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We present BioGraph, a data integration and data mining platform for the exploration and discovery of biomedical information. The platform offers prioritizations of putative disease genes, supported by functio...
Mapping of 5-hydroxylmethylcytosine in mammalian genomes has unveiled its unique role in the epigenetic regulation of gene expression.
Mounting evidence suggests a major role for epigenetic feedback in Plasmodium falciparum transcriptional regulation. Long non-coding RNAs (lncRNAs) have recently emerged as a new paradigm in epigenetic remodeling...
SNP (single nucleotide polymorphism) discovery using next-generation sequencing data remains difficult primarily because of redundant genomic regions, such as interspersed repetitive elements and paralogous ge...
5-Hydroxymethylcytosine (5hmC) was recently found to be abundantly present in certain cell types, including embryonic stem cells. There is growing evidence that TET proteins, which convert 5-methylcytosine (5m...
A report of the Systems Biology: Networks meeting, Cold Spring Harbor, USA, 22-26 March 2011.
Pollen development in flowering plants requires strict control of the gene expression program and genetic information stability by mechanisms possibly including the miRNA pathway. However, our understanding of...
A report on the British Yeast Group Meeting, Brighton, UK, 23-25 March 2011.
The lamins are the major architectural proteins of the animal cell nucleus. Lamins line the inside of the nuclear membrane, where they provide a platform for the binding of proteins and chromatin and confer me...
Copy number variants (CNVs), defined as losses and gains of segments of genomic DNA, are a major source of genomic variation.
Late Pleistocene North America hosted at least two divergent and ecologically distinct species of mammoth: the periglacial woolly mammoth (Mammuthus primigenius) and the subglacial Columbian mammoth (Mammuthus co...
Recent developments in high-throughput genotyping and whole-genome sequencing will enhance the identification of disease loci in admixed populations. We discuss how a more refined estimation of ancestry benefi...
The first detailed temporal study of the human microbiome shows that individual body habitats exhibit surprising variation over time yet maintain distinguishable community structures.
A recent phylogenomic study has provided new evidence for two ancient whole genome duplications in plants, with potential importance for the evolution of seed and flowering plants.
Understanding the normal temporal variation in the human microbiome is critical to developing treatments for putative microbiome-related afflictions such as obesity, Crohn's disease, inflammatory bowel disease...
Graph-based methods have been widely used for the analysis of biological networks. Their application to metabolic networks has been much discussed, in particular noting that an important weakness in such metho...
Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The A...
Previous molecular and mechanistic studies have identified several principles of prokaryotic transcription, but less is known about the global transcriptional architecture of bacterial genomes. Here we perform...
Recent studies have investigated the contribution of copy number variants (CNVs) to disease susceptibility in a multitude of complex disorders, including systemic lupus erythematosus, Crohn's disease, and vari...
Gene loss, inversions, translocations, and other chromosomal rearrangements vary among species, resulting in different rates of structural genome evolution. Major chromosomal rearrangements are rare in most eu...
Recovery of ribosomal small subunit genes by assembly of short read community DNA sequence data generally fails, making taxonomic characterization difficult. Here, we solve this problem with a novel iterative ...
The development of complex organisms is believed to involve progressive restrictions in cellular fate. Understanding the scope and features of chromatin dynamics during embryogenesis, and identifying regulator...
Despite its critical role for mammalian gene regulation, the basic structural landscape of chromatin in living cells remains largely unknown within chromosomal territories below the megabase scale.
MicroRNAs are pervasive in both plants and animals, but many aspects of their biogenesis, function and evolution differ. We reveal how these differences contribute to characteristic features of microRNA evolut...
Cullin proteins are molecular scaffolds that have crucial roles in the post-translational modification of cellular proteins involving ubiquitin. The mammalian cullin protein family comprises eight members (CUL...
Initiation sites for meiotic recombination have now been precisely mapped across the budding yeast genome using a widely applicable deep-sequencing approach.
We describe methods with enhanced power and specificity to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth. By separating SCNA profiles into underlying arm-level and...
A response to Dynamic cumulative activity of transcription factors as a mechanism of quantitative gene regulation by F He, J Buer, AP Zeng and R Balling. Genome Biol 2007, 8:R181.
A report of the Keystone Symposium 'DNA Replication and Recombination' held in Keystone, USA, 27 February to 4 March 2011.
The original article was published in Genome Biology 2009 10:R60
Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. ...
We describe the Yeast Kinase Interaction Database (KID, http://​www.​moseslab.​csb.​utoronto.​ca/​KID/​), which contains high- and low-throughput data relevant to p...
The Erratum to this article has been published in Genome Biology 2012 13:417
McLaughlin and Chadwick describe an X-linked tandem repeat that is transcribed, conserved and defies X inactivation. Is it selfish, functional or just an oddity?
As in eukaryotes, precursor transfer RNAs in Archaea often contain introns that are removed in tRNA maturation. Two unrelated archaeal species display unique pre-tRNA processing complexity in the form of split...
Comparative sequence analysis is a powerful means with which to identify functionally relevant non-coding DNA elements through conserved nucleotide sequence. The macrosatellite DXZ4 is a polymorphic, uninterru...
Gene regulatory networks (GRNs) are rapidly being delineated, but their quality and biological meaning are often questioned. Here, I argue that biological meaning is challenging to define and discuss reasons w...
When mismatches in heteroduplex DNA formed during meiotic recombination are left unrepaired, post-meiotic segregation of the two mismatched alleles occurs during the ensuing round of mitosis. This gives rise t...
We present an optimized probe design for copy number variation (CNV) and SNP genotyping in the Plasmodium falciparum genome. We demonstrate that variable length and isothermal probes are superior to static length...
In Drosophila embryos, many biochemically and functionally unrelated transcription factors bind quantitatively to highly overlapping sets of genomic regions, with much of the lowest levels of binding being incide...
The human malaria parasite Plasmodium falciparum survives pressures from the host immune system and antimalarial drugs by modifying its genome. Genetic recombination and nucleotide substitution are the two major ...
Biological data is often tabular but finding statistically valid connections between entities in a sequence of tables can be problematic - for example, connecting particular entities in a drug property table t...
The unparalleled efficiency of next-generation sequencing (NGS) has prompted widespread adoption, but significant problems remain in the use of NGS data for whole genome assembly. We explore the advantages and...
Comparison of gene expression from transgenes and endogenous genes with or without introns reveals a time-regulating role of introns in natural biological systems.
High-throughput phenotyping approaches (phenomics) are being combined with genome-wide genetic screens to identify alterations in phenotype that result from gene inactivation. Here we highlight promising techn...
Insertion sequences (ISs) play a key role in prokaryotic genome evolution but are seldom well annotated. We describe a web application pipeline, ISsaga (
Blastocystis is a highly prevalent anaerobic eukaryotic parasite of humans and animals that is associated with various gastrointestinal and extraintestinal disorders. Epidemiological studies have identified diffe...
Map based cloning in Arabidopsis thaliana can be a difficult and time-consuming process, specifically if the phenotype is subtle and scoring labour intensive. Here, we have re-sequenced the 120-Mb genome of a nov...
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