79 citations
6 papers
The Genomic HyperBrowser: inferential genomics at the sequence level
Geir K. Sandve, Sveinung Gundersen, Halfdan Rydbeck +11
The immense increase in the generation of genomic scale data poses an unmet analytical challenge, due to a lack of established methodology with the required flexibility and power.…
Application of new probabilistic graphical models in the genetic regulatory networks studies
Junbai Wang, Leo Wang-Kit Cheung, Jan Delabie
This paper introduces two new probabilistic graphical models for reconstruction of genetic regulatory networks using DNA microarray data. One is an Independence Graph (IG) model wi…
Segmentation of DNA sequences into twostate regions and melting fork regions
Eivind Tøstesen, Geir Kjetil Sandve, Fang Liu +1
The accurate prediction and characterization of DNA melting domains by computational tools could facilitate a broad range of biological applications. However, no algorithm for melt…
A stitch in time: Efficient computation of genomic DNA melting bubbles
Eivind Tøstesen
Background: It is of biological interest to make genome-wide predictions of the locations of DNA melting bubbles using statistical mechanics models. Computationally, this poses the…
Partly melted DNA conformations obtained with a probability peak finding method
E. Tostesen
Peaks in the probabilities of loops or bubbles, helical segments, and unzipping ends in melting DNA are found in this article using a peak finding method that maps the hierarchical…
Speed-Up of DNA Melting Algorithm with Complete Nearest Neighbor Properties
E. Tostesen, F. Liu, T. -K. Jenssen +1
We describe a faster and more accurate algorithm for computing the statistical mechanics of DNA denaturation according to the Poland-Scheraga type. Nearest neighbor thermodynamics…