Saccharina genomes provide novel insight into kelp biology

The Vanadium Iodoperoxidase from the Marine Flavobacteriaceae Species Zobellia galactanivorans Reveals Novel Molecular and Evolutionary Features of Halide Specificity in the Vanadium Haloperoxidase Enzyme Family

(2014) Jean-Baptiste Fournier et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

TreSpEx–-Detection of Misleading Signal in Phylogenetic Reconstructions Based on Tree Information

(2014) Torsten H. Struck   Evolutionary Bioinformatics

RepARK—de novo creation of repeat libraries from whole-genome NGS reads

(2014) Philipp Koch et al.   NUCLEIC ACIDS RESEARCH

Sex-biased gene expression in the brown alga Fucus vesiculosus

(2013) Maria João F Martins et al.   BMC GENOMICS

Mannitol metabolism in brown algae involves a new phosphatase family

(2013) Agnès Groisillier et al.   JOURNAL OF EXPERIMENTAL BOTANY

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data

(2012) Jianxing Feng et al.   BIOINFORMATICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Seasonal variation in Laminaria digitata and its impact on biochemical conversion routes to biofuels

(2011) J.M.M. Adams et al.   BIORESOURCE TECHNOLOGY

Seaweed Polysaccharides and Derived Oligosaccharides Stimulate Defense Responses and Protection Against Pathogens in Plants

(2011) Jeannette Vera et al.   Marine Drugs

Highly Dynamic Exon Shuffling in Candidate Pathogen Receptors ... What if Brown Algae Were Capable of Adaptive Immunity?

(2011) A. Zambounis et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data

(2011) Ji Qi et al.   NUCLEIC ACIDS RESEARCH

Toward Systems Biology in Brown Algae to Explore Acclimation and Adaptation to the Shore Environment

(2011) Thierry Tonon et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

The Discovery of Zinc Fingers and Their Applications in Gene Regulation and Genome Manipulation

(2010) Aaron Klug   Annual Review of Biochemistry

A multi-locus time-calibrated phylogeny of the brown algae (Heterokonta, Ochrophyta, Phaeophyceae): Investigating the evolutionary nature of the “brown algal crown radiation”

(2010) Thomas Silberfeld et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Ectocarpus genome and the independent evolution of multicellularity in brown algae

(2010) J. Mark Cock et al.   NATURE

Autotrophic carbon fixation in archaea

(2010) Ivan A. Berg et al.   NATURE REVIEWS MICROBIOLOGY

The cell wall polysaccharide metabolism of the brown alga Ectocarpus siliculosus. Insights into the evolution of extracellular matrix polysaccharides in Eukaryotes

(2010) Gurvan Michel et al.   NEW PHYTOLOGIST

Central and storage carbon metabolism of the brown alga Ectocarpus siliculosus: insights into the origin and evolution of storage carbohydrates in Eukaryotes

(2010) Gurvan Michel et al.   NEW PHYTOLOGIST

Molecular characterization and differential expression of β-1,3-glucanase during ripening in banana fruit in response to ethylene, auxin, ABA, wounding, cold and light–dark cycles

(2010) Swarup Roy Choudhury et al.   PLANT CELL REPORTS

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

(2010) Dapeng Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

inGAP: an integrated next-generation genome analysis pipeline

(2009) Ji Qi et al.   BIOINFORMATICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Tracking the past: Interspersed repeats in an extinct Afrotherian mammal, Mammuthus primigenius

(2009) F. Zhao et al.   GENOME RESEARCH

Inferring weak population structure with the assistance of sample group information

(2009) MELISSA J. HUBISZ et al.   Molecular Ecology Resources

Patterns of gene expression induced by oligoguluronates reveal conserved and environment-specific molecular defense responses in the brown alga Laminaria digitata

(2009) Audrey Cosse et al.   NEW PHYTOLOGIST

The genome of the brown alga Ectocarpus siliculosus contains a series of viral DNA pieces, suggesting an ancient association with large dsDNA viruses

(2008) Nicolas Delaroque et al.   BMC EVOLUTIONARY BIOLOGY

Life-cycle-generation-specific developmental processes are modified in the immediate upright mutant of the brown alga Ectocarpus siliculosus

(2008) A. F. Peters et al.   DEVELOPMENT

The genusLaminaria sensu lato: recent insights and developments

(2008) Inka Bartsch et al.   EUROPEAN JOURNAL OF PHYCOLOGY

The Roco protein family: a functional perspective

(2008) Ignacio Marín et al.   FASEB JOURNAL

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

(2008) V. Ter-Hovhannisyan et al.   GENOME RESEARCH

Iodide accumulation provides kelp with an inorganic antioxidant impacting atmospheric chemistry

(2008) F. C. Kupper et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY