Skip to main content

Articles

Page 1 of 140

  1. Although genome-wide DNA methylomes have demonstrated their clinical value as reliable biomarkers for tumor detection, subtyping, and classification, their direct biological impacts at the individual gene leve...

    Authors: Justin Williams, Beisi Xu, Daniel Putnam, Andrew Thrasher, Chunliang Li, Jun Yang and Xiang Chen

    Citation: Genome Biology 2021 22:24

    Content type: Method

    Published on:

  2. We report SPIN, an integrative computational method to reveal genome-wide intranuclear chromosome positioning and nuclear compartmentalization relative to multiple nuclear structures, which are pivotal for mod...

    Authors: Yuchuan Wang, Yang Zhang, Ruochi Zhang, Tom van Schaik, Liguo Zhang, Takayo Sasaki, Daniel Peric-Hupkes, Yu Chen, David M. Gilbert, Bas van Steensel, Andrew S. Belmont and Jian Ma

    Citation: Genome Biology 2021 22:36

    Content type: Method

    Published on:

  3. Alternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS in response to specific conditions, esp...

    Authors: Guiomar Martín, Yamile Márquez, Federica Mantica, Paula Duque and Manuel Irimia

    Citation: Genome Biology 2021 22:35

    Content type: Research

    Published on:

  4. The start and end sites of messenger RNAs (TSSs and TESs) are highly regulated, often in a cell-type-specific manner. Yet the contribution of transcript diversity in regulating gene expression remains largely ...

    Authors: Minghao Chia, Cai Li, Sueli Marques, Vicente Pelechano, Nicholas M. Luscombe and Folkert J. van Werven

    Citation: Genome Biology 2021 22:34

    Content type: Research

    Published on:

  5. Aberrant activation of the Hedgehog pathway drives tumorigenesis of many cancers, including glioblastoma. However, the sensitization mechanism of the G protein-coupled-like receptor smoothened (SMO), a key com...

    Authors: Xujia Wu, Songhua Xiao, Maolei Zhang, Lixuan Yang, Jian Zhong, Bo Li, Fanying Li, Xin Xia, Xixi Li, Huangkai Zhou, Dawei Liu, Nunu Huang, Xuesong Yang, Feizhe Xiao and Nu Zhang

    Citation: Genome Biology 2021 22:33

    Content type: Research

    Published on:

  6. GWAS summary statistics are fundamental for a variety of research applications yet no common storage format has been widely adopted. Existing tabular formats ambiguously or incompletely store information about...

    Authors: Matthew S. Lyon, Shea J. Andrews, Ben Elsworth, Tom R. Gaunt, Gibran Hemani and Edoardo Marcora

    Citation: Genome Biology 2021 22:32

    Content type: Method

    Published on:

  7. Tartary buckwheat (Fagopyrum tataricum) is a nutritionally balanced and flavonoid-rich crop plant that has been in cultivation for 4000 years and is now grown globally. Despite its nutraceutical and agricultural ...

    Authors: Kaixuan Zhang, Ming He, Yu Fan, Hui Zhao, Bin Gao, Keli Yang, Faliang Li, Yu Tang, Qiang Gao, Tao Lin, Muriel Quinet, Dagmar Janovská, Vladimir Meglič, Jacek Kwiatkowski, Olga Romanova, Nikhil Chrungoo…

    Citation: Genome Biology 2021 22:23

    Content type: Research

    Published on:

  8. Animal genomes contain thousands of long noncoding RNA (lncRNA) genes, a growing subset of which are thought to be functionally important. This functionality is often mediated by short sequence elements scatte...

    Authors: Caroline Jane Ross, Aviv Rom, Amit Spinrad, Dikla Gelbard-Solodkin, Neta Degani and Igor Ulitsky

    Citation: Genome Biology 2021 22:29

    Content type: Research

    Published on:

  9. A major challenge to long read sequencing data is their high error rate of up to 15%. We present Ratatosk, a method to correct long reads with short read data. We demonstrate on 5 human genome trios that Ratat...

    Authors: Guillaume Holley, Doruk Beyter, Helga Ingimundardottir, Peter L. Møller, Snædis Kristmundsdottir, Hannes P. Eggertsson and Bjarni V. Halldorsson

    Citation: Genome Biology 2021 22:28

    Content type: Method

    Published on:

  10. Polyploidization and introgression are major events driving plant genome evolution and influencing crop breeding. However, the mechanisms underlying the higher-order chromatin organization of subgenomes and al...

    Authors: Jizeng Jia, Yilin Xie, Jingfei Cheng, Chuizheng Kong, Meiyue Wang, Lifeng Gao, Fei Zhao, Jingyu Guo, Kai Wang, Guangwei Li, Dangqun Cui, Tiezhu Hu, Guangyao Zhao, Daowen Wang, Zhengang Ru and Yijing Zhang

    Citation: Genome Biology 2021 22:26

    Content type: Research

    Published on:

  11. Seminal studies of vertebrate protein evolution speculated that gene regulatory changes can drive anatomical innovations. However, very little is known about gene regulatory network (GRN) evolution associated ...

    Authors: Tarang K. Mehta, Christopher Koch, Will Nash, Sara A. Knaack, Padhmanand Sudhakar, Marton Olbei, Sarah Bastkowski, Luca Penso-Dolfin, Tamas Korcsmaros, Wilfried Haerty, Sushmita Roy and Federica Di-Palma

    Citation: Genome Biology 2021 22:25

    Content type: Research

    Published on:

  12. There are no comprehensive methods to identify N6-methyladenosine (m6A) at single-base resolution for every single transcript, which is necessary for the estimation of m6A abundance. We develop a new pipeline cal...

    Authors: Yubang Gao, Xuqing Liu, Bizhi Wu, Huihui Wang, Feihu Xi, Markus V. Kohnen, Anireddy S. N. Reddy and Lianfeng Gu

    Citation: Genome Biology 2021 22:22

    Content type: Method

    Published on:

  13. In any ‘omics study, the scale of analysis can dramatically affect the outcome. For instance, when clustering single-cell transcriptomes, is the analysis tuned to discover broad or specific cell types? Likewis...

    Authors: Fan Zheng, She Zhang, Christopher Churas, Dexter Pratt, Ivet Bahar and Trey Ideker

    Citation: Genome Biology 2021 22:21

    Content type: Short Report

    Published on:

  14. Transcription factor (TF) binding specificity is determined via a complex interplay between the transcription factor’s DNA binding preference and cell type-specific chromatin environments. The chromatin featur...

    Authors: Divyanshi Srivastava, Begüm Aydin, Esteban O. Mazzoni and Shaun Mahony

    Citation: Genome Biology 2021 22:20

    Content type: Research

    Published on:

  15. Metastatic progress is the primary cause of death in most cancers, yet the regulatory dynamics driving the cellular changes necessary for metastasis remain poorly understood. Multi-omics approaches hold great ...

    Authors: Saba Ghaffari, Casey Hanson, Remington E. Schmidt, Kelly J. Bouchonville, Steven M. Offer and Saurabh Sinha

    Citation: Genome Biology 2021 22:19

    Content type: Research

    Published on:

  16. Although the genomes of monozygotic twins are practically identical, their methylomes may evolve divergently throughout their lifetime as a consequence of factors such as the environment or aging. Particularly...

    Authors: Benjamin Planterose Jiménez, Fan Liu, Amke Caliebe, Diego Montiel González, Jordana T. Bell, Manfred Kayser and Athina Vidaki

    Citation: Genome Biology 2021 22:18

    Content type: Research

    Published on:

  17. N6-methyladenosine (m6A) modification is known to impact many aspects of RNA metabolism, including mRNA stability and translation, and is highly prevalent in the brain.

    Authors: Andrew M. Shafik, Feiran Zhang, Zhenxing Guo, Qing Dai, Kinga Pajdzik, Yangping Li, Yunhee Kang, Bing Yao, Hao Wu, Chuan He, Emily G. Allen, Ranhui Duan and Peng Jin

    Citation: Genome Biology 2021 22:17

    Content type: Research

    Published on:

  18. The folding of proteins is challenging in the highly crowded and sticky environment of a cell. Regulation of translation elongation may play a crucial role in ensuring the correct folding of proteins. Much of ...

    Authors: Taolan Zhao, Yan-Ming Chen, Yu Li, Jia Wang, Siyu Chen, Ning Gao and Wenfeng Qian

    Citation: Genome Biology 2021 22:16

    Content type: Research

    Published on:

  19. Small RNAs (sRNAs) including microRNAs (miRNAs) and small interfering RNAs (siRNAs) serve as core players in gene silencing at transcriptional and post-transcriptional levels in plants, but their subcellular l...

    Authors: Xiaoyu Yang, Chenjiang You, Xufeng Wang, Lei Gao, Beixin Mo, Lin Liu and Xuemei Chen

    Citation: Genome Biology 2021 22:15

    Content type: Research

    Published on:

  20. The regulation of messenger RNA (mRNA) stability has a profound impact on gene expression dynamics during embryogenesis. For example, in animals, maternally deposited mRNAs are degraded after fertilization to ...

    Authors: Santiago Gerardo Medina-Muñoz, Gopal Kushawah, Luciana Andrea Castellano, Michay Diez, Michelle Lynn DeVore, María José Blanco Salazar and Ariel Alejandro Bazzini

    Citation: Genome Biology 2021 22:14

    Content type: Research

    Published on:

  21. Structural variations (SVs), a major resource of genomic variation, can have profound consequences on phenotypic variation, yet the impacts of SVs remain largely unexplored in crops.

    Authors: Jiantao Guan, Yaoguang Xu, Yang Yu, Jun Fu, Fei Ren, Jiying Guo, Jianbo Zhao, Quan Jiang, Jianhua Wei and Hua Xie

    Citation: Genome Biology 2021 22:13

    Content type: Research

    Published on:

  22. Brown algae evolved complex multicellularity independently of the animal and land plant lineages and are the third most developmentally complex phylogenetic group on the planet. An understanding of development...

    Authors: Simon Bourdareau, Leila Tirichine, Bérangère Lombard, Damarys Loew, Delphine Scornet, Yue Wu, Susana M. Coelho and J. Mark Cock

    Citation: Genome Biology 2021 22:12

    Content type: Research

    Published on:

  23. mRNA processing is critical for gene expression. A challenge in regulating mRNA processing is how to recognize the actual mRNA processing sites, such as splice and polyadenylation sites, when the sequence cont...

    Authors: Zhenshan Liu, Qi Liu, Xiaofei Yang, Yueying Zhang, Matthew Norris, Xiaoxi Chen, Jitender Cheema, Huakun Zhang and Yiliang Ding

    Citation: Genome Biology 2021 22:11

    Content type: Research

    Published on:

  24. Long-read sequencing of full-length cDNAs enables the detection of structures of aberrant splicing isoforms in cancer cells. These isoforms are occasionally translated, presented by HLA molecules, and recogniz...

    Authors: Miho Oka, Liu Xu, Toshihiro Suzuki, Toshiaki Yoshikawa, Hiromi Sakamoto, Hayato Uemura, Akiyasu C. Yoshizawa, Yutaka Suzuki, Tetsuya Nakatsura, Yasushi Ishihama, Ayako Suzuki and Masahide Seki

    Citation: Genome Biology 2021 22:9

    Content type: Research

    Published on:

  25. Crosstalk between genetic, epigenetic, and immune alterations in upper tract urothelial carcinomas and their role in shaping muscle invasiveness and patient outcome are poorly understood.

    Authors: Xiaoping Su, Xiaofan Lu, Sehrish Khan Bazai, Eva Compérat, Roger Mouawad, Hui Yao, Morgan Rouprêt, Jean-Philippe Spano, David Khayat, Irwin Davidson, Nizar N. Tannir, Fangrong Yan and Gabriel G. Malouf

    Citation: Genome Biology 2021 22:7

    Content type: Research

    Published on:

  26. Plant genome engineering mediated by various CRISPR-based tools requires specific protospacer adjacent motifs (PAMs), such as the well-performed NGG, NG, and NNG, to initiate target recognition, which notably ...

    Authors: Ziyan Xu, Yongjie Kuang, Bin Ren, Daqi Yan, Fang Yan, Carl Spetz, Wenxian Sun, Guirong Wang, Xueping Zhou and Huanbin Zhou

    Citation: Genome Biology 2021 22:6

    Content type: Research

    Published on:

  27. Redundancy is a common feature of genomes, presumably to ensure robust growth under different and changing conditions. Genome compaction, removing sequences nonessential for given conditions, provides a novel ...

    Authors: Zhouqing Luo, Kang Yu, Shangqian Xie, Marco Monti, Daniel Schindler, Yuan Fang, Shijun Zhao, Zhenzhen Liang, Shuangying Jiang, Meiwei Luan, Chuanle Xiao, Yizhi Cai and Junbiao Dai

    Citation: Genome Biology 2021 22:5

    Content type: Research

    Published on:

  28. Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers due to its high metastasis rate in the liver. However, little is known about the molecular features of hepatic metastases due to diffic...

    Authors: Jianyu Yang, Ping Lin, Minwei Yang, Wei Liu, Xueliang Fu, Dejun Liu, Lingye Tao, Yanmiao Huo, Junfeng Zhang, Rong Hua, Zhigang Zhang, Yixue Li, Liwei Wang, Jing Xue, Hong Li and Yongwei Sun

    Citation: Genome Biology 2021 22:4

    Content type: Research

    Published on:

  29. Crop genomics has seen dramatic advances in recent years due to improvements in sequencing technology, assembly methods, and computational resources. These advances have led to the development of new tools to ...

    Authors: Rafael Della Coletta, Yinjie Qiu, Shujun Ou, Matthew B. Hufford and Candice N. Hirsch

    Citation: Genome Biology 2021 22:3

    Content type: Review

    Published on:

  30. Bone accrual impacts lifelong skeletal health, but genetic discovery has been primarily limited to cross-sectional study designs and hampered by uncertainty about target effector genes. Here, we capture this d...

    Authors: Diana L. Cousminer, Yadav Wagley, James A. Pippin, Ahmed Elhakeem, Gregory P. Way, Matthew C. Pahl, Shana E. McCormack, Alessandra Chesi, Jonathan A. Mitchell, Joseph M. Kindler, Denis Baird, April Hartley, Laura Howe, Heidi J. Kalkwarf, Joan M. Lappe, Sumei Lu…

    Citation: Genome Biology 2021 22:1

    Content type: Research

    Published on:

  31. Generating chromosome-level, haplotype-resolved assemblies of heterozygous genomes remains challenging. To address this, we developed gamete binning, a method based on single-cell sequencing of haploid gametes...

    Authors: José A. Campoy, Hequan Sun, Manish Goel, Wen-Biao Jiao, Kat Folz-Donahue, Nan Wang, Manuel Rubio, Chang Liu, Christian Kukat, David Ruiz, Bruno Huettel and Korbinian Schneeberger

    Citation: Genome Biology 2020 21:306

    Content type: Method

    Published on:

  32. A mechanistic understanding of the spread of SARS-CoV-2 and diligent tracking of ongoing mutagenesis are of key importance to plan robust strategies for confining its transmission. Large numbers of available s...

    Authors: Michael R. Garvin, Erica T. Prates, Mirko Pavicic, Piet Jones, B. Kirtley Amos, Armin Geiger, Manesh B. Shah, Jared Streich, Joao Gabriel Felipe Machado Gazolla, David Kainer, Ashley Cliff, Jonathon Romero, Nathan Keith, James B. Brown and Daniel Jacobson

    Citation: Genome Biology 2020 21:304

    Content type: Research

    Published on:

  33. The increasing availability of microbial genomes and environmental shotgun metagenomes provides unprecedented access to the genomic differences within related bacteria. The human oral microbiome with its diver...

    Authors: Daniel R. Utter, Gary G. Borisy, A. Murat Eren, Colleen M. Cavanaugh and Jessica L. Mark Welch

    Citation: Genome Biology 2020 21:293

    Content type: Research

    Published on:

  34. Microbial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and intriguing patterns of site specificity amidst the lack of dispersal limitati...

    Authors: Alon Shaiber, Amy D. Willis, Tom O. Delmont, Simon Roux, Lin-Xing Chen, Abigail C. Schmid, Mahmoud Yousef, Andrea R. Watson, Karen Lolans, Özcan C. Esen, Sonny T. M. Lee, Nora Downey, Hilary G. Morrison, Floyd E. Dewhirst, Jessica L. Mark Welch and A. Murat Eren

    Citation: Genome Biology 2020 21:292

    Content type: Research

    Published on:

  35. Tumor-specific genomic aberrations are routinely determined by high-throughput genomic measurements. It remains unclear how complex genome alterations affect molecular networks through changing protein levels ...

    Authors: Konstantina Charmpi, Tiannan Guo, Qing Zhong, Ulrich Wagner, Rui Sun, Nora C. Toussaint, Christine E. Fritz, Chunhui Yuan, Hao Chen, Niels J. Rupp, Ailsa Christiansen, Dorothea Rutishauser, Jan H. Rüschoff, Christian Fankhauser, Karim Saba, Cedric Poyet…

    Citation: Genome Biology 2020 21:302

    Content type: Research

    Published on:

  36. Staphylococcus aureus is a leading cause of healthcare- and community-associated infections and can be difficult to treat due to antimicrobial resistance. About 30% of individuals carry S. aureus asymptomatically...

    Authors: Emma K. Accorsi, Eric A. Franzosa, Tiffany Hsu, Regina Joice Cordy, Ayala Maayan-Metzger, Hanaa Jaber, Aylana Reiss-Mandel, Madeleine Kline, Casey DuLong, Marc Lipsitch, Gili Regev-Yochay and Curtis Huttenhower

    Citation: Genome Biology 2020 21:301

    Content type: Research

    Published on:

  37. STARR-seq technology has employed progressively more complex genomic libraries and increased sequencing depths. An issue with the increased complexity and depth is that the coverage in STARR-seq experiments is...

    Authors: Donghoon Lee, Manman Shi, Jennifer Moran, Martha Wall, Jing Zhang, Jason Liu, Dominic Fitzgerald, Yasuhiro Kyono, Lijia Ma, Kevin P. White and Mark Gerstein

    Citation: Genome Biology 2020 21:298

    Content type: Method

    Published on:

  38. Despite the long-observed correlation between H3K9me3, chromatin architecture, and transcriptional repression, how H3K9me3 regulates genome higher-order organization and transcriptional activity in living cell...

    Authors: Ying Feng, Yao Wang, Xiangnan Wang, Xiaohui He, Chen Yang, Ardalan Naseri, Thoru Pederson, Jing Zheng, Shaojie Zhang, Xiao Xiao, Wei Xie and Hanhui Ma

    Citation: Genome Biology 2020 21:296

    Content type: Research

    Published on:

  39. The accurate placement of an ancient whole-genome duplication (WGD) in relation to the lineage divergence is important. Here, we re-investigated the Aquilegia coerulea WGD and found it is more likely lineage-spec...

    Authors: Tao Shi and Jinming Chen

    Citation: Genome Biology 2020 21:295

    Content type: Correspondence

    Published on:

    The Correspondence to this article has been published in Genome Biology 2020 21:297