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  1. 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

    Published on:

  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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

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  10. 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

  11. 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

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  12. 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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  13. 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

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  14. 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

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  15. 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

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  16. 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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  17. 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:

  18. 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

  19. 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

  20. 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:

  21. 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

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  22. 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

    Published on:

  23. 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:

  24. 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

    Published on:

  25. 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:

  26. Technical variation in feature measurements, such as gene expression and locus accessibility, is a key challenge of large-scale single-cell genomic datasets. We show that this technical variation in both scRNA...

    Authors: Ruoxin Li and Gerald Quon

    Citation: Genome Biology 2019 20:193

    Content type: Method

    Published on:

    The Correction to this article has been published in Genome Biology 2019 20:247

  27. Polyadenylation plays a key role in producing mature mRNAs in eukaryotes. It is widely believed that the poly(A)-binding proteins (PABs) uniformly bind to poly(A)-tailed mRNAs, regulating their stability and t...

    Authors: Taolan Zhao, Qing Huan, Jing Sun, Chunyan Liu, Xiuli Hou, Xiang Yu, Ian M. Silverman, Yi Zhang, Brian D. Gregory, Chun-Ming Liu, Wenfeng Qian and Xiaofeng Cao

    Citation: Genome Biology 2019 20:189

    Content type: Research

    Published on:

  28. Following publication of the original article [1], it was noticed that the incorrect Fig. 2 and Fig. 3. were processed during production. It was also noticed that Fig. 4a was processed with a superfluous “1e7”...

    Authors: Michal Sadowski, Agnieszka Kraft, Przemyslaw Szalaj, Michal Wlasnowolski, Zhonghui Tang, Yijun Ruan and Dariusz Plewczynski

    Citation: Genome Biology 2019 20:188

    Content type: Correction

    Published on:

    The original article was published in Genome Biology 2019 20:148

  29. Tsetse flies (Glossina sp.) are the vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse flies are distinguished from other Diptera by unique adaptations, including lactation and the ...

    Authors: Geoffrey M. Attardo, Adly M. M. Abd-Alla, Alvaro Acosta-Serrano, James E. Allen, Rosemary Bateta, Joshua B. Benoit, Kostas Bourtzis, Jelle Caers, Guy Caljon, Mikkel B. Christensen, David W. Farrow, Markus Friedrich, Aurélie Hua-Van, Emily C. Jennings, Denis M. Larkin, Daniel Lawson…

    Citation: Genome Biology 2019 20:187

    Content type: Research

    Published on:

  30. Cytoscape is one of the most successful network biology analysis and visualization tools, but because of its interactive nature, its role in creating reproducible, scalable, and novel workflows has been limite...

    Authors: David Otasek, John H. Morris, Jorge Bouças, Alexander R. Pico and Barry Demchak

    Citation: Genome Biology 2019 20:185

    Content type: Software

    Published on:

  31. Two of the most important pathogens contributing to the global rise in antimicrobial resistance (AMR) are Klebsiella pneumoniae and Enterobacter cloacae. Despite this, most of our knowledge about the changing pat...

    Authors: Matthew J. Ellington, Eva Heinz, Alexander M. Wailan, Matthew J. Dorman, Marcus de Goffau, Amy K. Cain, Sonal P. Henson, Nicholas Gleadall, Christine J. Boinett, Gordon Dougan, Nicholas M. Brown, Neil Woodford, Julian Parkhill, M. Estée Török, Sharon J. Peacock and Nicholas R. Thomson

    Citation: Genome Biology 2019 20:184

    Content type: Research

    Published on:

  32. Massively parallel reporter assays (MPRAs) can measure the regulatory function of thousands of DNA sequences in a single experiment. Despite growing popularity, MPRA studies are limited by a lack of a unified ...

    Authors: Tal Ashuach, David S. Fischer, Anat Kreimer, Nadav Ahituv, Fabian J. Theis and Nir Yosef

    Citation: Genome Biology 2019 20:183

    Content type: Method

    Published on:

  33. Following publication of the original article [1], the authors reported that Additional file 4, “Table S5. Parent-of-origin RNAseq dataset of 4 DAP INTACT-purified endosperm of Col × Ler reciprocal crosses” had t...

    Authors: Jordi Moreno-Romero, Gerardo Del Toro-De León, Vikash Kumar Yadav, Juan Santos-González and Claudia Köhler

    Citation: Genome Biology 2019 20:182

    Content type: Correction

    Published on:

    The original article was published in Genome Biology 2019 20:41

  34. Birds of prey (raptors) are dominant apex predators in terrestrial communities, with hawks (Accipitriformes) and falcons (Falconiformes) hunting by day and owls (Strigiformes) hunting by night.

    Authors: Yun Sung Cho, Je Hoon Jun, Jung A Kim, Hak-Min Kim, Oksung Chung, Seung-Gu Kang, Jin-Young Park, Hwa-Jung Kim, Sunghyun Kim, Hee-Jong Kim, Jin-ho Jang, Ki-Jeong Na, Jeongho Kim, Seung Gu Park, Hwang-Yeol Lee, Andrea Manica…

    Citation: Genome Biology 2019 20:181

    Content type: Research

    Published on:

  35. Semi-automated genome annotation methods such as Segway take as input a set of genome-wide measurements such as of histone modification or DNA accessibility and output an annotation of genomic activity in the ...

    Authors: Maxwell W. Libbrecht, Oscar L. Rodriguez, Zhiping Weng, Jeffrey A. Bilmes, Michael M. Hoffman and William Stafford Noble

    Citation: Genome Biology 2019 20:180

    Content type: Database

    Published on:

  36. Funding research is a challenge faced by most scientists around the world. Genome Biology has invited four scientists based in three different countries to share their own experience and opinions regarding fun...

    Authors: Nick Wong

    Citation: Genome Biology 2019 20:178

    Content type: Editorial

    Published on:

    The Editorial to this article has been published in Genome Biology 2019 20:177

    The Editorial to this article has been published in Genome Biology 2019 20:176

  37. Funding research is a challenge faced by most scientists around the world. Genome Biology has invited four scientists based in three different countries to share their own experience and opinions regarding fun...

    Authors: Hui Yang

    Citation: Genome Biology 2019 20:177

    Content type: Editorial

    Published on:

    The Editorial to this article has been published in Genome Biology 2019 20:176

    The Editorial to this article has been published in Genome Biology 2019 20:178

  38. Funding research is a challenge faced by most scientists around the world. Genome Biology has invited four scientists based in three different countries to share their own experience and opinions regarding fun...

    Authors: Verena Jantsch and Michael Jantsch

    Citation: Genome Biology 2019 20:176

    Content type: Editorial

    Published on:

    The Editorial to this article has been published in Genome Biology 2019 20:178

    The Editorial to this article has been published in Genome Biology 2019 20:177

  39. Genomic global positioning system (GPS) applies the multilateration technique commonly used in the GPS to genomic data. In the framework we present here, investigators calculate genetic distances from their sa...

    Authors: Kunhee Kim, Hyungryul Baik, Chloe Soohyun Jang, Jin Kyung Roh, Eleazer Eskin and Buhm Han

    Citation: Genome Biology 2019 20:175

    Content type: Short Report

    Published on:

  40. CRISPR-Cas9 gene-editing technology has facilitated the generation of knockout mice, providing an alternative to cumbersome and time-consuming traditional embryonic stem cell-based methods. An earlier study re...

    Authors: Channabasavaiah B. Gurumurthy, Aidan R. O’Brien, Rolen M. Quadros, John Adams Jr, Pilar Alcaide, Shinya Ayabe, Johnathan Ballard, Surinder K. Batra, Marie-Claude Beauchamp, Kathleen A. Becker, Guillaume Bernas, David Brough, Francisco Carrillo-Salinas, Wesley Chan, Hanying Chen, Ruby Dawson…

    Citation: Genome Biology 2019 20:171

    Content type: Research

    Published on: