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  1. Content type: METHOD

    Allele-specific measurements of transcription factor binding from ChIP-seq data are key to dissecting the allelic effects of non-coding variants and their contribution to phenotypic diversity. However, most me...

    Authors: Ines de Santiago, Wei Liu, Ke Yuan, Martin O’Reilly, Chandra Sekhar Reddy Chilamakuri, Bruce A. J. Ponder, Kerstin B. Meyer and Florian Markowetz

    Citation: Genome Biology 2017 18:39

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  2. Content type: METHOD

    The study of epigenetic heterogeneity at the level of individual cells and in whole populations is the key to understanding cellular differentiation, organismal development, and the evolution of cancer. We dev...

    Authors: Martin Vincent, Kamilla Mundbjerg, Jakob Skou Pedersen, Gangning Liang, Peter A. Jones, Torben Falck Ørntoft, Karina Dalsgaard Sørensen and Carsten Wiuf

    Citation: Genome Biology 2017 18:38

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  3. Content type: Research

    The history of African indigenous cattle and their adaptation to environmental and human selection pressure is at the root of their remarkable diversity. Characterization of this diversity is an essential step...

    Authors: Jaemin Kim, Olivier Hanotte, Okeyo Ally Mwai, Tadelle Dessie, Salim Bashir, Boubacar Diallo, Morris Agaba, Kwondo Kim, Woori Kwak, Samsun Sung, Minseok Seo, Hyeonsoo Jeong, Taehyung Kwon, Mengistie Taye, Ki-Duk Song, Dajeong Lim…

    Citation: Genome Biology 2017 18:34

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  4. Content type: Research

    Distinct RNA species may compete for binding to microRNAs (miRNAs). This competition creates an indirect interaction between miRNA targets, which behave as miRNA sponges and eventually influence each other’s e...

    Authors: Carla Bosia, Francesco Sgrò, Laura Conti, Carlo Baldassi, Davide Brusa, Federica Cavallo, Ferdinando Di Cunto, Emilia Turco, Andrea Pagnani and Riccardo Zecchina

    Citation: Genome Biology 2017 18:37

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  5. Content type: Research

    Cotton has been cultivated and used to make fabrics for at least 7000 years. Two allotetraploid species of great commercial importance, Gossypium hirsutum and Gossypium barbadense, were domesticated after polyplo...

    Authors: Lei Fang, Hao Gong, Yan Hu, Chunxiao Liu, Baoliang Zhou, Tao Huang, Yangkun Wang, Shuqi Chen, David D. Fang, Xiongming Du, Hong Chen, Jiedan Chen, Sen Wang, Qiong Wang, Qun Wan, Bingliang Liu…

    Citation: Genome Biology 2017 18:33

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  6. Content type: Research

    Precise genome editing via homology-directed repair (HDR) after double-stranded DNA (dsDNA) cleavage facilitates functional genomic research and holds promise for gene therapy. However, HDR efficiency remains ...

    Authors: Jian-Ping Zhang, Xiao-Lan Li, Guo-Hua Li, Wanqiu Chen, Cameron Arakaki, Gary D. Botimer, David Baylink, Lu Zhang, Wei Wen, Ya-Wen Fu, Jing Xu, Noah Chun, Weiping Yuan, Tao Cheng and Xiao-Bing Zhang

    Citation: Genome Biology 2017 18:35

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  7. Content type: Research

    Monoubiquitination of H2B (H2Bub1) is a largely enigmatic histone modification that has been linked to transcriptional elongation. Because of this association, it has been commonly assumed that H2Bub1 is an ex...

    Authors: Wanhua Xie, Sankari Nagarajan, Simon J. Baumgart, Robyn Laura Kosinsky, Zeynab Najafova, Vijayalakshmi Kari, Magali Hennion, Daniela Indenbirken, Stefan Bonn, Adam Grundhoff, Florian Wegwitz, Ahmed Mansouri and Steven A. Johnsen

    Citation: Genome Biology 2017 18:32

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  8. Content type: Research Highlight

    Tumor cells have to overcome challenges in the host tissue microenvironment to metastasize successfully to distant organs. In a recent Nature study, a genome-wide functional screen demonstrated that deficiency of...

