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Here, we show that the related cytidine deaminase, APOBEC3G, induces site-specific C-to-U RNA editing in natural killer cells, lymphoma cell lines, and, to a lesser extent, CD8-positive T cells upon cellular crow...
Single-cell RNA-seq data allows insight into normal cellular function ... visualization and analysis, but single-cell RNA-seq data are challenging for classical dimensionality-reduction...
Mutations in myosin chaperones Unc45b and Hsp90aa1.1 as well as in the Unc45b-binding protein Smyd1b impair formation of myofibrils in skeletal muscle and lead to the accumulation of misfolded myosin. The conc...
To test whether alternative splicing in unicellular protists plays a role in cellular differentiation, we conduct RNA-seq to compare splicing in female and male...Plasmodium berghei. We find extensive changes in ...
The yellow potato cyst nematode, Globodera rostochiensis, is a devastating plant pathogen of global economic importance. This biotrophic parasite secretes effectors from pharyngeal glands, some of which were acqu...
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...
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...
DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has bee...
The flowering plant Primula veris is a common spring blooming perennial that is widely cultivated throughout Europe. This species is an established model system in the study of the genetics, evolution, and ecolog...
Geese were domesticated over 6,000 years ago, making them one of the first domesticated poultry. Geese are capable of rapid growth, disease resistance, and high liver lipid storage capacity, and can be easily ...
A comparison of transcriptional profiles derived from different tissues in a given species or among different species assumes that commonalities reflect evolutionarily conserved programs and that differences r...
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 ...
The Erratum to this article has been published in Genome Biology 2017 18:41
We analyze tumor-infiltrating immune cells in over 10,000 RNA-seq samples across 23 cancer types from The...http://​cistrome.​org/​TIMER.
The RNA helicase eIF4A1 is a key component of the translation initiation machinery and is required for the translation of many pro-oncogenic mRNAs. There is increasing interest in targeting eIF4A1 therapeutica...
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, ...
Massively parallel reporter assays (MPRAs) can measure the regulatory function of thousands of DNA sequences in a single experiment. Despite growing popularity, MPRA studies are limited by a lack of a unified ...
RNA contains over 150 types of chemical modifications. Although many of these chemical modifications were discovered several decades ago, their functions were not immediately apparent. Discoveries of RNA demet...
In the analysis of high-throughput data from complex samples, cell composition is an important factor that needs to be accounted for. Except for a limited number of tissues with known pure cell type profiles, ...
High-throughput single-cell gene expression experiments can be used to uncover branching dynamics in cell populations undergoing differentiation through pseudotime methods. We develop the branching Gaussian proce...
In studies of development and aging, the expression of many genes has been shown to undergo drastic changes at mRNA and protein levels. The connection between mRNA and protein expression level changes, as well...
Adenosine-to-inosine (A-to-I) RNA editing is an essential post-transcriptional mechanism mediated by ADAR enzymes that have been recently associated with cancer.
The isochore concept in human genome sequence was challenged in an analysis by the International Human Genome Sequencing Consortium (IHGSC). We argue here that a statement in IGHSC analysis concerning the existen...
Maintaining up-to-date annotation on reference genomes is becoming more important, not less, as the ability to rapidly and cheaply resequence genomes expands.
Piwi-interacting RNAs (piRNAs) originate from genomic regions dubbed piRNA clusters. How cluster transcripts are selected for processing into piRNAs is not understood. We discuss evidence for the involvement o...
Pleiotropy describes the phenomenon in which a gene affects multiple phenotypes. The extent of pleiotropy is still disputed, mainly because of issues of inadequate power of analyses. A further challenge is tha...
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 12 Supplement 1
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 12 Supplement 1
Integrated transcriptomic and high-resolution whole genome methylation analysis in a myeloid leukemia cell line defines genes that respond to clinically relevant DNA methyltransferase inhibitors.
The proliferation of web-based integrative analysis frameworks has enabled users to perform complex analyses directly through the web. Unfortunately, it also revoked the freedom to easily select the most appro...
A recent study reveals a surprisingly high degree of change in the occupancy patterns of two transcription factors in the livers of five vertebrates.
A report on the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 7th Special Interest Group meeting on Alternative Splicing, Boston, USA, 9-13 July 2010.
A report on the Advances in Genome Biology and Technology (AGBT) meeting, Marco Island, Florida, USA, 15-18 February 2012.
A report of the Wellcome Trust Functional Genomics and Systems Biology Conference, Hinxton, UK, 29 November to 1 December 2011.
A report on the EMBO/EMBL Symposium on The Non-Coding Genome, held in Heidelberg, Germany, 9-12 October, 2013.
Michael Snyder answers Genome Biology's questions on the human and professional stories underlying his Snyderome integrative omics project.
A recent study investigates the in vitro DNA binding behavior of PRDM9, a zinc finger protein involved in the localization of recombination hotspots in mammals.
A report on the Epigenetic Engineering Meeting hosted by the Barts Institute of Cancer, held in London, UK, May 7, 2014
A new study integrates genome-wide SNP genotyping, RNA-Seq and DNA methylation in human cells, revealing...
A new study in this issue of Genome Biology sheds light on why some pseudogenes persist in rodent, and other mammalian, genomes.
A report of the 2007 Cold Spring Harbor Laboratory/Wellcome Trust Conference on Functional Genomics and Systems Biology, Hinxton, UK, 10-13 October 2007.
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