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Article
Full-length single-molecule protein fingerprinting
Proteins are the primary functional actors of the cell. While proteoform diversity is known to be highly biologically relevant, current protein analysis methods are of limited use for distinguishing proteoform...
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Article
Open AccessReply to: On the statistical foundation of a recent single molecule FRET benchmark
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Article
Open AccessA blind benchmark of analysis tools to infer kinetic rate constants from single-molecule FRET trajectories
Single-molecule FRET (smFRET) is a versatile technique to study the dynamics and function of biomolecules since it makes nanoscale movements detectable as fluorescence signals. The powerful ability to infer qu...
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Article
Open AccessThe Pectobacterium pangenome, with a focus on Pectobacterium brasiliense, shows a robust core and extensive exchange of genes from a shared gene pool
Bacterial plant pathogens of the Pectobacterium genus are responsible for a wide spectrum of diseases in plants, including important crops such as potato, tomato, lettuce, and banana. Investigation of the genetic...
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Article
Open AccessCAPICE: a computational method for Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations
Exome sequencing is now mainstream in clinical practice. However, identification of pathogenic Mendelian variants remains time-consuming, in part, because the limited accuracy of current computational predicti...
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Article
Open AccessHap10: reconstructing accurate and long polyploid haplotypes using linked reads
Haplotype information is essential for many genetic and genomic analyses, including genotype-phenotype associations in human, animals and plants. Haplotype assembly is a method for reconstructing haplotypes fr...
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Article
Open AccesspCADD: SNV prioritisation in Sus scrofa
In animal breeding, identification of causative genetic variants is of major importance and high economical value. Usually, the number of candidate variants exceeds the number of variants that can be validated...
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Article
Open AccessHecaton: reliably detecting copy number variation in plant genomes using short read sequencing data
Copy number variation (CNV) is thought to actively contribute to adaptive evolution of plant species. While many computational algorithms are available to detect copy number variation from whole genome sequenc...
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Article
Open AccessCorrecting palindromes in long reads after whole-genome amplification
Next-generation sequencing requires sufficient DNA to be available. If limited, whole-genome amplification is applied to generate additional amounts of DNA. Such amplification often results in many chimeric DN...
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Article
Open AccessPredicting variant deleteriousness in non-human species: applying the CADD approach in mouse
Predicting the deleteriousness of observed genomic variants has taken a step forward with the introduction of the Combined Annotation Dependent Depletion (CADD) approach, which trains a classifier on the wealt...
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Article
Open AccessEfficient inference of homologs in large eukaryotic pan-proteomes
Identification of homologous genes is fundamental to comparative genomics, functional genomics and phylogenomics. Extensive public homology databases are of great value for investigating homology but need to b...
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Article
Open AccessA survey of functional genomic variation in domesticated chickens
Deleterious genetic variation can increase in frequency as a result of mutations, genetic drift, and genetic hitchhiking. Although individual effects are often small, the cumulative effect of deleterious genet...
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Article
Open AccessSelected proceedings of Machine Learning in Systems Biology: MLSB 2016
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Article
Open AccessHeritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants
Asexual reproduction has the potential to enhance deleterious mutation accumulation and to constrain adaptive evolution. One source of mutations that can be especially relevant in recent asexuals is activity o...
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Article
Open AccessCnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data
Identification of biological specimens is a requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but generally do not scale to...
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Article
Open AccessSPiCE: a web-based tool for sequence-based protein classification and exploration
Amino acid sequences and features extracted from such sequences have been used to predict many protein properties, such as subcellular localization or solubility, using classifier algorithms. Although software...
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Article
Open AccessBeyond genomic variation - comparison and functional annotation of three Brassica rapagenomes: a turnip, a rapid cycling and a Chinese cabbage
Brassica rapa is an economically important crop species. During its long breeding history, a large number of morphotypes have been generated, including leafy vegetables such as Chinese cabbage and pakchoi, turnip...
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Article
Open AccessTopology of molecular interaction networks
Molecular interactions are often represented as network models which have become the common language of many areas of biology. Graphs serve as convenient mathematical representations of network models and have...
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Chapter and Conference Paper
Conditional Random Fields for Protein Function Prediction
Markov Random Fields (MRF) have been shown to be good predictors of functional annotation, using protein-protein interaction data. Many other sources of data can also be used in this prediction task, but they ...
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Chapter and Conference Paper
Using Predictive Models to Engineer Biology: A Case Study in Codon Optimization
Given recent advances in synthetic biology and DNA synthesis, there is an increasing need for carefully engineered biological parts (e.g. genes, promoter sequences or enzymes) and circuits. However, forward en...
