Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types

Single-cell transcriptional analysis of normal, aberrant, and malignant hematopoiesis in zebrafish

(2016) Finola E. Moore et al.   JOURNAL OF EXPERIMENTAL MEDICINE

The heterogeneity of human CD127+ innate lymphoid cells revealed by single-cell RNA sequencing

(2016) Åsa K Björklund et al.   NATURE IMMUNOLOGY

T cell fate and clonality inference from single-cell transcriptomes

(2016) Michael J T Stubbington et al.   NATURE METHODS

A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation

(2016) C. K. Kaufman et al.   SCIENCE

Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells

(2016) Iain C. Macaulay et al.   Cell Reports

Zebrafish Nk-lysins: First insights about their cellular and functional diversification

(2015) P. Pereiro et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Index sorting resolves heterogeneous murine hematopoietic stem cell populations

(2015) Reiner Schulte et al.   EXPERIMENTAL HEMATOLOGY

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

The evolution of natural killer cell receptors

(2015) Paola Carrillo-Bustamante et al.   IMMUNOGENETICS

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction

(2014) Hilary S. Parker et al.   BIOINFORMATICS

Zebrafish as a model for understanding the evolution of the vertebrate immune system and human primary immunodeficiency

(2014) Norimasa Iwanami   EXPERIMENTAL HEMATOLOGY

The Ontogeny and Fate of NK Cells Marked by Permanent DNA Rearrangements

(2014) K. Pilbeam et al.   JOURNAL OF IMMUNOLOGY

Existence of Conventional Dendritic Cells in Gallus gallus Revealed by Comparative Gene Expression Profiling

(2014) T.-P. Vu Manh et al.   JOURNAL OF IMMUNOLOGY

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Single-cell RNA-seq: advances and future challenges

(2014) Antoine-Emmanuel Saliba et al.   NUCLEIC ACIDS RESEARCH

A Loss of Function Screen of Identified Genome-Wide Association Study Loci Reveals New Genes Controlling Hematopoiesis

(2014) Ewa Bielczyk-Maczyńska et al.   PLoS Genetics

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

IgBLAST: an immunoglobulin variable domain sequence analysis tool

(2013) Jian Ye et al.   NUCLEIC ACIDS RESEARCH

Conservation and divergence in the transcriptional programs of the human and mouse immune systems

(2013) T. Shay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Immunological Genome Project and systems immunology

(2013) Tal Shay et al.   TRENDS IN IMMUNOLOGY

Evolution of immune systems: Specificity and autoreactivity

(2012) Mick Bailey et al.   AUTOIMMUNITY REVIEWS

Evolution of Vertebrate Immunity

(2012) Thomas Boehm   CURRENT BIOLOGY

A model 450 million years in the making: zebrafish and vertebrate immunity

(2012) S. A. Renshaw et al.   Disease Models & Mechanisms

Genomic and functional characterization of the diverse immunoglobulin domain-containing protein (DICP) family

(2012) Robert N. Haire et al.   GENOMICS

Molecular definition of the identity and activation of natural killer cells

(2012) Natalie A Bezman et al.   NATURE IMMUNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution

(2011) Matteo Fumagalli et al.   PLoS Genetics

Identification of new populations of chicken natural killer (NK) cells

(2010) Christine A. Jansen et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Characterization of the zebrafish T cell receptor β locus

(2010) Nathan D. Meeker et al.   IMMUNOGENETICS

The phylogenetic origins of natural killer receptors and recognition: relationships, possibilities, and realities

(2010) Jeffrey A. Yoder et al.   IMMUNOGENETICS

A HaemAtlas: characterizing gene expression in differentiated human blood cells

(2009) Nicholas A. Watkins et al.   BLOOD

Natural killer cells remember: An evolutionary bridge between innate and adaptive immunity?

(2009) Joseph C. Sun et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

CD4 and CD8: an inside-out coreceptor model for innate immune cells

(2009) Derrick Gibbings et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Dual nature of the adaptive immune system in lampreys

(2009) Peng Guo et al.   NATURE

Adaptive immune features of natural killer cells

(2009) Joseph C. Sun et al.   NATURE

Origin and evolution of the adaptive immune system: genetic events and selective pressures

(2009) Martin F. Flajnik et al.   NATURE REVIEWS GENETICS

Hematopoietic cell kinase (Hck) isoforms and phagocyte duties – From signaling and actin reorganization to migration and phagocytosis

(2008) R GUIET et al.   EUROPEAN JOURNAL OF CELL BIOLOGY

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

Patterns of Positive Selection in Six Mammalian Genomes

(2008) Carolin Kosiol et al.   PLoS Genetics