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  1. Single-cell RNA-seq datasets are often first analyzed independently without harnessing model fits from previous studies, and are then contextualized with public data sets, requiring time-consuming data wrangli...

    Authors: David S. Fischer, Leander Dony, Martin König, Abdul Moeed, Luke Zappia, Lukas Heumos, Sophie Tritschler, Olle Holmberg, Hananeh Aliee and Fabian J. Theis

    Citation: Genome Biology 2021 22:248

    Content type: Software

    Published on:

  2. Genome-wide association studies have reported more than 100 risk loci for rheumatoid arthritis (RA). These loci are shown to be enriched in immune cell-specific enhancers, but the analysis so far has excluded ...

    Authors: Xiangyu Ge, Mojca Frank-Bertoncelj, Kerstin Klein, Amanda McGovern, Tadeja Kuret, Miranda Houtman, Blaž Burja, Raphael Micheroli, Chenfu Shi, Miriam Marks, Andrew Filer, Christopher D. Buckley, Gisela Orozco, Oliver Distler, Andrew P. Morris, Paul Martin…

    Citation: Genome Biology 2021 22:247

    Content type: Research

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  3. Authors: Kim-Anh Lê Cao, Al J. Abadi, Emily F. Davis-Marcisak, Lauren Hsu, Arshi Arora, Alexis Coullomb, Atul Deshpande, Yuzhou Feng, Pratheepa Jeganathan, Melanie Loth, Chen Meng, Wancen Mu, Vera Pancaldi, Kris Sankaran, Dario Righelli, Amrit Singh…

    Citation: Genome Biology 2021 22:246

    Content type: Author Correction

    Published on:

    The original article was published in Genome Biology 2021 22:220

  4. Nullomers and nullpeptides are short DNA or amino acid sequences that are absent from a genome or proteome, respectively. One potential cause for their absence could be their having a detrimental impact on an ...

    Authors: Ilias Georgakopoulos-Soares, Ofer Yizhar-Barnea, Ioannis Mouratidis, Martin Hemberg and Nadav Ahituv

    Citation: Genome Biology 2021 22:245

    Content type: Research

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  5. The transcription factor CTCF appears indispensable in defining topologically associated domain boundaries and maintaining chromatin loop structures within these domains, supported by numerous functional studi...

    Authors: Beisi Xu, Hong Wang, Shaela Wright, Judith Hyle, Yang Zhang, Ying Shao, Mingming Niu, Yiping Fan, Wojciech Rosikiewicz, Mohamed Nadhir Djekidel, Junmin Peng, Rui Lu and Chunliang Li

    Citation: Genome Biology 2021 22:244

    Content type: Research

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  6. To date, the locus with the most robust human genetic association to COVID-19 severity is 3p21.31. Here, we integrate genome-scale CRISPR loss-of-function screens and eQTLs in diverse cell types and tissues to...

    Authors: Silva Kasela, Zharko Daniloski, Sailalitha Bollepalli, Tristan X. Jordan, Benjamin R. tenOever, Neville E. Sanjana and Tuuli Lappalainen

    Citation: Genome Biology 2021 22:242

    Content type: Short Report

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  7. Genome-wide association studies reveal many non-coding variants associated with complex traits. However, model organism studies largely remain as an untapped resource for unveiling the effector genes of non-co...

    Authors: Chenyang Dong, Shane P. Simonett, Sunyoung Shin, Donnie S. Stapleton, Kathryn L. Schueler, Gary A. Churchill, Leina Lu, Xiaoxiao Liu, Fulai Jin, Yan Li, Alan D. Attie, Mark P. Keller and Sündüz Keleş

    Citation: Genome Biology 2021 22:241

    Content type: Method

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  8. The human genome encodes over 14,000 pseudogenes that are evolutionary relics of protein-coding genes and commonly considered as nonfunctional. Emerging evidence suggests that some pseudogenes may exert import...

