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  1. Content type: Method

    Some exciting biological questions require quantifying thousands of proteins in single cells. To achieve this goal, we develop Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS) and validate its ability to...

    Authors: Bogdan Budnik, Ezra Levy, Guillaume Harmange and Nikolai Slavov

    Citation: Genome Biology 2018 19:161

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  2. Content type: Research

    Many applications of CRISPR/Cas9-mediated genome editing require Cas9-induced non-homologous end joining (NHEJ), which was thought to be error prone. However, with directly ligatable ends, Cas9-induced DNA dou...

    Authors: Tao Guo, Yi-Li Feng, Jing-Jing Xiao, Qian Liu, Xiu-Na Sun, Ji-Feng Xiang, Na Kong, Si-Cheng Liu, Guo-Qiao Chen, Yue Wang, Meng-Meng Dong, Zhen Cai, Hui Lin, Xiu-Jun Cai and An-Yong Xie

    Citation: Genome Biology 2018 19:170

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  3. Content type: Method

    We present SeqOthello, an ultra-fast and memory-efficient indexing structure to support arbitrary sequence query against large collections of RNA-seq experiments. It takes SeqOthello only 5 min and 19.1 GB mem...

    Authors: Ye Yu, Jinpeng Liu, Xinan Liu, Yi Zhang, Eamonn Magner, Erik Lehnert, Chen Qian and Jinze Liu

    Citation: Genome Biology 2018 19:167

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  4. Content type: Method

    CRISPR/Cas9 pooled screening permits parallel evaluation of comprehensive guide RNA libraries to systematically perturb protein coding sequences in situ and correlate with functional readouts. For the analysis...

    Authors: Vivien A. C. Schoonenberg, Mitchel A. Cole, Qiuming Yao, Claudio Macias-Treviño, Falak Sher, Patrick G. Schupp, Matthew C. Canver, Takahiro Maeda, Luca Pinello and Daniel E. Bauer

    Citation: Genome Biology 2018 19:169

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  5. Content type: Research

    Cytokines are critical to human disease and are attractive therapeutic targets given their widespread influence on gene regulation and transcription. Defining the downstream regulatory mechanisms influenced by...

    Authors: Emma E. Davenport, Tiffany Amariuta, Maria Gutierrez-Arcelus, Kamil Slowikowski, Harm-Jan Westra, Yang Luo, Ciyue Shen, Deepak A. Rao, Ying Zhang, Stephen Pearson, David von Schack, Jean S. Beebe, Nan Bing, Sally John, Michael S. Vincent, Baohong Zhang…

    Citation: Genome Biology 2018 19:168

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  6. Content type: Research

    It has been proposed that more than 450 million years ago, two successive whole genome duplications took place in a marine chordate lineage before leading to the common ancestor of vertebrates. A precise recon...

    Authors: Christine Sacerdot, Alexandra Louis, Céline Bon, Camille Berthelot and Hugues Roest Crollius

    Citation: Genome Biology 2018 19:166

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  7. Content type: Method

    Current single-cell RNA-seq approaches are hindered by preamplification bias, loss of strand of origin information, and the inability to observe small-RNA and mRNA dual transcriptomes. Here, we introduce a sin...

    Authors: Zhengyun Xiao, Guo Cheng, Yang Jiao, Chen Pan, Ran Li, Danmei Jia, Jing Zhu, Chao Wu, Min Zheng and Junling Jia

    Citation: Genome Biology 2018 19:163

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  8. Content type: Short report

    In previous studies, CRISPR/Cas9 was shown to induce unexpected exon skipping; however, the mechanism by which this phenomenon is triggered is controversial. By analyzing 22 gene-edited rabbit lines generated ...

    Authors: Tingting Sui, Yuning Song, Zhiquan Liu, Mao Chen, Jichao Deng, Yuanyuan Xu, Liangxue Lai and Zhanjun Li

    Citation: Genome Biology 2018 19:164

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  9. Content type: Research

    There is substantial interest in the evolutionary forces that shaped the regulatory framework in early human development. Progress in this area has been slow because it is difficult to obtain relevant biologic...

