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  1. Although it is assumed that contamination in bacterial whole-genome sequencing causes errors, the influences of contamination on clustering analyses, such as single-nucleotide polymorphism discovery, phylogene...

    Authors: Arthur W. Pightling, James B. Pettengill, Yu Wang, Hugh Rand and Errol Strain

    Citation: Genome Biology 2019 20:286

    Content type: Short Report

    Published on:

  2. The lifelong accumulation of somatic mutations underlies age-related phenotypes and cancer. Mutagenic forces are thought to shape the genome of aging cells in a tissue-specific way. Whole genome analyses of so...

    Authors: Irene Franco, Hafdis T. Helgadottir, Aldo Moggio, Malin Larsson, Peter Vrtačnik, Anna Johansson, Nina Norgren, Pär Lundin, David Mas-Ponte, Johan Nordström, Torbjörn Lundgren, Peter Stenvinkel, Lars Wennberg, Fran Supek and Maria Eriksson

    Citation: Genome Biology 2019 20:285

    Content type: Research

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  3. Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembl...

    Authors: Cécile Monat, Sudharsan Padmarasu, Thomas Lux, Thomas Wicker, Heidrun Gundlach, Axel Himmelbach, Jennifer Ens, Chengdao Li, Gary J. Muehlbauer, Alan H. Schulman, Robbie Waugh, Ilka Braumann, Curtis Pozniak, Uwe Scholz, Klaus F. X. Mayer, Manuel Spannagl…

    Citation: Genome Biology 2019 20:284

    Content type: Method

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  4. The spatial organization of chromatin in the nucleus has been implicated in regulating gene expression. Maps of high-frequency interactions between different segments of chromatin have revealed topologically a...

    Authors: Lin An, Tao Yang, Jiahao Yang, Johannes Nuebler, Guanjue Xiang, Ross C. Hardison, Qunhua Li and Yu Zhang

    Citation: Genome Biology 2019 20:282

    Content type: Method

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  5. The Horvath epigenetic clock is widely used. It predicts age quite well from 353 CpG sites in the DNA methylation profile in unknown samples and has been used to calculate “age acceleration” in various tissues...

    Authors: Louis Y. El Khoury, Tyler Gorrie-Stone, Melissa Smart, Amanda Hughes, Yanchun Bao, Alexandria Andrayas, Joe Burrage, Eilis Hannon, Meena Kumari, Jonathan Mill and Leonard C. Schalkwyk

    Citation: Genome Biology 2019 20:283

    Content type: Research

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  6. High-throughput DNA sequencing enables large-scale metagenomic analyses of complex biological systems. Such analyses are not restricted to present-day samples and can also be applied to molecular data from arc...

    Authors: Ron Hübler, Felix M. Key, Christina Warinner, Kirsten I. Bos, Johannes Krause and Alexander Herbig

    Citation: Genome Biology 2019 20:280

    Content type: Method

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  7. Identification of functional elements for a protein of interest is important for achieving a mechanistic understanding. However, it remains cumbersome to assess each and every amino acid of a given protein in ...

    Authors: Xinyi Zhang, Di Yue, Yinan Wang, Yuexin Zhou, Ying Liu, Yeting Qiu, Feng Tian, Ying Yu, Zhuo Zhou and Wensheng Wei

    Citation: Genome Biology 2019 20:279

    Content type: Method

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  8. RNA sequencing using the latest single-molecule sequencing instruments produces reads that are thousands of nucleotides long. The ability to assemble these long reads can greatly improve the sensitivity of lon...

    Authors: Sam Kovaka, Aleksey V. Zimin, Geo M. Pertea, Roham Razaghi, Steven L. Salzberg and Mihaela Pertea

    Citation: Genome Biology 2019 20:278

    Content type: Method

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  9. Genomic differences range from single nucleotide differences to complex structural variations. Current methods typically annotate sequence differences ranging from SNPs to large indels accurately but do not un...

    Authors: Manish Goel, Hequan Sun, Wen-Biao Jiao and Korbinian Schneeberger

    Citation: Genome Biology 2019 20:277

    Content type: Software

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  10. Hemophilia A, a bleeding disorder resulting from F8 mutations, can only be cured by gene therapy. A promising strategy is CRISPR-Cas9-mediated precise insertion of F8 in hepatocytes at highly expressed gene loci,...

