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  1. The practical use of graph-based reference genomes depends on the ability to align reads to them. Performing substring queries to paths through these graphs lies at the core of this task. The combination of in...

    Authors: Tom Mokveld, Jasper Linthorst, Zaid Al-Ars, Henne Holstege and Marcel Reinders

    Citation: Genome Biology 2020 21:65

    Content type: Method

    Published on:

  2. How intestinal epithelial cells interact with the microbiota and how this is regulated at the gene expression level are critical questions. Smarcad1 is a conserved chromatin remodeling factor with a poorly und...

    Authors: Juri Kazakevych, Jérémy Denizot, Anke Liebert, Mariana Portovedo, Mia Mosavie, Payal Jain, Claudia Stellato, Claire Fraser, Renan Oliveira Corrêa, Marina Célestine, Raphaël Mattiuz, Hanneke Okkenhaug, J. Ross Miller, Marco Aurélio Ramirez Vinolo, Marc Veldhoen and Patrick Varga-Weisz

    Citation: Genome Biology 2020 21:64

    Content type: Research

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  3. Genome-wide pooled CRISPR-Cas-mediated knockout, activation, and repression screens are powerful tools for functional genomic investigations. Despite their increasing importance, there is currently little guid...

    Authors: Sunil Bodapati, Timothy P. Daley, Xueqiu Lin, James Zou and Lei S. Qi

    Citation: Genome Biology 2020 21:62

    Content type: Review

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  4. Hemispheric asymmetry in neuronal processes is a fundamental feature of the human brain and drives symptom lateralization in Parkinson’s disease (PD), but its molecular determinants are unknown. Here, we ident...

    Authors: Peipei Li, Elizabeth Ensink, Sean Lang, Lee Marshall, Meghan Schilthuis, Jared Lamp, Irving Vega and Viviane Labrie

    Citation: Genome Biology 2020 21:61

    Content type: Research

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  5. Mango is one of the world’s most important tropical fruits. It belongs to the family Anacardiaceae, which includes several other economically important species, notably cashew, sumac and pistachio from other g...

    Authors: Peng Wang, Yingfeng Luo, Jianfeng Huang, Shenghan Gao, Guopeng Zhu, Zhiguo Dang, Jiangtao Gai, Meng Yang, Min Zhu, Huangkai Zhang, Xiuxu Ye, Aiping Gao, Xinyu Tan, Sen Wang, Shuangyang Wu, Edgar B. Cahoon…

    Citation: Genome Biology 2020 21:60

    Content type: Research

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  6. The spatiotemporal control of 3D genome is fundamental for gene regulation, yet it remains challenging to profile high-resolution chromatin structure at cis-regulatory elements (CREs). Using C-terminally biotinyl...

    Authors: Xin Liu, Yong Chen, Yuannyu Zhang, Yuxuan Liu, Nan Liu, Giovanni A. Botten, Hui Cao, Stuart H. Orkin, Michael Q. Zhang and Jian Xu

    Citation: Genome Biology 2020 21:59

    Content type: Method

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  7. To understand diversity in enormous collections of genome sequences, we need computationally scalable tools that can quickly contextualize individual genomes based on their similarities and identify features o...

    Authors: Ahmed M. Moustafa and Paul J. Planet

    Citation: Genome Biology 2020 21:58

    Content type: Short Report

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  8. Droplet-based microfluidic devices have become widely used to perform single-cell RNA sequencing (scRNA-seq). However, ambient RNA present in the cell suspension can be aberrantly counted along with a cell’s n...

    Authors: Shiyi Yang, Sean E. Corbett, Yusuke Koga, Zhe Wang, W Evan Johnson, Masanao Yajima and Joshua D. Campbell

    Citation: Genome Biology 2020 21:57

    Content type: Method

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  9. The recent advent of third-generation sequencing technologies brings promise for better characterization of genomic structural variants by virtue of having longer reads. However, long-read applications are sti...

    Authors: Cheng Yong Tham, Roberto Tirado-Magallanes, Yufen Goh, Melissa J. Fullwood, Bryan T.H. Koh, Wilson Wang, Chin Hin Ng, Wee Joo Chng, Alexandre Thiery, Daniel G. Tenen and Touati Benoukraf

    Citation: Genome Biology 2020 21:56

    Content type: Software

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  10. While the physical and chemical properties of airborne particulate matter (PM) have been extensively studied, their associated microbiome remains largely unexplored. Here, we performed a longitudinal metagenom...

    Authors: Nan Qin, Peng Liang, Chunyan Wu, Guanqun Wang, Qian Xu, Xiao Xiong, Tingting Wang, Moreno Zolfo, Nicola Segata, Huanlong Qin, Rob Knight, Jack A. Gilbert and Ting F. Zhu

    Citation: Genome Biology 2020 21:55

    Content type: Research

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  11. We present long-read Tet-assisted pyridine borane sequencing (lrTAPS) for targeted base-resolution sequencing of DNA methylation and hydroxymethylation in regions up to 10 kb from nanogram-level input. Compati...

    Authors: Yibin Liu, Jingfei Cheng, Paulina Siejka-Zielińska, Carika Weldon, Hannah Roberts, Maria Lopopolo, Andrea Magri, Valentina D’Arienzo, James M. Harris, Jane A. McKeating and Chun-Xiao Song

    Citation: Genome Biology 2020 21:54

    Content type: Short Report

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  12. Pooled CRISPR screens are a powerful tool to probe genotype-phenotype relationships at genome-wide scale. However, criteria for optimal design are missing, and it remains unclear how experimental parameters af...

    Authors: Katharina Imkeller, Giulia Ambrosi, Michael Boutros and Wolfgang Huber

    Citation: Genome Biology 2020 21:53

    Content type: Method

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  13. Zebrafish can faithfully regenerate injured fins through the formation of a blastema, a mass of proliferative cells that can grow and develop into the lost body part. After amputation, various cell types contr...

    Authors: Hyung Joo Lee, Yiran Hou, Yujie Chen, Zea Z. Dailey, Aiyana Riddihough, Hyo Sik Jang, Ting Wang and Stephen L. Johnson

    Citation: Genome Biology 2020 21:52

    Content type: Research

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  14. The speed of translation elongation is primarily determined by the abundance of tRNAs. Thus, the codon usage influences the rate with which individual mRNAs are translated. As the nature of tRNA pools and modi...

    Authors: Joao C. Guimaraes, Nitish Mittal, Alexandra Gnann, Dominik Jedlinski, Andrea Riba, Katarzyna Buczak, Alexander Schmidt and Mihaela Zavolan

    Citation: Genome Biology 2020 21:44

    Content type: Research

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  15. CRISPR-Cas9 has been developed as a therapeutic agent for various infectious and genetic diseases. In many clinically relevant applications, constitutively active CRISPR-Cas9 is delivered into human cells with...

    Authors: Yan-ru Cui, Shao-jie Wang, Jun Chen, Jie Li, Wenzhang Chen, Shuyue Wang, Bing Meng, Wei Zhu, Zhuhong Zhang, Bei Yang, Biao Jiang, Guang Yang, Peixiang Ma and Jia Liu

    Citation: Genome Biology 2020 21:51

    Content type: Research

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  16. Following publication of the original paper [1], an error was reported in the third paragraph in the section “Analysis of GMB composition and its correlates” (page 3 of the PDF). The first sentence of the text sh...

    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 2020 21:50

    Content type: Author Correction

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    The original article was published in Genome Biology 2019 20:219

  17. Single-cell RNA sequencing has emerged as a powerful tool for characterizing cells, but not all phenotypes of interest can be observed through changes in gene expression. Linking sequencing with optical analys...

    Authors: Jesse Q. Zhang, Christian A. Siltanen, Leqian Liu, Kai-Chun Chang, Zev J. Gartner and Adam R. Abate

    Citation: Genome Biology 2020 21:49

    Content type: Method

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  18. Recently, several non-classical functions of histone modification regulators (HMRs), independent of their known histone modification substrates and products, have been reported to be essential for specific cel...

    Authors: Shengen Hu, Dawei Huo, Zhaowei Yu, Yujie Chen, Jing Liu, Lin Liu, Xudong Wu and Yong Zhang

    Citation: Genome Biology 2020 21:48

    Content type: Method

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  19. Microbial populations exhibit functional changes in response to different ambient environments. Although whole metagenome sequencing promises enough raw data to study those changes, existing tools are limited ...

    Authors: Sumaiya Nazeen, Yun William Yu and Bonnie Berger

    Citation: Genome Biology 2020 21:47

    Content type: Method

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  20. Following publication of the original paper [1], the authors reported an error in the affiliation of Xin-Tian Hu, who is also affiliated with “Kunming Primate Research Center, Kunming Institute of Zoology, Chi...

