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  1. 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

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  2. 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

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  3. 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

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  4. 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

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  5. 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

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  6. 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

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  7. Content type: Research

    Cisplatin resistance is a major challenge for advanced head and neck cancer (HNC). Understanding the underlying mechanisms and developing effective strategies against cisplatin resistance are highly desired in...

    Authors: Xing Qin, Haiyan Guo, Xiaoning Wang, Xueqin Zhu, Ming Yan, Xu Wang, Qin Xu, Jianbo Shi, Eryi Lu, Wantao Chen and Jianjun Zhang

    Citation: Genome Biology 2019 20:12

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  8. Content type: Correction

    Following publication of the original article [1], the authors reported the following error in the name of the fourth author.

    Authors: Pierre Murat, Giovanni Marsico, Barbara Herdy, Avazeh T. Ghanbarian, Guillem Portella and Shankar Balasubramanian

    Citation: Genome Biology 2019 20:11

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    The original article was published in Genome Biology 2018 19:229

  9. Content type: Method

    How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to demonstrate how virus concentra...

    Authors: Nathan D. Grubaugh, Karthik Gangavarapu, Joshua Quick, Nathaniel L. Matteson, Jaqueline Goes De Jesus, Bradley J. Main, Amanda L. Tan, Lauren M. Paul, Doug E. Brackney, Saran Grewal, Nikos Gurfield, Koen K. A. Van Rompay, Sharon Isern, Scott F. Michael, Lark L. Coffey, Nicholas J. Loman…

    Citation: Genome Biology 2019 20:8

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  10. Content type: Research

    Long intergenic RNAs (lincRNAs) play critical roles in eukaryotic cells, but systematic analyses of the lincRNAs of an animal for phenotypes are lacking. We generate CRISPR knockout strains for Caenorhabditis ele...

    Authors: Shuai Wei, He Chen, Emmanuel Enoch Dzakah, Bin Yu, Xiaolin Wang, Tao Fu, Jingxin Li, Lei Liu, Shucheng Fang, Weihong Liu and Ge Shan

    Citation: Genome Biology 2019 20:7

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  11. Content type: Research

    The nearly neutral theory of molecular evolution predicts that the efficacy of natural selection increases with the effective population size. This prediction has been verified by independent observations in d...

    Authors: Paulina Bolívar, Laurent Guéguen, Laurent Duret, Hans Ellegren and Carina F. Mugal

    Citation: Genome Biology 2019 20:5

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  12. Content type: Software

    Bioconductor is a widely used R-based platform for genomics, but its host of complex genomic data structures places a cognitive burden on the user. For most tasks, the GRanges object would suffice, but there a...

    Authors: Stuart Lee, Dianne Cook and Michael Lawrence

    Citation: Genome Biology 2019 20:4

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  13. Content type: Research

    Pseudomonas syringae is a highly diverse bacterial species complex capable of causing a wide range of serious diseases on numerous agronomically important crops. We examine the evolutionary relationships of 391 a...

    Authors: Marcus M. Dillon, Shalabh Thakur, Renan N. D. Almeida, Pauline W. Wang, Bevan S. Weir and David S. Guttman

    Citation: Genome Biology 2019 20:3

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  14. Content type: Research

    Maintenance of physiological circadian rhythm plays a crucial role in human health. Numerous studies have shown that disruption of circadian rhythm may increase risk for malignant, psychiatric, metabolic, and ...

    Authors: Gabriel Oh, Karolis Koncevičius, Sasha Ebrahimi, Matthew Carlucci, Daniel Erik Groot, Akhil Nair, Aiping Zhang, Algimantas Kriščiūnas, Edward S. Oh, Viviane Labrie, Albert H. C. Wong, Juozas Gordevičius, Peixin Jia, Miki Susic and Art Petronis

    Citation: Genome Biology 2019 20:2

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  15. Content type: Database

    The Network of Cancer Genes (NCG) is a manually curated repository of 2372 genes whose somatic modifications have known or predicted cancer driver roles. These genes were collected from 275 publications, inclu...

    Authors: Dimitra Repana, Joel Nulsen, Lisa Dressler, Michele Bortolomeazzi, Santhilata Kuppili Venkata, Aikaterini Tourna, Anna Yakovleva, Tommaso Palmieri and Francesca D. Ciccarelli

    Citation: Genome Biology 2019 20:1

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  16. Content type: Research

    RNA secondary structures in the 5′-untranslated regions (5′-UTR) of mRNAs are key to the post-transcriptional regulation of gene expression. While it is evident that non-canonical Hoogsteen-paired G-quadruplex...

    Authors: Pierre Murat, Giovanni Marsico, Barbara Herdy, Avazeh Ghanbarian, Guillem Portella and Shankar Balasubramanian

    Citation: Genome Biology 2018 19:229

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    The Correction to this article has been published in Genome Biology 2019 20:124

    The Correction to this article has been published in Genome Biology 2019 20:11

  17. Content type: Opinion

    Cells adapt to stress by altering gene expression at multiple levels. Here, we propose a new mechanism regulating stress-dependent gene expression at the level of translation, with coordinated interplay betwee...

    Authors: Cheryl Chan, Phuong Pham, Peter C. Dedon and Thomas J. Begley

    Citation: Genome Biology 2018 19:228

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  18. Content type: Short Report

    Biomarkers of aging can be used to assess the health of individuals and to study aging and age-related diseases. We generate a large dataset of genome-wide RNA-seq profiles of human dermal fibroblasts from 133...

    Authors: Jason G. Fleischer, Roberta Schulte, Hsiao H. Tsai, Swati Tyagi, Arkaitz Ibarra, Maxim N. Shokhirev, Ling Huang, Martin W. Hetzer and Saket Navlakha

    Citation: Genome Biology 2018 19:221

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  19. Content type: Method

    Despite rapid developments in single cell sequencing, sample-specific batch effects, detection of cell multiplets, and experimental costs remain outstanding challenges. Here, we introduce Cell Hashing, where o...

    Authors: Marlon Stoeckius, Shiwei Zheng, Brian Houck-Loomis, Stephanie Hao, Bertrand Z. Yeung, William M. Mauck III, Peter Smibert and Rahul Satija

    Citation: Genome Biology 2018 19:224

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  20. Content type: Research

    DNA methylation is influenced by both environmental and genetic factors and is increasingly thought to affect variation in complex traits and diseases. Yet, the extent of ancestry-related differences in DNA me...

    Authors: Lucas T. Husquin, Maxime Rotival, Maud Fagny, Hélène Quach, Nora Zidane, Lisa M. McEwen, Julia L. MacIsaac, Michael S. Kobor, Hugues Aschard, Etienne Patin and Lluis Quintana-Murci

    Citation: Genome Biology 2018 19:222

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  21. Content type: Software

    There is growing interest in using genetic variants to augment the reference genome into a graph genome, with alternative sequences, to improve read alignment accuracy and reduce allelic bias. While adding a v...

    Authors: Jacob Pritt, Nae-Chyun Chen and Ben Langmead

    Citation: Genome Biology 2018 19:220

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  22. Content type: Research

    The organization of chromatin in the nucleus plays an essential role in gene regulation. About half of the mammalian genome comprises transposable elements. Given their repetitive nature, reads associated with...

    Authors: Ramya Raviram, Pedro P. Rocha, Vincent M. Luo, Emily Swanzey, Emily R. Miraldi, Edward B. Chuong, Cédric Feschotte, Richard Bonneau and Jane A. Skok

    Citation: Genome Biology 2018 19:216

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  23. Content type: Research

    Friend leukemia virus integration 1 (FLI1), an ETS transcription factor family member, acts as an oncogenic driver in hematological malignancies and promotes tumor growth in solid tumors. However, little is kn...

    Authors: Naifei Chen, Gang Zhao, Xu Yan, Zheng Lv, Hongmei Yin, Shilin Zhang, Wei Song, Xueli Li, Lingyu Li, Zhonghua Du, Lin Jia, Lei Zhou, Wei Li, Andrew R. Hoffman, Ji-Fan Hu and Jiuwei Cui

    Citation: Genome Biology 2018 19:218

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  24. Content type: Research

    Chromatin folding gives rise to structural elements among which are clusters of densely interacting DNA regions termed topologically associating domains (TADs). TADs have been characterized across multiple spe...

    Authors: Marie Zufferey, Daniele Tavernari, Elisa Oricchio and Giovanni Ciriello

    Citation: Genome Biology 2018 19:217

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  25. Content type: Research

    The development of CRISPR genome editing has transformed biomedical research. Most applications reported thus far rely upon the Cas9 protein from Streptococcus pyogenes SF370 (SpyCas9). With many RNA guides, wild...

    Authors: Nadia Amrani, Xin D. Gao, Pengpeng Liu, Alireza Edraki, Aamir Mir, Raed Ibraheim, Ankit Gupta, Kanae E. Sasaki, Tong Wu, Paul D. Donohoue, Alexander H. Settle, Alexandra M. Lied, Kyle McGovern, Chris K. Fuller, Peter Cameron, Thomas G. Fazzio…

    Citation: Genome Biology 2018 19:214

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  26. Content type: Method

    We present here miRTrace, the first algorithm to trace microRNA sequencing data back to their taxonomic origins. This is a challenge with profound implications for forensics, parasitology, food control, and re...

    Authors: Wenjing Kang, Yrin Eldfjell, Bastian Fromm, Xavier Estivill, Inna Biryukova and Marc R. Friedländer

    Citation: Genome Biology 2018 19:213

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  27. Content type: Research

    Recently, DNA methylation was proposed to regulate fleshy fruit ripening. Fleshy fruits can be distinguished by their ripening process as climacteric fruits, such as tomatoes, or non-climacteric fruits, such a...

    Authors: Jingfei Cheng, Qingfeng Niu, Bo Zhang, Kunsong Chen, Ruihua Yang, Jian-Kang Zhu, Yijing Zhang and Zhaobo Lang

    Citation: Genome Biology 2018 19:212

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  28. Content type: Review

    Genome-editing tools provide advanced biotechnological techniques that enable the precise and efficient targeted modification of an organism’s genome. Genome-editing systems have been utilized in a wide variet...

    Authors: Yi Zhang, Karen Massel, Ian D. Godwin and Caixia Gao

    Citation: Genome Biology 2018 19:210

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    The Correction to this article has been published in Genome Biology 2019 20:13

  29. Content type: Database

    We assembled the sequences from deep RNA sequencing experiments by the Genotype-Tissue Expression (GTEx) project, to create a new catalog of human genes and transcripts, called CHESS. The new database contains...

    Authors: Mihaela Pertea, Alaina Shumate, Geo Pertea, Ales Varabyou, Florian P. Breitwieser, Yu-Chi Chang, Anil K. Madugundu, Akhilesh Pandey and Steven L. Salzberg

    Citation: Genome Biology 2018 19:208

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    The Research Highlight to this article has been published in Genome Biology 2018 19:223

  30. Content type: Method

    Mass and growth rate are highly integrative measures of cell physiology not discernable via genomic measurements. Here, we introduce a microfluidic platform enabling direct measurement of single-cell mass and ...

    Authors: Robert J. Kimmerling, Sanjay M. Prakadan, Alejandro J. Gupta, Nicholas L. Calistri, Mark M. Stevens, Selim Olcum, Nathan Cermak, Riley S. Drake, Kristine Pelton, Frederik De Smet, Keith L. Ligon, Alex K. Shalek and Scott R. Manalis

    Citation: Genome Biology 2018 19:207

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  31. Content type: Editorial

    We describe the results of our year-long trial of transparent peer review and announce the adoption of transparent review as permanent policy.

    Authors: Andrew Cosgrove and Barbara Cheifet

    Citation: Genome Biology 2018 19:206

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  32. Content type: Review

    The human population is growing, and as a result we need to produce more food whilst reducing the impact of farming on the environment. Selective breeding and genomic selection have had a transformational impa...

    Authors: Christine Tait-Burkard, Andrea Doeschl-Wilson, Mike J. McGrew, Alan L. Archibald, Helen M. Sang, Ross D. Houston, C. Bruce Whitelaw and Mick Watson

    Citation: Genome Biology 2018 19:204

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  33. Content type: Method

    Despite rapid progress of next-generation sequencing (NGS) technologies, the disease-causing genes underpinning about half of all Mendelian diseases remain elusive. One main challenge is the high genetic heter...

    Authors: Jun Wang, Li Zhao, Xia Wang, Yong Chen, Mingchu Xu, Zachry T. Soens, Zhongqi Ge, Peter Ronghan Wang, Fei Wang and Rui Chen

    Citation: Genome Biology 2018 19:203

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  34. Content type: Method

    High-throughput DNA sequencing enables detection of copy number variations (CNVs) on the genome-wide scale with finer resolution compared to array-based methods but suffers from biases and artifacts that lead ...

    Authors: Yuchao Jiang, Rujin Wang, Eugene Urrutia, Ioannis N. Anastopoulos, Katherine L. Nathanson and Nancy R. Zhang

    Citation: Genome Biology 2018 19:202

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  35. Content type: Research Highlight

    The study of the evolution of chromosomal number and structure has long been of interest to evolutionary biologists. However, this research has been hindered by the lack of chromosome-level genome assemblies f...

    Authors: Guojie Zhang

    Citation: Genome Biology 2018 19:201

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  36. Content type: Review

    Transposable elements (TEs) are major components of eukaryotic genomes. However, the extent of their impact on genome evolution, function, and disease remain a matter of intense interrogation. The rise of geno...

    Authors: Guillaume Bourque, Kathleen H. Burns, Mary Gehring, Vera Gorbunova, Andrei Seluanov, Molly Hammell, Michaël Imbeault, Zsuzsanna Izsvák, Henry L. Levin, Todd S. Macfarlan, Dixie L. Mager and Cédric Feschotte

    Citation: Genome Biology 2018 19:199

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