Phylotranscriptomics suggests the jawed vertebrate ancestor could generate diverse helper and regulatory T cell subsets

De novo assembly of the kidney and spleen transcriptomes of the cosmopolitan blue shark, Prionace glauca

(2018) André M. Machado et al.   Marine Genomics

Haptoglobin Is a Divergent MASP Family Member That Neofunctionalized To Recycle Hemoglobin via CD163 in Mammals

(2018) Anthony K. Redmond et al.   JOURNAL OF IMMUNOLOGY

Outgroup, alignment and modelling improvements indicate that two TNFSF13-like genes existed in the vertebrate ancestor

(2017) Anthony K . Redmond et al.   IMMUNOGENETICS

Phylotranscriptomic consolidation of the jawed vertebrate timetree

(2017) Iker Irisarri et al.   Nature Ecology & Evolution

Multi-tissue RNA-seq and transcriptome characterisation of the spiny dogfish shark (Squalus acanthias) provides a molecular tool for biological research and reveals new genes involved in osmoregulation

(2017) Andres Chana-Munoz et al.   PLoS One

Evidence of positive selection associated with placental loss in tiger sharks

(2016) Dominic G. Swift et al.   BMC EVOLUTIONARY BIOLOGY

The complement system of elasmobranches revealed by liver transcriptome analysis of a hammerhead shark, Sphyrna zygaena

(2016) Masayuki Goshima et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Adaptive phenotypic response to climate enabled by epigenetics in a K-strategy species, the fishLeucoraja ocellata(Rajidae)

(2016) Jackie Lighten et al.   Royal Society Open Science

Venom gland transcriptome analyses of two freshwater stingrays (Myliobatiformes: Potamotrygonidae) from Brazil

(2016) Nelson Gomes de Oliveira Júnior et al.   Scientific Reports

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

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

Type 1 regulatory T cells: a new mechanism of peripheral immune tolerance

(2015) Hanyu Zeng et al.   Cellular & Molecular Immunology

Characterisation of the TNF superfamily members CD40L and BAFF in the small-spotted catshark ( Scyliorhinus canicula )

(2015) Ronggai Li et al.   FISH & SHELLFISH IMMUNOLOGY

The CXC chemokine receptors of fish: Insights into CXCR evolution in the vertebrates

(2015) Jun Zou et al.   GENERAL AND COMPARATIVE ENDOCRINOLOGY

The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications

(2015) Jeramiah J. Smith et al.   GENOME RESEARCH

Rooting the tree of life: the phylogenetic jury is still out

(2015) Richard Gouy et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

Molecular mechanisms underlying the exceptional adaptations of batoid fins

(2015) Tetsuya Nakamura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plastid establishment did not require a chlamydial partner

(2015) Daryl Domman et al.   Nature Communications

The Treg/Th17 Axis: A Dynamic Balance Regulated by the Gut Microbiome

(2015) Sara Omenetti et al.   Frontiers in Immunology

Transcriptomic analysis of the lesser spotted catshark (Scyliorhinus canicula) pancreas, liver and brain reveals molecular level conservation of vertebrate pancreas function

(2014) John F Mulley et al.   BMC GENOMICS

The expanding repertoire of the IL-12 cytokine family in teleost fish: Identification of three paralogues each of the p35 and p40 genes in salmonids, and comparative analysis of their expression and modulation in Atlantic salmon Salmo salar

(2014) Tiehui Wang et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Differential expression, modulation and bioactivity of distinct fish IL-12 isoforms: Implication towards the evolution of Th1-like immune responses

(2014) Tiehui Wang et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

The Comb Jelly Opsins and the Origins of Animal Phototransduction

(2014) Roberto Feuda et al.   Genome Biology and Evolution

Analysis of the Opsin Repertoire in the Tardigrade Hypsibius dujardini Provides Insights into the Evolution of Opsin Genes in Panarthropoda

(2014) Lars Hering et al.   Genome Biology and Evolution

An Amino Acid Substitution-Selection Model Adjusts Residue Fitness to Improve Phylogenetic Estimation

(2014) H.-C. Wang 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

Venkatesh et al. reply

(2014) Byrappa Venkatesh et al.   NATURE

Ghost locus appears

(2014) James O. McInerney et al.   NATURE

Elephant shark genome provides unique insights into gnathostome evolution

(2014) Byrappa Venkatesh et al.   NATURE

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

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

TH2 and Treg candidate genes in elephant shark

(2014) Johannes M. Dijkstra   NATURE

Transcriptome Profiling Reveals Higher Vertebrate Orthologous of Intra-Cytoplasmic Pattern Recognition Receptors in Grey Bamboo Shark

(2014) Tirumurugaan Krishnaswamy Gopalan et al.   PLoS One

Host protective roles of type 2 immunity: Parasite killing and tissue repair, flip sides of the same coin

(2014) Judith E. Allen et al.   SEMINARS IN IMMUNOLOGY

Characterization of the definitive classical calpain family of vertebrates using phylogenetic, evolutionary and expression analyses

(2014) D. J. Macqueen et al.   Open Biology

Characterization of the heart transcriptome of the white shark (Carcharodon carcharias)

(2013) Vincent P Richards et al.   BMC GENOMICS

Identification of a gene for an ancient cytokine, interleukin 15-like, in mammals; interleukins 2 and 15 co-evolved with this third family member, all sharing binding motifs for IL-15Rα

(2013) Johannes M. Dijkstra et al.   IMMUNOGENETICS

Heterogeneous Models Place the Root of the Placental Mammal Phylogeny

(2013) Claire C. Morgan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ancient Origins of Vertebrate-Specific Innate Antiviral Immunity

(2013) Krishanu Mukherjee 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

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

(2013) Jeramiah J Smith et al.   NATURE GENETICS

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

Th9 cells, new players in adaptive immunity

(2013) Edgar Schmitt et al.   TRENDS IN IMMUNOLOGY

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

CD4+T Cells: Differentiation and Functions

(2012) Rishi Vishal Luckheeram et al.   Clinical & Developmental Immunology

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

IL-12 family cytokines: immunological playmakers

(2012) Dario A A Vignali et al.   NATURE IMMUNOLOGY

LIFR is a breast cancer metastasis suppressor upstream of the Hippo-YAP pathway and a prognostic marker

(2012) Dahu Chen et al.   NATURE MEDICINE

Evolution of JAK-STAT Pathway Components: Mechanisms and Role in Immune System Development

(2012) Clifford Liongue et al.   PLoS One

Follicular Helper CD4 T Cells (TFH)

(2011) Shane Crotty   Annual Review of Immunology

Co-orthology of Pax4 and Pax6 to the fly eyeless gene: molecular phylogenetic, comparative genomic, and embryological analyses

(2011) Tereza Manousaki et al.   EVOLUTION & DEVELOPMENT

Structure of a Domain-Swapped FOXP3 Dimer on DNA and Its Function in Regulatory T Cells

(2011) Hozefa S. Bandukwala et al.   IMMUNITY

Molecular characterization and expression analysis of the putative interleukin 6 receptor (IL-6Rα and glycoprotein-130) in rainbow trout (Oncorhynchus mykiss): Salmonid IL-6Rα possesses a polymorphic N-terminal Ig domain with variable numbers of two repeats

(2011) Maria M. Costa et al.   IMMUNOGENETICS

Acoelomorph flatworms are deuterostomes related to Xenoturbella

(2011) Hervé Philippe et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda

(2011) L. I. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Natural Deletion of the HoxC Cluster in Elasmobranch Fishes

(2011) B. L. King et al.   SCIENCE

Identification of Treg-like cells in Tetraodon: insight into the origin of regulatory T subsets during early vertebrate evolution

(2010) Yi Wen et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

gp130 at the nexus of inflammation, autoimmunity, and cancer

(2010) J. S. Silver et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Evolutionary Origin and Phylogeny of the Modern Holocephalans (Chondrichthyes: Chimaeriformes): A Mitogenomic Perspective

(2010) J. G. Inoue et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Human Th17 cells: Are they different from murine Th17 cells?

(2009) Francesco Annunziato et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

RORC2: The master of human Th17 cell programming

(2009) Derya Unutmaz   EUROPEAN JOURNAL OF IMMUNOLOGY

How do Regulatory T Cells Work?

(2009) A. Corthay   SCANDINAVIAN JOURNAL OF IMMUNOLOGY

Empirical profile mixture models for phylogenetic reconstruction

(2008) Le Si Quang et al.   BIOINFORMATICS

Expansion of signaling genes for adaptive immune system evolution in early vertebrates

(2008) Kinya Okada et al.   BMC GENOMICS

Characterization and expression analysis of an interleukin-7 homologue in the Japanese pufferfish, Takifugu rubripes

(2008) Tomoya Kono et al.   FEBS Journal

The conditioned reconstructed process

(2008) Tanja Gernhard   JOURNAL OF THEORETICAL BIOLOGY