Skip to main content



Page 4 of 131

  1. Content type: Method

    Droplet-based single-cell RNA sequencing protocols have dramatically increased the throughput of single-cell transcriptomics studies. A key computational challenge when processing these data is to distinguish ...

    Authors: Aaron T. L. Lun, Samantha Riesenfeld, Tallulah Andrews, The Phuong Dao, Tomas Gomes and John C. Marioni

    Citation: Genome Biology 2019 20:63

    Published on:

  2. Content type: Method

    Single-cell RNA-seq quantifies biological heterogeneity across both discrete cell types and continuous cell transitions. Partition-based graph abstraction (PAGA) provides an interpretable graph-like map of the...

    Authors: F. Alexander Wolf, Fiona K. Hamey, Mireya Plass, Jordi Solana, Joakim S. Dahlin, Berthold Göttgens, Nikolaus Rajewsky, Lukas Simon and Fabian J. Theis

    Citation: Genome Biology 2019 20:59

    Published on:

  3. Content type: Method

    Tandemly repeated DNA is highly mutable and causes at least 31 diseases, but it is hard to detect pathogenic repeat expansions genome-wide. Here, we report robust detection of human repeat expansions from care...

    Authors: Satomi Mitsuhashi, Martin C. Frith, Takeshi Mizuguchi, Satoko Miyatake, Tomoko Toyota, Hiroaki Adachi, Yoko Oma, Yoshihiro Kino, Hiroaki Mitsuhashi and Naomichi Matsumoto

    Citation: Genome Biology 2019 20:58

    Published on:

  4. Content type: Research

    Hi-C is currently the most widely used assay to investigate the 3D organization of the genome and to study its role in gene regulation, DNA replication, and disease. However, Hi-C experiments are costly to per...

    Authors: Galip Gürkan Yardımcı, Hakan Ozadam, Michael E. G. Sauria, Oana Ursu, Koon-Kiu Yan, Tao Yang, Abhijit Chakraborty, Arya Kaul, Bryan R. Lajoie, Fan Song, Ye Zhan, Ferhat Ay, Mark Gerstein, Anshul Kundaje, Qunhua Li, James Taylor…

    Citation: Genome Biology 2019 20:57

    Published on:

  5. Content type: Software

    DNA methylation is a widely investigated epigenetic mark with important roles in development and disease. High-throughput assays enable genome-scale DNA methylation analysis in large numbers of samples. Here, ...

    Authors: Fabian Müller, Michael Scherer, Yassen Assenov, Pavlo Lutsik, Jörn Walter, Thomas Lengauer and Christoph Bock

    Citation: Genome Biology 2019 20:55

    Published on:

  6. Content type: Research

    Sequencing errors are key confounding factors for detecting low-frequency genetic variants that are important for cancer molecular diagnosis, treatment, and surveillance using deep next-generation sequencing (...

    Authors: Xiaotu Ma, Ying Shao, Liqing Tian, Diane A. Flasch, Heather L. Mulder, Michael N. Edmonson, Yu Liu, Xiang Chen, Scott Newman, Joy Nakitandwe, Yongjin Li, Benshang Li, Shuhong Shen, Zhaoming Wang, Sheila Shurtleff, Leslie L. Robison…

    Citation: Genome Biology 2019 20:50

    Published on:

  7. Content type: Method

    Measuring gene expression of tumor clones at single-cell resolution links functional consequences to somatic alterations. Without scalable methods to simultaneously assay DNA and RNA from the same single cell,...

    Authors: Kieran R. Campbell, Adi Steif, Emma Laks, Hans Zahn, Daniel Lai, Andrew McPherson, Hossein Farahani, Farhia Kabeer, Ciara O’Flanagan, Justina Biele, Jazmine Brimhall, Beixi Wang, Pascale Walters, IMAXT Consortium, Alexandre Bouchard-Côté, Samuel Aparicio…

    Citation: Genome Biology 2019 20:54

    Published on:

  8. Content type: Correction

    Following publication of the original article [1], the authors reported the following errors.

    Authors: Hangnoh Lee, C. Joel McManus, Dong-Yeon Cho, Matthew Eaton, Fioranna Renda, Maria Patrizia Somma, Lucy Cherbas, Gemma May, Sara Powell, Dayu Zhang, Lijun Zhan, Alissa Resch, Justen Andrews, Susan E. Celniker, Peter Cherbas, Teresa M. Przytycka…

    Citation: Genome Biology 2019 20:53

    Published on:

    The original article was published in Genome Biology 2014 15:R70

  9. Content type: Method

    We propose a statistical boosting method, termed I-Boost, to integrate multiple types of high-dimensional genomics data with clinical data for predicting survival time. I-Boost provides substantially higher pr...

    Authors: Kin Yau Wong, Cheng Fan, Maki Tanioka, Joel S. Parker, Andrew B. Nobel, Donglin Zeng, Dan-Yu Lin and Charles M. Perou

    Citation: Genome Biology 2019 20:52

    Published on:

  10. Content type: Software

    The explosive growth in taxonomic metagenome profiling methods over the past years has created a need for systematic comparisons using relevant performance criteria. The Open-community Profiling Assessment too...

    Authors: Fernando Meyer, Andreas Bremges, Peter Belmann, Stefan Janssen, Alice C. McHardy and David Koslicki

    Citation: Genome Biology 2019 20:51

    Published on:

  11. Content type: Method

    Histone acetylation plays a central role in gene regulation and is sensitive to the levels of metabolic intermediates. However, predicting the impact of metabolic alterations on acetylation in pathological con...

    Authors: Fangzhou Shen, Luigi Boccuto, Rini Pauly, Sujata Srikanth and Sriram Chandrasekaran

    Citation: Genome Biology 2019 20:49

    Published on:

  12. Content type: Method

    Predicting the effects of genetic variants on splicing is highly relevant for human genetics. We describe the framework MMSplice (modular modeling of splicing) with which we built the winning model of the CAGI...

    Authors: Jun Cheng, Thi Yen Duong Nguyen, Kamil J. Cygan, Muhammed Hasan Çelik, William G. Fairbrother, žiga Avsec and Julien Gagneur

    Citation: Genome Biology 2019 20:48

    Published on:

  13. Content type: Method

    Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a simple protocol for detection of open chromatin. Computational footprinting, the search for regions with depletion of cleavage events due...

    Authors: Zhijian Li, Marcel H. Schulz, Thomas Look, Matthias Begemann, Martin Zenke and Ivan G. Costa

    Citation: Genome Biology 2019 20:45

    Published on:

  14. Content type: Correction

    Following publication of the original article [1], it was noticed that the author names were published with initials instead of full names. The article [1] has been updated.

    Authors: Agnieszka P. Lipinska, Martha L. Serrano-Serrano, Alexandre Cormier, Akira F. Peters, Kazuhiro Kogame, J. Mark Cock and Susana M. Coelho

    Citation: Genome Biology 2019 20:44

    Published on:

    The original article was published in Genome Biology 2019 20:35

  15. Content type: Correction

    Following publication of the original article [1], it was reported that the incorrect “Additional file 3” was published. The correct additional file is given below.

    Authors: Nelly Olova, Felix Krueger, Simon Andrews, David Oxley, Rebecca V. Berrens, Miguel R. Branco and Wolf Reik

    Citation: Genome Biology 2019 20:43

    Published on:

    The original article was published in Genome Biology 2018 19:33

  16. Content type: Research

    DNase-seq and ATAC-seq are broadly used methods to assay open chromatin regions genome-wide. The single nucleotide resolution of DNase-seq has been further exploited to infer transcription factor binding sites...

    Authors: Aslıhan Karabacak Calviello, Antje Hirsekorn, Ricardo Wurmus, Dilmurat Yusuf and Uwe Ohler

    Citation: Genome Biology 2019 20:42

    Published on:

  17. Content type: Research

    Imprinted genes are epigenetically modified during gametogenesis and maintain the established epigenetic signatures after fertilization, causing parental-specific gene expression.

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

    Citation: Genome Biology 2019 20:41

    Published on:

    The Correction to this article has been published in Genome Biology 2019 20:182

  18. Content type: Research

    The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying du...

    Authors: Xin Qiao, Qionghou Li, Hao Yin, Kaijie Qi, Leiting Li, Runze Wang, Shaoling Zhang and Andrew H. Paterson

    Citation: Genome Biology 2019 20:38

    Published on:

  19. Content type: Research

    Protein recoding by RNA editing is required for normal health and evolutionary adaptation. However, de novo induction of RNA editing in response to environmental factors is an uncommon phenomenon. While APOBEC...

    Authors: Shraddha Sharma, Jianmin Wang, Emad Alqassim, Scott Portwood, Eduardo Cortes Gomez, Orla Maguire, Per H. Basse, Eunice S. Wang, Brahm H. Segal and Bora E. Baysal

    Citation: Genome Biology 2019 20:37

    Published on:

  20. Content type: Research

    Human selection has a long history of transforming crop genomes. Peach (Prunus persica) has undergone more than 5000 years of domestication that led to remarkable changes in a series of agronomically important tr...

    Authors: Yong Li, Ke Cao, Gengrui Zhu, Weichao Fang, Changwen Chen, Xinwei Wang, Pei Zhao, Jian Guo, Tiyu Ding, Liping Guan, Qian Zhang, Wenwu Guo, Zhangjun Fei and Lirong Wang

    Citation: Genome Biology 2019 20:36

    Published on:

  21. Content type: Research

    Sexual life cycles in eukaryotes involve a cyclic alternation between haploid and diploid phases. While most animals possess a diploid life cycle, many plants and algae alternate between multicellular haploid ...

    Authors: Agnieszka P. Lipinska, Martha L. Serrano-Serrano, Alexandre Cormier, Akira F. Peters, Kazuhiro Kogame, J. Mark Cock and Susana M. Coelho

    Citation: Genome Biology 2019 20:35

    Published on:

    The Correction to this article has been published in Genome Biology 2019 20:44

  22. Content type: Method

    The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate and biodiversity changes. The recent genome-skimming approach extends current barcoding practices beyond short...

    Authors: Shahab Sarmashghi, Kristine Bohmann, M. Thomas P. Gilbert, Vineet Bafna and Siavash Mirarab

    Citation: Genome Biology 2019 20:34

    Published on:

  23. Content type: Research

    Adenosine-to-inosine (A-to-I) RNA editing is an essential post-transcriptional mechanism mediated by ADAR enzymes that have been recently associated with cancer.

    Authors: Domenico Alessandro Silvestris, Ernesto Picardi, Valeriana Cesarini, Bruno Fosso, Nicolò Mangraviti, Luca Massimi, Maurizio Martini, Graziano Pesole, Franco Locatelli and Angela Gallo

    Citation: Genome Biology 2019 20:33

    Published on:

  24. Content type: Method

    State-of-the-art methods assessing pathogenic non-coding variants have mostly been characterized on common disease-associated polymorphisms, yet with modest accuracy and strong positional biases. In this study...

    Authors: Barthélémy Caron, Yufei Luo and Antonio Rausell

    Citation: Genome Biology 2019 20:32

    Published on:

  25. Content type: Research

    Alternative splicing is a key regulatory mechanism in eukaryotic cells and increases the effective number of functionally distinct gene products. Using bulk RNA sequencing, splicing variation has been studied ...

    Authors: Stephanie M. Linker, Lara Urban, Stephen J. Clark, Mariya Chhatriwala, Shradha Amatya, Davis J. McCarthy, Ingo Ebersberger, Ludovic Vallier, Wolf Reik, Oliver Stegle and Marc Jan Bonder

    Citation: Genome Biology 2019 20:30

    Published on:

  26. Content type: Opinion

    How contemporary plant genomes originated and evolved is a fascinating question. One approach uses reference genomes from extant species to reconstruct the sequence and structure of their common ancestors over...

    Authors: Caroline Pont, Stefanie Wagner, Antoine Kremer, Ludovic Orlando, Christophe Plomion and Jerome Salse

    Citation: Genome Biology 2019 20:29

    Published on:

  27. Content type: Research

    Structural variants (SVs) are known to play important roles in a variety of cancers, but their origins and functional consequences are still poorly understood. Many SVs are thought to emerge from errors in the...

    Authors: Tracy J. Ballinger, Britta A. M. Bouwman, Reza Mirzazadeh, Silvano Garnerone, Nicola Crosetto and Colin A. Semple

    Citation: Genome Biology 2019 20:28

    Published on:

  28. Content type: Research

    CRISPR-Cas9 genome editing is widely used to study gene function, from basic biology to biomedical research. Structural rearrangements are a ubiquitous feature of cancer cells and their impact on the functiona...

    Authors: Emanuel Gonçalves, Fiona M. Behan, Sandra Louzada, Damien Arnol, Euan A. Stronach, Fengtang Yang, Kosuke Yusa, Oliver Stegle, Francesco Iorio and Mathew J. Garnett

    Citation: Genome Biology 2019 20:27

    Published on:

  29. Content type: Short Report

    CRISPR-Cas12a/Cpf1, a single RNA-guided endonuclease system, provides a promising tool for genome engineering. However, only three Cas12a orthologs have been employed for mammalian genome editing, and the edit...

    Authors: Fei Teng, Jing Li, Tongtong Cui, Kai Xu, Lu Guo, Qingqin Gao, Guihai Feng, Chuanyuan Chen, Dali Han, Qi Zhou and Wei Li

    Citation: Genome Biology 2019 20:15

    Published on:

  30. Content type: Research

    Recent studies have revealed thousands of A-to-I RNA editing events in primates, but the origination and general functions of these events are not well addressed.

    Authors: Ni A. An, Wanqiu Ding, Xin-Zhuang Yang, Jiguang Peng, Bin Z. He, Qing Sunny Shen, Fujian Lu, Aibin He, Yong E. Zhang, Bertrand Chin-Ming Tan, Jia-Yu Chen and Chuan-Yun Li

    Citation: Genome Biology 2019 20:24

    Published on:

  31. Content type: Research

    Altering the biochemical makeup of chromatin by the incorporation of histone variants during development represents a key mechanism in regulating gene expression. The histone variant H2A.B, H2A.B.3 in mice, ap...

    Authors: Nur Diana Anuar, Sebastian Kurscheid, Matt Field, Lei Zhang, Edward Rebar, Philip Gregory, Thierry Buchou, Josephine Bowles, Peter Koopman, David J. Tremethick and Tatiana A. Soboleva

    Citation: Genome Biology 2019 20:23

    Published on:

  32. Content type: Research

    Genome-wide loss-of-function screens using the CRISPR/Cas9 system allow the efficient discovery of cancer cell vulnerabilities. While several studies have focused on correcting for DNA cleavage toxicity biases...

    Authors: Jean-Philippe Fortin, Jenille Tan, Karen E. Gascoigne, Peter M. Haverty, William F. Forrest, Michael R. Costa and Scott E. Martin

    Citation: Genome Biology 2019 20:21

    Published on:

  33. Content type: Method

    We report a new method using re-designed guide RNAs with internal barcodes (iBARs) embedded in their loop regions. Our iBAR approach outperforms the conventional method by producing screening results with much...

    Authors: Shiyou Zhu, Zhongzheng Cao, Zhiheng Liu, Yuan He, Yinan Wang, Pengfei Yuan, Wei Li, Feng Tian, Ying Bao and Wensheng Wei

    Citation: Genome Biology 2019 20:20

    Published on:

  34. Content type: Short Report

    Trim-Away is a recent technique to rapidly deplete a protein from any cell type. Guided by antibodies, TRIM21 selects proteins for destruction. However, the applicability of this method in model organisms has ...

    Authors: Xiao Chen, Mi Liu, Hongyan Lou, Yiyi Lu, Meng-Tao Zhou, Rongying Ou, Yunsheng Xu and Kai-Fu Tang

    Citation: Genome Biology 2019 20:19

    Published on:

  35. Content type: Editorial

    We polled the Editorial Board of Genome Biology to ask where they see genomics going in the next few years. Here are some of their responses.

    Authors: Barbara Cheifet

    Citation: Genome Biology 2019 20:17

    Published on:

  36. Content type: Research

    Gut microbiota from individuals in rural, non-industrialized societies differ from those in individuals from industrialized societies. Here, we use 16S rRNA sequencing to survey the gut bacteria of seven non-i...

    Authors: Matthew E. B. Hansen, Meagan A. Rubel, Aubrey G. Bailey, Alessia Ranciaro, Simon R. Thompson, Michael C. Campbell, William Beggs, Jaanki R. Dave, Gaonyadiwe G. Mokone, Sununguko Wata Mpoloka, Thomas Nyambo, Christian Abnet, Stephen J. Chanock, Frederic D. Bushman and Sarah A. Tishkoff

    Citation: Genome Biology 2019 20:16

    Published on:

  37. Content type: Short Report

    Genome engineering methods have advanced greatly with the development of programmable nucleases, but methods for quantifying on- and off-target cleavage sites and associated deletions remain nascent. Here, we ...

    Authors: Christopher L. Nobles, Shantan Reddy, January Salas-McKee, Xiaojun Liu, Carl H. June, J. Joseph Melenhorst, Megan M. Davis, Yangbing Zhao and Frederic D. Bushman

    Citation: Genome Biology 2019 20:14

    Published on: