MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics

MMseqs2 desktop and local web server app for fast, interactive sequence searches

(2019) M Mirdita et al.   BIOINFORMATICS

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands

(2019) Joanna Warwick-Dugdale et al.   PeerJ

Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold

(2019) Martin Steinegger et al.   NATURE METHODS

Parallelization of MAFFT for large-scale multiple sequence alignments

(2018) Tsukasa Nakamura et al.   BIOINFORMATICS

BMC3C: binning metagenomic contigs using codon usage, sequence composition and read coverage

(2018) Guoxian Yu et al.   BIOINFORMATICS

Genome-reconstruction for eukaryotes from complex natural microbial communities

(2018) Patrick T. West et al.   GENOME RESEARCH

Clustering huge protein sequence sets in linear time

(2018) Martin Steinegger et al.   Nature Communications

A global ocean atlas of eukaryotic genes

(2018) Quentin Carradec et al.   Nature Communications

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes

(2018) Tom O. Delmont et al.   Nature Microbiology

A Novel Eukaryotic Denitrification Pathway in Foraminifera

(2018) Christian Woehle et al.   CURRENT BIOLOGY

Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes

(2018) Gordon Lax et al.   NATURE

Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes

(2018) Lisa K Johnson et al.   GigaScience

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

(2017) Sergey Koren et al.   GENOME RESEARCH

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

GenBank

(2017) Dennis A Benson et al.   NUCLEIC ACIDS RESEARCH

Big-data approaches to protein structure prediction

(2017) Johannes Söding   SCIENCE

Protein structure determination using metagenome sequence data

(2017) Sergey Ovchinnikov et al.   SCIENCE

Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture

(2017) Connor B. Driscoll et al.   Standards in Genomic Sciences

Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics

(2017) Karel Sedlar et al.   Computational and Structural Biotechnology Journal

The new micro-kingdoms of eukaryotes

(2017) Jan Pawlowski   BMC BIOLOGY

Phylogenetic Resolution of Deep Eukaryotic and Fungal Relationships Using Highly Conserved Low-Copy Nuclear Genes

(2016) Ren Ren et al.   Genome Biology and Evolution

Antimicrobial Compounds from Eukaryotic Microalgae against Human Pathogens and Diseases in Aquaculture

(2016) Charlotte Falaise et al.   Marine Drugs

Uniclust databases of clustered and deeply annotated protein sequences and alignments

(2016) Milot Mirdita et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data

(2016) J. A. Frank et al.   Scientific Reports

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Algae as production systems of bioactive compounds

(2015) Izabela Michalak et al.   ENGINEERING IN LIFE SCIENCES

Defensive symbioses of animals with prokaryotic and eukaryotic microorganisms

(2015) Laura V. Flórez et al.   NATURAL PRODUCT REPORTS

DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity

(2015) Matthieu Leray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics

(2015) Alejandra Escobar-Zepeda et al.   Frontiers in Genetics

Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities

(2015) Markus Majaneva et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Symbiosis as a General Principle in Eukaryotic Evolution

(2014) A. E. Douglas   Cold Spring Harbor Perspectives in Biology

The Eukaryotic Tree of Life from a Global Phylogenomic Perspective

(2014) F. Burki   Cold Spring Harbor Perspectives in Biology

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing

(2014) Patrick J. Keeling et al.   PLOS BIOLOGY

Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity

(2014) Laura Wegener Parfrey et al.   Frontiers in Microbiology

Recovery of soil unicellular eukaryotes: An efficiency and activity analysis on the single cell level

(2013) Guillaume Lentendu et al.   JOURNAL OF MICROBIOLOGICAL METHODS

WebAUGUSTUS--a web service for training AUGUSTUS and predicting genes in eukaryotes

(2013) K. J. Hoff et al.   NUCLEIC ACIDS RESEARCH

Sequencing our way towards understanding global eukaryotic biodiversity

(2012) Holly M. Bik et al.   TRENDS IN ECOLOGY & EVOLUTION

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

Microbial Eukaryotes in the Human Microbiome: Ecology, Evolution, and Future Directions

(2011) Laura Wegener Parfrey et al.   Frontiers in Microbiology

Eukaryotic Picoplankton in Surface Oceans

(2010) Ramon Massana   Annual Review of Microbiology

The voyage of the microbial eukaryote

(2010) Alexandra Z Worden et al.   CURRENT OPINION IN MICROBIOLOGY

Significant CO2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean

(2010) Ludwig Jardillier et al.   ISME Journal

An Overview of Nested Genes in Eukaryotic Genomes

(2009) Anuj Kumar   EUKARYOTIC CELL

Direct mapping and alignment of protein sequences onto genomic sequence

(2008) Osamu Gotoh   BIOINFORMATICS