    Authors: Toni Celià-Terrassa and Yibin Kang

    Citation: Genome Biology 2017 18:31

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  9. Content type: Research

    Comparative transcriptomics can answer many questions in developmental and evolutionary developmental biology. Most transcriptomic studies start by showing global patterns of variation in transcriptomes that d...

    Authors: Sophie Pantalacci, Laurent Guéguen, Coraline Petit, Anne Lambert, Renata Peterkovà and Marie Sémon

    Citation: Genome Biology 2017 18:29

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  10. Content type: Research

    The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contamina...

    Authors: Ronald P. de Vries, Robert Riley, Ad Wiebenga, Guillermo Aguilar-Osorio, Sotiris Amillis, Cristiane Akemi Uchima, Gregor Anderluh, Mojtaba Asadollahi, Marion Askin, Kerrie Barry, Evy Battaglia, Özgür Bayram, Tiziano Benocci, Susanna A. Braus-Stromeyer, Camila Caldana, David Cánovas…

    Citation: Genome Biology 2017 18:28

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  11. Content type: Research

    The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception and the majority have evolved to colonise a sm...

    Authors: Thomas C. Mathers, Yazhou Chen, Gemy Kaithakottil, Fabrice Legeai, Sam T. Mugford, Patrice Baa-Puyoulet, Anthony Bretaudeau, Bernardo Clavijo, Stefano Colella, Olivier Collin, Tamas Dalmay, Thomas Derrien, Honglin Feng, Toni Gabaldón, Anna Jordan, Irene Julca…

    Citation: Genome Biology 2017 18:27

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    The Erratum to this article has been published in Genome Biology 2017 18:63

  12. Content type: Review

    High-throughput assays for measuring the three-dimensional (3D) configuration of DNA have provided unprecedented insights into the relationship between DNA 3D configuration and function. Data interpretation fr...

    Authors: Galip Gürkan Yardımcı and William Stafford Noble

    Citation: Genome Biology 2017 18:26

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  13. Content type: Research

    The CRISPR-Cas9 system is a widely utilized platform for transgenic animal production in various species, although its off-target effects should be addressed. Several applications of this tool have been propos...

    Authors: Yuanpeng Gao, Haibo Wu, Yongsheng Wang, Xin Liu, Linlin Chen, Qian Li, Chenchen Cui, Xu Liu, Jingcheng Zhang and Yong Zhang

    Citation: Genome Biology 2017 18:13

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  14. Content type: Method

    Current three-dimensional (3D) genome modeling platforms are limited by their inability to account for radial placement of loci in the nucleus. We present Chrom3D, a user-friendly whole-genome 3D computational...

    Authors: Jonas Paulsen, Monika Sekelja, Anja R. Oldenburg, Alice Barateau, Nolwenn Briand, Erwan Delbarre, Akshay Shah, Anita L. Sørensen, Corinne Vigouroux, Brigitte Buendia and Philippe Collas

    Citation: Genome Biology 2017 18:21

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  15. Content type: Research

    Whole-exome sequencing (WES) has been successful in identifying genes that cause familial Parkinson’s disease (PD). However, until now this approach has not been deployed to study large cohorts of unrelated pa...

    Authors: Iris E. Jansen, Hui Ye, Sasja Heetveld, Marie C. Lechler, Helen Michels, Renée I. Seinstra, Steven J. Lubbe, Valérie Drouet, Suzanne Lesage, Elisa Majounie, J. Raphael Gibbs, Mike A. Nalls, Mina Ryten, Juan A. Botia, Jana Vandrovcova, Javier Simon-Sanchez…

    Citation: Genome Biology 2017 18:22

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  16. Content type: Editorial

    We summarize the remarkable progress that has been made in the identification and functional characterization of DNA sequence variants associated with disease.

    Authors: Mark I. McCarthy and Daniel G. MacArthur

    Citation: Genome Biology 2017 18:20

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  17. Content type: Research

    5-Hydroxymethyluracil (5hmU) is a thymine base modification found in the genomes of a diverse range of organisms. To explore the functional importance of 5hmU, we develop a method for the genome-wide mapping o...

    Authors: Fumiko Kawasaki, Dario Beraldi, Robyn E. Hardisty, Gordon R. McInroy, Pieter van Delft and Shankar Balasubramanian

    Citation: Genome Biology 2017 18:23

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  18. Content type: Correspondence

    We thank Hattab and colleagues for their correspondence and their investigation of cell-type mixture correction methods in methyl-CG binding domain sequencing. Here, we speculate on why surrogate variable anal...

