An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes

DolphinNext: a distributed data processing platform for high throughput genomics

(2020) Onur Yukselen et al.   BMC GENOMICS

DEBrowser: interactive differential expression analysis and visualization tool for count data

(2019) Alper Kucukural et al.   BMC GENOMICS

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Developing zebrafish disease models for in vivo small molecule screens

(2019) Pui-Ying Lam et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

foxc1 is required for embryonic head vascular smooth muscle differentiation in zebrafish

(2019) Thomas R. Whitesell et al.   DEVELOPMENTAL BIOLOGY

A single-cell transcriptome atlas for zebrafish development

(2019) Dylan R. Farnsworth et al.   DEVELOPMENTAL BIOLOGY

Fox proteins are modular competency factors for facial cartilage and tooth specification

(2018) Pengfei Xu et al.   DEVELOPMENT

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

(2018) Bushra Raj et al.   NATURE BIOTECHNOLOGY

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

(2018) Daniel E. Wagner et al.   SCIENCE

VCAM-1+ macrophages guide the homing of HSPCs to a vascular niche

(2018) Dantong Li et al.   NATURE

Robust Identification of Developmentally Active Endothelial Enhancers in Zebrafish Using FANS-Assisted ATAC-Seq

(2017) Aurelie Quillien et al.   Cell Reports

c-myb hyperactivity leads to myeloid and lymphoid malignancies in zebrafish

(2016) W Liu et al.   LEUKEMIA

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Tip cell-specific requirement for an atypical Gpr124- and Reck-dependent Wnt/β-catenin pathway during brain angiogenesis

(2015) Benoit Vanhollebeke et al.   eLife

Two independent transcription initiation codes overlap on vertebrate core promoters

(2014) Vanja Haberle et al.   NATURE

MARIS: Method for Analyzing RNA following Intracellular Sorting

(2014) Siniša Hrvatin et al.   PLoS One

Modelling of human Wiskott-Aldrich syndrome protein mutants in zebrafish larvae using in vivo live imaging

(2013) R. A. Jones et al.   JOURNAL OF CELL SCIENCE

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Erg is a crucial regulator of endocardial-mesenchymal transformation during cardiac valve morphogenesis

(2012) P. Vijayaraj et al.   DEVELOPMENT

Rac2 expression and its role in neutrophil functions of zebrafish (Danio rerio)

(2012) Rachel M. Tell et al.   FISH & SHELLFISH IMMUNOLOGY

Extensive alternative polyadenylation during zebrafish development

(2012) I. Ulitsky et al.   GENOME RESEARCH

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Forward and Reverse Genetic Approaches for the Analysis of Vertebrate Development in the Zebrafish

(2011) Nathan D. Lawson et al.   DEVELOPMENTAL CELL

Characterization of Sry-related HMG box group F genes in zebrafish hematopoiesis

(2011) Martin In Shing Chung et al.   EXPERIMENTAL HEMATOLOGY

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Loss of fish actinotrichia proteins and the fin-to-limb transition

(2010) Jing Zhang et al.   NATURE

Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs

(2010) Calvin H. Jan et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Essential role of c-myb in definitive hematopoiesis is evolutionarily conserved

(2010) C. Soza-Ried et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Specific expression and regulation of glucose transporters in zebrafish ionocytes

(2009) Yung-Che Tseng et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

Foxn4 directly regulates tbx2b expression and atrioventricular canal formation

(2008) N. C. Chi et al.   GENES & DEVELOPMENT

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS