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4,659 Newest Publications in bioinformatics

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Aligning dynamic networks with DynaWAVE

01-Feb-2018 | Vijayan V, Milenković T., Bioinformatics, 2018

Bioinformatics (2017) DOI: https://doi.org/10.1093/bioinformatics/btx841

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Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation

30-Jan-2018 | Armean I, Lilley K, Trotter M, et al., Bioinformatics, 2018

Abstract Motivation Protein–protein interactions (PPI) play a crucial role in our understanding of protein function and biological processes. The standardization and recording of experimental findings is increasingly stored in ontologies, with the Gene Ontology (GO) being one of the most ...

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DincRNA: a comprehensive web-based bioinformatics toolkit for exploring disease associations and ncRNA function

22-Jan-2018 | Cheng L, Hu Y, Sun J, et al., Bioinformatics, 2018

Abstract Summary DincRNA aims to provide a comprehensive web-based bioinformatics toolkit to elucidate the entangled relationships among diseases and non-coding RNAs (ncRNAs) from the perspective of disease similarity. The quantitative way to illustrate relationships of pair-wise diseases always ...

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ADEPTUS: a discovery tool for disease prediction, enrichment and network analysis based on profiles from many diseases

19-Jan-2018 | Amar D, Vizel A, Levy C, et al., Bioinformatics, 2018

Abstract Motivation Large-scale publicly available genomic data on many disease phenotypes could improve our understanding of the molecular basis of disease. Tools that undertake this challenge by jointly analyzing multiple phenotypes are needed. Results ADEPTUS is a web-tool that enables ...

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Sequanix: a dynamic graphical interface for Snakemake workflows

19-Jan-2018 | Desvillechabrol D, Legendre R, Rioualen C, et al., Bioinformatics, 2018

Abstract Summary We designed a PyQt graphical user interface—Sequanix—aimed at democratizing the use of Snakemake pipelines in the NGS space and beyond. By default, Sequanix includes Sequana NGS pipelines (Snakemake format) (http://sequana.readthedocs.io), and is also capable of loading any ...

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Primer3_masker: integrating masking of template sequence with primer design software

19-Jan-2018 | Kõressaar T, Lepamets M, Kaplinski L, et al., Bioinformatics, 2018

Abstract Summary Designing PCR primers for amplifying regions of eukaryotic genomes is a complicated task because the genomes contain a large number of repeat sequences and other regions unsuitable for amplification by PCR. We have developed a novel k-mer based masking method that uses a ...

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ST Spot Detector: a web-based application for automatic spot and tissue detection for spatial Transcriptomics image datasets

17-Jan-2018 | Wong K, Navarro J, Bergenstråhle L, et al., Bioinformatics, 2018

Abstract Motiviation Spatial Transcriptomics (ST) is a method which combines high resolution tissue imaging with high troughput transcriptome sequencing data. This data must be aligned with the images for correct visualization, a process that involves several manual steps. Results Here we ...

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Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer

12-Jan-2018 | Afsari B, Guo T, Considine M, et al., Bioinformatics, 2018

Abstract Motivation Current bioinformatics methods to detect changes in gene isoform usage in distinct phenotypes compare the relative expected isoform usage in phenotypes. These statistics model differences in isoform usage in normal tissues, which have stable regulation of gene splicing. ...

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QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction

12-Jan-2018 | Deveau P, Colmet Daage L, Oldridge D, et al., Bioinformatics, 2018

Abstract Motivation In cancer, clonal evolution is assessed based on information coming from single nucleotide variants and copy number alterations. Nonetheless, existing methods often fail to accurately combine information from both sources to truthfully reconstruct clonal populations in a ...

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LeNup: learning nucleosome positioning from DNA sequences with improved convolutional neural networks

10-Jan-2018 | Zhang J, Peng W, Wang L., Bioinformatics, 2018

Abstract Motivation Nucleosome positioning plays significant roles in proper genome packing and its accessibility to execute transcription regulation. Despite a multitude of nucleosome positioning resources available on line including experimental datasets of genome-wide nucleosome occupancy ...

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