Skip to main content

Articles

Page 3 of 139

  1. To provide a comprehensive mechanistic interpretation of how known trait-associated SNPs affect complex traits, we propose a method, Primo, for integrative analysis of GWAS summary statistics with multiple set...

    Authors: Kevin J. Gleason, Fan Yang, Brandon L. Pierce, Xin He and Lin S. Chen

    Citation: Genome Biology 2020 21:236

    Content type: Method

    Published on:

  2. We propose a new computational framework, probabilistic transcriptome-wide association study (PTWAS), to investigate causal relationships between gene expressions and complex traits. PTWAS applies the establis...

    Authors: Yuhua Zhang, Corbin Quick, Ketian Yu, Alvaro Barbeira, Francesca Luca, Roger Pique-Regi, Hae Kyung Im and Xiaoquan Wen

    Citation: Genome Biology 2020 21:232

    Content type: Method

    Published on:

  3. Enhancers are distal regulators of gene expression that shape cell identity and control cell fate transitions. In mouse embryonic stem cells (mESCs), the pluripotency network is maintained by the function of a...

    Authors: Tianran Peng, Yanan Zhai, Yaser Atlasi, Menno ter Huurne, Hendrik Marks, Hendrik G. Stunnenberg and Wout Megchelenbrink

    Citation: Genome Biology 2020 21:243

    Content type: Research

    Published on:

  4. Metagenomic profiling, predicting the presence and relative abundances of microbes in a sample, is a critical first step in microbiome analysis. Alignment-based approaches are often considered accurate yet com...

    Authors: Nathan LaPierre, Mohammed Alser, Eleazar Eskin, David Koslicki and Serghei Mangul

    Citation: Genome Biology 2020 21:242

    Content type: Software

    Published on:

  5. GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. It recruits organelle-associated reads using a modified “baiting and iterative mapping” ap...

    Authors: Jian-Jun Jin, Wen-Bin Yu, Jun-Bo Yang, Yu Song, Claude W. dePamphilis, Ting-Shuang Yi and De-Zhu Li

    Citation: Genome Biology 2020 21:241

    Content type: Software

    Published on:

  6. Compared to proteins, glycans, and lipids, much less is known about RNAs on the cell surface. We develop a series of technologies to test for any nuclear-encoded RNAs that are stably attached to the cell surfa...

    Authors: Norman Huang, Xiaochen Fan, Kathia Zaleta-Rivera, Tri C. Nguyen, Jiarong Zhou, Yingjun Luo, Jie Gao, Ronnie H. Fang, Zhangming Yan, Zhen Bouman Chen, Liangfang Zhang and Sheng Zhong

    Citation: Genome Biology 2020 21:225

    Content type: Research

    Published on:

  7. A key challenge in epigenetics is to determine the biological significance of epigenetic variation among individuals. We present Coordinate Covariation Analysis (COCOA), a computational framework that uses cov...

    Authors: John T. Lawson, Jason P. Smith, Stefan Bekiranov, Francine E. Garrett-Bakelman and Nathan C. Sheffield

    Citation: Genome Biology 2020 21:240

    Content type: Method

    Published on:

  8. The accuracy of transcript quantification using RNA-seq data depends on many factors, such as the choice of alignment or mapping method and the quantification model being adopted. While the choice of quantific...

    Authors: Avi Srivastava, Laraib Malik, Hirak Sarkar, Mohsen Zakeri, Fatemeh Almodaresi, Charlotte Soneson, Michael I. Love, Carl Kingsford and Rob Patro

    Citation: Genome Biology 2020 21:239

    Content type: Research

    Published on:

  9. Viral load is a major contributor to outcome in patients with Ebola virus disease (EVD), with high values leading to a fatal outcome. Evidence from the 2013–2016 Ebola virus (EBOV) outbreak indicated that diff...

    Authors: Xiaofeng Dong, Jordana Munoz-Basagoiti, Natasha Y. Rickett, Georgios Pollakis, William A. Paxton, Stephan Günther, Romy Kerber, Lisa F. P. Ng, Michael J. Elmore, N’faly Magassouba, Miles W. Carroll, David A. Matthews and Julian A. Hiscox

    Citation: Genome Biology 2020 21:238

    Content type: Research

    Published on:

  10. Several long noncoding RNAs (lncRNAs) have been shown to function as components of molecular machines that play fundamental roles in biology. While the number of annotated lncRNAs in mammalian genomes has grea...

    Authors: Jordan P. Lewandowski, Gabrijela Dumbović, Audrey R. Watson, Taeyoung Hwang, Emily Jacobs-Palmer, Nydia Chang, Christian Much, Kyle M. Turner, Christopher Kirby, Nimrod D. Rubinstein, Abigail F. Groff, Steve C. Liapis, Chiara Gerhardinger, Assaf Bester, Pier Paolo Pandolfi, John G. Clohessy…

    Citation: Genome Biology 2020 21:237

    Content type: Research

    Published on:

  11. A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. ...

    Authors: Hélène Badouin, Amandine Velt, François Gindraud, Timothée Flutre, Vincent Dumas, Sonia Vautrin, William Marande, Jonathan Corbi, Erika Sallet, Jérémy Ganofsky, Sylvain Santoni, Dominique Guyot, Eugenia Ricciardelli, Kristen Jepsen, Jos Käfer, Hélène Berges…

    Citation: Genome Biology 2020 21:223

    Content type: Research

    Published on:

  12. Cell type heterogeneity presents a challenge to the interpretation of epigenome data, compounded by the difficulty in generating reliable single-cell DNA methylomes for large numbers of cells and samples. We p...

    Authors: Andrew E. Teschendorff, Tianyu Zhu, Charles E. Breeze and Stephan Beck

    Citation: Genome Biology 2020 21:221

    Content type: Method

    Published on:

  13. Fine-tuning quantitative traits for continuous subtle phenotypes is highly advantageous. We engineer the highly conserved upstream open reading frame (uORF) of FvebZIPs1.1 in strawberry (Fragaria vesca), using ba...

    Authors: Sinian Xing, Kunling Chen, Haocheng Zhu, Rui Zhang, Huawei Zhang, Bingbing Li and Caixia Gao

    Citation: Genome Biology 2020 21:230

    Content type: Method

    Published on:

  14. The Boran (Bos indicus), indigenous Zebu cattle breed from sub-Saharan Africa, is remarkably well adapted to harsh tropical environments. Due to financial constraints and low-quality forage, African livestock are...

    Authors: Toby Wilkinson, Daniel Korir, Moses Ogugo, Robert D. Stewart, Mick Watson, Edith Paxton, John Goopy and Christelle Robert

    Citation: Genome Biology 2020 21:229

    Content type: Research

    Published on:

  15. The central nervous system (CNS) is vulnerable to viral infection, yet few host factors in the CNS are known to defend against invasion by neurotropic viruses. Long noncoding RNAs (lncRNAs) have been revealed ...

    Authors: Baokun Sui, Dong Chen, Wei Liu, Qiong Wu, Bin Tian, Yingying Li, Jing Hou, Shiyong Liu, Juan Xie, Hao Jiang, Zhaochen Luo, Lei Lv, Fei Huang, Ruiming Li, Chengguang Zhang, Yuling Tian…

    Citation: Genome Biology 2020 21:228

    Content type: Research

    Published on:

  16. We present pipeComp (https://​github.​com/​plger/​pipeComp), a flexible R framework for pipeline comparison handling interactions between analysis steps and relying on multi-level evaluation metrics. We apply it t...

    Authors: Pierre-Luc Germain, Anthony Sonrel and Mark D. Robinson

    Citation: Genome Biology 2020 21:227

    Content type: Method

    Published on:

  17. Guanine-rich sequences are able to form complex RNA structures termed RNA G-quadruplexes in vitro. Because of their high stability, RNA G-quadruplexes are proposed to exist in vivo and are suggested to be asso...

    Authors: Xiaofei Yang, Jitender Cheema, Yueying Zhang, Hongjing Deng, Susan Duncan, Mubarak Ishaq Umar, Jieyu Zhao, Qi Liu, Xiaofeng Cao, Chun Kit Kwok and Yiliang Ding

    Citation: Genome Biology 2020 21:226

    Content type: Research

    Published on:

  18. It is a major challenge to integrate single-cell sequencing data across experiments, conditions, batches, time points, and other technical considerations. New computational methods are required that can integr...

    Authors: Zhisong He, Agnieska Brazovskaja, Sebastian Ebert, J. Gray Camp and Barbara Treutlein

    Citation: Genome Biology 2020 21:224

    Content type: Method

    Published on:

  19. We present a base editing system, in which base editors are attached to different sites of sgRNA scaffold (sgBE). Each independent sgBE has its own specific editing pattern for a given target site. Among teste...

    Authors: Yanhong Wang, Lifang Zhou, Rui Tao, Nan Liu, Jie Long, Fengming Qin, Wenling Tang, Yang Yang, Qiang Chen and Shaohua Yao

    Citation: Genome Biology 2020 21:222

    Content type: Method

    Published on:

  20. DNA methylation is a key epigenetic modification in human development and disease, yet there is limited understanding of its highly coordinated regulation. Here, we identify 818 genes that affect DNA methylati...

    Authors: Paul J. Hop, René Luijk, Lucia Daxinger, Maarten van Iterson, Koen F. Dekkers, Rick Jansen, Joyce B. J. van Meurs, Peter A. C. ’t Hoen, M. Arfan Ikram, Marleen M. J. van Greevenbroek, Dorret I. Boomsma, P. Eline Slagboom, Jan H. Veldink, Erik W. van Zwet and Bastiaan T. Heijmans

    Citation: Genome Biology 2020 21:220

    Content type: Research

    Published on:

  21. An important unanswered question in chromatin biology is the extent to which long-range looping interactions change across developmental models, genetic perturbations, drug treatments, and disease states. Comp...

    Authors: Lindsey R. Fernandez, Thomas G. Gilgenast and Jennifer E. Phillips-Cremins

    Citation: Genome Biology 2020 21:219

    Content type: Method

    Published on:

  22. Germline disease-causing variants are generally more spatially clustered in protein 3-dimensional structures than benign variants. Motivated by this tendency, we develop a fast and powerful protein-structure-b...

    Authors: Zheng-Zheng Tang, Gregory R. Sliwoski, Guanhua Chen, Bowen Jin, William S. Bush, Bingshan Li and John A. Capra

    Citation: Genome Biology 2020 21:217

    Content type: Method

    Published on:

  23. Glioblastoma (GBM) is a complex disease with extensive molecular and transcriptional heterogeneity. GBM can be subcategorized into four distinct subtypes; tumors that shift towards the mesenchymal phenotype up...

    Authors: Jason K. Sa, Nakho Chang, Hye Won Lee, Hee Jin Cho, Michele Ceccarelli, Luigi Cerulo, Jinlong Yin, Sung Soo Kim, Francesca P. Caruso, Mijeong Lee, Donggeon Kim, Young Taek Oh, Yeri Lee, Nam-Gu Her, Byeongkwi Min, Hye-Jin Kim…

    Citation: Genome Biology 2020 21:216

    Content type: Research

    Published on:

  24. The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary a...

    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 2020 21:215

    Content type: Research

    Published on:

  25. Quantifying the genetic heterogeneity of a cell population is essential to understanding of biological systems. We develop a universal method to label individual DNA molecules for single-base-resolution haplot...

    Authors: Chongwei Bi, Lin Wang, Baolei Yuan, Xuan Zhou, Yu Li, Sheng Wang, Yuhong Pang, Xin Gao, Yanyi Huang and Mo Li

    Citation: Genome Biology 2020 21:213

    Content type: Method

    Published on:

  26. The observation that disease-associated genetic variants typically reside outside of exons has inspired widespread investigation into the genetic basis of transcriptional regulation. While associations between...

    Authors: Xuanyao Liu, Joel A. Mefford, Andrew Dahl, Yuan He, Meena Subramaniam, Alexis Battle, Alkes L. Price and Noah Zaitlen

    Citation: Genome Biology 2020 21:211

    Content type: Method

    Published on:

  27. Gene expression differences between species are driven by both cis and trans effects. Whereas cis effects are caused by genetic variants located on the same DNA molecule as the target gene, trans effects are due ...

    Authors: Kaia Mattioli, Winona Oliveros, Chiara Gerhardinger, Daniel Andergassen, Philipp G. Maass, John L. Rinn and Marta Melé

    Citation: Genome Biology 2020 21:210

    Content type: Research

    Published on:

  28. Deep mutational scanning (DMS) enables multiplexed measurement of the effects of thousands of variants of proteins, RNAs, and regulatory elements. Here, we present a customizable pipeline, DiMSum, that represe...

    Authors: Andre J. Faure, Jörn M. Schmiedel, Pablo Baeza-Centurion and Ben Lehner

    Citation: Genome Biology 2020 21:207

    Content type: Software

    Published on:

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

    Authors: Imran Noorani, Jorge de la Rosa, Yoon Ha Choi, Alexander Strong, Hannes Ponstingl, M. S. Vijayabaskar, Jusung Lee, Eunmin Lee, Angela Richard-Londt, Mathias Friedrich, Federica Furlanetto, Rocio Fuente, Ruby Banerjee, Fengtang Yang, Frances Law, Colin Watts…

    Citation: Genome Biology 2020 21:206

    Content type: Author Correction

    Published on:

    The original article was published in Genome Biology 2020 21:181

  30. Pigs are important animals for agricultural and biomedical research, and improvement is needed for use of the assisted reproductive technologies. Determining underlying mechanisms of epigenetic reprogramming i...

