User profiles for L. Arvestad

Lars Arvestad

Stockholm University; Dept of Mathematics, and Swedish e-Science Research Center
Verified email at math.su.se
Cited by 3970

[HTML][HTML] The Norway spruce genome sequence and conifer genome evolution

…, K Vanneste, ZQ Wu, B Zhang, P Zerbe, L Arvestad… - Nature, 2013 - nature.com
Conifers have dominated forests for more than 200 million years and are of huge ecological
and economic importance. Here we present the draft assembly of the 20-gigabase genome …

Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms

C Roth, S Rastogi, L Arvestad, K Dittmar… - … Zoology Part B …, 2007 - Wiley Online Library
Gene duplication is postulated to have played a major role in the evolution of biological
novelty. Here, gene duplication is examined across levels of biological organization in an …

Simultaneous Bayesian gene tree reconstruction and reconciliation analysis

Ö Åkerborg, B Sennblad, L Arvestad… - Proceedings of the …, 2009 - National Acad Sciences
… of obtaining the planted subtree G u and lengths l when (i) a single gene tree vertex starts to
… The function σ is defined as follows: (i) for a leaf l of G, σ(l) is the species for gene l and (ii) …

[PDF][PDF] Bayesian gene/species tree reconciliation and orthology analysis using MCMC

L Arvestad, AC Berglund, J Lagergren… - Bioinformatics-Oxford, 2003 - csc.kth.se
… denoted L(… L(G) → L(S). Intuitively, leaves in a gene tree G represent genes, leaves in a
species tree S represent species, and the gene lL(G) belongs to the genome of the species σ(l

[HTML][HTML] BESST-efficient scaffolding of large fragmented assemblies

…, F Vezzi, B Nystedt, J Lundeberg, L Arvestad - BMC bioinformatics, 2014 - Springer
… By aligning all reads in on we can define the graph as follows: Each contig gives rise to
precisely two vertices c i,L and c i,R in where c i,L denotes it’s 5’ end and c i,R denotes it’s 3’ end …

The genome sequence of black cottonwood (Populus trichocarpa) reveals 18 conserved cellulose synthase (CesA) genes

S Djerbi, M Lindskog, L Arvestad, F Sterky, TT Teeri - Planta, 2005 - Springer
The genome sequence of Populus trichocarpa was screened for genes encoding cellulose
synthases by using full-length cDNA sequences and ESTs previously identified in the tissue …

Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution

L Arvestad, AC Berglund, J Lagergren… - Proceedings of the …, 2004 - dl.acm.org
l leaves to be generated can, hence, be expressed as a product a(Т)h(Т), where a(Т) is the
probability that the labeled tree has l leaves and h(Т) is the fraction all of labeled trees with l

A Bayesian method for analyzing lateral gene transfer

J Sjöstrand, A Tofigh, V Daubin, L Arvestad… - Systematic …, 2014 - academic.oup.com
… Ratios between posterior densities of the form p[G,l,θ|D] are computed in order to determine
acceptance probabilities of proposed states in our Markov chain. Such a posterior density …

The gene evolution model and computing its associated probabilities

L Arvestad, J Lagergren, B Sennblad - Journal of the ACM (JACM), 2009 - dl.acm.org
… We describe in detail the gene evolution model [Arvestad et al. 2003], a probabilistic model
… define l and l to be orthologs if and only if lca(l,l ) is a speciation with respect to γ; otherwise …

[HTML][HTML] GAM-NGS: genomic assemblies merger for next generation sequencing

R Vicedomini, F Vezzi, S Scalabrin, L Arvestad… - BMC …, 2013 - Springer
… Moreover, high values of T c or T l allow us to filter more blocks, running the risk of discarding
… We decided to set B min = 10, T c = 0.75 and T l = 200 bp for all experiments on bacteria. …