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

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

(2018) Jordi Paps et al.   Nature Communications

The Evolutionary Loss of RNAi Key Determinants in Kinetoplastids as a Multiple Sporadic Phenomenon

(2017) Andrey V. Matveyev et al.   JOURNAL OF MOLECULAR 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

The SARM1 Toll/Interleukin-1 Receptor Domain Possesses Intrinsic NAD + Cleavage Activity that Promotes Pathological Axonal Degeneration

(2017) Kow Essuman et al.   NEURON

WormBase 2017: molting into a new stage

(2017) Raymond Y N Lee et al.   NUCLEIC ACIDS RESEARCH

The NBS-LRR architectures of plant R-proteins and metazoan NLRs evolved in independent events

(2017) Jonathan M. Urbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sea anemone model has a single Toll-like receptor that can function in pathogen detection, NF-κB signal transduction, and development

(2017) Joseph J. Brennan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Innovation and constraint leading to complex multicellularity in the Ascomycota

(2017) Tu Anh Nguyen et al.   Nature Communications

Dynamics of genomic innovation in the unicellular ancestry of animals

(2017) Xavier Grau-Bové et al.   eLife

Animal multicellularity and polarity without Wnt signaling

(2017) Quentin Schenkelaars et al.   Scientific Reports

The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity

(2016) Arnau Sebé-Pedrós et al.   CELL

High-Throughput Proteomics Reveals the Unicellular Roots of Animal Phosphosignaling and Cell Differentiation

(2016) Arnau Sebé-Pedrós et al.   DEVELOPMENTAL CELL

An automated system for evaluation of the potential functionome: MAPLE version 2.1.0

(2016) Hideto Takami et al.   DNA RESEARCH

Standardized benchmarking in the quest for orthologs

(2016) Adrian M Altenhoff et al.   NATURE METHODS

Evolution by gene loss

(2016) Ricard Albalat et al.   NATURE REVIEWS GENETICS

Database Resources of the National Center for Biotechnology Information

(2016)   NUCLEIC ACIDS RESEARCH

FlyBase at 25: looking to the future

(2016) L. Sian Gramates et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Phylogenetic evidence for the modular evolution of metazoan signalling pathways

(2016) Leslie S. Babonis et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Bacterial lipids activate, synergize, and inhibit a developmental switch in choanoflagellates

(2016) Arielle Woznica et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista

(2016) Fabien Burki et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Losing Complexity: The Role of Simplification in Macroevolution

(2016) Maureen A. O’Malley et al.   TRENDS IN ECOLOGY & EVOLUTION

The multicellularity genes of dictyostelid social amoebas

(2016) Gernot Glöckner et al.   Nature Communications

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

Genomic data do not support comb jellies as the sister group to all other animals

(2015) Davide Pisani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic insights into the evolutionary origin of Myxozoa within Cnidaria

(2015) E. Sally Chang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals

(2015) Alex de Mendoza et al.   eLife

Metabolic and Chaperone Gene Loss Marks the Origin of Animals: Evidence for Hsp104 and Hsp78 Chaperones Sharing Mitochondrial Enzymes as Clients

(2015) Albert J. Erives et al.   PLoS One

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

The Eukaryotic Ancestor Had a Complex Ubiquitin Signaling System of Archaeal Origin

(2014) Xavier Grau-Bové et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Analysis of Eight Transcriptomes from All Poriferan Classes Reveals Surprising Genetic Complexity in Sponges

(2014) Ana Riesgo et al.   MOLECULAR BIOLOGY AND EVOLUTION

The ctenophore genome and the evolutionary origins of neural systems

(2014) Leonid L. Moroz et al.   NATURE

Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes

(2014) Sofia A. V. Fortunato et al.   NATURE

Molecular evolutionary and structural analysis of the cytosolic DNA sensor cGAS and STING

(2014) Xiaomei Wu et al.   NUCLEIC ACIDS RESEARCH

Innate immune responses regulate morphogenesis and degeneration: roles of Toll-like receptors and Sarm1 in neurons

(2014) Hsin-Yu Liu et al.   Neuroscience Bulletin

The Genomic and Cellular Foundations of Animal Origins

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

Genome reduction as the dominant mode of evolution

(2013) Yuri I. Wolf et al.   BIOESSAYS

Evidence for Sex and Recombination in the Choanoflagellate Salpingoeca rosetta

(2013) Tera C. Levin et al.   CURRENT BIOLOGY

The Characterization of Sponge NLRs Provides Insight into the Origin and Evolution of This Innate Immune Gene Family in Animals

(2013) Benedict Yuen 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

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

The Innate Immunity Adaptor SARM Translocates to the Nucleus to Stabilize Lamins and Prevent DNA Fragmentation in Response to Pro-Apoptotic Signaling

(2013) Chad R. Sethman et al.   PLoS One

Early evolution of the T-box transcription factor family

(2013) A. Sebe-Pedros et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Animals in a bacterial world, a new imperative for the life sciences

(2013) Margaret McFall-Ngai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

The Capsaspora genome reveals a complex unicellular prehistory of animals

(2013) Hiroshi Suga et al.   Nature Communications

Regulated aggregative multicellularity in a close unicellular relative of metazoa

(2013) Arnau Sebé-Pedrós et al.   eLife

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

(2013) Stephen R Fairclough et al.   GENOME BIOLOGY

Recognition of Bacteria by Inflammasomes

(2012) Jakob von Moltke et al.   Annual Review of Immunology

How much does the amphioxus genome represent the ancestor of chordates?

(2012) A. Louis et al.   Briefings in Functional Genomics

NF-κB: where did it come from and why?

(2012) Thomas D. Gilmore et al.   IMMUNOLOGICAL REVIEWS

Streaming fragment assignment for real-time analysis of sequencing experiments

(2012) Adam Roberts et al.   NATURE METHODS

RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

(2012) M. Lohse et al.   NUCLEIC ACIDS RESEARCH

Enhanced Hippocampal Long-Term Potentiation and Fear Memory in Btbd9 Mutant Mice

(2012) Mark P. DeAndrade et al.   PLoS One

The Evolution and Origin of Animal Toll-Like Receptor Signaling Pathway Revealed by Network-Level Molecular Evolutionary Analyses

(2012) Xiaojun Song et al.   PLoS One

Origin of metazoan cadherin diversity and the antiquity of the classical cadherin/ -catenin complex

(2012) S. A. Nichols et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Premetazoan Origin of the Hippo Signaling Pathway

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

A bacterial sulfonolipid triggers multicellular development in the closest living relatives of animals

(2012) Rosanna A Alegado et al.   eLife

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

Cell differentiation and morphogenesis in the colony-forming choanoflagellate Salpingoeca rosetta

(2011) Mark J. Dayel et al.   DEVELOPMENTAL BIOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Reptile: representative tiling for short read error correction

(2010) X. Yang et al.   BIOINFORMATICS

Multicellular development in a choanoflagellate

(2010) Stephen R. Fairclough et al.   CURRENT BIOLOGY

The genome of the sponge Amphimedon queenslandica provides new perspectives into the origin of Toll-like and interleukin 1 receptor pathways

(2010) Marie E. A. Gauthier et al.   EVOLUTION & DEVELOPMENT

Complete Genome Sequence of Algoriphagus sp. PR1, Bacterial Prey of a Colony-Forming Choanoflagellate

(2010) R. A. Alegado et al.   JOURNAL OF BACTERIOLOGY

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

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

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

(2010) J. Mark Cock et al.   NATURE

The Amphimedon queenslandica genome and the evolution of animal complexity

(2010) Mansi Srivastava et al.   NATURE

A dicer-independent miRNA biogenesis pathway that requires Ago catalysis

(2010) Sihem Cheloufi et al.   NATURE

The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation

(2010) Sohail Malik et al.   NATURE REVIEWS GENETICS

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

Genomic Analysis of Organismal Complexity in the Multicellular Green Alga Volvox carteri

(2010) S. E. Prochnik et al.   SCIENCE

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

phyloXML: XML for evolutionary biology and comparative genomics

(2009) Mira V Han et al.   BMC BIOINFORMATICS

Origin and evolution of the Notch signalling pathway: an overview from eukaryotic genomes

(2009) Eve Gazave et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenomics Revives Traditional Views on Deep Animal Relationships

(2009) Hervé Philippe et al.   CURRENT BIOLOGY

The interleukin-1 receptor/Toll-like receptor superfamily: 10 years of progress

(2009) Luke A. J. O'Neill   IMMUNOLOGICAL REVIEWS

A three-dimensional view of the molecular machinery of RNA interference

(2009) Martin Jinek et al.   NATURE

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

(2009) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

RNAi in Budding Yeast

(2009) I. A. Drinnenberg et al.   SCIENCE

The Hedgehog Signaling Pathway: Where Did It Come From?

(2009) George Hausmann et al.   PLOS BIOLOGY

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

(2009) Adrian M. Altenhoff et al.   PLoS Computational Biology

Fast Statistical Alignment

(2009) Robert K. Bradley et al.   PLoS Computational Biology

The Origins of Multicellularity and the Early History of the Genetic Toolkit For Animal Development

(2008) Antonis Rokas   Annual Review of Genetics

Sponge Genes Provide New Insight into the Evolutionary Origin of the Neurogenic Circuit

(2008) Gemma S. Richards et al.   CURRENT BIOLOGY

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

(2008) Nicole King et al.   NATURE

Toll-like receptors — taking an evolutionary approach

(2008) François Leulier et al.   NATURE REVIEWS GENETICS

The protist, Monosiga brevicollis, has a tyrosine kinase signaling network more elaborate and diverse than found in any known metazoan

(2008) G. Manning et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages

(2008) D. Pincus et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enzymes of the shikimic acid pathway encoded in the genome of a basal metazoan, Nematostella vectensis, have microbial origins

(2008) A. Starcevic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Three Families of LTR Retrotransposons are Present in the Genome of the Choanoflagellate Monosiga brevicollis

(2008) Martin Carr et al.   PROTIST

The Premetazoan Ancestry of Cadherins

(2008) Monika Abedin et al.   SCIENCE

Origins and evolution of eukaryotic RNA interference

(2008) S SHABALINA et al.   TRENDS IN ECOLOGY & EVOLUTION