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  1. Content type: Method

    We developed a chemical cleavage method that releases single nucleosome dyad-containing fragments, allowing us to precisely map both single nucleosomes and linkers with high accuracy genome-wide in yeast. Our ...

    Authors: Răzvan V. Chereji, Srinivas Ramachandran, Terri D. Bryson and Steven Henikoff

    Citation: Genome Biology 2018 19:19

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  2. Content type: Research

    Previous studies showed that the majority of developmental genes are devoid of DNA methylation at promoters even when they are repressed. Such hypomethylated regions at developmental genes are unusually large ...

    Authors: Yuanyuan Li, Hui Zheng, Qiujun Wang, Chen Zhou, Lei Wei, Xuehui Liu, Wenhao Zhang, Yu Zhang, Zhenhai Du, Xiaowo Wang and Wei Xie

    Citation: Genome Biology 2018 19:18

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  3. Content type: Correction

    After publication of our article [1] it was brought to our attention that a line of code was missing from our program to combine the within-replicate variance and between-replicate variance. This led to an ove...

    Authors: Alan F. Rubin, Hannah Gelman, Nathan Lucas, Sandra M. Bajjalieh, Anthony T. Papenfuss, Terence P. Speed and Douglas M. Fowler

    Citation: Genome Biology 2018 19:17

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    The original article was published in Genome Biology 2017 18:150

  4. Content type: Software

    Scanpy is a scalable toolkit for analyzing single-cell gene expression data. It includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing,...

    Authors: F. Alexander Wolf, Philipp Angerer and Fabian J. Theis

    Citation: Genome Biology 2018 19:15

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  5. Content type: Open Letter

    On behalf of The Human Proteome Organization (HUPO) Proteomics Standards Initiative, we introduce here two novel standard data formats, proBAM and proBed, that have been developed to address the current challe...

    Authors: Gerben Menschaert, Xiaojing Wang, Andrew R. Jones, Fawaz Ghali, David Fenyö, Volodimir Olexiouk, Bing Zhang, Eric W. Deutsch, Tobias Ternent and Juan Antonio Vizcaíno

    Citation: Genome Biology 2018 19:12

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  6. Content type: Research

    Human immunity relies on the coordinated responses of many cellular subsets and functional states. Inter-individual variations in cellular composition and communication could thus potentially alter host protec...

    Authors: Enrique Martin-Gayo, Michael B. Cole, Kellie E. Kolb, Zhengyu Ouyang, Jacqueline Cronin, Samuel W. Kazer, Jose Ordovas-Montanes, Mathias Lichterfeld, Bruce D. Walker, Nir Yosef, Alex K. Shalek and Xu G. Yu

    Citation: Genome Biology 2018 19:10

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  7. Content type: Research

    In plants, the existence and possible role of epigenetic reprogramming has been questioned because of the occurrence of stably inherited epialleles. Evidence suggests that epigenetic reprogramming does occur d...

    Authors: Marc W. Schmid, Alejandro Giraldo-Fonseca, Moritz Rövekamp, Dmitry Smetanin, John L. Bowman and Ueli Grossniklaus

    Citation: Genome Biology 2018 19:9

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  8. Content type: Research

    The 3′ untranslated regions (UTRs) of mRNAs play a major role in post-transcriptional regulation of gene expression. Selection of transcript cleavage and polyadenylation sites is a dynamic process that produce...

    Authors: Sean M. West, Desirea Mecenas, Michelle Gutwein, David Aristizábal-Corrales, Fabio Piano and Kristin C. Gunsalus

    Citation: Genome Biology 2018 19:8

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  9. Content type: Research

    The gut microbiome, a key constituent of the colonic environment, has been implicated as an important modulator of human health. The eukaryotic epigenome is postulated to respond to environmental stimuli throu...

    Authors: Yufeng Qin, John D. Roberts, Sara A. Grimm, Fred B. Lih, Leesa J. Deterding, Ruifang Li, Kaliopi Chrysovergis and Paul A. Wade

    Citation: Genome Biology 2018 19:7

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  10. Content type: Research

    Endogenous retroviruses (ERVs), which are responsible for 10% of spontaneous mouse mutations, are kept under control via several epigenetic mechanisms. The H3K9 histone methyltransferase SETDB1 is essential fo...

    Authors: Özgen Deniz, Lorenzo de la Rica, Kevin C. L. Cheng, Dominik Spensberger and Miguel R. Branco

    Citation: Genome Biology 2018 19:6

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  11. Content type: Method

    We present a new method, Fine-Mapping of Adaptive Variation (FineMAV), which combines population differentiation, derived allele frequency, and molecular functionality to prioritize positively selected candidate ...

    Authors: Michał Szpak, Massimo Mezzavilla, Qasim Ayub, Yuan Chen, Yali Xue and Chris Tyler-Smith

    Citation: Genome Biology 2018 19:5

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  12. Content type: Research

    About 11% of all human genetic diseases are caused by nonsense mutations that generate premature translation termination codons (PTCs) in messenger RNAs (mRNA). PTCs not only lead to the production of truncate...

    Authors: Lulu Huang, Audrey Low, Sagar S. Damle, Melissa M. Keenan, Steven Kuntz, Susan F. Murray, Brett P. Monia and Shuling Guo

    Citation: Genome Biology 2018 19:4

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  13. Content type: Research

    Canonical Wnt/beta-catenin signalling regulates self-renewal and lineage selection within the mammalian epidermis. Although the transcriptional response of keratinocytes that receive a Wnt signal is well chara...

    Authors: Arsham Ghahramani, Giacomo Donati, Nicholas M. Luscombe and Fiona M. Watt

    Citation: Genome Biology 2018 19:3

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  14. Content type: Research

    Monozygotic twins have long been studied to estimate heritability and explore epigenetic influences on phenotypic variation. The phenotypic and epigenetic similarities of monozygotic twins have been assumed to...

    Authors: Timothy E. Van Baak, Cristian Coarfa, Pierre-Antoine Dugué, Giovanni Fiorito, Eleonora Laritsky, Maria S. Baker, Noah J. Kessler, Jianrong Dong, Jack D. Duryea, Matt J. Silver, Ayden Saffari, Andrew M. Prentice, Sophie E. Moore, Akram Ghantous, Michael N. Routledge, Yun Yun Gong…

    Citation: Genome Biology 2018 19:2

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  15. Content type: Research

    CRISPR/Cas systems confer immunity against invading nucleic acids and phages in bacteria and archaea. CRISPR/Cas13a (known previously as C2c2) is a class 2 type VI-A ribonuclease capable of targeting and cleav...

    Authors: Rashid Aman, Zahir Ali, Haroon Butt, Ahmed Mahas, Fatimah Aljedaani, Muhammad Zuhaib Khan, Shouwei Ding and Magdy Mahfouz

    Citation: Genome Biology 2018 19:1

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  16. Content type: Method

    The diversity of processed transcripts in eukaryotic genomes poses a challenge for the classification of their biological functions. Sparse sequence conservation in non-coding sequences and the unreliable natu...

    Authors: Martin A. Smith, Stefan E. Seemann, Xiu Cheng Quek and John S. Mattick

    Citation: Genome Biology 2017 18:244

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  17. Content type: Research

    Enhancers are modular regulatory elements that are central to the spatial and temporal regulation of gene expression. Bidirectional transcription initiating at enhancers has been proposed to mark active enhanc...

    Authors: Robert S. Young, Yatendra Kumar, Wendy A. Bickmore and Martin S. Taylor

    Citation: Genome Biology 2017 18:242

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  18. Content type: Research article

    Genotyping of large populations through genome-wide association studies (GWAS) has successfully identified many genomic variants associated with traits or disease risk. Unexpectedly, a large proportion of GWAS...

    Authors: N. Bartonicek, M. B. Clark, X. C. Quek, J. R. Torpy, A. L. Pritchard, J. L. V. Maag, B. S. Gloss, J. Crawford, R. J. Taft, N. K. Hayward, G. W. Montgomery, J. S. Mattick, T. R. Mercer and M. E. Dinger

    Citation: Genome Biology 2017 18:241

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  19. Content type: Research

    Organisms need to adapt to keep pace with a changing environment. Examining recent range expansion aids our understanding of how organisms evolve to overcome environmental constraints. However, how organisms a...

    Authors: Yu-Pan Zou, Xing-Hui Hou, Qiong Wu, Jia-Fu Chen, Zi-Wen Li, Ting-Shen Han, Xiao-Min Niu, Li Yang, Yong-Chao Xu, Jie Zhang, Fu-Min Zhang, Dunyan Tan, Zhixi Tian, Hongya Gu and Ya-Long Guo

    Citation: Genome Biology 2017 18:239

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  20. Content type: Method

    We introduce a k-mer-based computational protocol, DE-kupl, for capturing local RNA variation in a set of RNA-seq libraries, independently of a reference genome or transcriptome. DE-kupl extracts all k-mers with ...

    Authors: Jérôme Audoux, Nicolas Philippe, Rayan Chikhi, Mikaël Salson, Mélina Gallopin, Marc Gabriel, Jérémy Le Coz, Emilie Drouineau, Thérèse Commes and Daniel Gautheret

    Citation: Genome Biology 2017 18:243

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  21. Content type: Research

    Diverse molecular alterations associated with smoking in normal and precursor lung cancer cells have been reported, yet their role in lung cancer etiology remains unclear. A prominent example is hypomethylatio...

    Authors: Yuting Chen, Martin Widschwendter and Andrew E. Teschendorff

    Citation: Genome Biology 2017 18:236

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  22. Content type: Research

    Circular RNAs are a class of endogenous RNAs with various functions in eukaryotic cells. Worthy of note, circular RNAs play a critical role in cancer. Currently, nothing is known about their role in head and n...

    Authors: Lorena Verduci, Maria Ferraiuolo, Andrea Sacconi, Federica Ganci, Jlenia Vitale, Teresa Colombo, Paola Paci, Sabrina Strano, Giuseppe Macino, Nikolaus Rajewsky and Giovanni Blandino

    Citation: Genome Biology 2017 18:237

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  23. Content type: Research

    Tumor-associated macrophages (TAMs) are abundant in gliomas and immunosuppressive TAMs are a barrier to emerging immunotherapies. It is unknown to what extent macrophages derived from peripheral blood adopt th...

    Authors: Sören Müller, Gary Kohanbash, S. John Liu, Beatriz Alvarado, Diego Carrera, Aparna Bhaduri, Payal B. Watchmaker, Garima Yagnik, Elizabeth Di Lullo, Martina Malatesta, Nduka M. Amankulor, Arnold R. Kriegstein, Daniel A. Lim, Manish Aghi, Hideho Okada and Aaron Diaz

    Citation: Genome Biology 2017 18:234

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  24. Content type: Software

    The increase in available sequence data has advanced the field of microbiology; however, making sense of these data without bioinformatics skills is still problematic. We describe MICRA, an automatic pipeline,...

    Authors: Ségolène Caboche, Gaël Even, Alexandre Loywick, Christophe Audebert and David Hot

    Citation: Genome Biology 2017 18:233

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  25. Content type: Research Highlight

    Balancing selection maintains variation for evolution. A recent study investigated the extent of balancing selection in two Brassicaceae species and highlighted its importance for adaptation.

    Authors: Baosheng Wang and Thomas Mitchell-Olds

    Citation: Genome Biology 2017 18:231

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  26. Content type: Method

    We present a new method, OMSV, for accurately and comprehensively identifying structural variations (SVs) from optical maps. OMSV detects both homozygous and heterozygous SVs, SVs of various types and sizes, a...

    Authors: Le Li, Alden King-Yung Leung, Tsz-Piu Kwok, Yvonne Y. Y. Lai, Iris K. Pang, Grace Tin-Yun Chung, Angel C. Y. Mak, Annie Poon, Catherine Chu, Menglu Li, Jacob J. K. Wu, Ernest T. Lam, Han Cao, Chin Lin, Justin Sibert, Siu-Ming Yiu…

    Citation: Genome Biology 2017 18:230

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  27. Content type: Review

    Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for population-scale microbiome profiles. To link the res...

    Authors: Himel Mallick, Siyuan Ma, Eric A. Franzosa, Tommi Vatanen, Xochitl C. Morgan and Curtis Huttenhower

    Citation: Genome Biology 2017 18:228

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  28. Content type: Research

    The CRISPR/Cas9 system has become an efficient gene editing method for generating cells carrying precise gene mutations, including the rearrangement and deletion of chromosomal segments. However, whether an en...

    Authors: Erwei Zuo, Xiaona Huo, Xuan Yao, Xinde Hu, Yidi Sun, Jianhang Yin, Bingbing He, Xing Wang, Linyu Shi, Jie Ping, Yu Wei, Wenqin Ying, Wei Wei, Wenjia Liu, Cheng Tang, Yixue Li…

    Citation: Genome Biology 2017 18:224

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  29. Content type: Comment

    The recent shift of computational biologists from bioinformatics service providers to leaders of cutting-edge programs highlights the accompanying cultural and conceptual changes that should be implemented by ...

    Authors: Itai Yanai and Eva Chmielnicki

    Citation: Genome Biology 2017 18:223

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  30. Content type: Research

    Genome-wide quantification of enhancer activity in the human genome has proven to be a challenging problem. Recent efforts have led to the development of powerful tools for enhancer quantification. However, be...

    Authors: Yuwen Liu, Shan Yu, Vineet K. Dhiman, Tonya Brunetti, Heather Eckart and Kevin P. White

    Citation: Genome Biology 2017 18:219

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  31. Content type: Research

    Dendritic messenger RNA (mRNA) localization and subsequent local translation in dendrites critically contributes to synaptic plasticity and learning and memory. Little is known, however, about the contribution...

    Authors: Stefan M. Berger, Iván Fernández-Lamo, Kai Schönig, Sandra M. Fernández Moya, Janina Ehses, Rico Schieweck, Stefano Clementi, Thomas Enkel, Sascha Grothe, Oliver von Bohlen und Halbach, Inmaculada Segura, José María Delgado-García, Agnès Gruart, Michael A. Kiebler and Dusan Bartsch

    Citation: Genome Biology 2017 18:222

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  32. Content type: Research

    While intron retention (IR) is now widely accepted as an important mechanism of mammalian gene expression control, it remains the least studied form of alternative splicing. To delineate conserved features of ...

    Authors: Ulf Schmitz, Natalia Pinello, Fangzhi Jia, Sultan Alasmari, William Ritchie, Maria-Cristina Keightley, Shaniko Shini, Graham J. Lieschke, Justin J-L Wong and John E. J. Rasko

    Citation: Genome Biology 2017 18:216

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  33. Content type: Research

    In contrast to positive selection, which reduces genetic variation by fixing beneficial alleles, balancing selection maintains genetic variation within a population or species and plays crucial roles in adapta...

    Authors: Qiong Wu, Ting-Shen Han, Xi Chen, Jia-Fu Chen, Yu-Pan Zou, Zi-Wen Li, Yong-Chao Xu and Ya-Long Guo

    Citation: Genome Biology 2017 18:217

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  34. Content type: Comment

    Open Science is encouraged by the European Union and many other political and scientific institutions. However, scientific practice is proving slow to change. We propose, as early career researchers, that it i...

    Authors: Andrea Farnham, Christoph Kurz, Mehmet Ali Öztürk, Monica Solbiati, Oona Myllyntaus, Jordy Meekes, Tra My Pham, Clara Paz, Magda Langiewicz, Sophie Andrews, Liisa Kanninen, Chantal Agbemabiese, Arzu Tugce Guler, Jeffrey Durieux, Sarah Jasim, Olivia Viessmann…

    Citation: Genome Biology 2017 18:221

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  35. Content type: Research

    The history of maize has been characterized by major demographic events, including population size changes associated with domestication and range expansion, and gene flow with wild relatives. The interplay be...

    Authors: Li Wang, Timothy M. Beissinger, Anne Lorant, Claudia Ross-Ibarra, Jeffrey Ross-Ibarra and Matthew B. Hufford

    Citation: Genome Biology 2017 18:215

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  36. Content type: Correction

    Upon publication of the original article [1], it was noted that references 11 and 22 were miscited in the reference list.

    Authors: Chengping Wen, Zhijun Zheng, Tiejuan Shao, Lin Liu, Zhijun Xie, Emmanuelle Le Chatelier, Zhixing He, Wendi Zhong, Yongsheng Fan, Linshuang Zhang, Haichang Li, Chunyan Wu, Changfeng Hu, Qian Xu, Jia Zhou, Shunfeng Cai…

    Citation: Genome Biology 2017 18:214

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    The original article was published in Genome Biology 2017 18:142