    Authors: Lauren E. Blake, Samantha M. Thomas, John D. Blischak, Chiaowen Joyce Hsiao, Claudia Chavarria, Marsha Myrthil, Yoav Gilad and Bryan J. Pavlovic

    Citation: Genome Biology 2018 19:162

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  10. Content type: Method

    Pooled CRISPR screens allow researchers to interrogate genetic causes of complex phenotypes at the genome-wide scale and promise higher specificity and sensitivity compared to competing technologies. Unfortuna...

    Authors: Timothy P. Daley, Zhixiang Lin, Xueqiu Lin, Yanxia Liu, Wing Hung Wong and Lei S. Qi

    Citation: Genome Biology 2018 19:159

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  11. Content type: Research

    Recent genome-wide association studies (GWAS) have identified more than 100 loci associated with increased risk of prostate cancer, most of which are in non-coding regions of the genome. Understanding the func...

    Authors: Yu Guo, Andrew A. Perez, Dennis J. Hazelett, Gerhard A. Coetzee, Suhn Kyong Rhie and Peggy J. Farnham

    Citation: Genome Biology 2018 19:160

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  12. Content type: Method

    Spatial mapping of genomic data to tissue context in a high-throughput and high-resolution manner has been challenging due to technical limitations. Here, we describe PHLI-seq, a novel approach that enables hi...

    Authors: Sungsik Kim, Amos Chungwon Lee, Han-Byoel Lee, Jinhyun Kim, Yushin Jung, Han Suk Ryu, Yongju Lee, Sangwook Bae, Minju Lee, Kyungmin Lee, Ryong Nam Kim, Woong-Yang Park, Wonshik Han and Sunghoon Kwon

    Citation: Genome Biology 2018 19:158

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  14. Content type: Research

    Reconstruction of ancestral karyotypes is critical for our understanding of genome evolution, allowing for the identification of the gross changes that shaped extant genomes. The identification of such changes...

    Authors: Joana Damas, Jaebum Kim, Marta Farré, Darren K Griffin and Denis M Larkin

    Citation: Genome Biology 2018 19:155

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  15. Content type: Research

    The patterns of gene expression on highly differentiated sex chromosomes differ drastically from those on autosomes, due to sex-specific patterns of selection and inheritance. As a result, X chromosomes are of...

    Authors: Wen-Juan Ma, Paris Veltsos, Roberto Sermier, Darren J Parker and Nicolas Perrin

    Citation: Genome Biology 2018 19:156

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  16. Content type: Method

    Here, we introduce the 3D Genome Browser, http://​3dgenome.​org, which allows users to conveniently explore both their own and over 300 publicly available chro...

    Authors: Yanli Wang, Fan Song, Bo Zhang, Lijun Zhang, Jie Xu, Da Kuang, Daofeng Li, Mayank N. K. Choudhary, Yun Li, Ming Hu, Ross Hardison, Ting Wang and Feng Yue

    Citation: Genome Biology 2018 19:151

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  17. Content type: Software

    SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit shows that SKESA produces assemblies that have ...

    Authors: Alexandre Souvorov, Richa Agarwala and David J. Lipman

    Citation: Genome Biology 2018 19:153

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  18. Content type: Research

    Recently, increasing evidence shows that long noncoding RNAs (lncRNAs) play a significant role in human tumorigenesis. However, the function of lncRNAs in human gastric cancer remains largely unknown.

    Authors: Erbao Zhang, Xuezhi He, Chongguo Zhang, Jun Su, Xiyi Lu, Xinxin Si, Jinfei Chen, Dandan Yin, Liang Han and Wei De

    Citation: Genome Biology 2018 19:154

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  19. Content type: Research

    MicroRNAs (miRNAs) are short regulatory RNAs that derive from hairpin precursors. Important for understanding the functional roles of miRNAs is the ability to predict the messenger RNA (mRNA) targets most resp...

    Authors: Vikram Agarwal, Alexander O. Subtelny, Prathapan Thiru, Igor Ulitsky and David P. Bartel

    Citation: Genome Biology 2018 19:152

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  20. Content type: Research

    Partially methylated domains are extended regions in the genome exhibiting a reduced average DNA methylation level. They cover gene-poor and transcriptionally inactive regions and tend to be heterochromatic. W...

    Authors: Abdulrahman Salhab, Karl Nordström, Gilles Gasparoni, Kathrin Kattler, Peter Ebert, Fidel Ramirez, Laura Arrigoni, Fabian Müller, Julia K. Polansky, Cristina Cadenas, Jan G.Hengstler, Thomas Lengauer, Thomas Manke and Jörn Walter

    Citation: Genome Biology 2018 19:150

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  21. Content type: Research

    How regulatory networks incorporate additional components and how novel genes are functionally integrated into well-established developmental processes are two important and intertwined questions whose answers...

    Authors: Daniel Pers and Jeremy A. Lynch

    Citation: Genome Biology 2018 19:148

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  22. Content type: Research

    The CRISPR/Cas9 system, composed of a single-guide RNA for target recognition and a Cas9 protein for DNA cleavage, has the potential to revolutionize agriculture as well as medicine. Even though extensive work...

    Authors: Yanfei Mao, Xiaoxuan Yang, Yiting Zhou, Zhengjing Zhang, Jose Ramon Botella and Jian-Kang Zhu

    Citation: Genome Biology 2018 19:149

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  25. Content type: Research

    Genome-wide DNA methylation (DNAm) profiling has allowed for the development of molecular predictors for a multitude of traits and diseases. Such predictors may be more accurate than the self-reported phenotyp...

    Authors: Daniel L. McCartney, Robert F. Hillary, Anna J. Stevenson, Stuart J. Ritchie, Rosie M. Walker, Qian Zhang, Stewart W. Morris, Mairead L. Bermingham, Archie Campbell, Alison D. Murray, Heather C. Whalley, Catharine R. Gale, David J. Porteous, Chris S. Haley, Allan F. McRae, Naomi R. Wray…

    Citation: Genome Biology 2018 19:136

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  26. Content type: Method

    We introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel simulation-based composite likelihood method that uses the blockwise site frequency spectrum to jointly infer past demography and recomb...

    Authors: Champak R. Beeravolu, Michael J. Hickerson, Laurent A. F. Frantz and Konrad Lohse

    Citation: Genome Biology 2018 19:145

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  27. Content type: Research

    Histone lysine acylations by short-chain fatty acids are distinct from the widely studied histone lysine acetylation in chromatin, although both modifications are regulated by primary metabolism in mammalian c...

    Authors: Yue Lu, Qiutao Xu, Yuan Liu, Yue Yu, Zhong-Yi Cheng, Yu Zhao and Dao-Xiu Zhou

    Citation: Genome Biology 2018 19:144

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  28. Content type: Research

    Previous approaches to defining subtypes of colorectal carcinoma (CRC) and other cancers based on transcriptomes have assumed the existence of discrete subtypes. We analyze gene expression patterns of colorect...

    Authors: Siyuan Ma, Shuji Ogino, Princy Parsana, Reiko Nishihara, Zhirong Qian, Jeanne Shen, Kosuke Mima, Yohei Masugi, Yin Cao, Jonathan A. Nowak, Kaori Shima, Yujin Hoshida, Edward L. Giovannucci, Manish K. Gala, Andrew T. Chan, Charles S. Fuchs…

    Citation: Genome Biology 2018 19:142

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  29. Content type: Research Highlight

    Two articles recently described the development of CRISPR technologies that have the potential to fundamentally transform the barcoding and tracing of mammalian cells.

    Authors: Thomas Gaj and Pablo Perez-Pinera

    Citation: Genome Biology 2018 19:143

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  30. Content type: Method

    We introduce a Bayesian semi-supervised method for estimating cell counts from DNA methylation by leveraging an easily obtainable prior knowledge on the cell-type composition distribution of the studied tissue...

    Authors: Elior Rahmani, Regev Schweiger, Liat Shenhav, Theodora Wingert, Ira Hofer, Eilon Gabel, Eleazar Eskin and Eran Halperin

    Citation: Genome Biology 2018 19:141

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  31. Content type: Review

    Understanding how crop plants evolved from their wild relatives and spread around the world can inform about the origins of agriculture. Here, we review how the rapid development of genomic resources and tools...

    Authors: Mona Schreiber, Nils Stein and Martin Mascher

    Citation: Genome Biology 2018 19:140

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  32. Content type: Research

    The genetic origins of Uralic speakers from across a vast territory in the temperate zone of North Eurasia have remained elusive. Previous studies have shown contrasting proportions of Eastern and Western Eura...

    Authors: Kristiina Tambets, Bayazit Yunusbayev, Georgi Hudjashov, Anne-Mai Ilumäe, Siiri Rootsi, Terhi Honkola, Outi Vesakoski, Quentin Atkinson, Pontus Skoglund, Alena Kushniarevich, Sergey Litvinov, Maere Reidla, Ene Metspalu, Lehti Saag, Timo Rantanen, Monika Karmin…

    Citation: Genome Biology 2018 19:139

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  33. Content type: Research

    Clustered, regularly interspaced, short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) have recently opened a new avenue for gene therapy. Cas9 nuclease guided by a single-guide RNA (sgRNA) ...

    Authors: Raed Ibraheim, Chun-Qing Song, Aamir Mir, Nadia Amrani, Wen Xue and Erik J. Sontheimer

    Citation: Genome Biology 2018 19:137

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  34. Content type: Research

    The importance of transcription factors (TFs) and epigenetic modifications in the control of gene expression is widely accepted. However, causal relationships between changes in TF binding, histone modificatio...

    Authors: Alexis Vandenbon, Yutaro Kumagai, Mengjie Lin, Yutaka Suzuki and Kenta Nakai

    Citation: Genome Biology 2018 19:138

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  36. Content type: Research

    Mutation rates vary across the genome. Many trans factors that influence mutation rates have been identified, as have specific sequence motifs at the 1–7-bp scale, but cis elements remain poorly characterized. Th...

    Authors: Chaorui Duan, Qing Huan, Xiaoshu Chen, Shaohuan Wu, Lucas B. Carey, Xionglei He and Wenfeng Qian

    Citation: Genome Biology 2018 19:132

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  38. Content type: Meeting report

    A meeting report on the 14th Gordon Research Conference on Meiosis, held at Colby Sawyer College, New London, NH, USA, 9–15 June 2018, chaired by Monica Colaiacovo, Harvard Medical School.

    Authors: Weronika E. Borek and Adele L. Marston

    Citation: Genome Biology 2018 19:134

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  39. Content type: Review

    “Conservation genomics” encompasses the idea that genome-scale data will improve the capacity of resource managers to protect species. Although genetic approaches have long been used in conservation research, ...

    Authors: Megan A. Supple and Beth Shapiro

    Citation: Genome Biology 2018 19:131

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  40. Content type: Method

    Expression quantitative trait loci (eQTLs) identified using tumor gene expression data could affect gene expression in cancer cells, tumor-associated normal cells, or both. Here, we have demonstrated a method ...

    Authors: Paul Geeleher, Aritro Nath, Fan Wang, Zhenyu Zhang, Alvaro N. Barbeira, Jessica Fessler, Robert L. Grossman, Cathal Seoighe and R. Stephanie Huang

    Citation: Genome Biology 2018 19:130

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  41. Content type: Research

    In addition to genetic variation, epigenetic variation plays an important role in determining various biological processes. The importance of natural genetic variation to crop domestication and improvement has...

    Authors: Yanting Shen, Jixiang Zhang, Yucheng Liu, Shulin Liu, Zhi Liu, Zongbiao Duan, Zheng Wang, Baoge Zhu, Ya-Long Guo and Zhixi Tian

    Citation: Genome Biology 2018 19:128

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  42. Content type: Research

    DNA replication plays an important role in mutagenesis, yet little is known about how it interacts with other mutagenic processes. Here, we use somatic mutation signatures—each representing a mutagenic process...

    Authors: Marketa Tomkova, Jakub Tomek, Skirmantas Kriaucionis and Benjamin Schuster-Böckler

    Citation: Genome Biology 2018 19:129

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  43. Content type: Research

    Aging is characterized by loss of function of the adaptive immune system, but the underlying causes are poorly understood. To assess the molecular effects of aging on B cell development, we profiled gene expre...

    Authors: Hashem Koohy, Daniel J. Bolland, Louise S. Matheson, Stefan Schoenfelder, Claudia Stellato, Andrew Dimond, Csilla Várnai, Peter Chovanec, Tamara Chessa, Jeremy Denizot, Raquel Manzano Garcia, Steven W. Wingett, Paula Freire-Pritchett, Takashi Nagano, Phillip Hawkins, Len Stephens…

    Citation: Genome Biology 2018 19:126

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  44. Content type: Research

    Hybridization is an important evolutionary process that results in increased plant diversity. Flowering Prunus includes popular cherry species that are appreciated worldwide for their flowers. The ornamental char...

    Authors: Seunghoon Baek, Kyung Choi, Goon-Bo Kim, Hee-Ju Yu, Ara Cho, Hoyeol Jang, Changkyun Kim, Hyuk-Jin Kim, Kae Sun Chang, Joo-Hwan Kim and Jeong-Hwan Mun

    Citation: Genome Biology 2018 19:127

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  45. Content type: Method

    The ability to accurately quantify all the microRNAs (miRNAs) in a sample is important for understanding miRNA biology and for development of new biomarkers and therapeutic targets. We develop a new method for...

    Authors: Sergio Barberán-Soler, Jenny M. Vo, Ryan E. Hogans, Anne Dallas, Brian H. Johnston and Sergei A. Kazakov

    Citation: Genome Biology 2018 19:105

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  46. Content type: Research

    Lung cancer is the leading cancer diagnosis worldwide and the number one cause of cancer deaths. Exposure to cigarette smoke, the primary risk factor in lung cancer, reduces epithelial barrier integrity and in...

    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 2018 19:123

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  47. Content type: Research

    In the Lophotrochozoa/Spiralia superphylum, few organisms have as high a capacity for rapid testing of gene function and single-cell transcriptomics as the freshwater planaria. The species Schmidtea mediterranea ...

    Authors: Lakshmipuram Seshadri Swapna, Alyssa M. Molinaro, Nicole Lindsay-Mosher, Bret J. Pearson and John Parkinson

    Citation: Genome Biology 2018 19:124

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  48. Content type: Software

    We present HiGlass, an open source visualization tool built on web technologies that provides a rich interface for rapid, multiplex, and multiscale navigation of 2D genomic maps alongside 1D genomic tracks, al...

    Authors: Peter Kerpedjiev, Nezar Abdennur, Fritz Lekschas, Chuck McCallum, Kasper Dinkla, Hendrik Strobelt, Jacob M. Luber, Scott B. Ouellette, Alaleh Azhir, Nikhil Kumar, Jeewon Hwang, Soohyun Lee, Burak H. Alver, Hanspeter Pfister, Leonid A. Mirny, Peter J. Park…

    Citation: Genome Biology 2018 19:125

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  49. Content type: Correction

    The original version [1] of this article unfortunately contained a mistake. The additive effects of the eQTLs of lncRNAs were flipped, meaning that the base allele in the contrast to derive the additive effect...

    Authors: Lin Li, Steven R. Eichten, Rena Shimizu, Katherine Petsch, Cheng-Ting Yeh, Wei Wu, Antony M. Chettoor, Scott A. Givan, Rex A. Cole, John E. Fowler, Matthew M. S. Evans, Michael J. Scanlon, Jianming Yu, Patrick S. Schnable, Marja C. P. Timmermans, Nathan M. Springer…

    Citation: Genome Biology 2018 19:122

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    The original article was published in Genome Biology 2014 15:R40

  50. Content type: Method

    Short tandem repeat (STR) expansions have been identified as the causal DNA mutation in dozens of Mendelian diseases. Most existing tools for detecting STR variation with short reads do so within the read leng...

    Authors: Harriet Dashnow, Monkol Lek, Belinda Phipson, Andreas Halman, Simon Sadedin, Andrew Lonsdale, Mark Davis, Phillipa Lamont, Joshua S. Clayton, Nigel G. Laing, Daniel G. MacArthur and Alicia Oshlack

    Citation: Genome Biology 2018 19:121

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