Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish

Multi-level transcriptome sequencing identifies COL1A1 as a candidate marker in human heart failure progression

(2020) Xiumeng Hua et al.   BMC Medicine

The Genetic Basis of Morphological Diversity in Domesticated Goldfish

(2020) Tetsuo Kon et al.   CURRENT BIOLOGY

De novo transcriptome analysis of Lantana camara L. revealed candidate genes involved in phenylpropanoid biosynthesis pathway

(2020) Muzammil Shah et al.   Scientific Reports

Transcriptome analysis identifies candidate genes associated with skin color variation in Triplophysa siluroides

(2020) Yeyu Chen et al.   Comparative Biochemistry and Physiology D-Genomics & Proteomics

Full-length transcriptome analysis of Litopenaeus vannamei reveals transcript variants involved in the innate immune system

(2019) Xiujuan Zhang et al.   FISH & SHELLFISH IMMUNOLOGY

Characterization and analysis of the transcriptome in Gymnocypris selincuoensis on the Qinghai-Tibetan Plateau using single-molecule long-read sequencing and RNA-seq

(2019) Xiu Feng et al.   DNA RESEARCH

De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication

(2019) Zelin Chen et al.   Science Advances

Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp

(2019) Mingkun Luo et al.   BMC GENOMICS

Expression of genes for melanotropic peptides and their receptors for morphological color change in goldfish Carassius auratus

(2018) Kanta Mizusawa et al.   GENERAL AND COMPARATIVE ENDOCRINOLOGY

Teleost Fish-Specific Preferential Retention of Pigmentation Gene-Containing Families After Whole Genome Duplications in Vertebrates

(2018) Thibault Lorin et al.   G3-Genes Genomes Genetics

High resolution annotation of zebrafish transcriptome using long-read sequencing

(2018) German Nudelman et al.   GENOME RESEARCH

Goldfish: An old and new model system to study vertebrate development, evolution, and human disease

(2018) Yoshihiro Omori et al.   JOURNAL OF BIOCHEMISTRY

Full-length transcriptome of Misgurnus anguillicaudatus provides insights into evolution of genus Misgurnus

(2018) Shaokui Yi et al.   Scientific Reports

Cis -trans controls and regulatory novelty accompanying allopolyploidization

(2018) Guanjing Hu et al.   NEW PHYTOLOGIST

PacBio full-length cDNA sequencing integrated with RNA-seq reads drastically improves the discovery of splicing transcripts in rice

(2018) Guoqiang Zhang et al.   PLANT JOURNAL

Comparative transcriptome analysis of molecular mechanism underlying gray-to-red body color formation in red crucian carp (Carassius auratus, red var.)

(2017) Yongqin Zhang et al.   FISH PHYSIOLOGY AND BIOCHEMISTRY

The Nrf2/GCH1/BH4 Axis Ameliorates Radiation-Induced Skin Injury by Modulating the ROS Cascade

(2017) Jiao Xue et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Secretoneurin A regulates neurogenic and inflammatory transcriptional networks in goldfish (Carassius auratus) radial glia

(2017) Dillon F. Da Fonte et al.   Scientific Reports

Long read reference genome-free reconstruction of a full-length transcriptome from Astragalus membranaceus reveals transcript variants involved in bioactive compound biosynthesis

(2017) Jun Li et al.   Cell Discovery

A benchmark of gene expression tissue-specificity metrics

(2016) Nadezda Kryuchkova-Mostacci et al.   BRIEFINGS IN BIOINFORMATICS

A survey of the sorghum transcriptome using single-molecule long reads

(2016) Salah E. Abdel-Ghany et al.   Nature Communications

Goldfish morphology as a model for evolutionary developmental biology

(2016) Kinya G. Ota et al.   Wiley Interdisciplinary Reviews-Developmental Biology

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Leveraging transcript quantification for fast computation of alternative splicing profiles

(2015) Gael P. Alamancos et al.   RNA

Local adaptation of Gymnocypris przewalskii (Cyprinidae) on the Tibetan Plateau

(2015) Renyi Zhang et al.   Scientific Reports

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Transcriptome Assembly, Gene Annotation and Tissue Gene Expression Atlas of the Rainbow Trout

(2015) Mohamed Salem et al.   PLoS One

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

LoRDEC: accurate and efficient long read error correction

(2014) Leena Salmela et al.   BIOINFORMATICS

Genome sequence and genetic diversity of the common carp, Cyprinus carpio

(2014) Peng Xu et al.   NATURE GENETICS

Leucophores are similar to xanthophores in their specification and differentiation processes in medaka

(2014) T. Kimura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A single-molecule long-read survey of the human transcriptome

(2013) Donald Sharon et al.   NATURE BIOTECHNOLOGY

Alternative splicing regulation by Muscleblind proteins: from development to disease

(2011) Juan M. Fernandez-Costa et al.   BIOLOGICAL REVIEWS

Pigment-dispersing activities and cortisol-releasing activities of melanocortins and their receptors in xanthophores and head kidneys of the goldfish Carassius auratus

(2011) Yuki Kobayashi et al.   GENERAL AND COMPARATIVE ENDOCRINOLOGY

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

Interplay between Foxd3 and Mitf regulates cell fate plasticity in the zebrafish neural crest

(2010) Kevin Curran et al.   DEVELOPMENTAL BIOLOGY

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

(2009) Likun Wang et al.   BIOINFORMATICS

Morphological skin colour changes in teleosts

(2009) Eric Leclercq et al.   FISH AND FISHERIES

Pigmentation Pathway Evolution after Whole-Genome Duplication in Fish

(2009) Ingo Braasch et al.   Genome Biology and Evolution

Structural insights into RNA recognition by the alternative-splicing regulator muscleblind-like MBNL1

(2008) Marianna Teplova et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE