Articles

Sort by
Previous Page Page 1 of 235 Next Page
  1. METHOD

    BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

    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...

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

    Genome Biology 2017 18:39

    Published on: 24 February 2017

  2. METHOD

    epiG: statistical inference and profiling of DNA methylation from whole-genome bisulfite sequencing data

    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...

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

    Genome Biology 2017 18:38

    Published on: 21 February 2017

  3. Research

    Efficient precise knockin with a double cut HDR donor after CRISPR/Cas9-mediated double-stranded DNA cleavage

    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 ...

    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

    Genome Biology 2017 18:35

    Published on: 20 February 2017

  4. Research

    Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons

    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...

    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…

    Genome Biology 2017 18:33

    Published on: 20 February 2017

  5. Research

    RNAs competing for microRNAs mutually influence their fluctuations in a highly non-linear microRNA-dependent manner in single cells

    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...

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

    Genome Biology 2017 18:37

    Published on: 20 February 2017

  6. Research

    The genome landscape of indigenous African cattle

    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...

    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…

    Genome Biology 2017 18:34

    Published on: 20 February 2017

  7. Research Highlight

    Mouse genomic screen reveals novel host regulator of metastasis

    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...

    Toni Celià-Terrassa and Yibin Kang

    Genome Biology 2017 18:31

    Published on: 16 February 2017

  8. Research

    RNF40 regulates gene expression in an epigenetic context-dependent manner

    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...

    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

    Genome Biology 2017 18:32

    Published on: 16 February 2017

  9. Research

    Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

    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...

    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…

    Genome Biology 2017 18:28

    Published on: 14 February 2017

  10. Research

    Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species

    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...

    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…

    Genome Biology 2017 18:27

    Published on: 13 February 2017

  11. Review

    Software tools for visualizing Hi-C data

    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...

    Galip Gürkan Yardımcı and William Stafford Noble

    Genome Biology 2017 18:26

    Published on: 3 February 2017

  12. Research

    Single Cas9 nickase induced generation of NRAMP1 knockin cattle with reduced off-target effects

    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...

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

    Genome Biology 2017 18:13

    Published on: 1 February 2017

  13. Correspondence

    Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies

    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...

    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

    Genome Biology 2017 18:24

    Published on: 30 January 2017

  14. Correspondence

    Response to: Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies

    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...

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

    Genome Biology 2017 18:25

    Published on: 30 January 2017

  15. Editorial

    Human disease genomics: from variants to biology

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

    Mark I. McCarthy and Daniel G. MacArthur

    Genome Biology 2017 18:20

    Published on: 30 January 2017

  16. Research

    Genome-wide mapping of 5-hydroxymethyluracil in the eukaryote parasite Leishmania

    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...

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

    Genome Biology 2017 18:23

    Published on: 30 January 2017

  17. Research

    Discovery and functional prioritization of Parkinson’s disease candidate genes from large-scale whole exome sequencing

    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...

    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…

    Genome Biology 2017 18:22

    Published on: 30 January 2017

  18. Method

    Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts

    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...

    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

    Genome Biology 2017 18:21

    Published on: 30 January 2017

  19. Research

    Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types

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

    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…

    Genome Biology 2017 18:18

    Published on: 26 January 2017

  20. Research

    Integrated genome-wide analysis of expression quantitative trait loci aids interpretation of genomic association studies

    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...

    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…

    Genome Biology 2017 18:16

    Published on: 25 January 2017

  21. Research

    Allele-specific analysis of cell fusion-mediated pluripotent reprograming reveals distinct and predictive susceptibilities of human X-linked genes to reactivation

    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...

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

    Genome Biology 2017 18:2

    Published on: 25 January 2017

Previous Page Page 1 of 235 Next Page