Gene family expansions and contractions are associated with host range in plant pathogens of the genus Colletotrichum
...Published in BMC Genomics
Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network
Published in BMC Genomics
Background: The reconstruction of context-specific metabolic models from easily and reliably measurable features such as transcriptomics data will be increasingly important in research and medicine. Current reconstruction methods suffer from high computational effort and arbitrary threshold setting. Moreover, understanding the underlying epigenetic...
A single molecule scaffold for the maize genome.
...Published in PLoS genetics
About 85% of the maize genome consists of highly repetitive sequences that are interspersed by low-copy, gene-coding sequences. The maize community has dealt with this genomic complexity by the construction of an integrated genetic and physical map (iMap), but this resource alone was not sufficient for ensuring the quality of the current sequence b...
Fine mapping of V(D)J recombinase mediated rearrangements in human lymphoid malignancies.
Published in BMC genomics
Our results demonstrate the ability of next generation sequencing to describe human V(D)J recombinase activity and provide a scalable means to chronicle off-target, unexpressed, and non-amplifiable recombinations occurring in the development of lymphoid cancers.
Suppression of genetic recombination in the pseudoautosomal region and at subtelomeres in mice with a hypomorphic Spo11 ...
Published in BMC genomics
Our data suggest that specific, yet-unidentified factors influence the initiation of meiotic recombination at subtelomeric chromosomal regions.
Expression of concern: Subfunctionalization reduces the fitness cost of gene duplication in humans by buffering dosage i...
Published in BMC genomics
After publication of this article (Fernandez et al., BMC Genomics 2011, 12:604) it was brought to the Editors' attention that the data generated by the first author, Ariel Fernandez, seemed anomalous. One of the author's institutions found that the data were not reproducible from the described methods, but an investigation by the author's other ins...
Transcription-coupled methylation of histone H3 at lysine 36 regulates dosage compensation by enhancing recruitment of t...
Published in Molecular and cellular biology
In Drosophila melanogaster, dosage compensation relies on the targeting of the male-specific lethal (MSL) complex to hundreds of sites along the male X chromosome. Transcription-coupled methylation of histone H3 lysine 36 is enriched toward the 3' end of active genes, similar to the MSL proteins. Here, we have studied the link between histone H3 me...
Nuclear receptor unfulfilled regulates axonal guidance and cell identity of Drosophila mushroom body neurons.
Published in PloS one
Nuclear receptors (NRs) comprise a family of ligand-regulated transcription factors that control diverse critical biological processes including various aspects of brain development. Eighteen NR genes exist in the Drosophila genome. To explore their roles in brain development, we knocked down individual NRs through the development of the mushroom b...
Genome-wide analysis of H4K5 acetylation associated with fear memory in mice
Published in BMC Genomics
Background Histone acetylation has been implicated in learning and memory in the brain, however, its function at the level of the genome and at individual genetic loci remains poorly investigated. This study examines a key acetylation mark, histone H4 lysine 5 acetylation (H4K5ac), genome-wide and its role in activity-dependent gene transcription i...
Estimating DNA polymorphism from next generation sequencing data with high error rate by dual sequencing applications
Published in BMC Genomics
Background As the error rate is high and the distribution of errors across sites is non-uniform in next generation sequencing (NGS) data, it has been a challenge to estimate DNA polymorphism (θ) accurately from NGS data. Results By computer simulations, we compare the two methods of data acquisition - sequencing each diploid individual separately a...