    Authors: Ming Sun, Yunfei Wang, Caishang Zheng, Yanjun Wei, Jiakai Hou, Peng Zhang, Wei He, Xiangdong Lv, Yao Ding, Han Liang, Chung-Chau Hon, Xi Chen, Han Xu and Yiwen Chen

    Citation: Genome Biology 2021 22:240

    Content type: Research

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  9. Several bioinformatic tools have been developed for genome-wide identification of orthologous and paralogous genes. However, no corresponding tool allows the detection of exon homology relationships. Here, we ...

    Authors: Yamile Márquez, Federica Mantica, Luca Cozzuto, Demian Burguera, Antonio Hermoso-Pulido, Julia Ponomarenko, Scott W. Roy and Manuel Irimia

    Citation: Genome Biology 2021 22:239

    Content type: Software

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  10. Functional genomics experiments, like ChIP-Seq or ATAC-Seq, produce results that are summarized as a region set. There is no way to objectively evaluate the effectiveness of region set similarity metrics. We p...

    Authors: Aaron Gu, Hyun Jae Cho and Nathan C. Sheffield

    Citation: Genome Biology 2021 22:238

    Content type: Short Report

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  11. Structural variants (SVs) significantly drive genome diversity and environmental adaptation for diverse species. Unlike the prevalent small SVs (< kilobase-scale) in higher eukaryotes, large-size SVs rarely ex...

    Authors: Yumin Huang, Wei Huang, Zhuang Meng, Guilherme Tomaz Braz, Yunfei Li, Kai Wang, Hai Wang, Jinsheng Lai, Jiming Jiang, Zhaobin Dong and Weiwei Jin

    Citation: Genome Biology 2021 22:237

    Content type: Research

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  12. After repairing double-strand breaks (DSBs) caused by CRISPR-Cas9 cleavage, genomic damage, such as large deletions, may have pathogenic consequences.

    Authors: Wei Wen, Zi-Jun Quan, Si-Ang Li, Zhi-Xue Yang, Ya-Wen Fu, Feng Zhang, Guo-Hua Li, Mei Zhao, Meng-Di Yin, Jing Xu, Jian-Ping Zhang, Tao Cheng and Xiao-Bing Zhang

    Citation: Genome Biology 2021 22:236

    Content type: Research

    Published on:

  13. Prime editing is a revolutionary genome-editing technology that can make a wide range of precise edits in DNA. However, designing highly efficient prime editors (PEs) remains challenging. We develop Easy-Prime...

    Authors: Yichao Li, Jingjing Chen, Shengdar Q. Tsai and Yong Cheng

    Citation: Genome Biology 2021 22:235

    Content type: Software

    Published on:

  14. A specific 3-dimensional intrachromosomal architecture of core stem cell factor genes is required to reprogram a somatic cell into pluripotency. As little is known about the epigenetic readers that orchestrate...

    Authors: Zhonghua Du, Xue Wen, Yichen Wang, Lin Jia, Shilin Zhang, Yudi Liu, Lei Zhou, Hui Li, Wang Yang, Cong Wang, Jingcheng Chen, Yajing Hao, Daniela Salgado Figueroa, Huiling Chen, Dan Li, Naifei Chen…

    Citation: Genome Biology 2021 22:233

    Content type: Research

    Published on:

    The Author Correction to this article has been published in Genome Biology 2021 22:272

  15. Single-cell RNA sequencing (scRNA-seq) provides new opportunities to characterize cell populations, typically accomplished through some type of clustering analysis. Estimation of the optimal cluster number (K) is...

    Authors: Siyao Liu, Aatish Thennavan, Joseph P. Garay, J. S. Marron and Charles M. Perou

    Citation: Genome Biology 2021 22:232

    Content type: Method

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  16. Efficiently scaling genomic variant search indexes to thousands of samples is computationally challenging due to the presence of multiple coordinate systems to avoid reference biases. We present VariantStore, ...

    Authors: Prashant Pandey, Yinjie Gao and Carl Kingsford

    Citation: Genome Biology 2021 22:231

    Content type: Method

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  17. Biomolecular condensates have been implicated in multiple cellular processes. However, the global role played by condensates in 3D chromatin organization remains unclear. At present, 1,6-hexanediol (1,6-HD) is...

    Authors: Xinyi Liu, Shaoshuai Jiang, Lin Ma, Jiale Qu, Longying Zhao, Xing Zhu and Junjun Ding

    Citation: Genome Biology 2021 22:230

    Content type: Research

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  18. Liquid-liquid phase separation (LLPS) is an important organizing principle for biomolecular condensation and chromosome compartmentalization. However, while many proteins have been reported to undergo LLPS, qu...

    Authors: Minglei Shi, Kaiqiang You, Taoyu Chen, Chao Hou, Zhengyu Liang, Mingwei Liu, Jifeng Wang, Taotao Wei, Jun Qin, Yang Chen, Michael Q. Zhang and Tingting Li

    Citation: Genome Biology 2021 22:229

    Content type: Research

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  19. Chromatin interactions play important roles in regulating gene expression. However, the availability of genome-wide chromatin interaction data is limited. We develop a computational method, chromatin interacti...

    Authors: Fan Cao, Yu Zhang, Yichao Cai, Sambhavi Animesh, Ying Zhang, Semih Can Akincilar, Yan Ping Loh, Xinya Li, Wee Joo Chng, Vinay Tergaonkar, Chee Keong Kwoh and Melissa J. Fullwood

    Citation: Genome Biology 2021 22:226

    Content type: Method

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  20. Retrotransposons are genetic elements inducing mutations in all domains of life. Despite their detrimental effect, retrotransposons can become temporarily active during epigenetic reprogramming and cellular st...

    Authors: Antoine Porquier, Constance Tisserant, Francisco Salinas, Carla Glassl, Lucas Wange, Wolfgang Enard, Andreas Hauser, Matthias Hahn and Arne Weiberg

    Citation: Genome Biology 2021 22:225

    Content type: Research

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  21. Tandem repeat (TR) expansion is the underlying cause of over 40 neurological disorders. Long-read sequencing offers an exciting avenue over conventional technologies for detecting TR expansions. Here, we prese...

    Authors: Readman Chiu, Indhu-Shree Rajan-Babu, Jan M. Friedman and Inanc Birol

    Citation: Genome Biology 2021 22:224

    Content type: Software

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  22. Single-cell RNA-seq (scRNA-seq) profiles gene expression with high resolution. Here, we develop a stepwise computational method-called SCAPTURE to identify, evaluate, and quantify cleavage and polyadenylation ...

    Authors: Guo-Wei Li, Fang Nan, Guo-Hua Yuan, Chu-Xiao Liu, Xindong Liu, Ling-Ling Chen, Bin Tian and Li Yang

    Citation: Genome Biology 2021 22:221

    Content type: Method

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  23. Six million Jews were killed by Nazi Germany and its collaborators during World War II. Archaeological excavations in the area of the death camp in Sobibór, Poland, revealed ten sets of human skeletal remains ...

    Authors: Marta Diepenbroek, Christina Amory, Harald Niederstätter, Bettina Zimmermann, Maria Szargut, Grażyna Zielińska, Arne Dür, Iwona Teul, Wojciech Mazurek, Krzysztof Persak, Andrzej Ossowski and Walther Parson

    Citation: Genome Biology 2021 22:200

    Content type: Research

    Published on:

  24. Authors: Kim-Anh Lê Cao, Al J. Abadi, Emily F. Davis-Marcisak, Lauren Hsu, Arshi Arora, Alexis Coullomb, Atul Deshpande, Yuzhou Feng, Pratheepa Jeganathan, Melanie Loth, Chen Meng, Wancen Mu, Vera Pancaldi, Kris Sankaran, Dario Righelli, Amrit Singh…

    Citation: Genome Biology 2021 22:220

    Content type: Open Letter

    Published on:

    The Author Correction to this article has been published in Genome Biology 2021 22:246

  25. Precise splice junction calls are currently unavailable in scRNA-seq pipelines such as the 10x Chromium platform but are critical for understanding single-cell biology. Here, we introduce SICILIAN, a new metho...

    Authors: Roozbeh Dehghannasiri, Julia Eve Olivieri, Ana Damljanovic and Julia Salzman

    Citation: Genome Biology 2021 22:219

    Content type: Short Report

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  26. Human-to-human transmission of symbiotic, anaerobic bacteria is a fundamental evolutionary adaptation essential for membership of the human gut microbiota. However, despite its importance, the genomic and biol...

    Authors: Hilary P. Browne, Alexandre Almeida, Nitin Kumar, Kevin Vervier, Anne T. Adoum, Elisa Viciani, Nicholas J. R. Dawson, Samuel C. Forster, Claire Cormie, David Goulding and Trevor D. Lawley

    Citation: Genome Biology 2021 22:204

    Content type: Research

    Published on:

  27. Spatial interactions and insulation of chromatin regions are associated with transcriptional regulation. Domains of frequent chromatin contacts are proposed as functional units, favoring and delimiting gene re...

    Authors: Marie Zufferey, Yuanlong Liu, Daniele Tavernari, Marco Mina and Giovanni Ciriello

    Citation: Genome Biology 2021 22:218

    Content type: Research

    Published on:

  28. The phenotype of an individual can be affected not only by the individual’s own genotypes, known as direct genetic effects (DGE), but also by genotypes of interacting partners, indirect genetic effects (IGE). ...

    Authors: Amelie Baud, Francesco Paolo Casale, Amanda M. Barkley-Levenson, Nilgoun Farhadi, Charlotte Montillot, Binnaz Yalcin, Jerome Nicod, Abraham A. Palmer and Oliver Stegle

    Citation: Genome Biology 2021 22:216

    Content type: Research

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  29. We introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs),...

    Authors: Christopher Quince, Sergey Nurk, Sebastien Raguideau, Robert James, Orkun S. Soyer, J. Kimberly Summers, Antoine Limasset, A. Murat Eren, Rayan Chikhi and Aaron E. Darling

    Citation: Genome Biology 2021 22:214

    Content type: Method

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  30. With viral infections, multiple related viral strains are often present due to coinfection or within-host evolution. We describe Haploflow, a deBruijn graph-based assembler for de novo genome assembly of viral...

    Authors: Adrian Fritz, Andreas Bremges, Zhi-Luo Deng, Till Robin Lesker, Jasper Götting, Tina Ganzenmueller, Alexander Sczyrba, Alexander Dilthey, Frank Klawonn and Alice Carolyn McHardy

    Citation: Genome Biology 2021 22:212

    Content type: Method

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  31. Understanding the genetic architecture of temperature adaptation is key for characterizing and predicting the effect of climate change on natural populations. One particularly promising approach is Evolve and ...

    Authors: Kathrin A. Otte, Viola Nolte, François Mallard and Christian Schlötterer

    Citation: Genome Biology 2021 22:211

    Content type: Research

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  32. Authors: Zhi-Qiang Chen, Yanjun Zan, Pascal Milesi, Linghua Zhou, Jun Chen, Lili Li, BinBin Cui, Shihui Niu, Johan Westin, Bo Karlsson, Maria Rosario García-Gil, Martin Lascoux and Harry X. Wu

    Citation: Genome Biology 2021 22:210

    Content type: Publisher Correction

    Published on:

    The original article was published in Genome Biology 2021 22:179

  33. Akkermansia muciniphila is a human gut microbe with a key role in the physiology of the intestinal mucus layer and reported associations with decreased body mass and increased gut barrier function and health. Des...

    Authors: Nicolai Karcher, Eleonora Nigro, Michal Punčochář, Aitor Blanco-Míguez, Matteo Ciciani, Paolo Manghi, Moreno Zolfo, Fabio Cumbo, Serena Manara, Davide Golzato, Anna Cereseto, Manimozhiyan Arumugam, Thi Phuong Nam Bui, Hanne L. P. Tytgat, Mireia Valles-Colomer, Willem M. de Vos…

    Citation: Genome Biology 2021 22:209

    Content type: Research

    Published on:

  34. One challenge facing omics association studies is the loss of statistical power when adjusting for confounders and multiple testing. The traditional statistical procedure involves fitting a confounder-adjusted...

    Authors: Sangyoon Yi, Xianyang Zhang, Lu Yang, Jinyan Huang, Yuanhang Liu, Chen Wang, Daniel J. Schaid and Jun Chen

    Citation: Genome Biology 2021 22:208

    Content type: Method

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  35. The full biosphere structure and functional exploration of the microbial communities of the Challenger Deep of the Mariana Trench, the deepest known hadal zone on Earth, lag far behind that of other marine rea...

    Authors: Ping Chen, Hui Zhou, Yanyan Huang, Zhe Xie, Mengjie Zhang, Yuli Wei, Jia Li, Yuewei Ma, Min Luo, Wenmian Ding, Junwei Cao, Tao Jiang, Peng Nan, Jiasong Fang and Xuan Li

    Citation: Genome Biology 2021 22:207

    Content type: Research

    Published on:

  36. Metazoan cells only utilize a small subset of the potential DNA replication origins to duplicate the whole genome in each cell cycle. Origin choice is linked to cell growth, differentiation, and replication st...

    Authors: Yongzheng Li, Boxin Xue, Mengling Zhang, Liwei Zhang, Yingping Hou, Yizhi Qin, Haizhen Long, Qian Peter Su, Yao Wang, Xiaodong Guan, Yanyan Jin, Yuan Cao, Guohong Li and Yujie Sun

    Citation: Genome Biology 2021 22:206

    Content type: Research

    Published on:

  37. Authors: Umberto Palatini, Reem A. Masri, Luciano V. Cosme, Sergey Koren, Françoise Thibaud-Nissen, James K. Biedler, Flavia Krsticevic, J. Spencer Johnston, Rebecca Halbach, Jacob E. Crawford, Igor Antoshechkin, Anna-Bella Failloux, Elisa Pischedda, Michele Marconcini, Jay Ghurye, Arang Rhie…

    Citation: Genome Biology 2021 22:205

    Content type: Author Correction

    Published on:

    The original article was published in Genome Biology 2020 21:215

  38. The origin of sex chromosomes requires the establishment of recombination suppression between the proto-sex chromosomes. In many fish species, the sex chromosome pair is homomorphic with a recent origin, provi...

    Authors: Lingzhan Xue, Yu Gao, Meiying Wu, Tian Tian, Haiping Fan, Yongji Huang, Zhen Huang, Dapeng Li and Luohao Xu

    Citation: Genome Biology 2021 22:203

    Content type: Research

    Published on:

  39. GRIDSS2 is the first structural variant caller to explicitly report single breakends—breakpoints in which only one side can be unambiguously determined. By treating single breakends as a fundamental genomic re...

    Authors: Daniel L. Cameron, Jonathan Baber, Charles Shale, Jose Espejo Valle-Inclan, Nicolle Besselink, Arne van Hoeck, Roel Janssen, Edwin Cuppen, Peter Priestley and Anthony T. Papenfuss

    Citation: Genome Biology 2021 22:202

    Content type: Method

    Published on:

  40. Naïve and primed pluripotent stem cells (PSCs) represent two different pluripotent states. Primed PSCs following in vitro culture exhibit lower developmental potency as evidenced by failure in germline chimera...

    Authors: Haifeng Fu, Weiyu Zhang, Niannian Li, Jiao Yang, Xiaoying Ye, Chenglei Tian, Xinyi Lu and Lin Liu

    Citation: Genome Biology 2021 22:201

    Content type: Research

    Published on:

  41. Recent studies highlight the role of metabolites in immune diseases, but it remains unknown how much of this effect is driven by genetic and non-genetic host factors.

    Authors: Xiaojing Chu, Martin Jaeger, Joep Beumer, Olivier B. Bakker, Raul Aguirre-Gamboa, Marije Oosting, Sanne P. Smeekens, Simone Moorlag, Vera P. Mourits, Valerie A. C. M. Koeken, Charlotte de Bree, Trees Jansen, Ian T. Mathews, Khoi Dao, Mahan Najhawan, Jeramie D. Watrous…

    Citation: Genome Biology 2021 22:198

    Content type: Research

    Published on:

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