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  1. Homologous recombination (HR) repair deficiency arising from defects in BRCA1 or BRCA2 is associated with characteristic patterns of somatic mutations. In this genetic study, we ask whether inactivating mutati...

    Authors: Ádám Póti, Hella Gyergyák, Eszter Németh, Orsolya Rusz, Szilárd Tóth, Csenger Kovácsházi, Dan Chen, Bernadett Szikriszt, Sándor Spisák, Shunichi Takeda, Gergely Szakács, Zoltan Szallasi, Andrea L. Richardson and Dávid Szüts

    Citation: Genome Biology 2019 20:240

    Content type: Research

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  2. Technological limitations have hindered the large-scale genetic investigation of tandem repeats in disease. We show that long-read sequencing with a single Oxford Nanopore Technologies PromethION flow cell per...

    Authors: Arne De Roeck, Wouter De Coster, Liene Bossaerts, Rita Cacace, Tim De Pooter, Jasper Van Dongen, Svenn D’Hert, Peter De Rijk, Mojca Strazisar, Christine Van Broeckhoven and Kristel Sleegers

    Citation: Genome Biology 2019 20:239

    Content type: Method

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  3. Elucidation of regulatory networks, including identification of regulatory mechanisms specific to a given biological context, is a key aim in systems biology. This has motivated the move from co-expression to ...

    Authors: Dharmesh D. Bhuva, Joseph Cursons, Gordon K. Smyth and Melissa J. Davis

    Citation: Genome Biology 2019 20:236

    Content type: Research

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  4. A large number of analysis strategies are available for DNA methylation (DNAm) array and RNA-seq datasets, but it is unclear which strategies are best to use. We compare commonly used strategies and report how...

    Authors: Jeroen van Rooij, Pooja R. Mandaviya, Annique Claringbould, Janine F. Felix, Jenny van Dongen, Rick Jansen, Lude Franke, Peter A. C. ’t Hoen, Bas Heijmans and Joyce B. J. van Meurs

    Citation: Genome Biology 2019 20:235

    Content type: Research

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  5. We present the software Condition-specific Regulatory Units Prediction (CRUP) to infer from epigenetic marks a list of regulatory units consisting of dynamically changing enhancers with their target genes. The...

    Authors: Anna Ramisch, Verena Heinrich, Laura V. Glaser, Alisa Fuchs, Xinyi Yang, Philipp Benner, Robert Schöpflin, Na Li, Sarah Kinkley, Anja Römer-Hillmann, John Longinotto, Steffen Heyne, Beate Czepukojc, Sonja M. Kessler, Alexandra K. Kiemer, Cristina Cadenas…

    Citation: Genome Biology 2019 20:227

    Content type: Method

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  6. The driver tissues or cell types in which susceptibility genes initiate diseases remain elusive. We develop a unified framework to detect the causal tissues of complex diseases or traits according to selective...

    Authors: Lin Jiang, Chao Xue, Sheng Dai, Shangzhen Chen, Peikai Chen, Pak Chung Sham, Haijun Wang and Miaoxin Li

    Citation: Genome Biology 2019 20:233

    Content type: Method

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  7. The MinHash algorithm has proven effective for rapidly estimating the resemblance of two genomes or metagenomes. However, this method cannot reliably estimate the containment of a genome within a metagenome. H...

    Authors: Brian D. Ondov, Gabriel J. Starrett, Anna Sappington, Aleksandra Kostic, Sergey Koren, Christopher B. Buck and Adam M. Phillippy

    Citation: Genome Biology 2019 20:232

    Content type: Method

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  8. Molecular and cellular changes are intrinsic to aging and age-related diseases. Prior cross-sectional studies have investigated the combined effects of age and genetics on gene expression and alternative splic...

    Authors: Brunilda Balliu, Matthew Durrant, Olivia de Goede, Nathan Abell, Xin Li, Boxiang Liu, Michael J. Gloudemans, Naomi L. Cook, Kevin S. Smith, David A. Knowles, Mauro Pala, Francesco Cucca, David Schlessinger, Siddhartha Jaiswal, Chiara Sabatti, Lars Lind…

    Citation: Genome Biology 2019 20:230

    Content type: Research

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  9. Multiplex assays of variant effect (MAVEs), such as deep mutational scans and massively parallel reporter assays, test thousands of sequence variants in a single experiment. Despite the importance of MAVE data...

    Authors: Daniel Esposito, Jochen Weile, Jay Shendure, Lea M. Starita, Anthony T. Papenfuss, Frederick P. Roth, Douglas M. Fowler and Alan F. Rubin

    Citation: Genome Biology 2019 20:223

    Content type: Database

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  10. The ocean microbiome represents one of the largest microbiomes and produces nearly half of the primary energy on the planet through photosynthesis or chemosynthesis. Using recent advances in marine genomics, w...

    Authors: Yan Wang, Qiang Shi, Pengshuo Yang, Chengxin Zhang, S. M. Mortuza, Zhidong Xue, Kang Ning and Yang Zhang

    Citation: Genome Biology 2019 20:229

    Content type: Research

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  11. Current genomics methods are designed to handle tens to thousands of samples but will need to scale to millions to match the pace of data and hypothesis generation in biomedical science. Here, we show that hig...

    Authors: Amaro Taylor-Weiner, François Aguet, Nicholas J. Haradhvala, Sager Gosai, Shankara Anand, Jaegil Kim, Kristin Ardlie, Eliezer M. Van Allen and Gad Getz

    Citation: Genome Biology 2019 20:228

    Content type: Short Report

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  12. Hispanics living in the USA may have unrecognized potential birthplace and lifestyle influences on the gut microbiome. We report a cross-sectional analysis of 1674 participants from four centers of the Hispani...

    Authors: Robert C. Kaplan, Zheng Wang, Mykhaylo Usyk, Daniela Sotres-Alvarez, Martha L. Daviglus, Neil Schneiderman, Gregory A. Talavera, Marc D. Gellman, Bharat Thyagarajan, Jee-Young Moon, Yoshiki Vázquez-Baeza, Daniel McDonald, Jessica S. Williams-Nguyen, Michael C. Wu, Kari E. North, Justin Shaffer…

    Citation: Genome Biology 2019 20:219

    Content type: Research

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  13. As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from the assembly of abundant microbes in many samples, rather than the exhaustive assembly of fewe...

    Authors: Jon G. Sanders, Sergey Nurk, Rodolfo A. Salido, Jeremiah Minich, Zhenjiang Z. Xu, Qiyun Zhu, Cameron Martino, Marcus Fedarko, Timothy D. Arthur, Feng Chen, Brigid S. Boland, Greg C. Humphrey, Caitriona Brennan, Karenina Sanders, James Gaffney, Kristen Jepsen…

    Citation: Genome Biology 2019 20:226

    Content type: Method

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  14. Genomic imprinting is an epigenetic phenomenon that allows a subset of genes to be expressed mono-allelically based on the parent of origin and is typically regulated by differential DNA methylation inherited ...

    Authors: Courtney W. Hanna, Raquel Pérez-Palacios, Lenka Gahurova, Michael Schubert, Felix Krueger, Laura Biggins, Simon Andrews, Maria Colomé-Tatché, Deborah Bourc’his, Wendy Dean and Gavin Kelsey

    Citation: Genome Biology 2019 20:225

    Content type: Research

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  15. We present RaGOO, a reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies in minutes. After the pseudomolecu...

    Authors: Michael Alonge, Sebastian Soyk, Srividya Ramakrishnan, Xingang Wang, Sara Goodwin, Fritz J. Sedlazeck, Zachary B. Lippman and Michael C. Schatz

    Citation: Genome Biology 2019 20:224

    Content type: Method

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  16. Horizontal pleiotropy, where one variant has independent effects on multiple traits, is important for our understanding of the genetic architecture of human phenotypes. We develop a method to quantify horizont...

    Authors: Daniel M. Jordan, Marie Verbanck and Ron Do

    Citation: Genome Biology 2019 20:222

    Content type: Method

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  17. Soils are a key component of agricultural productivity, and soil microbiota determine the availability of many essential plant nutrients. Agricultural domestication of soils, that is, the conversion of previou...

    Authors: Joseph Edwards, Christian Santos-Medellín, Bao Nguyen, John Kilmer, Zachary Liechty, Esteban Veliz, Jiadong Ni, Gregory Phillips and Venkatesan Sundaresan

    Citation: Genome Biology 2019 20:221

    Content type: Research

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  18. Identifying genetic variants that are associated with methylation variation—an analysis commonly referred to as methylation quantitative trait locus (mQTL) mapping—is important for understanding the epigenetic...

    Authors: Yue Fan, Tauras P. Vilgalys, Shiquan Sun, Qinke Peng, Jenny Tung and Xiang Zhou

    Citation: Genome Biology 2019 20:220

    Content type: Method

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  19. A variety of base editors have been developed to achieve C-to-T editing in different genomic contexts. Here, we compare a panel of five base editors on their C-to-T editing efficiencies and product purity at c...

    Authors: Ying Wang, Runze Gao, Jing Wu, Yi-Chun Xiong, Jia Wei, Sipin Zhang, Bei Yang, Jia Chen and Li Yang

    Citation: Genome Biology 2019 20:218

    Content type: Short Report

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  20. Current-day metagenomics analyses increasingly involve de novo taxonomic classification of long DNA sequences and metagenome-assembled genomes. Here, we show that the conventional best-hit approach often leads...

    Authors: F. A. Bastiaan von Meijenfeldt, Ksenia Arkhipova, Diego D. Cambuy, Felipe H. Coutinho and Bas E. Dutilh

    Citation: Genome Biology 2019 20:217

    Content type: Method

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  21. Cells have evolved quality control mechanisms to ensure protein homeostasis by detecting and degrading aberrant mRNAs and proteins. A common source of aberrant mRNAs is premature polyadenylation, which can res...

    Authors: Andrea Hildebrandt, Mirko Brüggemann, Cornelia Rücklé, Susan Boerner, Jan B. Heidelberger, Anke Busch, Heike Hänel, Andrea Voigt, Martin M. Möckel, Stefanie Ebersberger, Anica Scholz, Annabelle Dold, Tobias Schmid, Ingo Ebersberger, Jean-Yves Roignant, Kathi Zarnack…

    Citation: Genome Biology 2019 20:216

    Content type: Research

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  22. Despite the tremendous growth of the DNA sequencing data in the last decade, our understanding of the human genome is still in its infancy. To understand the implications of genetic variants in the light of po...

    Authors: Chao Zhang, Yang Gao, Zhilin Ning, Yan Lu, Xiaoxi Zhang, Jiaojiao Liu, Bo Xie, Zhe Xue, Xiaoji Wang, Kai Yuan, Xueling Ge, Yuwen Pan, Chang Liu, Lei Tian, Yuchen Wang, Dongsheng Lu…

    Citation: Genome Biology 2019 20:215

    Content type: Database

    Published on:

  23. Following publication of the original paper [1], Dr. Nayfach kindly pointed out an error and the authors would like to report the following correction.

    Authors: Zifan Zhu, Jie Ren, Sonia Michail and Fengzhu Sun

    Citation: Genome Biology 2019 20:214

    Content type: Correction

    Published on:

    The original article was published in Genome Biology 2019 20:154

  24. Human tissue is increasingly being whole genome sequenced as we transition into an era of genomic medicine. With this arises the potential to detect sequences originating from microorganisms, including pathoge...

    Authors: Abraham Gihawi, Ghanasyam Rallapalli, Rachel Hurst, Colin S. Cooper, Richard M. Leggett and Daniel S. Brewer

    Citation: Genome Biology 2019 20:208

    Content type: Research

    Published on:

  25. Accurate fusion transcript detection is essential for comprehensive characterization of cancer transcriptomes. Over the last decade, multiple bioinformatic tools have been developed to predict fusions from RNA...

    Authors: Brian J. Haas, Alexander Dobin, Bo Li, Nicolas Stransky, Nathalie Pochet and Aviv Regev

    Citation: Genome Biology 2019 20:213

    Content type: Research

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  26. Single-cell RNA sequencing (scRNA-seq) offers new opportunities to study gene expression of tens of thousands of single cells simultaneously. We present DeepImpute, a deep neural network-based imputation algor...

    Authors: Cédric Arisdakessian, Olivier Poirion, Breck Yunits, Xun Zhu and Lana X. Garmire

    Citation: Genome Biology 2019 20:211

    Content type: Method

    Published on:

  27. Single-cell RNA sequencing (scRNA-seq) is a powerful tool for studying complex biological systems, such as tumor heterogeneity and tissue microenvironments. However, the sources of technical and biological var...

    Authors: Ciara H. O’Flanagan, Kieran R. Campbell, Allen W. Zhang, Farhia Kabeer, Jamie L. P. Lim, Justina Biele, Peter Eirew, Daniel Lai, Andrew McPherson, Esther Kong, Cherie Bates, Kelly Borkowski, Matt Wiens, Brittany Hewitson, James Hopkins, Jenifer Pham…

    Citation: Genome Biology 2019 20:210

    Content type: Research

    Published on:

  28. Genomic rearrangements exert a heavy influence on the molecular landscape of cancer. New analytical approaches integrating somatic structural variants (SSVs) with altered gene features represent a framework by...

    Authors: Yiqun Zhang, Lixing Yang, Melanie Kucherlapati, Angela Hadjipanayis, Angeliki Pantazi, Christopher A. Bristow, Eunjung Alice Lee, Harshad S. Mahadeshwar, Jiabin Tang, Jianhua Zhang, Sahil Seth, Semin Lee, Xiaojia Ren, Xingzhi Song, Huandong Sun, Jonathan Seidman…

    Citation: Genome Biology 2019 20:209

    Content type: Research

    Published on:

  29. Large palindromes (inverted repeats) make up substantial proportions of mammalian sex chromosomes, often contain genes, and have high rates of structural variation arising via ectopic recombination. As a resul...

    Authors: Wentao Shi, Andrea Massaia, Sandra Louzada, Juliet Handsaker, William Chow, Shane McCarthy, Joanna Collins, Pille Hallast, Kerstin Howe, Deanna M. Church, Fengtang Yang, Yali Xue and Chris Tyler-Smith

    Citation: Genome Biology 2019 20:207

    Content type: Research

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  30. scRNA-seq profiles each represent a highly partial sample of mRNA molecules from a unique cell that can never be resampled, and robust analysis must separate the sampling effect from biological variance. We de...

    Authors: Yael Baran, Akhiad Bercovich, Arnau Sebe-Pedros, Yaniv Lubling, Amir Giladi, Elad Chomsky, Zohar Meir, Michael Hoichman, Aviezer Lifshitz and Amos Tanay

    Citation: Genome Biology 2019 20:206

    Content type: Method

    Published on:

  31. Following publication of the original article [1], a typographical error in the formula for calculating di in the “Scans for local adaptation” subsection in the Method section, was identified. The correct formula...

    Authors: Shaohua Fan, Derek E. Kelly, Marcia H. Beltrame, Matthew E. B. Hansen, Swapan Mallick, Alessia Ranciaro, Jibril Hirbo, Simon Thompson, William Beggs, Thomas Nyambo, Sabah A. Omar, Dawit Wolde Meskel, Gurja Belay, Alain Froment, Nick Patterson, David Reich…

    Citation: Genome Biology 2019 20:204

    Content type: Correction

    Published on:

    The original article was published in Genome Biology 2019 20:82

  32. Many high-throughput experiments compare two phenotypes such as disease vs. healthy, with the goal of understanding the underlying biological phenomena characterizing the given phenotype. Because of the import...

    Authors: Tuan-Minh Nguyen, Adib Shafi, Tin Nguyen and Sorin Draghici

    Citation: Genome Biology 2019 20:203

    Content type: Research

    Published on:

    The Correction to this article has been published in Genome Biology 2019 20:234

  33. A series of miRNA-disease association prediction methods have been proposed to prioritize potential disease-associated miRNAs. Independent benchmarking of these methods is warranted to assess their effectivene...

    Authors: Zhou Huang, Leibo Liu, Yuanxu Gao, Jiangcheng Shi, Qinghua Cui, Jianwei Li and Yuan Zhou

    Citation: Genome Biology 2019 20:202

    Content type: Research

    Published on:

  34. Comparative data from non-human primates provide insight into the processes that shaped the evolution of the human gut microbiome and highlight microbiome traits that differentiate humans from other primates. ...

    Authors: Katherine R. Amato, Elizabeth K. Mallott, Daniel McDonald, Nathaniel J. Dominy, Tony Goldberg, Joanna E. Lambert, Larissa Swedell, Jessica L. Metcalf, Andres Gomez, Gillian A. O. Britton, Rebecca M. Stumpf, Steven R. Leigh and Rob Knight

    Citation: Genome Biology 2019 20:201

    Content type: Research

    Published on:

  35. DNA methylation (DNAm) is a critical regulator of both development and cellular identity and shows unique patterns in neurons. To better characterize maturational changes in DNAm patterns in these cells, we pr...

    Authors: Amanda J. Price, Leonardo Collado-Torres, Nikolay A. Ivanov, Wei Xia, Emily E. Burke, Joo Heon Shin, Ran Tao, Liang Ma, Yankai Jia, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger and Andrew E. Jaffe

    Citation: Genome Biology 2019 20:196

    Content type: Research

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  36. Micrococcal nuclease (MNase) is widely used to map nucleosomes. However, its aggressive endo-/exo-nuclease activities make MNase-seq unreliable for determining nucleosome occupancies, because cleavages within ...

    Authors: Răzvan V. Chereji, Terri D. Bryson and Steven Henikoff

    Citation: Genome Biology 2019 20:198

    Content type: Method

    Published on:

  37. Challenges are achieving broad acceptance for addressing many biomedical questions and enabling tool assessment. But ensuring that the methods evaluated are reproducible and reusable is complicated by the dive...

    Authors: Kyle Ellrott, Alex Buchanan, Allison Creason, Michael Mason, Thomas Schaffter, Bruce Hoff, James Eddy, John M. Chilton, Thomas Yu, Joshua M. Stuart, Julio Saez-Rodriguez, Gustavo Stolovitzky, Paul C. Boutros and Justin Guinney

    Citation: Genome Biology 2019 20:195

    Content type: Open Letter

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  38. Single-cell transcriptomics is rapidly advancing our understanding of the cellular composition of complex tissues and organisms. A major limitation in most analysis pipelines is the reliance on manual annotati...

    Authors: Tamim Abdelaal, Lieke Michielsen, Davy Cats, Dylan Hoogduin, Hailiang Mei, Marcel J. T. Reinders and Ahmed Mahfouz

    Citation: Genome Biology 2019 20:194

    Content type: Research

    Published on: