I work computational problems in molecular biology, primarily related to evolution and genomics. The work on evolution has focused on models, methods, and software for estimating phylogenetic trees (and related parameters) for genes with the additional information of a species tree. Such additional information turns out to be highly valuable and inferred gene trees are far more accurate than based only on gene sequences. In genomics, we have recently paid a lot of attention to the scaffolding problem and have provided the scaffolder that was used in the spruce genome project.
Sahlin K, Chikhi R, Arvestad L (2016) “Assembly scaffolding with PE-contaminated mate-pair libraries.” Bioinformatics 32(13), 1925-1932
Sahlin K, Franberg M, Arvestad L (2016) “Structural Variation Detection with Read Pair Information: An Improved Null Hypothesis Reduces Bias.” J Comput Biol
Sahlin et al (2014) “BESST-Efficient scaffolding of large fragmented assemblies”, BMC Bioinformatics
- Ali R, Muhammad S, Khan M, Arvestad L (2013) “Quantitative synteny scoring improves homology inference and partitioning of gene families.” BMC Bioinformatics 14 Suppl 15, S12
- Sjöstrand J, Sennblad B, Arvestad L, Lagergren J (2012) “DLRS: gene tree evolution in light of a species tree.” Bioinformatics 28(22), 2994-2995