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  1. Rhinoviruses (RVs) cause more than half of common colds and, in some cases, more severe diseases. Functional genomics analyses of RVs using siRNA or genome-wide CRISPR screen uncovered a limited set of host fa...

    Authors: Hong Mei, Zhao Zha, Wei Wang, Yusang Xie, Yuege Huang, Wenping Li, Dong Wei, Xinxin Zhang, Jieming Qu and Jia Liu

    Citation: Genome Biology 2021 22:297

    Content type: Research

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  2. Calling fusion genes from RNA-seq data is well established, but other transcriptional variants are difficult to detect using existing approaches. To identify all types of variants in transcriptomes we develope...

    Authors: Marek Cmero, Breon Schmidt, Ian J. Majewski, Paul G. Ekert, Alicia Oshlack and Nadia M. Davidson

    Citation: Genome Biology 2021 22:296

    Content type: Method

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  3. Nanopore long-read sequencing technology greatly expands the capacity of long-range, single-molecule DNA-modification detection. A growing number of analytical tools have been developed to detect DNA methylati...

    Authors: Yang Liu, Wojciech Rosikiewicz, Ziwei Pan, Nathaniel Jillette, Ping Wang, Aziz Taghbalout, Jonathan Foox, Christopher Mason, Martin Carroll, Albert Cheng and Sheng Li

    Citation: Genome Biology 2021 22:295

    Content type: Research

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  4. The 3′ untranslated region (UTR) plays critical roles in determining the level of gene expression through effects on activities such as mRNA stability and translation. Functional elements within this region ha...

    Authors: Andrew Savinov, Benjamin M. Brandsen, Brooke E. Angell, Josh T. Cuperus and Stanley Fields

    Citation: Genome Biology 2021 22:293

    Content type: Research

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  5. The endoplasmic reticulum (ER) is a membranous organelle that maintains proteostasis and cellular homeostasis, controlling the fine balance between health and disease. Dysregulation of the ER stress response h...

    Authors: Xiaobo Ke, Kwontae You, Matthieu Pichaud, Henry J. Haiser, Daniel B. Graham, Hera Vlamakis, Jeffrey A. Porter and Ramnik J. Xavier

    Citation: Genome Biology 2021 22:292

    Content type: Research

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  6. Alternative cleavage and polyadenylation (APA), an RNA processing event, occurs in over 70% of human protein-coding genes. APA results in mRNA transcripts with distinct 3′ ends. Most APA occurs within 3′ UTRs,...

    Authors: Ankeeta Shah, Briana E. Mittleman, Yoav Gilad and Yang I. Li

    Citation: Genome Biology 2021 22:291

    Content type: Research

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  7. Cellular RNA-binding proteins (RBPs) have multiple roles in post-transcriptional control, and some are shown to bind DNA. However, the global localization and the general chromatin-binding ability of RBPs are ...

    Authors: Yue Ren, Yue Huo, Weiqian Li, Manman He, Siqi Liu, Jiabin Yang, Hongmei Zhao, Lingjie Xu, Yuehong Guo, Yanmin Si, Hualu Zhao, Shuan Rao, Jing Wang, Yanni Ma, Xiaoshuang Wang, Jia Yu…

    Citation: Genome Biology 2021 22:290

    Content type: Research

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  8. Pancreatic ductal adenocarcinoma initiation is most frequently caused by Kras mutations.

    Authors: Angela J. Mathison, Romica Kerketta, Thiago Milech de Assuncao, Elise Leverence, Atefeh Zeighami, Guillermo Urrutia, Timothy J. Stodola, Marina Pasca di Magliano, Juan L. Iovanna, Michael T. Zimmermann, Gwen Lomberk and Raul Urrutia

    Citation: Genome Biology 2021 22:289

    Content type: Research

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  9. High-throughput biological data analysis commonly involves identifying features such as genes, genomic regions, and proteins, whose values differ between two conditions, from numerous features measured simulta...

    Authors: Xinzhou Ge, Yiling Elaine Chen, Dongyuan Song, MeiLu McDermott, Kyla Woyshner, Antigoni Manousopoulou, Ning Wang, Wei Li, Leo D. Wang and Jingyi Jessica Li

    Citation: Genome Biology 2021 22:288

    Content type: Method

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  10. The diversity of genomic alterations in cancer poses challenges to fully understanding the etiologies of the disease. Recent interest in infrequent mutations, in genes that reside in the “long tail” of the mut...

    Authors: Hussein Mohsen, Vignesh Gunasekharan, Tao Qing, Montrell Seay, Yulia Surovtseva, Sahand Negahban, Zoltan Szallasi, Lajos Pusztai and Mark B. Gerstein

    Citation: Genome Biology 2021 22:287

    Content type: Research

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  11. The rise in throughput and quality of long-read sequencing should allow unambiguous identification of full-length transcript isoforms. However, its application to single-cell RNA-seq has been limited by throug...