    Authors: Kevin McGregor, Aurélie Labbe and Celia M. T. Greenwood

    Citation: Genome Biology 2017 18:25

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  19. Content type: Correspondence

    Based on an extensive simulation study, McGregor and colleagues recently recommended the use of surrogate variable analysis (SVA) to control for the confounding effects of cell-type heterogeneity in DNA methyl...

    Authors: Mohammad W. Hattab, Andrey A. Shabalin, Shaunna L. Clark, Min Zhao, Gaurav Kumar, Robin F. Chan, Lin Ying Xie, Rick Jansen, Laura K. M. Han, Patrik K. E. Magnusson, Gerard van Grootheest, Christina M. Hultman, Brenda W. J. H. Penninx, Karolina A. Aberg and Edwin J. C. G. van den Oord

    Citation: Genome Biology 2017 18:24

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  20. Content type: METHOD

    We show that epigenome- and transcriptome-wide association studies (EWAS and TWAS) are prone to significant inflation and bias of test statistics, an unrecognized phenomenon introducing spurious findings if le...

    Authors: Maarten van Iterson, Erik W. van Zwet and Bastiaan T. Heijmans

    Citation: Genome Biology 2017 18:19

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  21. Content type: Research

    A healthy immune system requires immune cells that adapt rapidly to environmental challenges. This phenotypic plasticity can be mediated by transcriptional and epigenetic variability.

    Authors: Simone Ecker, Lu Chen, Vera Pancaldi, Frederik O. Bagger, José María Fernández, Enrique Carrillo de Santa Pau, David Juan, Alice L. Mann, Stephen Watt, Francesco Paolo Casale, Nikos Sidiropoulos, Nicolas Rapin, Angelika Merkel, Hendrik G. Stunnenberg, Oliver Stegle, Mattia Frontini…

    Citation: Genome Biology 2017 18:18

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  22. Content type: Research

    Inactivation of one X chromosome is established early in female mammalian development and can be reversed in vivo and in vitro when pluripotency factors are re-expressed. The extent of reactivation along the i...

    Authors: Irene Cantone, Gopuraja Dharmalingam, Yi-Wah Chan, Anne-Celine Kohler, Boris Lenhard, Matthias Merkenschlager and Amanda G. Fisher

    Citation: Genome Biology 2017 18:2

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  23. Content type: Research

    Identification of single nucleotide polymorphisms (SNPs) associated with gene expression levels, known as expression quantitative trait loci (eQTLs), may improve understanding of the functional role of phenoty...

    Authors: Roby Joehanes, Xiaoling Zhang, Tianxiao Huan, Chen Yao, Sai-xia Ying, Quang Tri Nguyen, Cumhur Yusuf Demirkale, Michael L. Feolo, Nataliya R. Sharopova, Anne Sturcke, Alejandro A. Schäffer, Nancy Heard-Costa, Han Chen, Po-ching Liu, Richard Wang, Kimberly A. Woodhouse…

    Citation: Genome Biology 2017 18:16

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  24. Content type: Research

    Organophosphates are the most frequently and largely applied insecticide in the world due to their biodegradable nature. Gut microbes were shown to degrade organophosphates and cause intestinal dysfunction. Th...

    Authors: Ganesan Velmurugan, Tharmarajan Ramprasath, Krishnan Swaminathan, Gilles Mithieux, Jeyaprakash Rajendhran, Mani Dhivakar, Ayothi Parthasarathy, D.D. Venkatesh Babu, Leishman John Thumburaj, Allen J. Freddy, Vasudevan Dinakaran, Shanavas Syed Mohamed Puhari, Balakrishnan Rekha, Yacob Jenifer Christy, Sivakumar Anusha, Ganesan Divya…

    Citation: Genome Biology 2017 18:8

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  25. Content type: Research

    Cell-to-cell heterogeneity is a major driver of cancer evolution, progression, and emergence of drug resistance. Epigenomic variation at the single-cell level can rapidly create cancer heterogeneity but is dif...

