Chamber Specific Gene Expression Landscape of the Zebrafish Heart

Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data

(2015) Wuming Gong et al.   BMC BIOINFORMATICS

Gene Expression Profile in the Early Stage of Angiotensin II-induced Cardiac Remodeling: a Time Series Microarray Study in a Mouse Model

(2015) Meng-Qiu Dang et al.   CELLULAR PHYSIOLOGY AND BIOCHEMISTRY

Cardiac Transcriptome and Dilated Cardiomyopathy Genes in ZebrafishCLINICAL PERSPECTIVE

(2015) Yu-Huan Shih et al.   Circulation-Cardiovascular Genetics

RNA-Seq identifies novel myocardial gene expression signatures of heart failure

(2015) Yichuan Liu et al.   GENOMICS

Cardiac Transcriptome and Dilated Cardiomyopathy Genes in ZebrafishCLINICAL PERSPECTIVE

(2015) Yu-Huan Shih et al.   Circulation-Cardiovascular Genetics

Chromosome microarray testing for patients with congenital heart defects reveals novel disease causing loci and high diagnostic yield

(2015) Juan Geng et al.   BMC GENOMICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Atrial fibrillation alters the microRNA expression profiles of the left atria of patients with mitral stenosis

(2014) Hai Liu et al.   BMC Cardiovascular Disorders

Transcriptional response to cardiac injury in the zebrafish: systematic identification of genes with highly concordant activity across in vivo models

(2014) Sophie Rodius et al.   BMC GENOMICS

Identification of the microRNA Expression Profile in the Regenerative Neonatal Mouse Heart by Deep Sequencing

(2014) H. L. Liu et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

Deep RNA Sequencing Reveals Dynamic Regulation of Myocardial Noncoding RNAs in Failing Human Heart and Remodeling With Mechanical Circulatory Support

(2014) Kai-Chien Yang et al.   CIRCULATION

Expression profiling and ontology analysis of long noncoding RNAs in post-ischemic heart and their implied roles in ischemia/reperfusion injury

(2014) Youbin Liu et al.   GENE

Human Atrium Transcript Analysis of Permanent Atrial Fibrillation

(2014) Jian Zhou et al.   International Heart Journal

MicroRNA-539 Is Up-regulated in Failing Heart, and SuppressesO-GlcNAcase Expression

(2014) Senthilkumar Muthusamy et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Metabolic gene profile in early human fetal heart development

(2014) J.I. Iruretagoyena et al.   MOLECULAR HUMAN REPRODUCTION

Early lineage restriction in temporally distinct populations of Mesp1 progenitors during mammalian heart development

(2014) Fabienne Lescroart et al.   NATURE CELL BIOLOGY

Dynamic Expression of Long Non-Coding RNAs (lncRNAs) in Adult Zebrafish

(2014) Kriti Kaushik et al.   PLoS One

Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs

(2013) Guo-Liang Chew et al.   DEVELOPMENT

Transcriptome network analysis of potential candidate genes for heart failure

(2013) J. Chen et al.   GENETICS AND MOLECULAR RESEARCH

WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013

(2013) Jing Wang et al.   NUCLEIC ACIDS RESEARCH

A Deep Sequencing Approach to Uncover the miRNOME in the Human Heart

(2013) Stefanos Leptidis et al.   PLoS One

Transcriptome Analysis Reveals Distinct Patterns of Long Noncoding RNAs in Heart and Plasma of Mice with Heart Failure

(2013) Danhua Li et al.   PLoS One

Integrated Analysis of Dysregulated lncRNA Expression in Fetal Cardiac Tissues with Ventricular Septal Defect

(2013) Guixian Song et al.   PLoS One

A Sequence-Based Variation Map of Zebrafish

(2013) Ashok Patowary et al.   Zebrafish

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Association and Functional Follow-Up Reveals New Loci for Kidney Function

(2012) Cristian Pattaro et al.   PLoS Genetics

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

Microarrays, deep sequencing and the true measure of the transcriptome

(2011) John H Malone et al.   BMC BIOLOGY

Zebrafish as a model to study cardiac development and human cardiac disease

(2011) J. Bakkers   CARDIOVASCULAR RESEARCH

Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution

(2011) Igor Ulitsky et al.   CELL

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

Deep sequencing reveals 50 novel genes for recessive cognitive disorders

(2011) Hossein Najmabadi et al.   NATURE

Heart regeneration

(2011) Michael A. Laflamme et al.   NATURE

A rare variant in MYH6 is associated with high risk of sick sinus syndrome

(2011) Hilma Holm et al.   NATURE GENETICS

The Pfam protein families database

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

Cardiac Alpha-Myosin (MYH6) Is the Predominant Sarcomeric Disease Gene for Familial Atrial Septal Defects

(2011) Maximilian G. Posch et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

Distinct troponin C isoform requirements in cardiac and skeletal muscle

(2010) Vanessa M. Sogah et al.   DEVELOPMENTAL DYNAMICS

The Rho Guanine Nucleotide Exchange Factor AKAP13 (BRX) Is Essential for Cardiac Development in Mice

(2010) Chantal M. Mayers et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Anaplastic Lymphoma Kinase Inhibition in Non–Small-Cell Lung Cancer

(2010) Eunice L. Kwak et al.   NEW ENGLAND JOURNAL OF MEDICINE

Transient and transgenic analysis of the zebrafish ventricular myosin heavy chain (vmhc) promoter: An inhibitory mechanism of ventricle-specific gene expression

(2009) Ruilin Zhang et al.   DEVELOPMENTAL DYNAMICS

Mutations and polymorphisms of the skeletal muscle α-actin gene (ACTA1)

(2009) Nigel G. Laing et al.   HUMAN MUTATION

Adult zebrafish heart as a model for human heart? An electrophysiological study

(2009) Petros Nemtsas et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

EML4-ALK Fusion Gene and Efficacy of an ALK Kinase Inhibitor in Lung Cancer

(2008) J. P. Koivunen et al.   CLINICAL CANCER RESEARCH

Deletion of the Protein Kinase A/Protein Kinase G Target SMTNL1 Promotes an Exercise-adapted Phenotype in Vascular Smooth Muscle

(2008) Anne A. Wooldridge et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

The beginning of the end for microarrays?

(2008) Jay Shendure   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

(2008) M. Sultan et al.   SCIENCE

High-resolution in situ hybridization to whole-mount zebrafish embryos

(2007) Christine Thisse et al.   Nature Protocols