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  1. 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:

  2. 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

  3. 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

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  4. 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

  5. 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:

  6. 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

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  7. 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:

  8. 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

  9. 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:

  10. 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:

  11. 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

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  12. 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

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  13. 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

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  14. 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:

  15. 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

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  16. riboCIRC is a translatome data-oriented circRNA database specifically designed for hosting, exploring, analyzing, and visualizing translatable circRNAs from multi-species. The database provides a comprehensive...

    Authors: Huihui Li, Mingzhe Xie, Yan Wang, Ludong Yang, Zhi Xie and Hongwei Wang

    Citation: Genome Biology 2021 22:79

    Content type: Database

    Published on:

  17. Spatial transcriptomic and proteomic technologies have provided new opportunities to investigate cells in their native microenvironment. Here we present Giotto, a comprehensive and open-source toolbox for spat...

    Authors: Ruben Dries, Qian Zhu, Rui Dong, Chee-Huat Linus Eng, Huipeng Li, Kan Liu, Yuntian Fu, Tianxiao Zhao, Arpan Sarkar, Feng Bao, Rani E. George, Nico Pierson, Long Cai and Guo-Cheng Yuan

    Citation: Genome Biology 2021 22:78

    Content type: Method

    Published on:

  18. The discovery that somatic cells can be reprogrammed to induced pluripotent stem cells (iPSCs) has provided a foundation for in vitro human disease modelling, drug development and population genetics studies. ...

    Authors: Drew Neavin, Quan Nguyen, Maciej S. Daniszewski, Helena H. Liang, Han Sheng Chiu, Yong Kiat Wee, Anne Senabouth, Samuel W. Lukowski, Duncan E. Crombie, Grace E. Lidgerwood, Damián Hernández, James C. Vickers, Anthony L. Cook, Nathan J. Palpant, Alice Pébay, Alex W. Hewitt…

    Citation: Genome Biology 2021 22:76

    Content type: Research

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  19. Controlling quality of next-generation sequencing (NGS) data files is a necessary but complex task. To address this problem, we statistically characterize common NGS quality features and develop a novel qualit...

    Authors: Steffen Albrecht, Maximilian Sprang, Miguel A. Andrade-Navarro and Jean-Fred Fontaine

    Citation: Genome Biology 2021 22:75

    Content type: Software

    Published on:

  20. Single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) identifies regulated chromatin accessibility modules at the single-cell resolution. Robust evaluation is critical to the developme...

    Authors: Zeinab Navidi, Lin Zhang and Bo Wang

    Citation: Genome Biology 2021 22:74

    Content type: Method

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  21. Many neurodegenerative diseases develop only later in life, when cells in the nervous system lose their structure or function. In many forms of neurodegenerative diseases, this late-onset phenomenon remains la...

    Authors: Matan Sorek, Walaa Oweis, Malka Nissim-Rafinia, Moria Maman, Shahar Simon, Cynthia C. Hession, Xian Adiconis, Sean K. Simmons, Neville E. Sanjana, Xi Shi, Congyi Lu, Jen Q. Pan, Xiaohong Xu, Mahmoud A. Pouladi, Lisa M. Ellerby, Feng Zhang…

    Citation: Genome Biology 2021 22:73

    Content type: Research

    Published on:

  22. Transcription of eukaryotic genomes involves complex alternative processing of RNAs. Sequencing of full-length RNAs using long reads reveals the true complexity of processing. However, the relatively high erro...

    Authors: Matthew T. Parker, Katarzyna Knop, Geoffrey J. Barton and Gordon G. Simpson

    Citation: Genome Biology 2021 22:72

    Content type: Software

    Published on:

  23. We present a Minimal Event Distance Aneuploidy Lineage Tree (MEDALT) algorithm that infers the evolution history of a cell population based on single-cell copy number (SCCN) profiles, and a statistical routine...

    Authors: Fang Wang, Qihan Wang, Vakul Mohanty, Shaoheng Liang, Jinzhuang Dou, Jincheng Han, Darlan Conterno Minussi, Ruli Gao, Li Ding, Nicholas Navin and Ken Chen

    Citation: Genome Biology 2021 22:70

    Content type: Research

    Published on:

  24. The ability of nanopore sequencing to simultaneously detect modified nucleotides while producing long reads makes it ideal for detecting and phasing allele-specific methylation. However, there is currently no ...

    Authors: Vahid Akbari, Jean-Michel Garant, Kieran O’Neill, Pawan Pandoh, Richard Moore, Marco A. Marra, Martin Hirst and Steven J. M. Jones

    Citation: Genome Biology 2021 22:68

    Content type: Software

    Published on:

  25. The broad application of single-cell RNA profiling in plants has been hindered by the prerequisite of protoplasting that requires digesting the cell walls from different types of plant tissues. Here, we presen...

    Authors: Yanping Long, Zhijian Liu, Jinbu Jia, Weipeng Mo, Liang Fang, Dongdong Lu, Bo Liu, Hong Zhang, Wei Chen and Jixian Zhai

    Citation: Genome Biology 2021 22:66

    Content type: Method

    Published on:

  26. The integration of single-cell RNA-sequencing datasets from multiple sources is critical for deciphering cell-to-cell heterogeneities and interactions in complex biological systems. We present a novel unsuperv...

    Authors: Dongfang Wang, Siyu Hou, Lei Zhang, Xiliang Wang, Baolin Liu and Zemin Zhang

    Citation: Genome Biology 2021 22:63

    Content type: Method

    Published on:

  27. To investigate the mechanisms driving regulatory evolution across tissues, we experimentally mapped promoters, enhancers, and gene expression in the liver, brain, muscle, and testis from ten diverse mammals.

    Authors: Maša Roller, Ericca Stamper, Diego Villar, Osagie Izuogu, Fergal Martin, Aisling M. Redmond, Raghavendra Ramachanderan, Louise Harewood, Duncan T. Odom and Paul Flicek

    Citation: Genome Biology 2021 22:62

    Content type: Research

    Published on:

  28. Authors: Teppo Felin, Jan Koenderink, Joachim I. Krueger, Denis Noble and George F. R. Ellis

    Citation: Genome Biology 2021 22:59

    Content type: Correspondence

    Published on:

    The original article was published in Genome Biology 2021 22:58

  29. Transcription in mammalian cells is a complex stochastic process involving shuttling of polymerase between genes and phase-separated liquid condensates. It occurs in bursts, which results in vastly different n...

    Authors: Massimo Cavallaro, Mark D. Walsh, Matt Jones, James Teahan, Simone Tiberi, Bärbel Finkenstädt and Daniel Hebenstreit

    Citation: Genome Biology 2021 22:56

    Content type: Research

    Published on:

  30. A bottleneck in high-throughput functional genomics experiments is identifying the most important genes and their relevant functions from a list of gene hits. Gene Ontology (GO) enrichment methods provide insi...

    Authors: Robert Ietswaart, Benjamin M. Gyori, John A. Bachman, Peter K. Sorger and L. Stirling Churchman

    Citation: Genome Biology 2021 22:55

    Content type: Research

    Published on:

  31. Frequent activation of the co-transcriptional factor YAP is observed in a large number of solid tumors. Activated YAP associates with enhancer loci via TEAD4-DNA-binding protein and stimulates cancer aggressiv...

    Authors: Li Li, Alejandro P. Ugalde, Colinda L. G. J. Scheele, Sebastian M. Dieter, Remco Nagel, Jin Ma, Abhijeet Pataskar, Gozde Korkmaz, Ran Elkon, Miao-Ping Chien, Li You, Pin-Rui Su, Onno B. Bleijerveld, Maarten Altelaar, Lyubomir Momchev, Zohar Manber…

    Citation: Genome Biology 2021 22:54

    Content type: Research

    Published on:

  32. Massive genome sequencing data have inspired new challenges in personalized treatments and facilitated oncological drug discovery. We present a comprehensive database, My Personal Mutanome (MPM), for accelerat...

    Authors: Yadi Zhou, Junfei Zhao, Jiansong Fang, William Martin, Lang Li, Ruth Nussinov, Timothy A. Chan, Charis Eng and Feixiong Cheng

    Citation: Genome Biology 2021 22:53

    Content type: Database

    Published on:

  33. N6-methyladenosine (m6A) and adenosine-to-inosine (A-to-I) RNA editing are two of the most abundant RNA modification events affecting adenosines in mammals. Both these RNA modifications determine mRNA fate and p....

    Authors: Valentina Tassinari, Valeriana Cesarini, Sara Tomaselli, Zaira Ianniello, Domenico Alessandro Silvestris, Lavinia Ceci Ginistrelli, Maurizio Martini, Biagio De Angelis, Gabriele De Luca, Lucia Ricci Vitiani, Alessandro Fatica, Franco Locatelli and Angela Gallo

    Citation: Genome Biology 2021 22:51

    Content type: Research

    Published on:

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