Browsing Department of Informatics by Journals "Bioinformatics"

Now showing items 1-7 of 7

    • Characteristics of 454 pyrosequencing data—enabling realistic simulation with flowsim 

      Balzer, Susanne Mignon; Malde, Ketil; Lanzén, Anders; Sharma, Animesh; Jonassen, Inge (Peer reviewed; Journal article, 2010)
      Motivation: The commercial launch of 454 pyrosequencing in 2005was a milestone in genome sequencing in terms of performance and cost. Throughout the three available releases, average read lengths have increased to ∼500 ...

    • Filtering duplicate reads from 454 pyrosequencing data 

      Balzer, Susanne Mignon; Malde, Ketil; Grohme, Markus A.; Jonassen, Inge (Peer reviewed; Journal article, 2013)
      Motivation: Throughout the recent years, 454 pyrosequencing has emerged as an efficient alternative to traditional Sanger sequencing and is widely used in both de novo whole-genome sequencing and metagenomics. Especially ...

    • Model-based clustering of multi-tissue gene expression data 

      Erola, Pau; Björkegren, Johan L.M.; Michoel, Tom Luk Robert (Journal article; Peer reviewed, 2020)
      Motivation Recently, it has become feasible to generate large-scale, multi-tissue gene expression data, where expression profiles are obtained from multiple tissues or organs sampled from dozens to hundreds of individuals. ...

    • Precrec: fast and accurate precision-recall and ROC curve calculations in R 

      Saito, Takaya; Rehmsmeier, Marc (Peer reviewed; Journal article, 2017)
      The precision–recall plot is more informative than the ROC plot when evaluating classifiers on imbalanced datasets, but fast and accurate curve calculation tools for precision–recall plots are currently not available. We ...

    • Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data 

      Xue, Yaxin; Lanzén, Anders; Jonassen, Inge (Journal article; Peer reviewed, 2020-03-13)
      Motivation Technological advances in meta-transcriptomics have enabled a deeper understanding of the structure and function of microbial communities. ‘Total RNA’ meta-transcriptomics, sequencing of total reverse transcribed ...

    • SeeCiTe: a method to assess CNV calls from SNP arrays using trio data 

      Lavrichenko, Ksenia; Helgeland, Øyvind; Njølstad, Pål Rasmus; Jonassen, Inge; Johansson, Stefan (Journal article; Peer reviewed, 2021)
      Motivation Single nucleotide polymorphism (SNP) genotyping arrays remain an attractive platform for assaying copy number variants (CNVs) in large population-wide cohorts. However, current tools for calling CNVs are still ...

    • Systematic exploration of error sources in pyrosequencing flowgram data 

      Balzer, Susanne Mignon; Malde, Ketil; Jonassen, Inge (Peer reviewed; Journal article, 2011)
      Motivation: 454 pyrosequencing, by Roche Diagnostics, has emerged as an alternative to Sanger sequencing when it comes to read lengths, performance and cost, but shows higher per-base error rates. Although there are several ...