    Authors: Ming-Li Li, Shi-Hao Wu, Jin-Jin Zhang, Hang-Yu Tian, Yong Shao, Zheng-Bo Wang, David M. Irwin, Jia-Li Li, Xin-Tian Hu and Dong-Dong Wu

    Citation: Genome Biology 2020 21:46

    Content type: Author Correction

    Published on:

    The original article was published in Genome Biology 2019 20:258

  21. H3K27ac is well recognized as a marker for active enhancers and a great indicator of enhancer activity. However, its functional impact on transcription has not been characterized. By substituting lysine 27 in ...

    Authors: Tiantian Zhang, Zhuqiang Zhang, Qiang Dong, Jun Xiong and Bing Zhu

    Citation: Genome Biology 2020 21:45

    Content type: Short Report

    Published on:

  22. The initiation and subsequent evolution of cancer are largely driven by a relatively small number of somatic mutations with critical functional impacts, so-called driver mutations. Identifying driver mutations...

    Authors: Hu Chen, Jun Li, Yumeng Wang, Patrick Kwok-Shing Ng, Yiu Huen Tsang, Kenna R. Shaw, Gordon B. Mills and Han Liang

    Citation: Genome Biology 2020 21:43

    Content type: Research

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  23. The relationship between germline genetic variation and breast cancer survival is largely unknown, especially in understudied minority populations who often have poorer survival. Genome-wide association studie...

    Authors: Arjun Bhattacharya, Montserrat García-Closas, Andrew F. Olshan, Charles M. Perou, Melissa A. Troester and Michael I. Love

    Citation: Genome Biology 2020 21:42

    Content type: Research

    Published on:

  24. Following publication of the original paper [1], the authors submitted a new Additional file 5 to replace the one containing formatting issues. The updated Additional file 5 is published in this correction.

    Authors: K. Leigh Greathouse, James R. White, Ashely J. Vargas, Valery V. Bliskovsky, Jessica A. Beck, Natalia von Muhlinen, Eric C. Polley, Elise D. Bowman, Mohammed A. Khan, Ana I. Robles, Tomer Cooks, Bríd M. Ryan, Noah Padgett, Amiran H. Dzutsev, Giorgio Trinchieri, Marbin A. Pineda…

    Citation: Genome Biology 2020 21:41

    Content type: Author Correction

    Published on:

    The original article was published in Genome Biology 2018 19:123

  25. Following publication of the original paper [1], it was reported that an error in the processing of Fig. 8 occurred. In the online HTML version of the article, Fig. 8 was presented as a duplication of Fig. 7. ...

    Authors: Douglas C. Woodhams, Molly C. Bletz, C. Guilherme Becker, Hayden A. Bender, Daniel Buitrago-Rosas, Hannah Diebboll, Roger Huynh, Patrick J. Kearns, Jordan Kueneman, Emmi Kurosawa, Brandon C. LaBumbard, Casandra Lyons, Kerry McNally, Klaus Schliep, Nachiket Shankar, Amanda G. Tokash-Peters…

    Citation: Genome Biology 2020 21:40

    Content type: Publisher Correction

    Published on:

    The original article was published in Genome Biology 2020 21:23

  26. Sex chromosomes have arisen independently in a wide variety of species, yet they share common characteristics, including the presence of suppressed recombination surrounding sex determination loci. Mammalian s...

    Authors: Ran Zhou, David Macaya-Sanz, Craig H. Carlson, Jeremy Schmutz, Jerry W. Jenkins, David Kudrna, Aditi Sharma, Laura Sandor, Shengqiang Shu, Kerrie Barry, Gerald A. Tuskan, Tao Ma, Jianquan Liu, Matthew Olson, Lawrence B. Smart and Stephen P. DiFazio

    Citation: Genome Biology 2020 21:38

    Content type: Research

    Published on:

  27. Many functional analysis tools have been developed to extract functional and mechanistic insight from bulk transcriptome data. With the advent of single-cell RNA sequencing (scRNA-seq), it is in principle poss...

    Authors: Christian H. Holland, Jovan Tanevski, Javier Perales-Patón, Jan Gleixner, Manu P. Kumar, Elisabetta Mereu, Brian A. Joughin, Oliver Stegle, Douglas A. Lauffenburger, Holger Heyn, Bence Szalai and Julio Saez-Rodriguez

    Citation: Genome Biology 2020 21:36

    Content type: Research

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  28. Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide a...

    Authors: Glenn Hickey, David Heller, Jean Monlong, Jonas A. Sibbesen, Jouni Sirén, Jordan Eizenga, Eric T. Dawson, Erik Garrison, Adam M. Novak and Benedict Paten

    Citation: Genome Biology 2020 21:35

    Content type: Method

    Published on:

  29. Chickens are a highly important source of protein for a large proportion of the human population. The caecal microbiota plays a crucial role in chicken nutrition through the production of short-chain fatty aci...

    Authors: Laura Glendinning, Robert D. Stewart, Mark J. Pallen, Kellie A. Watson and Mick Watson

    Citation: Genome Biology 2020 21:34

    Content type: Research

    Published on:

  30. Quiescence (G0) is a transient, cell cycle-arrested state. By entering G0, cancer cells survive unfavorable conditions such as chemotherapy and cause relapse. While G0 cells have been studied at the transcript...

    Authors: Sooncheol Lee, Douglas Micalizzi, Samuel S. Truesdell, Syed I. A. Bukhari, Myriam Boukhali, Jennifer Lombardi-Story, Yasutaka Kato, Min-Kyung Choo, Ipsita Dey-Guha, Fei Ji, Benjamin T. Nicholson, David T. Myers, Dongjun Lee, Maria A. Mazzola, Radhika Raheja, Adam Langenbucher…

    Citation: Genome Biology 2020 21:33

    Content type: Research

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  31. We developed Lisa (http://​lisa.​cistrome.​org/​) to predict the transcriptional regulators (TRs) of differentially expressed or co-expressed gene sets. Based on the input gene sets, Lisa first uses histone mark ChIP...

    Authors: Qian Qin, Jingyu Fan, Rongbin Zheng, Changxin Wan, Shenglin Mei, Qiu Wu, Hanfei Sun, Myles Brown, Jing Zhang, Clifford A. Meyer and X. Shirley Liu

    Citation: Genome Biology 2020 21:32

    Content type: Method

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  32. The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell sequencing technology. Thousands—or even millions—of cells analyzed in a si...

    Authors: David Lähnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson, Catalina A. Vallejos, Kieran R. Campbell, Niko Beerenwinkel, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn Baaijens…

    Citation: Genome Biology 2020 21:31

    Content type: Review

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  33. Long-read technologies are overcoming early limitations in accuracy and throughput, broadening their application domains in genomics. Dedicated analysis tools that take into account the characteristics of long...

    Authors: Shanika L. Amarasinghe, Shian Su, Xueyi Dong, Luke Zappia, Matthew E. Ritchie and Quentin Gouil

    Citation: Genome Biology 2020 21:30

    Content type: Review

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  34. Admixture occurs when previously isolated populations come together and exchange genetic material. We hypothesize that admixture can enable rapid adaptive evolution in human populations by introducing novel ge...

    Authors: Emily T. Norris, Lavanya Rishishwar, Aroon T. Chande, Andrew B. Conley, Kaixiong Ye, Augusto Valderrama-Aguirre and I. King Jordan

    Citation: Genome Biology 2020 21:29

    Content type: Research

    Published on:

  35. Following publication of the original paper [1], an error was reported in the processing of Fig. 2. The correct Fig. 2 is supplied below and the original article [1] has been corrected. The publishers apologiz...

    Authors: Mayank N. K. Choudhary, Ryan Z. Friedman, Julia T. Wang, Hyo Sik Jang, Xiaoyu Zhuo and Ting Wang

    Citation: Genome Biology 2020 21:28

    Content type: Publisher Correction

    Published on:

    The original article was published in Genome Biology 2020 21:16

  36. Drug resistance is a major obstacle in cancer therapy. To elucidate the genetic factors that regulate sensitivity to anti-cancer drugs, we performed CRISPR-Cas9 knockout screens for resistance to a spectrum of...

    Authors: Man-Tat Lau, Shila Ghazanfar, Ashleigh Parkin, Angela Chou, Jourdin R. Rouaen, Jamie B. Littleboy, Danielle Nessem, Thang M. Khuong, Damien Nevoltris, Peter Schofield, David Langley, Daniel Christ, Jean Yang, Marina Pajic and G. Gregory Neely

    Citation: Genome Biology 2020 21:27

    Content type: Research

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  37. Mobile elements comprise a large fraction of metazoan genomes. Accumulation of mobile elements is bound to produce multiple putative double-stranded RNA (dsRNA) structures within the transcriptome. These endog...

    Authors: Michal Barak, Hagit T. Porath, Gilad Finkelstein, Binyamin A. Knisbacher, Ilana Buchumenski, Shalom Hillel Roth, Erez Y. Levanon and Eli Eisenberg

    Citation: Genome Biology 2020 21:26

    Content type: Research

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  38. The circum-basmati group of cultivated Asian rice (Oryza sativa) contains many iconic varieties and is widespread in the Indian subcontinent. Despite its economic and cultural importance, a high-quality reference...

    Authors: Jae Young Choi, Zoe N. Lye, Simon C. Groen, Xiaoguang Dai, Priyesh Rughani, Sophie Zaaijer, Eoghan D. Harrington, Sissel Juul and Michael D. Purugganan

    Citation: Genome Biology 2020 21:21

    Content type: Research

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  39. Regulation of transcription depends on interactions between cis-regulatory elements (CREs) and regulatory proteins. Active CREs are imbedded in open chromatin that are accessible to nucleases. Several techniques,...

    Authors: Hainan Zhao, Wenli Zhang, Tao Zhang, Yuan Lin, Yaodong Hu, Chao Fang and Jiming Jiang

    Citation: Genome Biology 2020 21:24

    Content type: Research

    Published on:

  40. Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolis...

    Authors: Douglas C. Woodhams, Molly C. Bletz, C. Guilherme Becker, Hayden A. Bender, Daniel Buitrago-Rosas, Hannah Diebboll, Roger Huynh, Patrick J. Kearns, Jordan Kueneman, Emmi Kurosawa, Brandon C. LaBumbard, Casandra Lyons, Kerry McNally, Klaus Schliep, Nachiket Shankar, Amanda G. Tokash-Peters…

    Citation: Genome Biology 2020 21:23

    Content type: Research

    Published on:

  41. Authors: K. C. Kent Lloyd, David J. Adams, Gareth Baynam, Arthur L. Beaudet, Fatima Bosch, Kym M. Boycott, Robert E. Braun, Mark Caulfield, Ronald Cohn, Mary E. Dickinson, Michael S. Dobbie, Ann M. Flenniken, Paul Flicek, Sanjeev Galande, Xiang Gao, Anne Grobler…

    Citation: Genome Biology 2020 21:18

    Content type: Editorial

    Published on:

  42. Identifying genotype-phenotype links and causative genes from quantitative trait loci (QTL) is challenging for complex agronomically important traits. To accelerate maize gene discovery and breeding, we presen...

    Authors: Hai-Jun Liu, Xiaqing Wang, Yingjie Xiao, Jingyun Luo, Feng Qiao, Wenyu Yang, Ruyang Zhang, Yijiang Meng, Jiamin Sun, Shijuan Yan, Yong Peng, Luyao Niu, Liumei Jian, Wei Song, Jiali Yan, Chunhui Li…

    Citation: Genome Biology 2020 21:20

    Content type: Research

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  43. We present scMAGeCK, a computational framework to identify genomic elements associated with multiple expression-based phenotypes in CRISPR/Cas9 functional screening that uses single-cell RNA-seq as readout. sc...

    Authors: Lin Yang, Yuqing Zhu, Hua Yu, Xiaolong Cheng, Sitong Chen, Yulan Chu, He Huang, Jin Zhang and Wei Li

    Citation: Genome Biology 2020 21:19

    Content type: Method

    Published on:

  44. Transposable elements (TEs) make up half of mammalian genomes and shape genome regulation by harboring binding sites for regulatory factors. These include binding sites for architectural proteins, such as CTCF...

    Authors: Mayank NK Choudhary, Ryan Z. Friedman, Julia T. Wang, Hyo Sik Jang, Xiaoyu Zhuo and Ting Wang

    Citation: Genome Biology 2020 21:16

    Content type: Research

    Published on:

    The Publisher Correction to this article has been published in Genome Biology 2020 21:28

  45. Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recor...

    Authors: Gregg W. C. Thomas, Elias Dohmen, Daniel S. T. Hughes, Shwetha C. Murali, Monica Poelchau, Karl Glastad, Clare A. Anstead, Nadia A. Ayoub, Phillip Batterham, Michelle Bellair, Greta J. Binford, Hsu Chao, Yolanda H. Chen, Christopher Childers, Huyen Dinh, Harsha Vardhan Doddapaneni…

    Citation: Genome Biology 2020 21:15

    Content type: Research

    Published on: