasper D. Hansen and Andrew P. Feinberg

    Citation: Genome Biology 2021 22:116

    Content type: Research

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  10. Our assembly-free linkage analysis pipeline (AFLAP) identifies segregating markers as k-mers in the raw reads without using a reference genome assembly for calling variants and provides genotype tables for the...

    Authors: Kyle Fletcher, Lin Zhang, Juliana Gil, Rongkui Han, Keri Cavanaugh and Richard Michelmore

    Citation: Genome Biology 2021 22:115

    Content type: Method

    Published on:

  11. High-throughput single-cell measurements of DNA methylomes can quantify methylation heterogeneity and uncover its role in gene regulation. However, technical limitations and sparse coverage can preclude this t...

    Authors: Chantriolnt-Andreas Kapourani, Ricard Argelaguet, Guido Sanguinetti and Catalina A. Vallejos

    Citation: Genome Biology 2021 22:114

    Content type: Method

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  12. Castor bean (Ricinus communis L.) is an important oil crop, which belongs to the Euphorbiaceae family. The seed oil of castor bean is currently the only commercial source of ricinoleic acid that can be used for p...

    Authors: Wei Xu, Di Wu, Tianquan Yang, Chao Sun, Zaiqing Wang, Bing Han, Shibo Wu, Anmin Yu, Mark A. Chapman, Sammy Muraguri, Qing Tan, Wenbo Wang, Zhigui Bao, Aizhong Liu and De-Zhu Li

    Citation: Genome Biology 2021 22:113

    Content type: Research

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  13. Genetic maps have been fundamental to building our understanding of disease genetics and evolutionary processes. The gametes of an individual contain all of the information required to perform a de novo chromo...

    Authors: Ruqian Lyu, Vanessa Tsui, Davis J. McCarthy and Wayne Crismani

    Citation: Genome Biology 2021 22:112

    Content type: Review

    Published on:

  14. Oncopanel genomic testing, which identifies important somatic variants, is increasingly common in medical practice and especially in clinical trials. Currently, there is a paucity of reliable genomic reference...

    Authors: Wendell Jones, Binsheng Gong, Natalia Novoradovskaya, Dan Li, Rebecca Kusko, Todd A. Richmond, Donald J. Johann Jr, Halil Bisgin, Sayed Mohammad Ebrahim Sahraeian, Pierre R. Bushel, Mehdi Pirooznia, Katherine Wilkins, Marco Chierici, Wenjun Bao, Lee Scott Basehore, Anne Bergstrom Lucas…

    Citation: Genome Biology 2021 22:111

    Content type: Research

    Published on:

    The Research to this article has been published in Genome Biology 2021 22:109

  15. X-chromosomal genes contribute to sex differences, in particular during early development, when both X chromosomes are active in females. Double X-dosage shifts female pluripotent cells towards the naive stem ...

    Authors: Oriana Genolet, Anna A. Monaco, Ilona Dunkel, Michael Boettcher and Edda G. Schulz

    Citation: Genome Biology 2021 22:110

    Content type: Research

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  16. Targeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and ...

    Authors: Binsheng Gong, Dan Li, Rebecca Kusko, Natalia Novoradovskaya, Yifan Zhang, Shangzi Wang, Carlos Pabón-Peña, Zhihong Zhang, Kevin Lai, Wanshi Cai, Jennifer S. LoCoco, Eric Lader, Todd A. Richmond, Vinay K. Mittal, Liang-Chun Liu, Donald J. Johann Jr…

    Citation: Genome Biology 2021 22:109

    Content type: Research

    Published on:

    The Research to this article has been published in Genome Biology 2021 22:111

  17. Differential gene expression mechanisms ensure cellular differentiation and plasticity to shape ontogenetic and phylogenetic diversity of cell types. A key regulator of differential gene expression programs ar...

    Authors: Anil Panigrahi and Bert W. O’Malley

    Citation: Genome Biology 2021 22:108

    Content type: Review

    Published on:

  18. Muscle-invasive bladder cancers are characterized by their distinct expression of luminal and basal genes, which could be used to predict key clinical features such as disease progression and overall survival....

    Authors: Tejaswi Iyyanki, Baozhen Zhang, Qixuan Wang, Ye Hou, Qiushi Jin, Jie Xu, Hongbo Yang, Tingting Liu, Xiaotao Wang, Fan Song, Yu Luan, Hironobu Yamashita, Ruby Chien, Huijue Lyu, Lijun Zhang, Lu Wang…

    Citation: Genome Biology 2021 22:105

    Content type: Research

    Published on:

  19. Although using a blockade of programmed death-ligand 1 (PD-L1) to enhance T cell immune responses shows great promise in tumor immunotherapy, the immune-checkpoint inhibition strategy is limited for patients w...

    Authors: Shuang Qu, Zichen Jiao, Geng Lu, Bing Yao, Ting Wang, Weiwei Rong, Jiahan Xu, Ting Fan, Xinlei Sun, Rong Yang, Jun Wang, Yongzhong Yao, Guifang Xu, Xin Yan, Tao Wang, Hongwei Liang…

    Citation: Genome Biology 2021 22:104

    Content type: Research

    Published on:

  20. Whole genome duplication (WGD) events have played a major role in eukaryotic genome evolution, but the consequence of these extreme events in adaptive genome evolution is still not well understood. To address ...

    Authors: Gareth B. Gillard, Lars Grønvold, Line L. Røsæg, Matilde Mengkrog Holen, Øystein Monsen, Ben F. Koop, Eric B. Rondeau, Manu Kumar Gundappa, John Mendoza, Daniel J. Macqueen, Rori V. Rohlfs, Simen R. Sandve and Torgeir R. Hvidsten

    Citation: Genome Biology 2021 22:103

    Content type: Research

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  21. Single-cell sequencing technologies are revolutionizing biology, but they are limited by the need to dissociate live samples. Here, we present ACME (ACetic-MEthanol), a dissociation approach for single-cell tr...

    Authors: Helena García-Castro, Nathan J. Kenny, Marta Iglesias, Patricia Álvarez-Campos, Vincent Mason, Anamaria Elek, Anna Schönauer, Victoria A. Sleight, Jakke Neiro, Aziz Aboobaker, Jon Permanyer, Manuel Irimia, Arnau Sebé-Pedrós and Jordi Solana

    Citation: Genome Biology 2021 22:89

    Content type: Method

    Published on:

  22. Authors: Channabasavaiah B. Gurumurthy, Aidan R. O’Brien, Rolen M. Quadros, John Adams Jr, Pilar Alcaide, Shinya Ayabe, Johnathan Ballard, Surinder K. Batra, Marie-Claude Beauchamp, Kathleen A. Becker, Guillaume Bernas, David Brough, Francisco Carrillo-Salinas, Wesley Chan, Hanying Chen, Ruby Dawson…

    Citation: Genome Biology 2021 22:99

    Content type: Correspondence

    Published on:

    The original article was published in Genome Biology 2021 22:98

  23. The integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal...

    Authors: Maria Artesi, Vincent Hahaut, Basiel Cole, Laurens Lambrechts, Fereshteh Ashrafi, Ambroise Marçais, Olivier Hermine, Philip Griebel, Natasa Arsic, Frank van der Meer, Arsène Burny, Dominique Bron, Elettra Bianchi, Philippe Delvenne, Vincent Bours, Carole Charlier…

    Citation: Genome Biology 2021 22:97

    Content type: Method

    Published on:

  24. We develop the free and open-source model Multi-tissue Splicing (MTSplice) to predict the effects of genetic variants on splicing of cassette exons in 56 human tissues. MTSplice combines MMSplice, which models...

    Authors: Jun Cheng, Muhammed Hasan Çelik, Anshul Kundaje and Julien Gagneur

    Citation: Genome Biology 2021 22:94

    Content type: Method

    Published on:

    The Publisher Correction to this article has been published in Genome Biology 2021 22:107

  25. The human microbiome is increasingly mined for diagnostic and therapeutic biomarkers using machine learning (ML). However, metagenomics-specific software is scarce, and overoptimistic evaluation and limited cr...

    Authors: Jakob Wirbel, Konrad Zych, Morgan Essex, Nicolai Karcher, Ece Kartal, Guillem Salazar, Peer Bork, Shinichi Sunagawa and Georg Zeller

    Citation: Genome Biology 2021 22:93

    Content type: Software

    Published on:

  26. Post-zygotic mutations incurred during DNA replication, DNA repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. How...

    Authors: Yifan Wang, Taejeong Bae, Jeremy Thorpe, Maxwell A. Sherman, Attila G. Jones, Sean Cho, Kenneth Daily, Yanmei Dou, Javier Ganz, Alon Galor, Irene Lobon, Reenal Pattni, Chaggai Rosenbluh, Simone Tomasi, Livia Tomasini, Xiaoxu Yang…

    Citation: Genome Biology 2021 22:92

    Content type: Research

    Published on:

  27. People with neurodegenerative disorders show diverse clinical syndromes, genetic heterogeneity, and distinct brain pathological changes, but studies report overlap between these features. DNA methylation (DNAm...

    Authors: Marta F. Nabais, Simon M. Laws, Tian Lin, Costanza L. Vallerga, Nicola J. Armstrong, Ian P. Blair, John B. Kwok, Karen A. Mather, George D. Mellick, Perminder S. Sachdev, Leanne Wallace, Anjali K. Henders, Ramona A. J. Zwamborn, Paul J. Hop, Katie Lunnon, Ehsan Pishva…

    Citation: Genome Biology 2021 22:90

    Content type: Research

    Published on:

  28. An amendment to this paper has been published and can be accessed via the original article.

    Authors: Rebecca Davies, Ling Liu, Sheng Taotao, Natasha Tuano, Richa Chaturvedi, Kie Kyon Huang, Catherine Itman, Amit Mandoli, Aditi Qamra, Changyuan Hu, David Powell, Roger J. Daly, Patrick Tan and Joseph Rosenbluh

    Citation: Genome Biology 2021 22:88

    Content type: Author Correction

    Published on:

    The original article was published in Genome Biology 2021 22:47

  29. Aging, noise, infection, and ototoxic drugs are the major causes of human acquired sensorineural hearing loss, but treatment options are limited. CRISPR/Cas9 technology has tremendous potential to become a new...

    Authors: Xi Gu, Daqi Wang, Zhijiao Xu, Jinghan Wang, Luo Guo, Renjie Chai, Genglin Li, Yilai Shu and Huawei Li

    Citation: Genome Biology 2021 22:86

    Content type: Research

    Published on:

  30. Histone lactylation, a metabolic stress-related histone modification, plays an important role in the regulation of gene expression during M1 macrophage polarization. However, the role of histone lactylation in...

    Authors: Jie Yu, Peiwei Chai, Minyue Xie, Shengfang Ge, Jing Ruan, Xianqun Fan and Renbing Jia

    Citation: Genome Biology 2021 22:85

    Content type: Research

    Published on:

  31. Here, we develop k -mer substring space decomposition (Kssd), a sketching technique which is significantly faster and more accurate than current sketching methods. We show that it is the only method that can b...

    Authors: Huiguang Yi, Yanling Lin, Chengqi Lin and Wenfei Jin

    Citation: Genome Biology 2021 22:84

    Content type: Software

    Published on:

  32. Most single nucleotide variants (SNVs) occur in noncoding sequence where millions of transcription factor binding sites (TFBS) reside. Here, a comparative analysis of CRISPR-mediated homology-directed repair (...

    Authors: Pan Gao, Qing Lyu, Amr R. Ghanam, Cicera R. Lazzarotto, Gregory A. Newby, Wei Zhang, Mihyun Choi, Orazio J. Slivano, Kevin Holden, John A. Walker II, Anastasia P. Kadina, Rob J. Munroe, Christian M. Abratte, John C. Schimenti, David R. Liu, Shengdar Q. Tsai…

    Citation: Genome Biology 2021 22:83

    Content type: Research

    Published on:

  33. Alternative polyadenylation (APA) refers to the regulated selection of polyadenylation sites (PASs) in transcripts, which determines the length of their 3′ untranslated regions (3′UTRs). We have recently shown...

    Authors: Oliver Daniel Schwich, Nicole Blümel, Mario Keller, Marius Wegener, Samarth Thonta Setty, Melinda Elaine Brunstein, Ina Poser, Igor Ruiz De Los Mozos, Beatrix Suess, Christian Münch, François McNicoll, Kathi Zarnack and Michaela Müller-McNicoll

    Citation: Genome Biology 2021 22:82

    Content type: Research

    Published on:

  34. Genome-scale metabolic models of microorganisms are powerful frameworks to predict phenotypes from an organism’s genotype. While manual reconstructions are laborious, automated reconstructions often fail to re...

    Authors: Johannes Zimmermann, Christoph Kaleta and Silvio Waschina

    Citation: Genome Biology 2021 22:81

    Content type: Software

    Published on:

  35. Millions of nucleotide variants are identified through cancer genome sequencing and it is clinically important to identify the pathogenic variants among them. By introducing base substitutions at guide RNA tar...

    Authors: Changcai Huang, Guangyu Li, Jiayu Wu, Junbo Liang and Xiaoyue Wang

    Citation: Genome Biology 2021 22:80

    Content type: Research

    Published on:

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