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Previous studies have used different methods in an effort to extract the modular organization of transcriptional regulatory networks. However, these approaches are not natural, as they try to cluster strongly ...
The genomes of pathogens are thought to have evolved under selective pressure provided by the host in a coevolutionary arms race (the 'Red Queen's Hypothesis'). Traditionally, adaptation by pathogens is though...
A report of the meeting 'Translational Control', Cold Spring Harbor, USA, 3-7 September 2008.
Plant pathogenic bacteria encounter host defenses mediated by a variety of small RNAs. Bacterial suppressors of silencing that inhibit multiple steps of plant microRNA biogenesis and function have recently bee...
A report of the meeting 'Molecular Genetics of Bacteria and Phages', Cold Spring Harbor, USA, 20-24 August 2008.
The draft genome sequence of the ascidian Ciona intestinalis, along with associated gene models, has been a valuable research resource. However, recently accumulated expressed sequence tag (EST)/cDNA data have re...
The explosive growth of genomic data provides an opportunity to make increased use of protein markers for phylogenetic inference. We have developed an automated pipeline for phylogenomic analysis (AMPHORA) tha...
Amplified MYCN oncogene resulting in deregulated MYCN transcriptional activity is observed in 20% of neuroblastomas and identifies a highly aggressive subtype. In MYCN single-copy neuroblastomas, elevated MYCN mR...
Protein phosphorylation regulates a multitude of biological processes. However, the large number of protein kinases and their substrates generates an enormously complex phosphoproteome. The cyclin-dependent ki...
Because of its polygenic nature, Alzheimer's disease is believed to be caused not by defects in single genes, but rather by variations in a large number of genes and their complex interactions. A systems biolo...
Controlled simulations of genome evolution are useful for benchmarking tools. However, many simulators lack extensibility and cannot measure parameters directly from data. These issues are addressed by three n...
Condensin and cohesin are loaded onto yeast chromosomes by a common mechanism at RNA polymerase III transcribed genes. Whereas cohesin translocates from these loading sites to mediate cohesion at secondary loc...
Telomeres prevent the ends of eukaryotic chromosomes from being recognized as damaged DNA and protect against cancer and ageing. When telomere structure is perturbed, a co-ordinated series of events promote ar...
The pax2/5/8 genes belonging to the PAX family of transcription factors are key developmental regulators that are involved in the patterning of various embryonic tissues. More particularly, their function in inne...
Reversible phosphorylation of proteins is involved in a wide range of processes, ranging from signaling cascades to regulation of protein complex assembly. Little is known about the structure and evolution of ...
A report of the Biochemical Society meeting 'The Molecular Biology of Archaea', St Andrews, UK, 19-21 August 2008.
Defensins, small endogenous peptides with antimicrobial activity, are pivotal components of the innate immune response. A large cluster of defensin genes is located on human chromosome 8p; among them the beta ...
The evolutionary rate of a protein is a basic measure of evolution at the molecular level. Previous studies have shown that genes expressed in the brain have significantly lower evolutionary rates than those e...
A large proportion of species-specific exons are alternatively spliced. In primates, Alu elements play a crucial role in the process of exon creation but many new exons have appeared through other mechanisms. Des...
Understanding the response of complex biochemical networks to genetic perturbations and environmental variability is a fundamental challenge in biology. Integration of high-throughput experimental assays and g...
A report of the Cold Spring Harbor Laboratory meeting 'Mechanisms and Models of Cancer', Cold Spring Harbor, USA, 13-17 August 2008.
Our knowledge on tissue- and disease-specific functions of human genes is rather limited and highly context-specific. Here, we have developed a method for the comparison of mRNA expression levels of most human...
Massively parallel short-tag sequencing of cDNA libraries - RNAseq - is being used to study the dynamics and complexity of eukaryotic transcriptomes, giving new biological insights into the 'active genome'.
The telomeres that cap the ends of eukaryotic chromosomes serve a dual role in protecting the chromosome ends and in intracellular signaling for regulating cell proliferation. A complex of six telomere-associa...
NetGrep (http://​genomics.​princeton.​edu/​singhlab/​netgrep/​) is a system for searching protein interaction networks for matches to user-supplied 'network schema...
We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and use...
The Related Article to this article has been published in Nature Protocols 2012 7:nprot.2012.101
A circuit of transcription factors has been discovered in Caenorhabditis elegans that could provide a link between laboratory-defined intracellular 'longevity pathways', gene dysregulation and the process of norm...
We present a strategy for detection of loss-of-heterozygosity and allelic imbalance in cancer cells from whole genome single nucleotide polymorphism genotyping data. Using a dilution series of a tumor cell lin...
Synthetic lethality defines a genetic interaction where the combination of mutations in two or more genes leads to cell death. The implications of synthetic lethal screens have been discussed in the context of...
A report of the joint American Society of Plant Biologists/Sociedad Mexicana De BioquÃmica meeting held in Mérida, Mexico, 26 June-1 July 2008.
The trithorax group (trxG) and Polycomb group (PcG) proteins are responsible for the maintenance of stable transcriptional patterns of many developmental regulators. They bind to specific regions of DNA and di...
The power of massively parallel sequencing has been harnessed to map cytosine methylation patterns in the mouse genome, allowing insights into the relationship of methylation with DNA sequence, histone modific...
The goal of text mining is to make the information conveyed in scientific publications accessible to structured search and automatic analysis. Two important subtasks of text mining are entity mention normaliza...
This article is part of a Supplement: Volume 9 Supplement 2
Research scientists and companies working in the domains of biomedicine and genomics are increasingly faced with the problem of efficiently locating, within the vast body of published scientific findings, the ...
This article is part of a Supplement: Volume 9 Supplement 2
Deciphering physical protein-protein interactions is fundamental to elucidating both the functions of proteins and biological processes. The development of high-throughput experimental technologies such as the...
This article is part of a Supplement: Volume 9 Supplement 2
We participated in three of the protein-protein interaction subtasks of the Second BioCreative Challenge: classification of abstracts relevant for protein-protein interaction (interaction article subtask [IAS]...
This article is part of a Supplement: Volume 9 Supplement 2
The tasks in BioCreative II were designed to approximate some of the laborious work involved in curating biomedical research papers. The approach to these tasks taken by the University of Edinburgh team was to...
This article is part of a Supplement: Volume 9 Supplement 2
Reliable information extraction applications have been a long sought goal of the biomedical text mining community, a goal that if reached would provide valuable tools to benchside biologists in their increasin...
This article is part of a Supplement: Volume 9 Supplement 2
Efficient access to information contained in online scientific literature collections is essential for life science research, playing a crucial role from the initial stage of experiment planning to the final i...
This article is part of a Supplement: Volume 9 Supplement 2
This article collects opinions from leading scientists about how text mining can provide better access to the biological literature, how the scientific community can help with this process, what the next steps...
This article is part of a Supplement: Volume 9 Supplement 2
We introduce the first meta-service for information extraction in molecular biology, the BioCreative MetaServer (BCMS; http://​bcms.​bioinfo.​cnio.​es/​). This pr...
This article is part of a Supplement: Volume 9 Supplement 2
In the absence of consolidated pipelines to archive biological data electronically, information dispersed in the literature must be captured by manual annotation. Unfortunately, manual annotation is time consu...
This article is part of a Supplement: Volume 9 Supplement 2
The biomedical literature is the primary information source for manual protein-protein interaction annotations. Text-mining systems have been implemented to extract binary protein interactions from articles, b...
This article is part of a Supplement: Volume 9 Supplement 2
The goal of the gene normalization task is to link genes or gene products mentioned in the literature to biological databases. This is a key step in an accurate search of the biological literature. It is a cha...
This article is part of a Supplement: Volume 9 Supplement 2
Nineteen teams presented results for the Gene Mention Task at the BioCreative II Workshop. In this task participants designed systems to identify substrings in sentences corresponding to gene name mentions. A ...
This article is part of a Supplement: Volume 9 Supplement 2
Genome sciences have experienced an increasing demand for efficient text-processing tools that can extract biologically relevant information from the growing amount of published literature. In response, a rang...
This article is part of a Supplement: Volume 9 Supplement 2
Proteins of the phytochrome superfamily of red/far-red light receptors have a variety of biological roles in plants, algae, bacteria and fungi and demonstrate a diversity of spectral sensitivities and output s...
Accumulating evidence points to the mosaic nature of the mouse genome. However, little is known about the way the introgressed segments are regulated within the context of the recipient genetic background. To ...
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