Genomic insights into the coupling of a Chlorella-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno

Bacterial, Phytoplankton, and Viral Distributions and Their Biogeochemical Contexts in Meromictic Lake Cadagno Offer Insights into the Proterozoic Ocean Microbial Loop

(2022) Jaspreet S. Saini et al.   mBio

OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity

(2022) Dmitry Kuznetsov et al.   NUCLEIC ACIDS RESEARCH

Persistence of bioconvection‐induced mixed layers in a stratified lake

(2021) Oscar Sepúlveda Steiner et al.   LIMNOLOGY AND OCEANOGRAPHY

Sensitive protein alignments at tree-of-life scale using DIAMOND

(2021) Benjamin Buchfink et al.   NATURE METHODS

Nitrate and nitrite as mixed source of nitrogen for Chlorella vulgaris: Growth, nitrogen uptake and pigment contents

(2021) Victor Pozzobon et al.   BIORESOURCE TECHNOLOGY

KEGG mapping tools for uncovering hidden features in biological data

(2021) Minoru Kanehisa et al.   PROTEIN SCIENCE

Purple sulfur bacteria fix N2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue

(2021) Miriam Philippi et al.   Nature Communications

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

BlobToolKit - Interactive Quality Assessment of Genome Assemblies

(2020) Richard Challis et al.   G3-Genes Genomes Genetics

Accurate and complete genomes from metagenomes

(2020) Lin-Xing Chen et al.   GENOME RESEARCH

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

(2020) Eli Levy Karin et al.   Microbiome

OrthoDB in 2020: evolutionary and functional annotations of orthologs

(2020) Evgeny M Zdobnov et al.   NUCLEIC ACIDS RESEARCH

Characterization and expression profiles of small heat shock proteins in the marine red alga Pyropia yezoensis

(2019) Toshiki Uji et al.   CELL STRESS & CHAPERONES

Mixotrophic Growth Under Micro-Oxic Conditions in the Purple Sulfur Bacterium “Thiodictyon syntrophicum”

(2019) Samuel M. Luedin et al.   Frontiers in Microbiology

Draft Genome Sequence of Chromatium okenii Isolated from the Stratified Alpine Lake Cadagno

(2019) Samuel M. Luedin et al.   Scientific Reports

Dark aerobic sulfide oxidation by anoxygenic phototrophs in anoxic waters

(2019) Jasmine S. Berg et al.   ENVIRONMENTAL MICROBIOLOGY

Small heat shock protein genes of the green algae Closterium ehrenbergii : Cloning and differential expression under heat and heavy metal stresses

(2019) Sofia Abassi et al.   ENVIRONMENTAL TOXICOLOGY

Phosphorus cycling in Lake Cadagno, Switzerland: A low sulfate euxinic ocean analogue

(2019) Yijun Xiong et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Heat shock protein genes in the green alga Tetraselmis suecica and their role against redox and non-redox active metals

(2019) Ramaraj Sathasivam et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Iron isotope transformations in the meromictic Lake Cadagno

(2019) Michael J. Ellwood et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

New perspectives on crassulacean acid metabolism biology

(2019) Kevin R Hultine et al.   JOURNAL OF EXPERIMENTAL BOTANY

Combining morphology, behaviour and genomics to understand the evolution and ecology of microbial eukaryotes

(2019) Patrick J. Keeling   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Nanoplanktonic diatoms are globally overlooked but play a role in spring blooms and carbon export

(2018) Karine Leblanc et al.   Nature Communications

Complete genome sequence of “Thiodictyon syntrophicum” sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno

(2018) Samuel M. Luedin et al.   Standards in Genomic Sciences

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Removal of H 2 S by a continuous microalgae-based photosynthetic biogas upgrading process

(2018) Leslie Meier et al.   PROCESS SAFETY AND ENVIRONMENTAL PROTECTION

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs

(2018) Evgenia V Kriventseva et al.   NUCLEIC ACIDS RESEARCH

Bacterial diversity in the water column of meromictic Lake Cadagno and evidence for seasonal dynamics

(2018) Francesco Danza et al.   PLoS One

Carbon isotope fractionation by anoxygenic phototrophic bacteria in euxinic Lake Cadagno

(2017) N. R. Posth et al.   Geobiology

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

More protist genomes needed

(2017) Shannon J. Sibbald et al.   Nature Ecology & Evolution

Intensive cryptic microbial iron cycling in the low iron water column of the meromictic Lake Cadagno

(2016) Jasmine S. Berg et al.   ENVIRONMENTAL MICROBIOLOGY

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

The BIG Data Center: from deposition to integration to translation

(2016)   NUCLEIC ACIDS RESEARCH

AMAS: a fast tool for alignment manipulation and computing of summary statistics

(2016) Marek L. Borowiec   PeerJ

Methane oxidation coupled to oxygenic photosynthesis in anoxic waters

(2015) Jana Milucka et al.   ISME Journal

Diversity of nitrogen assimilation pathways among microbial photosynthetic eukaryotes

(2015) Ramon Terrado et al.   JOURNAL OF PHYCOLOGY

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea, Antarctica

(2015) Tom O. Delmont et al.   Frontiers in Microbiology

Nitrate Storage and Dissimilatory Nitrate Reduction by Eukaryotic Microbes

(2015) Anja Kamp et al.   Frontiers in Microbiology

Understanding nitrate assimilation and its regulation in microalgae

(2015) Emanuel Sanz-Luque et al.   Frontiers in Plant Science

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

Algae Sense Exact Temperatures: Small Heat Shock Proteins Are Expressed at the Survival Threshold Temperature in Cyanidioschyzon merolae and Chlamydomonas reinhardtii

(2014) Yusuke Kobayashi et al.   Genome Biology and Evolution

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Phylogeny of C4-Photosynthesis Enzymes Based on Algal Transcriptomic and Genomic Data Supports an Archaeal/Proteobacterial Origin and Multiple Duplication for Most C4-Related Genes

(2014) Shan Chi et al.   PLoS One

Achieving pH control in microalgal cultures through fed-batch addition of stoichiometrically-balanced growth media

(2013) Megerle L Scherholz et al.   BMC BIOTECHNOLOGY

C4 photosynthesis

(2013) Elizabeth A. Kellogg   CURRENT BIOLOGY

CO2assimilation in the chemocline of Lake Cadagno is dominated by a few types of phototrophic purple sulfur bacteria

(2013) Nicola Storelli et al.   FEMS MICROBIOLOGY ECOLOGY

Combining sedimentological, trace metal (Mn, Mo) and molecular evidence for reconstructing past water-column redox conditions: The example of meromictic Lake Cadagno (Swiss Alps)

(2013) Stefanie B. Wirth et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Removal of nitrogen and phosphorus by Chlorella sorokiniana cultured heterotrophically in ammonia and nitrate

(2013) Sunjin Kim et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

Sonication-based isolation and enrichment of Chlorella protothecoides chloroplasts for Illumina genome sequencing

(2013) Angelina Angelova et al.   JOURNAL OF APPLIED PHYCOLOGY

aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity

(2013) Shigehiro Kuraku et al.   NUCLEIC ACIDS RESEARCH

Domain enhanced lookup time accelerated BLAST

(2012) Grzegorz M Boratyn et al.   Biology Direct

Heat shock protein HSP70B as a marker for genotype resistance to environmental stress in Chlorella species from contrasting habitats

(2012) Stephka Chankova et al.   GENE

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fine scale analysis of shifts in bacterial community structure in the chemocline of meromictic Lake Cadagno, Switzerland

(2012) Paola M.A. DECRISTOPHORIS et al.   JOURNAL OF LIMNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

(2012) Daniel H. Huson et al.   SYSTEMATIC BIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Comparative proteomics and activity of a green sulfur bacterium through the water column of Lake Cadagno, Switzerland

(2010) Kirsten S. Habicht et al.   ENVIRONMENTAL MICROBIOLOGY

High isotope fractionations during sulfate reduction in a low-sulfate euxinic ocean analog

(2010) Donald E. Canfield et al.   GEOLOGY

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

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Co-occurrence of denitrification and nitrogen fixation in a meromictic lake, Lake Cadagno (Switzerland)

(2009) Hannah Halm et al.   ENVIRONMENTAL MICROBIOLOGY

Dominance of a clonal green sulfur bacterial population in a stratified lake

(2009) Lea H. Gregersen et al.   FEMS MICROBIOLOGY ECOLOGY

The behavior of molybdenum and its isotopes across the chemocline and in the sediments of sulfidic Lake Cadagno, Switzerland

(2009) Tais W. Dahl et al.   GEOCHIMICA ET COSMOCHIMICA ACTA