User profiles for L. Arvestad
Lars ArvestadStockholm 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
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 …
and economic importance. Here we present the draft assembly of the 20-gigabase genome …
Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms
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 …
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) …
… 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 l ∈ L(G) belongs to the genome of the species σ(l…
species tree S represent species, and the gene l ∈ L(G) belongs to the genome of the species σ(l…
[HTML][HTML] BESST-efficient scaffolding of large fragmented assemblies
… 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 …
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 …
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 …
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
… 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 …
acceptance probabilities of proposed states in our Markov chain. Such a posterior density …
The gene evolution model and computing its associated probabilities
… 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 …
… 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. …
… We decided to set B min = 10, T c = 0.75 and T l = 200 bp for all experiments on bacteria. …