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Lars Arvestad, Ph.D. - Publications

Affiliations: 
KTH Royal Institute of Technology, Stockholm, Stockholms län, Sweden 
Website:
http://www.nada.kth.se/~arve/
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34 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Sullivan AR, Eldfjell Y, Schiffthaler B, Delhomme N, Asp T, Hebelstrup KH, Keech O, Öberg L, Møller IM, Arvestad L, Street NR, Wang XR. The mitogenome of Norway spruce and a reappraisal of mitochondrial recombination in plants. Genome Biology and Evolution. PMID 31774499 DOI: 10.1093/Gbe/Evz263  0.376
2019 Klinter S, Bulone V, Arvestad L. Diversity and evolution of chitin synthases in oomycetes (Straminipila: Oomycota). Molecular Phylogenetics and Evolution. 106558. PMID 31288106 DOI: 10.1016/J.Ympev.2019.106558  0.319
2018 Duchemin W, Gence G, Arigon Chifolleau AM, Arvestad L, Bansal MS, Berry V, Boussau B, Chevenet F, Comte N, Davín AA, Dessimoz C, Dylus D, Hasic D, Mallo D, Planel R, et al. RecPhyloXML - a format for reconciled gene trees. Bioinformatics (Oxford, England). PMID 29762653 DOI: 10.1093/Bioinformatics/Bty389  0.394
2017 Ali RH, Bark M, Miró J, Muhammad SA, Sjöstrand J, Zubair SM, Abbas RM, Arvestad L. VMCMC: a graphical and statistical analysis tool for Markov chain Monte Carlo traces. Bmc Bioinformatics. 18: 97. PMID 28187712 DOI: 10.1186/S12859-017-1505-3  0.312
2016 Sahlin K, Frånberg M, Arvestad L. Structural Variation Detection with Read Pair Information: An Improved Null Hypothesis Reduces Bias. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 27681236 DOI: 10.1089/Cmb.2016.0124  0.373
2016 Ali RH, Muhammad SA, Arvestad L. GenFamClust: an accurate, synteny-aware and reliable homology inference algorithm. Bmc Evolutionary Biology. 16: 120. PMID 27260514 DOI: 10.1186/S12862-016-0684-2  0.458
2016 Sahlin K, Chikhi R, Arvestad L. Assembly scaffolding with PE-contaminated mate-pair libraries. Bioinformatics (Oxford, England). PMID 27153683 DOI: 10.1093/Bioinformatics/Btw064  0.351
2015 Mahmudi O, Sennblad B, Arvestad L, Nowick K, Lagergren J. Gene-pseudogene evolution: a probabilistic approach. Bmc Genomics. 16: S12. PMID 26449131 DOI: 10.1186/1471-2164-16-S10-S12  0.397
2014 Sahlin K, Vezzi F, Nystedt B, Lundeberg J, Arvestad L. BESST--efficient scaffolding of large fragmented assemblies. Bmc Bioinformatics. 15: 281. PMID 25128196 DOI: 10.1186/1471-2105-15-281  0.379
2014 Sjöstrand J, Tofigh A, Daubin V, Arvestad L, Sennblad B, Lagergren J. A Bayesian method for analyzing lateral gene transfer. Systematic Biology. 63: 409-20. PMID 24562812 DOI: 10.1093/Sysbio/Syu007  0.461
2013 Khan MA, Elias I, Sjölund E, Nylander K, Guimera RV, Schobesberger R, Schmitzberger P, Lagergren J, Arvestad L. Fastphylo: fast tools for phylogenetics. Bmc Bioinformatics. 14: 334. PMID 24255987 DOI: 10.1186/1471-2105-14-334  0.336
2013 Kahles A, Sarqume F, Savolainen P, Arvestad L. Excap: maximization of haplotypic diversity of linked markers. Plos One. 8: e79012. PMID 24244403 DOI: 10.1371/Journal.Pone.0079012  0.328
2013 Vicedomini R, Vezzi F, Scalabrin S, Arvestad L, Policriti A. GAM-NGS: genomic assemblies merger for next generation sequencing. Bmc Bioinformatics. 14: S6. PMID 23815503 DOI: 10.1186/1471-2105-14-S7-S6  0.376
2013 Sjöstrand J, Arvestad L, Lagergren J, Sennblad B. GenPhyloData: realistic simulation of gene family evolution. Bmc Bioinformatics. 14: 209. PMID 23803001 DOI: 10.1186/1471-2105-14-209  0.412
2013 Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin YC, Scofield DG, Vezzi F, Delhomme N, Giacomello S, Alexeyenko A, Vicedomini R, Sahlin K, Sherwood E, Elfstrand M, Gramzow L, ... ... Arvestad L, et al. The Norway spruce genome sequence and conifer genome evolution. Nature. 497: 579-84. PMID 23698360 DOI: 10.1038/Nature12211  0.408
2012 Sjöstrand J, Sennblad B, Arvestad L, Lagergren J. DLRS: gene tree evolution in light of a species tree. Bioinformatics (Oxford, England). 28: 2994-5. PMID 22982573 DOI: 10.1093/Bioinformatics/Bts548  0.457
2012 Sahlin K, Street N, Lundeberg J, Arvestad L. Improved gap size estimation for scaffolding algorithms. Bioinformatics (Oxford, England). 28: 2215-22. PMID 22923455 DOI: 10.1093/Bioinformatics/Bts441  0.348
2010 Frygelius J, Arvestad L, Wedell A, Töhönen V. Evolution and human tissue expression of the Cres/Testatin subgroup genes, a reproductive tissue specific subgroup of the type 2 cystatins. Evolution & Development. 12: 329-42. PMID 20565543 DOI: 10.1111/J.1525-142X.2010.00418.X  0.388
2010 Stranneheim H, Käller M, Allander T, Andersson B, Arvestad L, Lundeberg J. Classification of DNA sequences using Bloom filters. Bioinformatics (Oxford, England). 26: 1595-600. PMID 20472541 DOI: 10.1093/Bioinformatics/Btq230  0.389
2009 Fugelstad J, Bouzenzana J, Djerbi S, Guerriero G, Ezcurra I, Teeri TT, Arvestad L, Bulone V. Identification of the cellulose synthase genes from the Oomycete Saprolegnia monoica and effect of cellulose synthesis inhibitors on gene expression and enzyme activity. Fungal Genetics and Biology : Fg & B. 46: 759-67. PMID 19589393 DOI: 10.1016/J.Fgb.2009.07.001  0.342
2009 Akerborg O, Sennblad B, Arvestad L, Lagergren J. Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proceedings of the National Academy of Sciences of the United States of America. 106: 5714-9. PMID 19299507 DOI: 10.1073/Pnas.0806251106  0.463
2009 Arvestad L, Lagergren J, Sennblad B. The gene evolution model and computing its associated probabilities Journal of the Acm. 56. DOI: 10.1145/1502793.1502796  0.454
2007 Sennblad B, Schreil E, Berglund Sonnhammer AC, Lagergren J, Arvestad L. primetv: a viewer for reconciled trees. Bmc Bioinformatics. 8: 148. PMID 17484781 DOI: 10.1186/1471-2105-8-148  0.379
2007 Roth C, Rastogi S, Arvestad L, Dittmar K, Light S, Ekman D, Liberles DA. Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 308: 58-73. PMID 16838295 DOI: 10.1002/Jez.B.21124  0.415
2006 Arvestad L. Efficient methods for estimating amino acid replacement rates. Journal of Molecular Evolution. 62: 663-73. PMID 16752207 DOI: 10.1007/S00239-004-0113-9  0.386
2006 Svensson O, Arvestad L, Lagergren J. Genome-wide survey for biologically functional pseudogenes. Plos Computational Biology. 2: e46. PMID 16680195 DOI: 10.1371/Journal.Pcbi.0020046  0.419
2005 Arvestad L, Visa N, Lundeberg J, Wieslander L, Savolainen P. Expressed sequence tags from the midgut and an epithelial cell line of Chironomus tentans: annotation, bioinformatic classification of unknown transcripts and analysis of expression levels. Insect Molecular Biology. 14: 689-95. PMID 16313569 DOI: 10.1111/J.1365-2583.2005.00600.X  0.441
2005 Savolainen P, Fitzsimmons C, Arvestad L, Andersson L, Lundeberg J. ESTs from brain and testis of White Leghorn and red junglefowl: annotation, bioinformatic classification of unknown transcripts and analysis of expression levels. Cytogenetic and Genome Research. 111: 79-87. PMID 16093725 DOI: 10.1159/000085674  0.425
2005 Hollich V, Milchert L, Arvestad L, Sonnhammer EL. Assessment of protein distance measures and tree-building methods for phylogenetic tree reconstruction. Molecular Biology and Evolution. 22: 2257-64. PMID 16049194 DOI: 10.1093/Molbev/Msi224  0.422
2005 Djerbi S, Lindskog M, Arvestad L, Sterky F, Teeri TT. The genome sequence of black cottonwood (Populus trichocarpa) reveals 18 conserved cellulose synthase (CesA) genes. Planta. 221: 739-46. PMID 15940463 DOI: 10.1007/S00425-005-1498-4  0.476
2004 Arvestad L, Berglund AC, Lagergren J, Sennblad B. Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 8: 326-335.  0.369
2003 Arvestad L, Berglund AC, Lagergren J, Sennblad B. Bayesian gene/species tree reconciliation and orthology analysis using MCMC. Bioinformatics (Oxford, England). 19: i7-15. PMID 12855432 DOI: 10.1093/Bioinformatics/Btg1000  0.368
2000 Savolainen P, Arvestad L, Lundeberg J. A novel method for forensic DNA investigations: repeat-type sequence analysis of tandemly repeated mtDNA in domestic dogs. Journal of Forensic Sciences. 45: 990-9. PMID 11005171 DOI: 10.1520/Jfs14820J  0.391
1997 Arvestad L, Bruno WJ. Estimation of reversible substitution matrices from multiple pairs of sequences. Journal of Molecular Evolution. 45: 696-703. PMID 9419247 DOI: 10.1007/Pl00006274  0.573
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