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  2. Content type: Research

    Glioma stem cells (GSCs) are a subpopulation of stem-like cells that contribute to glioblastoma (GBM) aggressiveness, recurrence, and resistance to radiation and chemotherapy. Therapeutically targeting the GSC...

    Authors: Dan Zhou, Bonnie M. Alver, Shuang Li, Ryan A. Hlady, Joyce J. Thompson, Mark A. Schroeder, Jeong-Heon Lee, Jingxin Qiu, Philip H. Schwartz, Jann N. Sarkaria and Keith D. Robertson

    Citation: Genome Biology 2018 19:43

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  4. Content type: Correction

    In the recent Research Highlight [1], it has been highlighted that part b of Fig. 1 was incorrectly labelled as “sgRNA + tracrRNA” instead of “sgRNA (crRNA + tracrRNA)”. An updated Figure 1, including also the...

    Authors: Gaetan Burgio

    Citation: Genome Biology 2018 19:41

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    The original article was published in Genome Biology 2018 19:27

  5. Content type: Method

    Despite the many approaches to study differential splicing from RNA-seq, many challenges remain unsolved, including computing capacity and sequencing depth requirements. Here we present SUPPA2, a new method th...

    Authors: Juan L. Trincado, Juan C. Entizne, Gerald Hysenaj, Babita Singh, Miha Skalic, David J. Elliott and Eduardo Eyras

    Citation: Genome Biology 2018 19:40

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  7. Content type: Method

    Comprehensive and accurate identification of structural variations (SVs) from next generation sequencing data remains a major challenge. We develop FusorSV, which uses a data mining approach to assess performance...

    Authors: Timothy Becker, Wan-Ping Lee, Joseph Leone, Qihui Zhu, Chengsheng Zhang, Silvia Liu, Jack Sargent, Kritika Shanker, Adam Mil-homens, Eliza Cerveira, Mallory Ryan, Jane Cha, Fabio C. P. Navarro, Timur Galeev, Mark Gerstein, Ryan E. Mills…

    Citation: Genome Biology 2018 19:38

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  8. Content type: Research

    Genomic instability promotes evolution and heterogeneity of tumors. Unraveling its mechanistic basis is essential for the design of appropriate therapeutic strategies. In a previous study, we reported an unexp...

    Authors: Panagiotis Galanos, George Pappas, Alexander Polyzos, Athanassios Kotsinas, Ioanna Svolaki, Nickolaos N. Giakoumakis, Christina Glytsou, Ioannis S. Pateras, Umakanta Swain, Vassilis L. Souliotis, Alexandros G. Georgakilas, Nicholas Geacintov, Luca Scorrano, Claudia Lukas, Jiri Lukas, Zvi Livneh…

    Citation: Genome Biology 2018 19:37

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  9. Content type: Research

    Ovarian cancer constitutes one of the most lethal gynecologic malignancies for females. Currently, early detection strategies and therapeutic options for ovarian cancer are far from satisfactory, leading to hi...

    Authors: Linjie Zhao, Wei Wang, Shuang Huang, Zhengnan Yang, Lian Xu, Qilian Yang, Xiu Zhou, Jinjin Wang, Qiuhong Shen, Chenlu Wang, Xiaobing Le, Min Feng, Nianxin Zhou, Wayne Bond Lau, Bonnie Lau, Shaohua Yao…

    Citation: Genome Biology 2018 19:35

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  11. Content type: Research

    Whole-genome bisulfite sequencing (WGBS) is becoming an increasingly accessible technique, used widely for both fundamental and disease-oriented research. Library preparation methods benefit from a variety of ...

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

    Citation: Genome Biology 2018 19:33

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  12. Content type: Research

    The mammalian genome is transcribed into large numbers of long noncoding RNAs (lncRNAs), but the definition of functional lncRNA groups has proven difficult, partly due to their low sequence conservation and l...

    Authors: Paulo P. Amaral, Tommaso Leonardi, Namshik Han, Emmanuelle Viré, Dennis K. Gascoigne, Raúl Arias-Carrasco, Magdalena Büscher, Luca Pandolfini, Anda Zhang, Stefano Pluchino, Vinicius Maracaja-Coutinho, Helder I. Nakaya, Martin Hemberg, Ramin Shiekhattar, Anton J. Enright and Tony Kouzarides

    Citation: Genome Biology 2018 19:32

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  13. Content type: Research article

    Organogenesis is crucial for proper organ formation during mammalian embryonic development. However, the similarities and shared features between different organs and the cellular heterogeneity during this pro...

    Authors: Ji Dong, Yuqiong Hu, Xiaoying Fan, Xinglong Wu, Yunuo Mao, Boqiang Hu, Hongshan Guo, Lu Wen and Fuchou Tang

    Citation: Genome Biology 2018 19:31

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  15. Content type: Method

    High-throughput single-cell RNA-seq methods assign limited unique molecular identifier (UMI) counts as gene expression values to single cells from shallow sequence reads and detect limited gene counts. We thus...

    Authors: Yohei Sasagawa, Hiroki Danno, Hitomi Takada, Masashi Ebisawa, Kaori Tanaka, Tetsutaro Hayashi, Akira Kurisaki and Itoshi Nikaido

    Citation: Genome Biology 2018 19:29

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  17. Content type: Research

    Amongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance and developmental and regenerative biology. However, compared to other echinoderms, ...

    Authors: David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R. Elphick and Paola Oliveri

    Citation: Genome Biology 2018 19:26

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  18. Content type: Research Highlight

    The generation of genetically modified alleles in mice using conventional transgenesis technologies is a long and inefficient process. A new study shows that the in situ delivery of CRISPR/Cas9 reagents into p...

    Authors: Gaetan Burgio

    Citation: Genome Biology 2018 19:27

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    The Correction to this article has been published in Genome Biology 2018 19:41

  19. Content type: Method

    We present a robust method called improved-Genome editing via Oviductal Nucleic Acids Delivery (i-GONAD) that delivers CRISPR ribonucleoproteins to E0.7 embryos via in situ electroporation. The method generates m...

    Authors: Masato Ohtsuka, Masahiro Sato, Hiromi Miura, Shuji Takabayashi, Makoto Matsuyama, Takayuki Koyano, Naomi Arifin, Shingo Nakamura, Kenta Wada and Channabasavaiah B. Gurumurthy

    Citation: Genome Biology 2018 19:25

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  20. Content type: Method

    Dropout events in single-cell RNA sequencing (scRNA-seq) cause many transcripts to go undetected and induce an excess of zero read counts, leading to power issues in differential expression (DE) analysis. This...

    Authors: Koen Van den Berge, Fanny Perraudeau, Charlotte Soneson, Michael I. Love, Davide Risso, Jean-Philippe Vert, Mark D. Robinson, Sandrine Dudoit and Lieven Clement

    Citation: Genome Biology 2018 19:24

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  21. Content type: Research

    The plant immune system is innate and encoded in the germline. Using it efficiently, plants are capable of recognizing a diverse range of rapidly evolving pathogens. A recently described phenomenon shows that ...

    Authors: Paul C. Bailey, Christian Schudoma, William Jackson, Erin Baggs, Gulay Dagdas, Wilfried Haerty, Matthew Moscou and Ksenia V. Krasileva

    Citation: Genome Biology 2018 19:23

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  22. Content type: Research

    Mammalian species exhibit a wide range of lifespans. To date, a robust and dynamic molecular readout of these lifespan differences has not yet been identified. Recent studies have established the existence of ...

    Authors: Robert Lowe, Carl Barton, Christopher A. Jenkins, Christina Ernst, Oliver Forman, Denise S. Fernandez-Twinn, Christoph Bock, Stephen J. Rossiter, Chris G. Faulkes, Susan E. Ozanne, Lutz Walter, Duncan T. Odom, Cathryn Mellersh and Vardhman K. Rakyan

    Citation: Genome Biology 2018 19:22

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  23. Content type: Open Letter

    The accurate description of ancestry is essential to interpret, access, and integrate human genomics data, and to ensure that these benefit individuals from all ancestral backgrounds. However, there are no est...

    Authors: Joannella Morales, Danielle Welter, Emily H. Bowler, Maria Cerezo, Laura W. Harris, Aoife C. McMahon, Peggy Hall, Heather A. Junkins, Annalisa Milano, Emma Hastings, Cinzia Malangone, Annalisa Buniello, Tony Burdett, Paul Flicek, Helen Parkinson, Fiona Cunningham…

    Citation: Genome Biology 2018 19:21

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  24. Content type: Method

    High-throughput RNA-sequencing (RNA-seq) technologies provide an unprecedented opportunity to explore the individual transcriptome. Unmapped reads are a large and often overlooked output of standard RNA-seq an...

    Authors: Serghei Mangul, Harry Taegyun Yang, Nicolas Strauli, Franziska Gruhl, Hagit T. Porath, Kevin Hsieh, Linus Chen, Timothy Daley, Stephanie Christenson, Agata Wesolowska-Andersen, Roberto Spreafico, Cydney Rios, Celeste Eng, Andrew D. Smith, Ryan D. Hernandez, Roel A. Ophoff…

    Citation: Genome Biology 2018 19:36

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  25. Content type: Research

    Little is known about the peopling of the Sahara during the Holocene climatic optimum, when the desert was replaced by a fertile environment.

    Authors: Eugenia D’Atanasio, Beniamino Trombetta, Maria Bonito, Andrea Finocchio, Genny Di Vito, Mara Seghizzi, Rita Romano, Gianluca Russo, Giacomo Maria Paganotti, Elizabeth Watson, Alfredo Coppa, Paolo Anagnostou, Jean-Michel Dugoujon, Pedro Moral, Daniele Sellitto, Andrea Novelletto…

    Citation: Genome Biology 2018 19:20

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  26. 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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  27. 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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  29. 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

  31. 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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  32. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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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  47. 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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  48. 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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  49. 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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  50. 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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