Anders Larsson

• PhD
• Bioinformatician at Uppsala University

AliView is an alignment viewer and editor designed to meet the requirements of next-generation sequencing era phylogenetic datasets. AliView handles alignments of unlimited size in the formats most commonly used, i.e. FASTA, Phylip, Nexus, Clustal and MSF. The intuitive graphical interface makes it easy to inspect, sort, delete, merge and realign s...

Backbone relationships within the large eupolypod II clade, which includes nearly a third of extant fern species, have resisted elucidation by both molecular and morphological data. Earlier studies suggest that much of the phylogenetic intractability of this group is due to three factors: (i) a long root that reduces apparent levels of support in t...

We present a family-level classification for the eupolypod II clade of leptosporangiate ferns, one of the two major lineages within the Eupolypods, and one of the few parts of the fern tree of life where family-level relationships were not well understood at the time of publication of the 2006 fern classification by Smith & al. Comprising over 2500...

Background: Molecular phylogenetic investigations have revolutionized our understanding of the evolutionary history of ferns-the second-most species-rich major group of vascular plants, and the sister clade to seed plants. The general absence of genomic resources available for this important group of plants, however, has resulted in the strong dep...

Significance Despite being one of the oldest groups of land plants, the majority of living ferns resulted from a relatively recent diversification following the rise of angiosperms. To exploit fully the new habitats created by angiosperm-dominated ecosystems, ferns had to evolve novel adaptive strategies to cope with the low-light conditions exerte...

Containers are gaining popularity in life science research as they provide a solution for encompassing dependencies of provisioned tools, simplify software installations for end users and offer a form of isolation between processes. Scientific workflows are ideal for chaining containers into data analysis pipelines to aid in creating reproducible a...

Background Identifying and assessing ligand-target binding is a core component in early drug discovery as one or more unwanted interactions may be associated with safety issues. Contributions We present an open-source, extendable web service for predicting target profiles with confidence using machine learning for a panel of 7 targets, where model...

Background Identifying and assessing ligand-target binding is a core component in early drug discovery as one or more unwanted interactions may be associated with safety issues. Contributions We present an open-source, extendable web service for predicting target profiles with confidence using machine learning for a panel of 7 targets, where models...

Background: Identifying and assessing ligand-target binding is a core component in early drug discovery as one or more unwanted interactions may be associated with safety issues. Contributions: We present an open-source, extendable web service for predicting target profiles with confidence using machine learning for a panel of 7 targets, where mode...

Containers are gaining popularity in life science research as they provide a solution for encompassing dependencies of provisioned tools, simplify software installations for end users and offer a form of isolation between processes. Scientific workflows are ideal for chaining containers into data analysis pipelines to aid in creating reproducible a...

Premise: Phylogenetic trees of bryophytes provide important evolutionary context for land plants. However, published inferences of overall embryophyte relationships vary considerably. We performed phylogenomic analyses of bryophytes and relatives using both mitochondrial and plastid gene sets, and investigated bryophyte plastome evolution. Method...

The computational demands for scientific applications are continuously increasing. The emergence of cloud computing has enabled on-demand resource allocation. However, relying solely on infrastructure as a service does not achieve the degree of flexibility required by the scientific community. Here we present a microservice-oriented methodology, wh...

Green plants (Viridiplantae) include around 450,000–500,000 species1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida),...

Green plants (Viridiplantae) include around 450,000–500,000 species1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida),...

Green plants (Viridiplantae) include around 450,000–500,000 species1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida),...

Background: Metabolomics datasets are becoming increasingly large and complex, with multiple types of algorithms and workflows needed to process and analyse the data. A cloud infrastructure with portable software tools can provide much needed resources enabling faster processing of much larger datasets than would be possible at any individual lab....

Motivation: Developing a robust and performant data analysis workflow that integrates all necessary components whilst still being able to scale over multiple compute nodes is a challenging task. We introduce a generic method based on the microservice architecture, where software tools are encapsulated as Docker containers that can be connected int...

Background Metabolomics is the comprehensive study of a multitude of small molecules to gain insight into an organism's metabolism. The research field is dynamic and expanding with applications across biomedical, biotechnological and many other applied biological domains. Its computationally-intensive nature has driven requirements for open data fo...

Making reproducible, auditable and scalable data-processing analysis workflows is an important challenge in the field of bioinformatics. Recently, software containers and cloud computing introduced a novel solution to address these challenges. They simplify software installation, management and reproducibility by packaging tools and their dependenc...

The new species Cucumis omissus Thulin from Yemen, Oman and Ethiopia is described and illustrated. According to phylogenetic analyses based mainly on nuclear ribosomal ITS sequences and chloroplast trnG sequences, the new species is sister to C. hastatus from Somalia and Ethiopia. A map showing the distributions of both C. omissus and C. hastatus i...

Background: Metabolomics is the comprehensive study of a multitude of small molecules to gain insight into an organism's metabolism. The research field is dynamic and expanding with applications across biomedical, biotechnological and many other applied biological domains. Its computationally-intensive nature has driven requirements for open data f...

Containers are gaining popularity in life science research as they encompass all dependencies of provisioned tools and simplifies software installations for end users, as well as offering a form of isolation between processes. Scientific workflows are ideal to chain containers into data analysis pipelines to sustain reproducible science. In this ma...

Containers are gaining popularity in life science research as they encompass all dependencies of provisioned tools and simplifies software installations for end users, as well as offering a form of isolation between processes. Scientific workflows are ideal to chain containers into data analysis pipelines to sustain reproducible science. In this ma...

Supplementary methods, tables and figures.

The genus Kewa in the monogeneric family Kewaceae (Caryophyllales) is revised. Six species are recognized, K. acida on St. Helena, K. angrae-pequenae in Namibia and South Africa, K. arenicola (incl. K. trachysperma) in South Africa, K. bowkeriana (incl. K. suffruticosa) widespread in eastern and southern Africa and inMadagascar, K. caespitosa in An...

Developing a robust and performant data analysis workflow that integrates all necessary components whilst still being able to scale over multiple compute nodes is a challenging task. We introduce a generic method based on the microservice architecture, where software tools are encapsulated as Docker containers that can be connected into scientific...

Microservices platforms, such as Kubernetes, have received a great deal of attention lately as they offer elastic and resilient orchestration for services implemented as portable, light-weight, software containers. While current solutions for cloud-based Kubernetes deployments are mainly focusing on maintaining long-running infrastructure, aimed to...

The draft genome of the moss model, Physcomitrella patens, comprised approximately 2,000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable ele...

Davalliaceae have been classified on the basis of morphological data or morphological and molecular data. The family has been divided into various genera, the circumscription of which may differ between authors. Previous phylogenetic analyses used limited numbers of genes and taxa. We studied the molecular phylogeny of the family by using two nucle...

Phylogeny has long informed pteridophyte classification. As our ability to infer evolutionary trees has improved, classifications aimed at recognizing natural groups have become increasingly predictive and stable. Here, we provide a modern, comprehensive classification for lycophytes and ferns, down to the genus level, utilizing a community-based a...

Significance Terpenoids are ubiquitous products made by land plants with diverse biological functions. Their formation in seed plants is catalyzed by typical plant terpene synthases (TPSs), a well-characterized group of enzymes. In contrast, our knowledge of terpenoid biosynthesis in nonseed plants is very limited. By systematically analyzing the t...

The circumscription of Molluginaceae has changed radically in recent years, with Corbichonia being moved to Lophiocarpaceae, Limeum to Limeaceae, Macarthuria to Macarthuriaceae and all species of Hypertelis, except the type, to Kewa in Kewaceae. In a broad analysis of core Caryophyllales using plastid trnK-matK and rbcL sequences, the position of M...

The anatomically simple plants that first colonised land must have acquired molecular and biochemical adaptations to drought stress. Abscisic acid (ABA) coordinates responses leading to desiccation tolerance in all land plants. We identified ABA non-responsive mutants in the model bryophyte Physcomitrella patens and genotyped a segregating populati...

• Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern ph...

We isolated Sindbis virus (SINV) from the enzootic mosquito vectors Culex torrentium, Cx. pipiens, and Culiseta morsitans collected in an area of Sweden where SINV disease is endemic. The infection rate in Cx. torrentium mosquitoes was exceptionally high (36 infections/1,000 mosquitoes), defining Cx. torrentium as the main enzootic vector of SINV i...