A draft genome assembly of the solar-powered sea slug Elysia chlorotica

Active Host Response to Algal Symbionts in the Sea Slug Elysia chlorotica

(2018) Cheong Xin Chan et al.   MOLECULAR BIOLOGY AND EVOLUTION

UniProt: the universal protein knowledgebase

(2018) The UniProt Consortium   NUCLEIC ACIDS RESEARCH

The Whole-Genome and Transcriptome of the Manila Clam (Ruditapes philippinarum)

(2017) Seyoung Mun et al.   Genome Biology and Evolution

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Whole genome analysis of a schistosomiasis-transmitting freshwater snail

(2017) Coen M. Adema et al.   Nature Communications

Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes

(2017) Jin Sun et al.   Nature Ecology & Evolution

Scallop genome provides insights into evolution of bilaterian karyotype and development

(2017) Shi Wang et al.   Nature Ecology & Evolution

DOGMA: domain-based transcriptome and proteome quality assessment

(2016) Elias Dohmen et al.   BIOINFORMATICS

A Preliminary Molecular and Phylogenetic Analysis of the Genome of a Novel Endogenous Retrovirus in the Sea Slug Elysia chlorotica

(2016) Sidney K. Pierce et al.   BIOLOGICAL BULLETIN

Draft genome of the leopard gecko, Eublepharis macularius

(2016) Zijun Xiong et al.   GigaScience

Molecular Phylogeny of the Sacoglossa, With a Discussion of Gain and Loss of Kleptoplasty in the Evolution of the Group

(2016) Taro Maeda et al.   BIOLOGICAL BULLETIN

FISH Labeling Reveals a Horizontally Transferred Algal (Vaucheria litorea) Nuclear Gene on a Sea Slug (Elysia chlorotica) Chromosome

(2016) Julie A. Schwartz et al.   BIOLOGICAL BULLETIN

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Sacoglossan sea slugs make routine use of photosynthesis by a variety of species-specific adaptations

(2015) Sidney K. Pierce et al.   INVERTEBRATE BIOLOGY

The octopus genome and the evolution of cephalopod neural and morphological novelties

(2015) Caroline B. Albertin et al.   NATURE

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

PANTHER version 10: expanded protein families and functions, and analysis tools

(2015) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

PBHoney: identifying genomic variants via long-read discordance and interrupted mapping

(2014) Adam C English et al.   BMC BIOINFORMATICS

SMART: recent updates, new developments and status in 2015

(2014) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

High-Resolution Linkage and Quantitative Trait Locus Mapping Aided by Genome Survey Sequencing: Building Up An Integrative Genomic Framework for a Bivalve Mollusc

(2013) W. Jiao et al.   DNA RESEARCH

Genome Analysis of Elysia chlorotica Egg DNA Provides No Evidence for Horizontal Gene Transfer into the Germ Line of This Kleptoplastic Mollusc

(2013) Debashish Bhattacharya et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

REAPR: a universal tool for genome assembly evaluation

(2013) Martin Hunt et al.   GENOME BIOLOGY

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

LIGHT-REGULATED PHOTOSYNTHETIC GENE EXPRESSION AND PHOSPHORIBULOKINASE ENZYME ACTIVITY IN THE HETEROKONT ALGA VAUCHERIA LITOREA (XANTHOPHYCEAE) AND ITS SYMBIOTIC MOLLUSKAN PARTNER ELYSIA CHLOROTICA (GASTROPODA)1

(2012) Kara M. Soule et al.   JOURNAL OF PHYCOLOGY

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

Insights into bilaterian evolution from three spiralian genomes

(2012) Oleg Simakov et al.   NATURE

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

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

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Transcriptomic Evidence for the Expression of Horizontally Transferred Algal Nuclear Genes in the Photosynthetic Sea Slug, Elysia chlorotica

(2011) Sidney K. Pierce et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sea Slug Kleptoplasty and Plastid Maintenance in a Metazoan

(2011) K. N. Pelletreau et al.   PLANT PHYSIOLOGY

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Using Algal Transcriptome Sequences to Identify Transferred Genes in the Sea Slug, Elysia chlorotica

(2010) Julie A. Schwartz et al.   Evolutionary Biology

The making of a photosynthetic animal

(2010) M. E. Rumpho et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chlorophyll a synthesis by an animal using transferred algal nuclear genes

(2010) Sidney K. Pierce et al.   SYMBIOSIS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Molecular Characterization of the Calvin Cycle Enzyme Phosphoribulokinase in the Stramenopile Alga Vaucheria litorea and the Plastid Hosting Mollusc Elysia chlorotica

(2009) Mary E. Rumpho et al.   Molecular Plant

PROSITE, a protein domain database for functional characterization and annotation

(2009) Christian J. A. Sigrist et al.   NUCLEIC ACIDS RESEARCH

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica

(2008) M. E. Rumpho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA