Reconstruction of protein domain evolution using single-cell amplified genomes of uncultured choanoflagellates sheds light on the origin of animals

Origin and evolution of plexins, semaphorins, and Met receptor tyrosine kinases

(2019) Chrystian Junqueira Alves et al.   Scientific Reports

Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty

(2018) Jordi Paps et al.   Nature Communications

Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity

(2018) David López-Escardó et al.   Scientific Reports

Gene family innovation, conservation and loss on the animal stem lineage

(2018) Daniel J Richter et al.   eLife

Mitochondrial Genome Evolution and a Novel RNA Editing System in Deep-Branching Heteroloboseids

(2017) Jiwon Yang et al.   Genome Biology and Evolution

A six-gene phylogeny provides new insights into choanoflagellate evolution

(2017) Martin Carr et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The origin of Metazoa: a unicellular perspective

(2017) Arnau Sebé-Pedrós et al.   NATURE REVIEWS GENETICS

Dynamics of genomic innovation in the unicellular ancestry of animals

(2017) Xavier Grau-Bové et al.   eLife

Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells

(2017) Jean-François Mangot et al.   Scientific Reports

Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis

(2017) David López-Escardó et al.   Scientific Reports

Nucleophosmin: from structure and function to disease development

(2016) Joseph K. Box et al.   BMC MOLECULAR BIOLOGY

The Evolution of Silicon Transport in Eukaryotes

(2016) Alan O. Marron et al.   MOLECULAR BIOLOGY AND EVOLUTION

Origin of animal multicellularity: precursors, causes, consequences—the choanoflagellate/sponge transition, neurogenesis and the Cambrian explosion

(2016) Thomas Cavalier-Smith   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Conserved expression of vertebrate microvillar gene homologs in choanocytes of freshwater sponges

(2016) Jesús F. Peña et al.   EvoDevo

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi

(2015) Guifré Torruella et al.   CURRENT BIOLOGY

Bacterial proteins pinpoint a single eukaryotic root

(2015) Romain Derelle 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

Open science resources for the discovery and analysis of Tara Oceans data

(2015) Stéphane Pesant et al.   Scientific Data

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The Early Expansion and Evolutionary Dynamics of POU Class Genes

(2014) David A. Gold et al.   MOLECULAR BIOLOGY AND EVOLUTION

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

The others: our biased perspective of eukaryotic genomes

(2014) Javier del Campo et al.   TRENDS IN ECOLOGY & EVOLUTION

The Robustness of a Signaling Complex to Domain Rearrangements Facilitates Network Evolution

(2014) Paloma M. Sato et al.   PLOS BIOLOGY

The Genomic and Cellular Foundations of Animal Origins

(2013) Daniel J. Richter et al.   Annual Review of Genetics

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Strikingly Bacteria-Like and Gene-Rich Mitochondrial Genomes throughout Jakobid Protists

(2013) Gertraud Burger et al.   Genome Biology and Evolution

Neuroglobins, Pivotal Proteins Associated with Emerging Neural Systems and Precursors of Metazoan Globin Diversity

(2013) Christophe Lechauve et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Insights into the Origin of Metazoan Filopodia and Microvilli

(2013) Arnau Sebé-Pedrós et al.   MOLECULAR BIOLOGY AND EVOLUTION

Environmental Survey Meta-analysis Reveals Hidden Diversity among Unicellular Opisthokonts

(2013) Javier del Campo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages

(2013) A. de Mendoza et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Capsaspora genome reveals a complex unicellular prehistory of animals

(2013) Hiroshi Suga et al.   Nature Communications

Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta

(2013) Stephen R Fairclough et al.   GENOME BIOLOGY

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

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Unveiling Trophic Functions of Uncultured Protist Taxa by Incubation Experiments in the Brackish Baltic Sea

(2012) Felix Weber et al.   PLoS One

Molecular Phylogeny of Unikonts: New Insights into the Position of Apusomonads and Ancyromonads and the Internal Relationships of Opisthokonts

(2012) Jordi Paps et al.   PROTIST

Genomic Survey of Premetazoans Shows Deep Conservation of Cytoplasmic Tyrosine Kinases and Multiple Radiations of Receptor Tyrosine Kinases

(2012) H. Suga et al.   Science Signaling

Premetazoan Origin of the Hippo Signaling Pathway

(2012) Arnau Sebé-Pedrós et al.   Cell Reports

The Essential Role of Centrosomal NDE1 in Human Cerebral Cortex Neurogenesis

(2011) Mehmet Bakircioglu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Multiple Origins of Complex Multicellularity

(2011) Andrew H. Knoll   Annual Review of Earth and Planetary Sciences

Amino acids biosynthesis and nitrogen assimilation pathways: a great genomic deletion during eukaryotes evolution

(2011) RLM Guedes et al.   BMC GENOMICS

Unveiling in situ interactions between marine protists and bacteria through single cell sequencing

(2011) Manuel Martinez-Garcia et al.   ISME Journal

Primordial neurosecretory apparatus identified in the choanoflagellate Monosiga brevicollis

(2011) P. Burkhardt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A bacterial proteorhodopsin proton pump in marine eukaryotes

(2011) Claudio H. Slamovits et al.   Nature Communications

A Holistic Approach to Marine Eco-Systems Biology

(2011) Eric Karsenti et al.   PLOS BIOLOGY

Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires

(2011) Christian M Zmasek et al.   GENOME BIOLOGY

Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood

(2010) M. Csuos   BIOINFORMATICS

Somatic stem cells express Piwi and Vasa genes in an adult ctenophore: Ancient association of “germline genes” with stemness

(2010) Alexandre Alié et al.   DEVELOPMENTAL BIOLOGY

Capturing diversity of marine heterotrophic protists: one cell at a time

(2010) Jane L Heywood et al.   ISME Journal

Unexpected Repertoire of Metazoan Transcription Factors in the Unicellular Holozoan Capsaspora owczarzaki

(2010) A. Sebe-Pedros et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Amphimedon queenslandica genome and the evolution of animal complexity

(2010) Mansi Srivastava et al.   NATURE

Ancient origin of the integrin-mediated adhesion and signaling machinery

(2010) A. Sebe-Pedros et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

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

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Empirical profile mixture models for phylogenetic reconstruction

(2008) Le Si Quang et al.   BIOINFORMATICS

Unicellular Ca2+ Signaling 'Toolkit' at the Origin of Metazoa

(2008) X. Cai   MOLECULAR BIOLOGY AND EVOLUTION

The genetic and molecular basis of Fanconi anemia

(2008) Johan P. de Winter et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans

(2008) Nicole King et al.   NATURE

Multigene Phylogeny of Choanozoa and the Origin of Animals

(2008) Kamran Shalchian-Tabrizi et al.   PLoS One

Molecular phylogeny of choanoflagellates, the sister group to Metazoa

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

Three-dimensional images of choanoflagellate loricae

(2008) B. S.C Leadbeater et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES