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

OUP accepted manuscript

(2018)   BIOINFORMATICS

A high-resolution genetic linkage map and QTL fine mapping for growth-related traits and sex in the Yangtze River common carp (Cyprinus carpio haematopterus)

(2018) Xiu Feng et al.   BMC GENOMICS

De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species

(2018) Madeleine Carruthers et al.   BMC GENOMICS

A survey of transcriptome complexity in Sus scrofa using single-molecule long-read sequencing

(2018) Yao Li et al.   DNA RESEARCH

Strong evidence for changing fish reproductive phenology under climate warming on the Tibetan Plateau

(2018) Juan Tao et al.   GLOBAL CHANGE BIOLOGY

Single-molecule, full-length transcript sequencing provides insight into the extreme metabolism of the ruby-throated hummingbird Archilochus colubris

(2018) Rachael E Workman et al.   GigaScience

Analysis of the biological features of the goldfish Carassius auratus auratus in Lake Trasimeno (Umbria, Italy) with a view to drawing up plans for population control

(2018) Massimo Lorenzoni et al.   FOLIA ZOOLOGICA

High resolution annotation of zebrafish transcriptome using long-read sequencing

(2018) German Nudelman et al.   GENOME RESEARCH

The Role of Alternative Splicing and Differential Gene Expression in Cichlid Adaptive Radiation

(2017) Pooja Singh et al.   Genome Biology and Evolution

Detecting alternatively spliced transcript isoforms from single-molecule long-read sequences without a reference genome

(2017) Xiaoxian Liu et al.   Molecular Ecology Resources

De novo assembly, characterization and annotation for the transcriptome of Sarcocheilichthys sinensis

(2017) Chuankun Zhu et al.   PLoS One

Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts

(2017) Bing Cheng et al.   GigaScience

A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing

(2017) Shi-Yi Chen et al.   Scientific Reports

Multi-tissue transcriptome profiles for coho salmon ( Oncorhynchus kisutch ), a species undergoing rediploidization following whole-genome duplication

(2016) Jin-Hyoung Kim et al.   Marine Genomics

Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks

(2016) Yun Huang et al.   MOLECULAR ECOLOGY

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

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

Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing

(2016) Bo Wang et al.   Nature Communications

Comparative Transcriptome Analysis Identifies Candidate Genes Related to Skin Color Differentiation in Red Tilapia

(2016) Wenbin Zhu et al.   Scientific Reports

Transcriptome profiling analysis of naked carp (Gymnocypris przewalskii) provides insights into the immune-related genes in highland fish

(2015) Chao Tong et al.   FISH & SHELLFISH IMMUNOLOGY

De novo assembly and characterization of the spleen transcriptome of common carp (Cyprinus carpio) using Illumina paired-end sequencing

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

Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing

(2015) Jason L. Weirather et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Renyi Zhang et al.   Scientific Reports

Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella)

(2015) Quanyuan Wan et al.   Scientific Reports

Validation of daily increment formation in otoliths forGymnocypris selincuoensisin the Tibetan Plateau, China

(2015) Chengzhi Ding et al.   Ecology and Evolution

Relationships between climate and growth ofGymnocypris selincuoensisin the Tibetan Plateau

(2015) Juan Tao et al.   Ecology and Evolution

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

PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme

(2014) Aimin Li et al.   BMC BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Defining a personal, allele-specific, and single-molecule long-read transcriptome

(2014) Hagen Tilgner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics

(2013) Linn Fagerberg et al.   MOLECULAR & CELLULAR PROTEOMICS

Transcriptome sequencing of sea cucumber (Apostichopus japonicus) and the identification of gene-associated markers

(2013) Z. C. Zhou et al.   Molecular Ecology Resources

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

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts

(2013) Liang Sun et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Transcriptome Sequencing and Analysis of Wild Amur Ide (Leuciscus waleckii) Inhabiting an Extreme Alkaline-Saline Lake Reveals Insights into Stress Adaptation

(2013) Jian Xu et al.   PLoS One

Characterization of the human ESC transcriptome by hybrid sequencing

(2013) K. F. Au et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ParaAT: A parallel tool for constructing multiple protein-coding DNA alignments

(2012) Zhang Zhang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Transcriptome Analysis of Silver Carp (Hypophthalmichthys molitrix) by Paired-End RNA Sequencing

(2012) B. Fu et al.   DNA RESEARCH

Exploring local immunological adaptation of two stickleback ecotypes by experimental infection and transcriptome-wide digital gene expression analysis

(2012) Tobias L. Lenz et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Characterization of Common Carp Transcriptome: Sequencing, De Novo Assembly, Annotation and Comparative Genomics

(2012) Peifeng Ji et al.   PLoS One

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms

(2011) J. E. SEEB et al.   Molecular Ecology Resources

The genome sequence of Atlantic cod reveals a unique immune system

(2011) Bastiaan Star et al.   NATURE

KEGG for integration and interpretation of large-scale molecular data sets

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

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Applications of next generation sequencing in molecular ecology of non-model organisms

(2010) R Ekblom et al.   HEREDITY

Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes

(2010) K. R. ELMER et al.   MOLECULAR ECOLOGY

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

(2010) Dapeng Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

(2009) Daniel Ramsköld et al.   PLoS Computational Biology