Gramene 2013: comparative plant genomics resources.

Gramene (http://www.gramene.org) is a curated online resource for comparative functional genomics in crops and model plant species, currently hosting 27 fully and 10 partially sequenced reference genomes in its build number 38.

Exploiting disjointness axioms to improve semantic similarity measures.

Motivation: Representing domain knowledge in biology has traditionally been accomplished by creating simple hierarchies of classes with textual annotations. Recently, expressive ontology languages, such as Web Ontology Language, have become more widely adopted, supporting axioms that express logical relationships other than class-subclass, e.g.

The impact of mathematical modeling on the understanding of diabetes and related complications.

Diabetes is a chronic and complex multifactorial disease caused by persistent hyperglycemia and for which underlying pathogenesis is still not completely understood. The mathematical modeling of glucose homeostasis, diabetic condition, and its associated complications is rapidly growing and provides new insights into the underlying mechanisms involved. Here, we discuss contributions to the diabetes modeling field over the past five decades, highlighting the areas where more focused research is required.

Unlocking the potential of survival data for model organisms through a new database and online analysis platform: SurvCurv.

Lifespan measurements, also called survival records, are a key phenotype in research on aging. If external hazards are excluded, aging alone determines the mortality in a population of model organisms. Understanding the biology of aging is highly desirable because of the benefits for the wide range of aging-related diseases.

Kraken: a set of tools for quality control and analysis of high-throughput sequence data.

New sequencing technologies pose significant challenges in terms of data complexity and magnitude. It is essential that efficient software is developed with performance that scales with this growth in sequence information. Here we present a comprehensive and integrated set of tools for the analysis of data from large scale sequencing experiments.

Analysing variation in Drosophila aging across independent experimental studies: a meta-analysis of survival data.

Survival records of longevity experiments are a key component in research on aging. However, surprisingly there have been very few cross-study analyses, besides comparisons of median lifespans or similar summary information. Here, we use a large set of full survival data from various studies to address questions in aging, which are beyond the scope of individual studies.

Bioinformatics goes to school--new avenues for teaching contemporary biology.

Since 2010, the European Molecular Biology Laboratory's (EMBL) Heidelberg laboratory and the European Bioinformatics Institute (EMBL-EBI) have jointly run bioinformatics training courses developed specifically for secondary school science teachers within Europe and EMBL member states. These courses focus on introducing bioinformatics, databases, and data-intensive biology, allowing participants to explore resources and providing classroom-ready materials to support them in sharing this new knowledge with their students. In this article, we chart our progress made in creating and running three bioinformatics training courses, including how the course resources are received by participants and how these, and bioinformatics in general, are subsequently used in the classroom.

GEE for multinomial responses using a local odds ratios parameterization.

In this article, we propose a generalized estimating equations (GEE) approach for correlated ordinal or nominal multinomial responses using a local odds ratios parameterization. Our motivation lies upon observing that: (i) modeling the dependence between correlated multinomial responses via the local odds ratios is meaningful both for ordinal and nominal response scales and (ii) ordinary GEE methods might not ensure the joint existence of the estimates of the marginal regression parameters and of the dependence structure. To avoid (ii), we treat the so-called "working" association vector α as a "nuisance" parameter vector that defines the local odds ratios structure at the marginalized contingency tables after tabulating the responses without a covariate adjustment at each time pair.

Controlled annotations for systems biology.

The aim of this chapter is to provide sufficient information to enable a reader, new to the subject of Systems Biology, to create and use effectively controlled annotations, using resolvable Identifiers.org Uniform Resource Identifiers (URIs). The text details the underlying requirements that have led to the development of such an identification scheme and infrastructure, the principles that underpin its syntax and the benefits derived through its use.

A new reference implementation of the PSICQUIC web service.

The Proteomics Standard Initiative Common QUery InterfaCe (PSICQUIC) specification was created by the Human Proteome Organization Proteomics Standards Initiative (HUPO-PSI) to enable computational access to molecular-interaction data resources by means of a standard Web Service and query language. Currently providing >150 million binary interaction evidences from 28 servers globally, the PSICQUIC interface allows the concurrent search of multiple molecular-interaction information resources using a single query. Here, we present an extension of the PSICQUIC specification (version 1.

Approaches to querying bacterial genomes with transposon-insertion sequencing.

In this review, we discuss transposon-insertion sequencing, variously known in the literature as TraDIS, Tn-seq, INSeq, and HITS. By monitoring a large library of single transposon-insertion mutants with high-throughput sequencing, these methods can rapidly identify genomic regions that contribute to organismal fitness under any condition assayable in the laboratory with exquisite resolution. We discuss the various protocols that have been developed and methods for analysis.

Transcriptional feedback in the insulin signalling pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster.

Several components have been previously identified, that modulate longevity in several species, including the target of rapamycin (TOR) and the Insulin/IGF-1 (IIS) signalling pathways. In order to infer paths and transcriptional feedback loops that are likely to modulate ageing, we manually built a comprehensive and computationally efficient signalling network model of the IIS and TOR pathways in worms. The core insulin transduction is signalling from the sole insulin receptor daf-2 to ultimately inhibit the translocation of the transcription factor daf-16 into the nucleus.

The challenge of increasing Pfam coverage of the human proteome.

It is a worthy goal to completely characterize all human proteins in terms of their domains. Here, using the Pfam database, we asked how far we have progressed in this endeavour. Ninety per cent of proteins in the human proteome matched at least one of 5494 manually curated Pfam-A families.

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions.

Detection of protein homology via sequence similarity has important applications in biology, from protein structure and function prediction to reconstruction of phylogenies. Although current methods for aligning protein sequences are powerful, challenges remain, including problems with homologous overextension of alignments and with regions under convergent evolution. Here, we test the ability of the profile hidden Markov model method HMMER3 to correctly assign homologous sequences to >13,000 manually curated families from the Pfam database.

Protein complexes are under evolutionary selection to assemble via ordered pathways.

Is the order in which proteins assemble into complexes important for biological function? Here, we seek to address this by searching for evidence of evolutionary selection for ordered protein complex assembly. First, we experimentally characterize the assembly pathways of several heteromeric complexes and show that they can be simply predicted from their three-dimensional structures. Then, by mapping gene fusion events identified from fully sequenced genomes onto protein complex assembly pathways, we demonstrate evolutionary selection for conservation of assembly order.

SMIM1 underlies the Vel blood group and influences red blood cell traits.

The blood group Vel was discovered 60 years ago, but the underlying gene is unknown. Individuals negative for the Vel antigen are rare and are required for the safe transfusion of patients with antibodies to Vel. To identify the responsible gene, we sequenced the exomes of five individuals negative for the Vel antigen and found that four were homozygous and one was heterozygous for a low-frequency 17-nucleotide frameshift deletion in the gene encoding the 78-amino-acid transmembrane protein SMIM1.

Shorthand notation for lipid structures derived from mass spectrometry.

There is a need for a standardized, practical annotation for structures of lipid species derived from mass spectrometric approaches; i.e., for high-throughput data obtained from instruments operating in either high- or low-resolution modes.

Brain: biomedical knowledge manipulation.

Summary: Brain is a Java software library facilitating the manipulation and creation of ontologies and knowledge bases represented with the Web Ontology Language (OWL).

Availability And Implementation: The Java source code and the library are freely available at https://github.com/loopasam/Brain and on the Maven Central repository (GroupId: uk.

Drosophila americana as a model species for comparative studies on the molecular basis of phenotypic variation.

Understanding the molecular basis of within and between species phenotypic variation is one of the main goals of Biology. In Drosophila, most of the work regarding this issue has been performed in D. melanogaster, but other distantly related species must also be studied to verify the generality of the findings obtained for this species.

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats.

Motivation: Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore required.

Results: EDAM is an ontology of bioinformatics operations (tool or workflow functions), types of data and identifiers, application domains and data formats.

Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements.

There are ~650,000 Alu elements in transcribed regions of the human genome. These elements contain cryptic splice sites, so they are in constant danger of aberrant incorporation into mature transcripts. Despite posing a major threat to transcriptome integrity, little is known about the molecular mechanisms preventing their inclusion.

CySBGN: a Cytoscape plug-in to integrate SBGN maps.

Background: A standard graphical notation is essential to facilitate exchange of network representations of biological processes. Towards this end, the Systems Biology Graphical Notation (SBGN) has been proposed, and it is already supported by a number of tools. However, support for SBGN in Cytoscape, one of the most widely used platforms in biology to visualise and analyse networks, is limited, and in particular it is not possible to import SBGN diagrams.

Facing growth in the European Nucleotide Archive.

The European Nucleotide Archive (ENA; http://www.ebi.ac.

Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB.

We describe Vivaldi (VIsualization and VALidation DIsplay; http://pdbe.org/vivaldi), a web-based service for the analysis, visualization, and validation of NMR structures in the Protein Data Bank (PDB). Vivaldi provides access to model coordinates and several types of experimental NMR data using interactive visualization tools, augmented with structural annotations and model-validation information.

Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival.

Background: Glioblastoma multiforme, the most common type of primary brain tumor in adults, is driven by cells with neural stem (NS) cell characteristics. Using derivation methods developed for NS cells, it is possible to expand tumorigenic stem cells continuously in vitro. Although these glioblastoma-derived neural stem (GNS) cells are highly similar to normal NS cells, they harbor mutations typical of gliomas and initiate authentic tumors following orthotopic xenotransplantation.