    Authors: Ulrike M. Litzenburger, Jason D. Buenrostro, Beijing Wu, Ying Shen, Nathan C. Sheffield, Arwa Kathiria, William J. Greenleaf and Howard Y. Chang

    Citation: Genome Biology 2017 18:15

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  26. Content type: Research

    Respiratory illness caused by viral infection is associated with the development and exacerbation of childhood asthma. Little is known about the effects of respiratory viral infections in the absence of illnes...

    Authors: Agata Wesolowska-Andersen, Jamie L. Everman, Rebecca Davidson, Cydney Rios, Rachelle Herrin, Celeste Eng, William J. Janssen, Andrew H. Liu, Sam S. Oh, Rajesh Kumar, Tasha E. Fingerlin, Jose Rodriguez-Santana, Esteban G. Burchard and Max A. Seibold

    Citation: Genome Biology 2017 18:12

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    The Correction to this article has been published in Genome Biology 2018 19:49

  27. Content type: Research

    In 2014, Western Africa experienced an unanticipated explosion of Ebola virus infections. What distinguishes fatal from non-fatal outcomes remains largely unknown, yet is key to optimising personalised treatme...

    Authors: Xuan Liu, Emily Speranza, César Muñoz-Fontela, Sam Haldenby, Natasha Y. Rickett, Isabel Garcia-Dorival, Yongxiang Fang, Yper Hall, Elsa-Gayle Zekeng, Anja Lüdtke, Dong Xia, Romy Kerber, Ralf Krumkamp, Sophie Duraffour, Daouda Sissoko, John Kenny…

    Citation: Genome Biology 2017 18:4

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  28. Content type: Method

    The mechanistic details of most disease-causing mutations remain poorly explored within the context of regulatory networks. We present a high-resolution three-dimensional integrated regulatory network (iRegNet...

    Authors: Siqi Liang, Nathaniel D. Tippens, Yaoda Zhou, Matthew Mort, Peter D. Stenson, David N. Cooper and Haiyuan Yu

    Citation: Genome Biology 2017 18:10

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  29. Content type: Erratum

    Authors: Alexie Papanicolaou, Marc F. Schetelig, Peter Arensburger, Peter W. Atkinson, Joshua B. Benoit, Kostas Bourtzis, Pedro Castañera, John P. Cavanaugh, Hsu Chao, Christopher Childers, Ingrid Curril, Huyen Dinh, HarshaVardhan Doddapaneni, Amanda Dolan, Shannon Dugan, Markus Friedrich…

    Citation: Genome Biology 2017 18:11

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    The original article was published in Genome Biology 2016 17:192

  30. Content type: Research

    Ultraviolet (UV) crosslinking and immunoprecipitation (CLIP) identifies the sites on RNAs that are in direct contact with RNA-binding proteins (RBPs). Several variants of CLIP exist, which require different co...

    Authors: Nejc Haberman, Ina Huppertz, Jan Attig, Julian König, Zhen Wang, Christian Hauer, Matthias W. Hentze, Andreas E. Kulozik, Hervé Le Hir, Tomaž Curk, Christopher R. Sibley, Kathi Zarnack and Jernej Ule

    Citation: Genome Biology 2017 18:7

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    The Erratum to this article has been published in Genome Biology 2017 18:154

  31. Content type: Method

    We present Gene-Aware Variant INterpretation (GAVIN), a new method that accurately classifies variants for clinical diagnostic purposes. Classifications are based on gene-specific calibrations of allele freque...

    Authors: K. Joeri van der Velde, Eddy N. de Boer, Cleo C. van Diemen, Birgit Sikkema-Raddatz, Kristin M. Abbott, Alain Knopperts, Lude Franke, Rolf H. Sijmons, Tom J. de Koning, Cisca Wijmenga, Richard J. Sinke and Morris A. Swertz

    Citation: Genome Biology 2017 18:6

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  32. Content type: MEETING REPORT

    A report on the Genome Informatics conference, held at the Wellcome Genome Campus Conference Centre, Hinxton, United Kingdom, 19–22 September 2016.

    Authors: Davide Chicco and Michael M. Hoffman

    Citation: Genome Biology 2017 18:5

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  33. Content type: Research

    Slow-growing prostate cancer (PC) can be aggressive in a subset of cases. Therefore, prognostic tools to guide clinical decision-making and avoid overtreatment of indolent PC and undertreatment of aggressive d...

    Authors: Kamilla Mundbjerg, Sameer Chopra, Mehrdad Alemozaffar, Christopher Duymich, Ranjani Lakshminarasimhan, Peter W. Nichols, Manju Aron, Kimberly D. Siegmund, Osamu Ukimura, Monish Aron, ‬Mariana Stern, Parkash Gill, John D. Carpten, Torben F. Ørntoft, Karina D. Sørensen, Daniel J. Weisenberger…

    Citation: Genome Biology 2017 18:3

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  34. Content type: Research

    Recent work has identified and mapped a range of posttranscriptional modifications in mRNA, including methylation of the N6 and N1 positions in adenine, pseudouridylation, and methylation of carbon 5 in cytosi...

    Authors: Thomas Amort, Dietmar Rieder, Alexandra Wille, Daria Khokhlova-Cubberley, Christian Riml, Lukas Trixl, Xi-Yu Jia, Ronald Micura and Alexandra Lusser

    Citation: Genome Biology 2017 18:1

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  35. Content type: Research

    Gene annotations, such as those in GENCODE, are derived primarily from alignments of spliced cDNA sequences and protein sequences. The impact of RNA-seq data on annotation has been confined to major projects l...

    Authors: Abhinav Nellore, Andrew E. Jaffe, Jean-Philippe Fortin, José Alquicira-Hernández, Leonardo Collado-Torres, Siruo Wang, Robert A. Phillips III, Nishika Karbhari, Kasper D. Hansen, Ben Langmead and Jeffrey T. Leek

    Citation: Genome Biology 2016 17:266

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  36. Content type: Research Highlight

    Alternative splice isoforms are common and important and have been shown to impact many human diseases. A new study by Nellore et al. offers a comprehensive study of splice junctions in humans by re-analyzing ...

    Authors: Christelle Robert and Mick Watson

    Citation: Genome Biology 2016 17:265

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  37. Content type: Review

    Despite major progress in dissecting the molecular pathways that control DNA methylation patterns in plants, little is known about the mechanisms that shape plant methylomes over evolutionary time. Drawing on ...

    Authors: Amaryllis Vidalis, Daniel Živković, René Wardenaar, David Roquis, Aurélien Tellier and Frank Johannes

    Citation: Genome Biology 2016 17:264

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    The Erratum to this article has been published in Genome Biology 2017 18:41

  38. Content type: Research

    Evolutionary origins of derived morphologies ultimately stem from changes in protein structure, gene regulation, and gene content. A well-assembled, annotated reference genome is a central resource for pursuin...

    Authors: C. M. Small, S. Bassham, J. Catchen, A. Amores, A. M. Fuiten, R. S. Brown, A. G. Jones and W. A. Cresko

    Citation: Genome Biology 2016 17:258

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  39. Content type: Erratum

    Authors: Linda Szabo, Robert Morey, Nathan J. Palpant, Peter L. Wang, Nastaran Afari, Chuan Jiang, Mana M. Parast, Charles E. Murry, Louise C. Laurent and Julia Salzman

    Citation: Genome Biology 2016 17:263

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    The original article was published in Genome Biology 2015 16:126

  40. Content type: METHOD

    In cancer, mutually exclusive or co-occurring somatic alterations across genes can suggest functional interactions. Existing tests for such patterns make the unrealistic assumption of identical gene alteration...

    Authors: Sander Canisius, John W. M. Martens and Lodewyk F. A. Wessels

    Citation: Genome Biology 2016 17:261

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  41. Content type: Software

    Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated an...

    Authors: Shaman Narayanasamy, Yohan Jarosz, Emilie E. L. Muller, Anna Heintz-Buschart, Malte Herold, Anne Kaysen, Cédric C. Laczny, Nicolás Pinel, Patrick May and Paul Wilmes

    Citation: Genome Biology 2016 17:260

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  42. Content type: Research

    Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective con...

    Authors: Federico Abascal, André Corvelo, Fernando Cruz, José L. Villanueva-Cañas, Anna Vlasova, Marina Marcet-Houben, Begoña Martínez-Cruz, Jade Yu Cheng, Pablo Prieto, Víctor Quesada, Javier Quilez, Gang Li, Francisca García, Miriam Rubio-Camarillo, Leonor Frias, Paolo Ribeca…

    Citation: Genome Biology 2016 17:251

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