    Authors: Feifei Li, Danyang Wang, Ruigao Song, Chunwei Cao, Zhihua Zhang, Yu Wang, Xiaoli Li, Jiaojiao Huang, Qiang Liu, Naipeng Hou, Bingxiang Xu, Xiao Li, Xiaomeng Gao, Yan Jia, Jianguo Zhao and Yanfang Wang

    Citation: Genome Biology 2020 21:203

    Content type: Research

    Published on:

  31. The complex interspersed pattern of segmental duplications in humans is responsible for rearrangements associated with neurodevelopmental disease, including the emergence of novel genes important in human brai...

    Authors: Stuart Cantsilieris, Susan M. Sunkin, Matthew E. Johnson, Fabio Anaclerio, John Huddleston, Carl Baker, Max L. Dougherty, Jason G. Underwood, Arvis Sulovari, PingHsun Hsieh, Yafei Mao, Claudia Rita Catacchio, Maika Malig, AnneMarie E. Welch, Melanie Sorensen, Katherine M. Munson…

    Citation: Genome Biology 2020 21:202

    Content type: Research

    Published on:

  32. Although tuberculosis accounts for the highest mortality from a bacterial infection on a global scale, questions persist regarding its origin. One hypothesis based on modern Mycobacterium tuberculosis complex (MT...

    Authors: Susanna Sabin, Alexander Herbig, Åshild J. Vågene, Torbjörn Ahlström, Gracijela Bozovic, Caroline Arcini, Denise Kühnert and Kirsten I. Bos

    Citation: Genome Biology 2020 21:201

    Content type: Research

    Published on:

  33. Wintersweet (Chimonanthus praecox), an important ornamental plant, has evolved unique fragrant aroma and winter-flowering properties, which are critical for its successful sexual reproduction. However, the molecu...

    Authors: Junzhong Shang, Jingpu Tian, Huihui Cheng, Qiaomu Yan, Lai Li, Abbas Jamal, Zhongping Xu, Lin Xiang, Christopher A. Saski, Shuangxia Jin, Kaige Zhao, Xiuqun Liu and Longqing Chen

    Citation: Genome Biology 2020 21:200

    Content type: Research

    Published on:

  34. We report a method called ContamLD for estimating autosomal ancient DNA (aDNA) contamination by measuring the breakdown of linkage disequilibrium in a sequenced individual due to the introduction of contaminan...

    Authors: Nathan Nakatsuka, Éadaoin Harney, Swapan Mallick, Matthew Mah, Nick Patterson and David Reich

    Citation: Genome Biology 2020 21:199

    Content type: Software

    Published on:

  35. We present Model-based AnalysEs of Transcriptome and RegulOme (MAESTRO), a comprehensive open-source computational workflow (http://​github.​com/​liulab-dfci/​MAESTRO)...

    Authors: Chenfei Wang, Dongqing Sun, Xin Huang, Changxin Wan, Ziyi Li, Ya Han, Qian Qin, Jingyu Fan, Xintao Qiu, Yingtian Xie, Clifford A. Meyer, Myles Brown, Ming Tang, Henry Long, Tao Liu and X. Shirley Liu

    Citation: Genome Biology 2020 21:198

    Content type: Software

    Published on:

  36. Many existing pipelines for scRNA-seq data apply pre-processing steps such as normalization or imputation to account for excessive zeros or “drop-outs." Here, we extensively analyze diverse UMI data sets to sh...

    Authors: Tae Hyun Kim, Xiang Zhou and Mengjie Chen

    Citation: Genome Biology 2020 21:196

    Content type: Research

    Published on:

  37. RNA-binding proteins (RBPs) function as master regulators of gene expression. Alterations in RBP expression and function are often observed in cancer and influence critical pathways implicated in tumor initiat...

    Authors: Adam Kosti, Patricia Rosa de Araujo, Wei-Qing Li, Gabriela D. A. Guardia, Jennifer Chiou, Caihong Yi, Debashish Ray, Fabiana Meliso, Yi-Ming Li, Talia Delambre, Mei Qiao, Suzanne S. Burns, Franziska K. Lorbeer, Fanny Georgi, Markus Flosbach, Sarah Klinnert…

    Citation: Genome Biology 2020 21:195

    Content type: Research

    Published on:

  38. Long-read sequencing is promising for the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high yields and performance simultaneously due to the complex SV si...

    Authors: Tao Jiang, Yongzhuang Liu, Yue Jiang, Junyi Li, Yan Gao, Zhe Cui, Yadong Liu, Bo Liu and Yadong Wang

    Citation: Genome Biology 2020 21:189

    Content type: Method

    Published on: