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

Deep developmental transcriptome sequencing uncovers numerous new genes and enhances gene annotation in the sponge Amphimedon queenslandica

(2015) Selene L Fernandez-Valverde et al.   BMC GENOMICS

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

(2015) Guifré Torruella et al.   CURRENT BIOLOGY

Dynamic and Widespread lncRNA Expression in a Sponge and the Origin of Animal Complexity

(2015) Federico Gaiti et al.   MOLECULAR BIOLOGY AND EVOLUTION

Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species

(2015) Hadas Hezroni et al.   Cell Reports

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains

(2014) Manuel Irimia et al.   CELL

New Tricks for “Old” Domains: How Novel Architectures and Promiscuous Hubs Contributed to the Organization and Evolution of the ECM

(2014) Graham Cromar et al.   Genome Biology and Evolution

The Evolution of the GPCR Signaling System in Eukaryotes: Modularity, Conservation, and the Transition to Metazoan Multicellularity

(2014) Alex de Mendoza et al.   Genome Biology and Evolution

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

Profiling the Secretome and Extracellular Proteome of the Potato Late Blight PathogenPhytophthora infestans

(2014) Harold J. G. Meijer et al.   MOLECULAR & CELLULAR PROTEOMICS

Evolutionary Insights into Premetazoan Functions of the Neuronal Protein Homer

(2014) Pawel Burkhardt et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transferred interbacterial antagonism genes augment eukaryotic innate immune function

(2014) Seemay Chou et al.   NATURE

Comparative analysis of the transcriptome across distant species

(2014) Mark B. Gerstein et al.   NATURE

Evolutionary dynamics of coding and non-coding transcriptomes

(2014) Anamaria Necsulea et al.   NATURE REVIEWS GENETICS

The rise of regulatory RNA

(2014) Kevin V. Morris et al.   NATURE REVIEWS GENETICS

Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications

(2014) Aurélie Kapusta et al.   TRENDS IN GENETICS

Origin of Spliceosomal Introns and Alternative Splicing

(2014) M. Irimia et al.   Cold Spring Harbor Perspectives in Biology

Antibacterial gene transfer across the tree of life

(2014) Jason A Metcalf et al.   eLife

The Genomic and Cellular Foundations of Animal Origins

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

lincRNAs: Genomics, Evolution, and Mechanisms

(2013) Igor Ulitsky et al.   CELL

Development of ichthyosporeans sheds light on the origin of metazoan multicellularity

(2013) Hiroshi Suga et al.   DEVELOPMENTAL BIOLOGY

Phylogenetic interpretations and ecological potentials of the Mesomycetozoea (Ichthyosporea)

(2013) Sally L. Glockling et al.   Fungal Ecology

Insights into the Origin of Metazoan Filopodia and Microvilli

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

Earliest Holozoan Expansion of Phosphotyrosine Signaling

(2013) Hiroshi Suga 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

MBNL proteins repress ES-cell-specific alternative splicing and reprogramming

(2013) Hong Han et al.   NATURE

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

Horizontal gene transfer in osmotrophs: playing with public goods

(2013) Thomas A. Richards et al.   NATURE REVIEWS MICROBIOLOGY

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

Cell cycle control across the eukaryotic kingdom

(2013) Hirofumi Harashima et al.   TRENDS IN CELL 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

Early evolution of eukaryote feeding modes, cell structural diversity, and classification of the protozoan phyla Loukozoa, Sulcozoa, and Choanozoa

(2012) Thomas Cavalier-Smith   EUROPEAN JOURNAL OF PROTISTOLOGY

Molecular Signatures of the Three Stem Cell Lineages in Hydra and the Emergence of Stem Cell Function at the Base of Multicellularity

(2012) Georg Hemmrich et al.   MOLECULAR BIOLOGY AND EVOLUTION

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

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

Physico-Genetic Determinants in the Evolution of Development

(2012) S. A. Newman   SCIENCE

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

(2012) N. L. Barbosa-Morais et al.   SCIENCE

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

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

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

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Metalloproteinase-mediated Shedding of Integrin β2 Promotes Macrophage Efflux from Inflammatory Sites

(2011) Ivan G. Gomez et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Phylogenetic Relationships within the Opisthokonta Based on Phylogenomic Analyses of Conserved Single-Copy Protein Domains

(2011) G. Torruella et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

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

Evolution of networks and sequences in eukaryotic cell cycle control

(2011) F. R. Cross et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes

(2011) T. A. Richards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene transfer into the fungi

(2011) Thomas A. Richards et al.   Fungal Biology Reviews

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Six major steps in animal evolution: are we derived sponge larvae?

(2010) Claus Nielsen   EVOLUTION & DEVELOPMENT

Duplication Frequency in a Population of Salmonella enterica Rapidly Approaches Steady State With or Without Recombination

(2010) A. B. Reams et al.   GENETICS

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

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

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

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The origin of Metazoa: a transition from temporal to spatial cell differentiation

(2009) Kirill V. Mikhailov et al.   BIOESSAYS

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

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

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

The Fungi

(2009) Jason E. Stajich et al.   CURRENT BIOLOGY

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Phylogeny of the "Forgotten" Cellular Slime Mold, Fonticula alba, Reveals a Key Evolutionary Branch within Opisthokonta

(2009) M. W. Brown et al.   MOLECULAR BIOLOGY AND EVOLUTION

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads

(2009) Iain MacCallum et al.   GENOME BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration

(2008) S. Bauer et al.   BIOINFORMATICS

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

(2008) Mario Stanke et al.   BIOINFORMATICS

PredGPI: a GPI-anchor predictor

(2008) Andrea Pierleoni et al.   BMC BIOINFORMATICS

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

The evolution of cell types in animals: emerging principles from molecular studies

(2008) Detlev Arendt   NATURE REVIEWS GENETICS

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

Multiple Isolations of a Culturable, Motile Ichthyosporean (Mesomycetozoa, Opisthokonta), Creolimax fragrantissima n. gen., n. sp., from Marine Invertebrate Digestive Tracts

(2008) Wyth L. Marshall et al.   PROTIST

Cross-kingdom patterns of alternative splicing and splice recognition

(2008) Abigail M McGuire et al.   GENOME BIOLOGY