    Authors: Jian-Ping Zhang, Xin-Xin Cheng, Mei Zhao, Guo-Hua Li, Jing Xu, Feng Zhang, Meng-Di Yin, Fei-Ying Meng, Xin-Yue Dai, Ya-Wen Fu, Zhi-Xue Yang, Cameron Arakaki, Ruijun Jeanna Su, Wei Wen, Wen-Tian Wang, Wanqiu Chen…

    Citation: Genome Biology 2019 20:276

    Content type: Research

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  11. Sequencing technology and assembly algorithms have matured to the point that high-quality de novo assembly is possible for large, repetitive genomes. Current assemblies traverse transposable elements (TEs) and...

    Authors: Shujun Ou, Weija Su, Yi Liao, Kapeel Chougule, Jireh R. A. Agda, Adam J. Hellinga, Carlos Santiago Blanco Lugo, Tyler A. Elliott, Doreen Ware, Thomas Peterson, Ning Jiang, Candice N. Hirsch and Matthew B. Hufford

    Citation: Genome Biology 2019 20:275

    Content type: Research

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  12. The alignment of long-read RNA sequencing reads is non-trivial due to high sequencing errors and complicated gene structures. We propose deSALT, a tailored two-pass alignment approach, which constructs graph-b...

    Authors: Bo Liu, Yadong Liu, Junyi Li, Hongzhe Guo, Tianyi Zang and Yadong Wang

    Citation: Genome Biology 2019 20:274

    Content type: Method

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  13. Genomic imprinting is essential for mammalian development and provides a unique paradigm to explore intra-cellular differences in chromatin configuration. So far, the detailed allele-specific chromatin organiz...

    Authors: David Llères, Benoît Moindrot, Rakesh Pathak, Vincent Piras, Mélody Matelot, Benoît Pignard, Alice Marchand, Mallory Poncelet, Aurélien Perrin, Virgile Tellier, Robert Feil and Daan Noordermeer

    Citation: Genome Biology 2019 20:272

    Content type: Research

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  14. Single-cell RNA sequencing has enabled the characterization of highly specific cell types in many tissues, as well as both primary and stem cell-derived cell lines. An important facet of these studies is the a...

    Authors: Jose Alquicira-Hernandez, Anuja Sathe, Hanlee P. Ji, Quan Nguyen and Joseph E. Powell

    Citation: Genome Biology 2019 20:264

    Content type: Method

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  15. Multicellular animals and bacteria frequently engage in predator-prey and host-pathogen interactions, such as the well-studied relationship between Pseudomonas aeruginosa and the nematode Caenorhabditis elegans. ...

    Authors: Alejandro Vasquez-Rifo, Isana Veksler-Lublinsky, Zhenyu Cheng, Frederick M. Ausubel and Victor Ambros

    Citation: Genome Biology 2019 20:270

    Content type: Research

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  16. Chromosome evolution is an important driver of speciation and species evolution. Previous studies have detected chromosome rearrangement events among different Carnivora species using chromosome painting strat...

    Authors: Huizhong Fan, Qi Wu, Fuwen Wei, Fengtang Yang, Bee Ling Ng and Yibo Hu

    Citation: Genome Biology 2019 20:267

    Content type: Research

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  17. CRISPR-Cas systems endow bacterial and archaeal species with adaptive immunity mechanisms to fend off invading phages and foreign genetic elements. CRISPR-Cas9 has been harnessed to confer virus interference a...

    Authors: Ahmed Mahas, Rashid Aman and Magdy Mahfouz

    Citation: Genome Biology 2019 20:263

    Content type: Research

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  18. Regulation of the mRNA life cycle is central to gene expression control and determination of cell fate. miRNAs represent a critical mRNA regulatory mechanism, but despite decades of research, their mode of act...

    Authors: Ania Wilczynska, Sarah L. Gillen, Tobias Schmidt, Hedda A. Meijer, Rebekah Jukes-Jones, Claudia Langlais, Kari Kopra, Wei-Ting Lu, Jack D. Godfrey, Benjamin R. Hawley, Kelly Hodge, Sara Zanivan, Kelvin Cain, John Le Quesne and Martin Bushell

    Citation: Genome Biology 2019 20:262

    Content type: Research

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  19. We describe ReorientExpress, a method to perform reference-free orientation of transcriptomic long sequencing reads. ReorientExpress uses deep learning to correctly predict the orientation of the majority of r...

    Authors: Angel Ruiz-Reche, Akanksha Srivastava, Joel A. Indi, Ivan de la Rubia and Eduardo Eyras

    Citation: Genome Biology 2019 20:260

    Content type: Method

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  20. Nucleotide composition bias plays an important role in the 1D and 3D organization of the human genome. Here, we investigate the potential interplay between nucleotide composition bias and the regulation of exo...

    Authors: Sébastien Lemaire, Nicolas Fontrodona, Fabien Aubé, Jean-Baptiste Claude, Hélène Polvèche, Laurent Modolo, Cyril F. Bourgeois, Franck Mortreux and Didier Auboeuf

    Citation: Genome Biology 2019 20:259

    Content type: Research

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  21. Brain aging is a complex process that depends on the precise regulation of multiple brain regions; however, the underlying molecular mechanisms behind this process remain to be clarified in non-human primates.

    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 2019 20:258

    Content type: Research

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    The Author Correction to this article has been published in Genome Biology 2020 21:46

  22. Although Kraken’s k-mer-based approach provides a fast taxonomic classification of metagenomic sequence data, its large memory requirements can be limiting for some applications. Kraken 2 improves upon Kraken 1 b...

    Authors: Derrick E. Wood, Jennifer Lu and Ben Langmead

    Citation: Genome Biology 2019 20:257

    Content type: Short Report

    Published on:

  23. The 3-dimensional (3D) conformation of chromatin inside the nucleus is integral to a variety of nuclear processes including transcriptional regulation, DNA replication, and DNA damage repair. Aberrations in 3D...

    Authors: David U. Gorkin, Yunjiang Qiu, Ming Hu, Kipper Fletez-Brant, Tristin Liu, Anthony D. Schmitt, Amina Noor, Joshua Chiou, Kyle J. Gaulton, Jonathan Sebat, Yun Li, Kasper D. Hansen and Bing Ren

    Citation: Genome Biology 2019 20:255

    Content type: Research

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  24. Single nucleotide variants (SNVs) in intronic regions have yet to be systematically investigated for their disease-causing potential. Using known pathogenic and neutral intronic SNVs (iSNVs) as training data, ...

    Authors: Hai Lin, Katherine A. Hargreaves, Rudong Li, Jill L. Reiter, Yue Wang, Matthew Mort, David N. Cooper, Yaoqi Zhou, Chi Zhang, Michael T. Eadon, M. Eileen Dolan, Joseph Ipe, Todd C. Skaar and Yunlong Liu

    Citation: Genome Biology 2019 20:254

    Content type: Method

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  25. Gynecologic malignancy is one of the leading causes of mortality in female adults worldwide. Comprehensive genomic analysis has revealed a list of molecular aberrations that are essential to tumorigenesis, pro...

    Authors: Jason K. Sa, Jae Ryoung Hwang, Young-Jae Cho, Ji-Yoon Ryu, Jung-Joo Choi, Soo Young Jeong, Jihye Kim, Myeong Seon Kim, E. Sun Paik, Yoo-Young Lee, Chel Hun Choi, Tae-Joong Kim, Byoung-Gie Kim, Duk-Soo Bae, Yeri Lee, Nam-Gu Her…

    Citation: Genome Biology 2019 20:253

    Content type: Research

    Published on:

  26. Recent metagenomic analyses have revealed dysbiosis of the gut microbiota of ulcerative colitis (UC) patients. However, the impacts of this dysbiosis are not fully understood, particularly at the strain level.

    Authors: Jun Seishima, Noriho Iida, Kazuya Kitamura, Masahiro Yutani, Ziyu Wang, Akihiro Seki, Taro Yamashita, Yoshio Sakai, Masao Honda, Tatsuya Yamashita, Takashi Kagaya, Yukihiro Shirota, Yukako Fujinaga, Eishiro Mizukoshi and Shuichi Kaneko

    Citation: Genome Biology 2019 20:252

    Content type: Research

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  27. The single-molecule multiplex chromatin interaction data are generated by emerging 3D genome mapping technologies such as GAM, SPRITE, and ChIA-Drop. These datasets provide insights into high-dimensional chrom...

    Authors: Minji Kim, Meizhen Zheng, Simon Zhongyuan Tian, Byoungkoo Lee, Jeffrey H. Chuang and Yijun Ruan

    Citation: Genome Biology 2019 20:251

    Content type: Method

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  28. Epigenetic clocks comprise a set of CpG sites whose DNA methylation levels measure subject age. These clocks are acknowledged as a highly accurate molecular correlate of chronological age in humans and other v...

    Authors: Christopher G. Bell, Robert Lowe, Peter D. Adams, Andrea A. Baccarelli, Stephan Beck, Jordana T. Bell, Brock C. Christensen, Vadim N. Gladyshev, Bastiaan T. Heijmans, Steve Horvath, Trey Ideker, Jean-Pierre J. Issa, Karl T. Kelsey, Riccardo E. Marioni, Wolf Reik, Caroline L. Relton…

    Citation: Genome Biology 2019 20:249

    Content type: Review

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  29. Activation of regulatory elements is thought to be inversely correlated with DNA methylation levels. However, it is difficult to determine whether DNA methylation is compatible with chromatin accessibility or ...

    Authors: Priscillia Lhoumaud, Gunjan Sethia, Franco Izzo, Theodore Sakellaropoulos, Valentina Snetkova, Simon Vidal, Sana Badri, Macintosh Cornwell, Dafne Campigli Di Giammartino, Kyu-Tae Kim, Effie Apostolou, Matthias Stadtfeld, Dan Avi Landau and Jane Skok

    Citation: Genome Biology 2019 20:248

    Content type: Method

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  30. Recent research into structural variants (SVs) has established their importance to medicine and molecular biology, elucidating their role in various diseases, regulation of gene expression, ethnic diversity, a...

    Authors: Medhat Mahmoud, Nastassia Gobet, Diana Ivette Cruz-Dávalos, Ninon Mounier, Christophe Dessimoz and Fritz J. Sedlazeck

    Citation: Genome Biology 2019 20:246

    Content type: Review

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  31. The epigenetic modifications of histones are versatile marks that are intimately connected to development and disease pathogenesis including human cancers. In this review, we will discuss the many different ty...

    Authors: Zibo Zhao and Ali Shilatifard

    Citation: Genome Biology 2019 20:245

    Content type: Review

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  32. The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function.

    Authors: Naihui Zhou, Yuxiang Jiang, Timothy R. Bergquist, Alexandra J. Lee, Balint Z. Kacsoh, Alex W. Crocker, Kimberley A. Lewis, George Georghiou, Huy N. Nguyen, Md Nafiz Hamid, Larry Davis, Tunca Dogan, Volkan Atalay, Ahmet S. Rifaioglu, Alperen Dalkıran, Rengul Cetin Atalay…

    Citation: Genome Biology 2019 20:244

    Content type: Research

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  33. DNA methylation can provide a source of heritable information that is sometimes entirely uncoupled from genetic variation. However, the extent of this uncoupling and the roles of DNA methylation in shaping div...

    Authors: Jing Xu, Guo Chen, Peter J. Hermanson, Qiang Xu, Changshuo Sun, Wenqing Chen, Qiuxin Kan, Minqi Li, Peter A. Crisp, Jianbing Yan, Lin Li, Nathan M. Springer and Qing Li

    Citation: Genome Biology 2019 20:243

    Content type: Research

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  34. Systematic interrogation of single-nucleotide variants (SNVs) is one of the most promising approaches to delineate the cellular heterogeneity and phylogenetic relationships at the single-cell level. While SNV ...

    Authors: Fenglin Liu, Yuanyuan Zhang, Lei Zhang, Ziyi Li, Qiao Fang, Ranran Gao and Zemin Zhang

    Citation: Genome Biology 2019 20:242

    Content type: Research

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  35. Recent innovations in single-cell Assay for Transposase Accessible Chromatin using sequencing (scATAC-seq) enable profiling of the epigenetic landscape of thousands of individual cells. scATAC-seq data analysi...

    Authors: Huidong Chen, Caleb Lareau, Tommaso Andreani, Michael E. Vinyard, Sara P. Garcia, Kendell Clement, Miguel A. Andrade-Navarro, Jason D. Buenrostro and Luca Pinello

    Citation: Genome Biology 2019 20:241

    Content type: Research

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  36. 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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  37. 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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  38. 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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