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bcROCsurface: an R package for correcting verification bias in estimation of the ROC surface and its volume for continuous diagnostic tests

BMC Bioinformatics - Sat, 18/11/2017 - 5:30am
Receiver operating characteristic (ROC) surface analysis is usually employed to assess the accuracy of a medical diagnostic test when there are three ordered disease status (e.g. non-diseased, intermediate, di...
Categories: Bioinformatics Trends

GPU-based detection of protein cavities using Gaussian surfaces

BMC Bioinformatics - Thu, 16/11/2017 - 5:30am
Protein cavities play a key role in biomolecular recognition and function, particularly in protein-ligand interactions, as usual in drug discovery and design. Grid-based cavity detection methods aim at finding...
Categories: Bioinformatics Trends

dbMDEGA: a database for meta-analysis of differentially expressed genes in autism spectrum disorder

BMC Bioinformatics - Thu, 16/11/2017 - 5:30am
Autism spectrum disorders (ASD) are hereditary, heterogeneous and biologically complex neurodevelopmental disorders. Individual studies on gene expression in ASD cannot provide clear consensus conclusions. The...
Categories: Bioinformatics Trends

ANAT 2.0: reconstructing functional protein subnetworks

BMC Bioinformatics - Thu, 16/11/2017 - 5:30am
ANAT is a graphical, Cytoscape-based tool for the inference of protein networks that underlie a process of interest. The ANAT tool allows the user to perform network reconstruction under several scenarios in a...
Categories: Bioinformatics Trends

Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks

Bioinformatics Oxford Journals - Thu, 16/11/2017 - 12:00am
AbstractMotivationRegulatory sequences are not solely defined by their nucleic acid sequence but also by their relative distances to genomic landmarks such as transcription start site, exon boundaries, or polyadenylation site. Deep learning has become the approach of choice for modeling regulatory sequences because of its strength to learn complex sequence features. However, modeling relative distances to genomic landmarks in deep neural networks has not been addressed.ResultsHere we developed spline transformation, a neural network module based on splines to flexibly and robustly model distances. Modeling distances to various genomic landmarks with spline transformations significantly increased state-of-the-art prediction accuracy of in vivo RNA-binding protein binding sites for 120 out of 123 proteins. We also developed a deep neural network for human splice branchpoint based on spline transformations that outperformed the current best, already distance-based, machine learning model. Compared to piecewise linear transformation, as obtained by composition of rectified linear units, spline transformation yields higher prediction accuracy as well as faster and more robust training. As spline transformation can be applied to further quantities beyond distances, such as methylation or conservation, we foresee it as a versatile component in the genomics deep learning toolbox.AvailabilitySpline transformation is implemented as a Keras layer in the CONCISE python package: https://github.com/gagneurlab/concise. Analysis code is available at goo.gl/3yMY5w.Contactavsec@in.tum.de; gagneur@in.tum.deSupplementary InformationSupplementary data are available at Bioinformatics online.
Categories: Bioinformatics Trends

Reconstructing cancer karyotypes from short read data: the half empty and half full glass

BMC Bioinformatics - Wed, 15/11/2017 - 5:30am
During cancer progression genomes undergo point mutations as well as larger segmental changes. The latter include, among others, segmental deletions duplications, translocations and inversions.The result is a ...
Categories: Bioinformatics Trends

SPRINT: ultrafast protein-protein interaction prediction of the entire human interactome

BMC Bioinformatics - Wed, 15/11/2017 - 5:30am
Proteins perform their functions usually by interacting with other proteins. Predicting which proteins interact is a fundamental problem. Experimental methods are slow, expensive, and have a high rate of error...
Categories: Bioinformatics Trends

Usability of human Infinium MethylationEPIC BeadChip for mouse DNA methylation studies

BMC Bioinformatics - Wed, 15/11/2017 - 5:30am
The advent of array-based genome-wide DNA methylation methods has enabled quantitative measurement of single CpG methylation status at relatively low cost and sample input. Whereas the use of Infinium Human Me...
Categories: Bioinformatics Trends

TRAVeLer: a tool for template-based RNA secondary structure visualization

BMC Bioinformatics - Wed, 15/11/2017 - 5:30am
Visualization of RNA secondary structures is a complex task, and, especially in the case of large RNA structures where the expected layout is largely habitual, the existing visualization tools often fail to pr...
Categories: Bioinformatics Trends

Correction to: Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2017: bioinformatics

BMC Bioinformatics - Wed, 15/11/2017 - 5:30am
After publication of this supplement [1], it was brought to our attention that the wrong year was used in the title of the supplement. The 16th Annual UT-KBRIN Bioinformatics Summit was held in 2017.
Categories: Bioinformatics Trends

ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data

BMC Bioinformatics - Tue, 14/11/2017 - 5:30am
With the development of chromosomal conformation capturing techniques, particularly, the Hi-C technique, the study of the spatial conformation of a genome is becoming an important topic in bioinformatics and c...
Categories: Bioinformatics Trends

Random walks on mutual microRNA-target gene interaction network improve the prediction of disease-associated microRNAs

BMC Bioinformatics - Tue, 14/11/2017 - 5:30am
MicroRNAs (miRNAs) have been shown to play an important role in pathological initiation, progression and maintenance. Because identification in the laboratory of disease-related miRNAs is not straightforward, ...
Categories: Bioinformatics Trends

Analysis of breast cancer subtypes by AP-ISA biclustering

BMC Bioinformatics - Tue, 14/11/2017 - 5:30am
Gene expression profiling has led to the definition of breast cancer molecular subtypes: Basal-like, HER2-enriched, LuminalA, LuminalB and Normal-like. Different subtypes exhibit diverse responses to treatment...
Categories: Bioinformatics Trends

GFF3sort: a novel tool to sort GFF3 files for tabix indexing

BMC Bioinformatics - Tue, 14/11/2017 - 5:30am
The traditional method of visualizing gene annotation data in JBrowse is converting GFF3 files to JSON format, which is time-consuming. The latest version of JBrowse supports rendering sorted GFF3 files indexe...
Categories: Bioinformatics Trends

fLPS: Fast discovery of compositional biases for the protein universe

BMC Bioinformatics - Mon, 13/11/2017 - 5:30am
Proteins often contain regions that are compositionally biased (CB), i.e., they are made from a small subset of amino-acid residue types. These CB regions can be functionally important, e.g., the prion-forming...
Categories: Bioinformatics Trends

The interplay of demography and selection during maize domestication and expansion

Genome Biology - BiomedCentral - Mon, 13/11/2017 - 5:30am
The history of maize has been characterized by major demographic events, including population size changes associated with domestication and range expansion, and gene flow with wild relatives. The interplay be...
Categories: Bioinformatics Trends

The interplay of demography and selection during maize domestication and expansion

Genome Biology - Mon, 13/11/2017 - 5:30am
The history of maize has been characterized by major demographic events, including population size changes associated with domestication and range expansion, and gene flow with wild relatives. The interplay be...
Categories: Bioinformatics Trends

A fragment based method for modeling of protein segments into cryo-EM density maps

BMC Bioinformatics - Mon, 13/11/2017 - 5:30am
Single-particle analysis of electron cryo-microscopy (cryo-EM) is a key technology for elucidation of macromolecular structures. Recent technical advances in hardware and software developments significantly en...
Categories: Bioinformatics Trends

BugMat and FindNeighbour: command line and server applications for investigating bacterial relatedness

BMC Bioinformatics - Mon, 13/11/2017 - 5:30am
Large scale bacterial sequencing has made the determination of genetic relationships within large sequence collections of bacterial genomes derived from the same microbial species an increasingly common task. ...
Categories: Bioinformatics Trends

Reference-guided de novo assembly approach improves genome reconstruction for related species

BMC Bioinformatics - Fri, 10/11/2017 - 5:30am
The development of next-generation sequencing has made it possible to sequence whole genomes at a relatively low cost. However, de novo genome assemblies remain challenging due to short read length, missing da...
Categories: Bioinformatics Trends
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