Emergence of distinct syntenic density regimes is associated with early metazoan genomic transitions

Whole-genome microsynteny-based phylogeny of angiosperms

(2021) Tao Zhao et al.   Nature Communications

Widespread patterns of gene loss in the evolution of the animal kingdom

(2020) Cristina Guijarro-Clarke et al.   Nature Ecology & Evolution

Gene gain and loss across the metazoan tree of life

(2020) Rosa Fernández et al.   Nature Ecology & Evolution

Ancient genomic regulatory blocks are a source for regulatory gene deserts in vertebrates after whole genome duplications

(2020) María Touceda-Suárez et al.   MOLECULAR BIOLOGY AND EVOLUTION

Symbiotic organs shaped by distinct modes of genome evolution in cephalopods

(2019) Mahdi Belcaid et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genome of the jellyfish Clytia hemisphaerica and the evolution of the cnidarian life-cycle

(2019) Lucas Leclère et al.   Nature Ecology & Evolution

Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria

(2019) Hervé Philippe et al.   CURRENT BIOLOGY

Chromosome-wide co-fluctuation of stochastic gene expression in mammalian cells

(2019) Mengyi Sun et al.   PLoS Genetics

Ancient animal genome architecture reflects cell type identities

(2019) Bob Zimmermann et al.   Nature Ecology & Evolution

Homeobox Gene Duplication and Divergence in Arachnids

(2018) Daniel J Leite et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2018) Jordi Paps et al.   Nature Communications

GOATOOLS: A Python library for Gene Ontology analyses

(2018) D. V. Klopfenstein et al.   Scientific Reports

Tandem Duplicate Genes in Maize Are Abundant and Date to Two Distinct Periods of Time

(2018) Thomas J. Y. Kono et al.   G3-Genes Genomes Genetics

Early metazoan cell type diversity and the evolution of multicellular gene regulation

(2018) Arnau Sebé-Pedrós et al.   Nature Ecology & Evolution

Xenacoelomorpha Survey Reveals That All 11 Animal Homeobox Gene Classes Were Present in the First Bilaterians

(2018) Michael Brauchle et al.   Genome Biology and Evolution

The genome of the jellyfish Aurelia and the evolution of animal complexity

(2018) David A. Gold et al.   Nature Ecology & Evolution

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation

(2017) Nathan Harmston et al.   Nature Communications

Dynamics of genomic innovation in the unicellular ancestry of animals

(2017) Xavier Grau-Bové et al.   eLife

Ctenophore relationships and their placement as the sister group to all other animals

(2017) Nathan V. Whelan et al.   Nature Ecology & Evolution

Scallop genome provides insights into evolution of bilaterian karyotype and development

(2017) Shi Wang et al.   Nature Ecology & Evolution

A Comprehensive Mouse Transcriptomic BodyMap across 17 Tissues by RNA-seq

(2017) Bin Li et al.   Scientific Reports

Sex Determination, Sex Chromosomes, and Karyotype Evolution in Insects

(2016) Heath Blackmon et al.   JOURNAL OF HEREDITY

A sisterly dispute

(2016) Maximilian J. Telford et al.   NATURE

Xenacoelomorpha is the sister group to Nephrozoa

(2016) Johanna Taylor Cannon et al.   NATURE

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation

(2016) Rafael D Acemel et al.   NATURE GENETICS

HOX gene complement and expression in the planarian Schmidtea mediterranea

(2016) Ko W. Currie et al.   EvoDevo

Composition and genomic organization of arthropod Hox clusters

(2016) Ryan M. Pace et al.   EvoDevo

The Role of Chromosome Domains in Shaping the Functional Genome

(2015) Tom Sexton et al.   CELL

Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales

(2015) Mario dos Reis et al.   CURRENT BIOLOGY

Hemichordate genomes and deuterostome origins

(2015) Oleg Simakov et al.   NATURE

The Homeobox Genes of Caenorhabditis elegans and Insights into Their Spatio-Temporal Expression Dynamics during Embryogenesis

(2015) Jürgen Hench et al.   PLoS One

Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders

(2015) Carlos Gómez-Marín et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Animal Phylogeny and Its Evolutionary Implications

(2014) Casey W. Dunn et al.   Annual Review of Ecology Evolution and Systematics

Evolution of Hox gene clusters in deuterostomes

(2013) Juan Pascual-Anaya et al.   BMC DEVELOPMENTAL BIOLOGY

The African coelacanth genome provides insights into tetrapod evolution

(2013) Chris T. Amemiya et al.   NATURE

Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints

(2012) M. Irimia et al.   GENOME RESEARCH

Coral Comparative Genomics Reveal Expanded Hox Cluster in the Cnidarian-Bilaterian Ancestor

(2012) T. Q. DuBuc et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains

(2012) Chunhui Hou et al.   MOLECULAR CELL

Insights into bilaterian evolution from three spiralian genomes

(2012) Oleg Simakov et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

The chromatin insulator CTCF and the emergence of metazoan diversity

(2012) P. Heger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes

(2011) Jie Lv et al.   BMC BIOINFORMATICS

Phylogenetic and regulatory region analysis of Wnt5 genes reveals conservation of a regulatory module with putative implication in pancreas development

(2010) Maria Kapasa et al.   Biology Direct

The Amphimedon queenslandica genome and the evolution of animal complexity

(2010) Mansi Srivastava et al.   NATURE

Positive correlation between gene coexpression and positional clustering in the zebrafish genome

(2009) Yen Kaow Ng et al.   BMC GENOMICS

Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories

(2009) D. M. Larkin et al.   GENOME RESEARCH

Consequences of Lineage-Specific Gene Loss on Functional Evolution of Surviving Paralogs: ALDH1A and Retinoic Acid Signaling in Vertebrate Genomes

(2009) Cristian Cañestro et al.   PLoS Genetics

Transcriptional features of genomic regulatory blocks

(2009) Altuna Akalin et al.   GENOME BIOLOGY

The amphioxus genome and the evolution of the chordate karyotype

(2008) Nicholas H. Putnam et al.   NATURE

The Trichoplax genome and the nature of placozoans

(2008) Mansi Srivastava et al.   NATURE