    Authors: Elisabeth Rebboah, Fairlie Reese, Katherine Williams, Gabriela Balderrama-Gutierrez, Cassandra McGill, Diane Trout, Isaryhia Rodriguez, Heidi Liang, Barbara J. Wold and Ali Mortazavi

    Citation: Genome Biology 2021 22:286

    Content type: Method

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  12. Regulation of protein output at the level of translation allows for a rapid adaptation to dynamic changes to the cell’s requirements. This precise control of gene expression is achieved by complex and interlin...

    Authors: Sarah L. Gillen, Chiara Giacomelli, Kelly Hodge, Sara Zanivan, Martin Bushell and Ania Wilczynska

    Citation: Genome Biology 2021 22:284

    Content type: Research

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  13. Balancing the yield, quality and resistance to disease is a daunting challenge in crop breeding due to the negative relationship among these traits. Large-scale genomic landscape analysis of germplasm resource...

    Authors: Ning Xiao, Cunhong Pan, Yuhong Li, Yunyu Wu, Yue Cai, Yue Lu, Ruyi Wang, Ling Yu, Wei Shi, Houxiang Kang, Zhaobing Zhu, Niansheng Huang, Xiaoxiang Zhang, Zichun Chen, Jianju Liu, Zefeng Yang…

    Citation: Genome Biology 2021 22:283

    Content type: Research

    Published on:

  14. Zebrafish pigment cell differentiation provides an attractive model for studying cell fate progression as a neural crest progenitor engenders diverse cell types, including two morphologically distinct pigment ...

    Authors: Hyo Sik Jang, Yujie Chen, Jiaxin Ge, Alicia N. Wilkening, Yiran Hou, Hyung Joo Lee, You Rim Choi, Rebecca F. Lowdon, Xiaoyun Xing, Daofeng Li, Charles K. Kaufman, Stephen L. Johnson and Ting Wang

    Citation: Genome Biology 2021 22:282

    Content type: Research

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  15. The adaptive CRISPR-Cas immune system stores sequences from past invaders as spacers in CRISPR arrays and thereby provides direct evidence that links invaders to hosts. Mapping CRISPR spacers has revealed many...

    Authors: Jochem N. A. Vink, Jan H. L. Baijens and Stan J. J. Brouns

    Citation: Genome Biology 2021 22:281

    Content type: Research

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  16. Deep learning has proven to be a powerful technique for transcription factor (TF) binding prediction but requires large training datasets. Transfer learning can reduce the amount of data required for deep lear...

    Authors: Gherman Novakovsky, Manu Saraswat, Oriol Fornes, Sara Mostafavi and Wyeth W. Wasserman

    Citation: Genome Biology 2021 22:280

    Content type: Research

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  17. Mammalian development is associated with extensive changes in gene expression, chromatin accessibility, and nuclear structure. Here, we follow such changes associated with mouse embryonic stem cell differentia...

    Authors: Giancarlo Bonora, Vijay Ramani, Ritambhara Singh, He Fang, Dana L. Jackson, Sanjay Srivatsan, Ruolan Qiu, Choli Lee, Cole Trapnell, Jay Shendure, Zhijun Duan, Xinxian Deng, William S. Noble and Christine M. Disteche

    Citation: Genome Biology 2021 22:279

    Content type: Research

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  18. Here we describe a new integrative approach for accurate annotation and quantification of circRNAs named Short Read circRNA Pipeline (SRCP). Our strategy involves two steps: annotation of validated circRNAs fo...

    Authors: Avigayel Rabin, Michela Zaffagni, Reut Ashwal-Fluss, Ines Lucia Patop, Aarti Jajoo, Shlomo Shenzis, Liran Carmel and Sebastian Kadener

    Citation: Genome Biology 2021 22:277

    Content type: Method

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  19. The bacillus Calmette-Guérin (BCG) vaccine protects against tuberculosis and heterologous infections but elicits high inter-individual variation in specific and nonspecific, or trained, immune responses. While...

    Authors: Martin Stražar, Vera P. Mourits, Valerie A. C. M. Koeken, L. Charlotte J. de Bree, Simone J. C. F. M. Moorlag, Leo A. B. Joosten, Reinout van Crevel, Hera Vlamakis, Mihai G. Netea and Ramnik J. Xavier

    Citation: Genome Biology 2021 22:275

    Content type: Research

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  20. Illumina DNA methylation microarrays enable epigenome-wide analysis vastly used for the discovery of novel DNA methylation variation in health and disease. However, the microarrays’ probe design cannot fully c...

    Authors: Benjamin Planterose Jiménez, Manfred Kayser and Athina Vidaki

    Citation: Genome Biology 2021 22:274

    Content type: Research

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  21. Spatiotemporal changes in the chromatin accessibility landscape are essential to cell differentiation, development, health, and disease. The quest of identifying regulatory elements in open chromatin regions a...

    Authors: Pâmela A. Alexandre, Marina Naval-Sánchez, Moira Menzies, Loan T. Nguyen, Laercio R. Porto-Neto, Marina R. S. Fortes and Antonio Reverter

    Citation: Genome Biology 2021 22:273

    Content type: Research

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  22. 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 22:272

    Content type: Author Correction

    Published on:

    The original article was published in Genome Biology 2021 22:233

  23. LightGBM is an ensemble model of decision trees for classification and regression prediction. We demonstrate its utility in genomic selection-assisted breeding with a large dataset of inbred and hybrid maize l...

    Authors: Jun Yan, Yuetong Xu, Qian Cheng, Shuqin Jiang, Qian Wang, Yingjie Xiao, Chuang Ma, Jianbing Yan and Xiangfeng Wang

    Citation: Genome Biology 2021 22:271

    Content type: Method

    Published on:

  24. Sequence Read Archive submissions to the National Center for Biotechnology Information often lack useful metadata, which limits the utility of these submissions. We describe the Sequence Taxonomic Analysis Too...

    Authors: Kenneth S. Katz, Oleg Shutov, Richard Lapoint, Michael Kimelman, J. Rodney Brister and Christopher O’Sullivan

    Citation: Genome Biology 2021 22:270

    Content type: Method

    Published on:

  25. Super-enhancers are clusters of enhancer elements that play critical roles in the maintenance of cell identity. Current investigations on super-enhancers are centered on the established ones in static cell typ...

    Authors: Yan Kai, Bin E. Li, Ming Zhu, Grace Y. Li, Fei Chen, Yingli Han, Hye Ji Cha, Stuart H. Orkin, Wenqing Cai, Jialiang Huang and Guo-Cheng Yuan

    Citation: Genome Biology 2021 22:269

    Content type: Research

    Published on:

  26. We present pandora, a novel pan-genome graph structure and algorithms for identifying variants across the full bacterial pan-genome. As much bacterial adaptability hinges on the accessory genome, methods which an...

    Authors: Rachel M. Colquhoun, Michael B. Hall, Leandro Lima, Leah W. Roberts, Kerri M. Malone, Martin Hunt, Brice Letcher, Jane Hawkey, Sophie George, Louise Pankhurst and Zamin Iqbal

    Citation: Genome Biology 2021 22:267

    Content type: Method

    Published on:

  27. While long-read sequencing allows for the complete assembly of bacterial genomes, long-read assemblies contain a variety of errors. Here, we present Trycycler, a tool which produces a consensus assembly from m...

    Authors: Ryan R. Wick, Louise M. Judd, Louise T. Cerdeira, Jane Hawkey, Guillaume Méric, Ben Vezina, Kelly L. Wyres and Kathryn E. Holt

    Citation: Genome Biology 2021 22:266

    Content type: Software

    Published on:

  28. Variation in gene expression underlies interindividual variability in relevant traits including immune response. However, the genetic variation responsible for these gene expression changes remains largely unk...

    Authors: Anna Ullastres, Miriam Merenciano and Josefa González

    Citation: Genome Biology 2021 22:265

    Content type: Research

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  29. Cell type identification is one of the most important questions in single-cell RNA sequencing (scRNA-seq) data analysis. With the accumulation of public scRNA-seq data, supervised cell type identification meth...

    Authors: Wenjing Ma, Kenong Su and Hao Wu

    Citation: Genome Biology 2021 22:264

    Content type: Research

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  30. With the recent increase in RNA sequencing efforts using large cohorts of individuals, surveying allele-specific gene expression is becoming increasingly frequent. Here, we report that, despite not containing ...

    Authors: Gamze Gürsoy, Nancy Lu, Sarah Wagner and Mark Gerstein

    Citation: Genome Biology 2021 22:263

    Content type: Short Report

    Published on:

  31. Local genetic correlation quantifies the genetic similarity of complex traits in specific genomic regions. However, accurate estimation of local genetic correlation remains challenging, due to linkage disequil...

    Authors: Yiliang Zhang, Qiongshi Lu, Yixuan Ye, Kunling Huang, Wei Liu, Yuchang Wu, Xiaoyuan Zhong, Boyang Li, Zhaolong Yu, Brittany G. Travers, Donna M. Werling, James J. Li and Hongyu Zhao

    Citation: Genome Biology 2021 22:262

    Content type: Method

    Published on:

  32. Long-read sequencing enables variant detection in genomic regions that are considered difficult-to-map by short-read sequencing. To fully exploit the benefits of longer reads, here we present a deep learning m...

    Authors: Mian Umair Ahsan, Qian Liu, Li Fang and Kai Wang

    Citation: Genome Biology 2021 22:261

    Content type: Method

    Published on:

  33. Drought is a major environmental disaster that causes crop yield loss worldwide. Metabolites are involved in various environmental stress responses of plants. However, the genetic control of metabolomes underl...

    Authors: Fei Zhang, Jinfeng Wu, Nir Sade, Si Wu, Aiman Egbaria, Alisdair R. Fernie, Jianbing Yan, Feng Qin, Wei Chen, Yariv Brotman and Mingqiu Dai

    Citation: Genome Biology 2021 22:260

    Content type: Research

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  34. Polygenic risk scores (PRSs) have wide applications in human genetics research, but often include tuning parameters which are difficult to optimize in practice due to limited access to individual-level data. H...

    Authors: Zijie Zhao, Yanyao Yi, Jie Song, Yuchang Wu, Xiaoyuan Zhong, Yupei Lin, Timothy J. Hohman, Jason Fletcher and Qiongshi Lu

    Citation: Genome Biology 2021 22:257

    Content type: Method

    Published on:

  35. We develop the Oncogene Concatenated Enriched Amplicon Nanopore Sequencing (OCEANS) method, in which variants with low variant allele frequency (VAFs) are amplified and subsequently concatenated for Nanopore S...

    Authors: Deepak Thirunavukarasu, Lauren Y. Cheng, Ping Song, Sherry X. Chen, Mitesh J. Borad, Lawrence Kwong, Phillip James, Daniel J. Turner and David Yu Zhang

    Citation: Genome Biology 2021 22:227

    Content type: Method

    Published on:

  36. Currently, different sequencing platforms are used to generate plant genomes and no workflow has been properly developed to optimize time, cost, and assembly quality. We present LeafGo, a complete de novo plan...

    Authors: Patrick Driguez, Salim Bougouffa, Karen Carty, Alexander Putra, Kamel Jabbari, Muppala Reddy, Richard Soppe, Ming Sin Cheung, Yoshinori Fukasawa and Luca Ermini

    Citation: Genome Biology 2021 22:256

    Content type: Method

    Published on:

  37. Introgressive hybridization can reassort genetic variants into beneficial combinations, permitting adaptation to new ecological niches. To evaluate evolutionary patterns and dynamics that contribute to introgr...

    Authors: Abraham Morales-Cruz, Jonas A. Aguirre-Liguori, Yongfeng Zhou, Andrea Minio, Summaira Riaz, Andrew M. Walker, Dario Cantu and Brandon S. Gaut

    Citation: Genome Biology 2021 22:254

    Content type: Research

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  38. Polycomb repressive complex 1 (PRC1) and PRC2 are chromatin regulators maintaining transcriptional repression. The deposition of H3 lysine 27 tri-methylation (H3K27me3) by PRC2 is known to be required for tran...

    Authors: Shujing Liu, Minerva S. Trejo-Arellano, Yichun Qiu, D. Magnus Eklund, Claudia Köhler and Lars Hennig

    Citation: Genome Biology 2021 22:253

    Content type: Research

    Published on:

  39. Detecting multiplets in single nucleus (sn)ATAC-seq data is challenging due to data sparsity and limited dynamic range. AMULET (ATAC-seq MULtiplet Estimation Tool) enumerates regions with greater than two uniq...

    Authors: Asa Thibodeau, Alper Eroglu, Christopher S. McGinnis, Nathan Lawlor, Djamel Nehar-Belaid, Romy Kursawe, Radu Marches, Daniel N. Conrad, George A. Kuchel, Zev J. Gartner, Jacques Banchereau, Michael L. Stitzel, A. Ercument Cicek and Duygu Ucar

    Citation: Genome Biology 2021 22:252

    Content type: Method

    Published on:

  40. We develop a novel computational method, NucHMM, to identify functional nucleosome states associated with cell type-specific combinatorial histone marks and nucleosome organization features such as phasing, sp...

    Authors: Kun Fang, Tianbao Li, Yufei Huang and Victor X. Jin

    Citation: Genome Biology 2021 22:250

    Content type: Method

    Published on:

  41. Aligning sequencing reads onto a reference is an essential step of the majority of genomic analysis pipelines. Computational algorithms for read alignment have evolved in accordance with technological advances...

    Authors: Mohammed Alser, Jeremy Rotman, Dhrithi Deshpande, Kodi Taraszka, Huwenbo Shi, Pelin Icer Baykal, Harry Taegyun Yang, Victor Xue, Sergey Knyazev, Benjamin D. Singer, Brunilda Balliu, David Koslicki, Pavel Skums, Alex Zelikovsky, Can Alkan, Onur Mutlu…

    Citation: Genome Biology 2021 22:249

    Content type: Review

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