Systematic Identification and Characterization of Long Non-Coding RNAs in the Silkworm, Bombyx mori

Long non-coding RNA discovery across the genus anopheles reveals conserved secondary structures within and beyond the Gambiae complex

(2015) Adam M Jenkins et al.   BMC GENOMICS

Genome-wide characterization of long intergenic non-coding RNAs (lincRNAs) provides new insight into viral diseases in honey bees Apis cerana and Apis mellifera

(2015) Murukarthick Jayakodi et al.   BMC GENOMICS

Positionally-conserved but sequence-diverged: identification of long non-coding RNAs in the Brassicaceae and Cleomaceae

(2015) Setareh Mohammadin et al.   BMC PLANT BIOLOGY

Loss of function of the yellow-e gene causes dehydration-induced mortality of adult Tribolium castaneum

(2015) Mi Young Noh et al.   DEVELOPMENTAL BIOLOGY

miR-184 is Critical for the motility-related PNS development in Drosophila

(2015) Jianjian Peng et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL NEUROSCIENCE

miR-184Regulates Pancreatic β-Cell Function According to Glucose Metabolism

(2015) Sudhir G. Tattikota et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Comparative proteomic analysis of the silkworm middle silk gland reveals the importance of ribosome biogenesis in silk protein production

(2015) Jian-ying Li et al.   Journal of Proteomics

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypiumspp.)

(2015) Maojun Wang et al.   NEW PHYTOLOGIST

Genome-Wide Identification, Characterization and Evolutionary Analysis of Long Intergenic Noncoding RNAs in Cucumber

(2015) Zhiqiang Hao et al.   PLoS One

Regulation of Transcription by Long Noncoding RNAs

(2014) Roberto Bonasio et al.   Annual Review of Genetics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

In depth annotation of the Anopheles gambiae mosquito midgut transcriptome

(2014) Alejandro Padrón et al.   BMC GENOMICS

Identification and functional analysis of long non-coding RNAs in mouse cleavage stage embryonic development based on single cell transcriptome data

(2014) Kunshan Zhang et al.   BMC GENOMICS

MicroRNA expression profiling of the fifth-instar posterior silk gland of Bombyx mori

(2014) Jisheng Li et al.   BMC GENOMICS

Genome-Wide Identification of Long Intergenic Noncoding RNA Genes and Their Potential Association with Domestication in Pigs

(2014) Zhong-Yin Zhou et al.   Genome Biology and Evolution

A Juvenile Hormone Transcription Factor Bmdimm-Fibroin H Chain Pathway Is Involved in the Synthesis of Silk Protein in Silkworm,Bombyx mori

(2014) Xiao-Ming Zhao et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A single female-specific piRNA is the primary determiner of sex in the silkworm

(2014) Takashi Kiuchi et al.   NATURE

Diversity and dynamics of the Drosophila transcriptome

(2014) James B. Brown et al.   NATURE

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea et al.   NATURE

lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse

(2014) Jing Gong et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Transcriptome Analysis of Integument Differentially Expressed Genes in the Pigment Mutant (quail) during Molting of Silkworm, Bombyx mori

(2014) Hongyi Nie et al.   PLoS One

lnCeDB: Database of Human Long Noncoding RNA Acting as Competing Endogenous RNA

(2014) Shaoli Das et al.   PLoS One

Genome-wide discovery and characterization of maize long non-coding RNAs

(2014) Lin Li et al.   GENOME BIOLOGY

Advances in Silkworm Studies Accelerated by the Genome Sequencing ofBombyx mori

(2013) Qingyou Xia et al.   Annual Review of Entomology

Linc2GO: a human LincRNA function annotation resource based on ceRNA hypothesis

(2013) Ke Liu et al.   BIOINFORMATICS

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Liang Sun et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

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

Sequence and Expression Characteristics of Long Noncoding RNAs in Honey Bee Caste Development – Potential Novel Regulators for Transgressive Ovary Size

(2013) Fernanda C. Humann et al.   PLoS One

Long Non-Coding RNA Expression Profiling of Mouse Testis during Postnatal Development

(2013) Jin Sun et al.   PLoS One

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Identification and Properties of 1,119 Candidate LincRNA Loci in the Drosophila melanogaster Genome

(2012) Robert S. Young et al.   Genome Biology and Evolution

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Identification of kakusei, a Nuclear Non-Coding RNA, as an Immediate Early Gene from the Honeybee, and Its Application for Neuroethological Study

(2012) Taketoshi Kiya et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

The novel long non-coding RNA CRG regulates Drosophila locomotor behavior

(2012) Meixia Li et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

(2012) J. Liu et al.   PLANT CELL

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

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

(2011) Igor Ulitsky et al.   CELL

A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA

(2011) Marcella Cesana et al.   CELL

The large noncoding hsrω-n transcripts are essential for thermotolerance and remobilization of hnRNPs, HP1 and RNA polymerase II during recovery from heat shock in Drosophila

(2011) Subhash C. Lakhotia et al.   CHROMOSOMA

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

A Conserved Long Noncoding RNA Affects Sleep Behavior inDrosophila

(2011) Alexey A. Soshnev et al.   GENETICS

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes

(2011) B. J. Parker et al.   GENOME RESEARCH

Identification and characterization of a novel nuclear noncoding RNA, Fben-1, which is preferentially expressed in the higher brain center of the female silkworm moth, Bombyx mori

(2011) Syusaku Taguchi et al.   NEUROSCIENCE LETTERS

Experimental RNomics and genomic comparative analysis reveal a large group of species-specific small non-message RNAs in the silkworm Bombyx mori

(2011) Dandan Li et al.   NUCLEIC ACIDS RESEARCH

Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network

(2011) Qi Liao et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

Highly Tissue Specific Expression of Sphinx Supports Its Male Courtship Related Role in Drosophila melanogaster

(2011) Ying Chen et al.   PLoS One

The silkworm W chromosome is a source of female-enriched piRNAs

(2011) S. Kawaoka et al.   RNA

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

MicroRNAs show diverse and dynamic expression patterns in multiple tissues of Bombyx mori

(2010) Shiping Liu et al.   BMC GENOMICS

MicroRNAs of Bombyx mori identified by Solexa sequencing

(2010) Shiping Liu et al.   BMC GENOMICS

Novel genes differentially expressed between posterior and median silk gland identified by SAGE-aided transcriptome analysis

(2010) Corinne Royer et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Evolution of the Insect Yellow Gene Family

(2010) L. C. Ferguson et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

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

(2010) Matthew D Young et al.   GENOME BIOLOGY

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

(2009) Likun Wang et al.   BIOINFORMATICS

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

miR-184 Has Multiple Roles in Drosophila Female Germline Development

(2009) Nicola Iovino et al.   DEVELOPMENTAL CELL

Age- and division-of-labour-dependent differential expression of a novel non-coding RNA,Nb-1, in the brain of worker honeybees,Apis melliferaL.

(2009) H. Tadano et al.   INSECT MOLECULAR BIOLOGY

SilkDB v2.0: a platform for silkworm (Bombyx mori) genome biology

(2009) Jun Duan et al.   NUCLEIC ACIDS RESEARCH

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Inducible- and constitutive-type transcript variants ofkakusei, a novel non-coding immediate early gene, in the honeybee brain

(2008) Taketoshi Kiya et al.   INSECT MOLECULAR BIOLOGY