Expression of lncRNAs in response to bacterial infections of goat mammary epithelial cells reveals insights into mammary gland diseases

Gene regulation by long non-coding RNAs and its biological functions

(2020) Luisa Statello et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Long non-coding RNAs in diseases related to inflammation and immunity

(2019) Jiao Chen et al.   Annals of Translational Medicine

Long noncoding RNAs are associated with metabolic and cellular processes in the jejunum mucosa of pre-weaning calves in response to different diets

(2018) Rosemarie Weikard et al.   Oncotarget

Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species

(2018) Colin Kern et al.   BMC GENOMICS

LncRNA XIST mediates bovine mammary epithelial cell inflammatory response via NF-κB/NLRP3 inflammasome pathway

(2018) Mengru Ma et al.   CELL PROLIFERATION

Transcriptome Analysis of Long Non-Coding RNA in the Bovine Mammary Gland Following Dietary Supplementation with Linseed Oil and Safflower Oil

(2018) Eveline Ibeagha-Awemu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Ensembl 2019

(2018) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Analyses of long non-coding RNAs and mRNA profiling through RNA sequencing of MDBK cells at different stages of bovine viral diarrhea virus infection

(2017) Qiman Ma et al.   RESEARCH IN VETERINARY SCIENCE

Intersecting transcriptomic profiling technologies and long non-coding RNA function in lung adenocarcinoma: discovery, mechanisms, and therapeutic applications

(2017) Jonathan Castillo et al.   Oncotarget

A Long Journey Ahead: Long Non-coding RNAs in Bacterial Infections

(2017) Jennifer zur Bruegge et al.   Frontiers in Cellular and Infection Microbiology

Survey of High Throughput RNA-Seq Data Reveals Potential Roles for lncRNAs during Development and Stress Response in Bread Wheat

(2017) Shumayla et al.   Frontiers in Plant Science

lncRNA H19 is involved in TGF-β1-induced epithelial to mesenchymal transition in bovine epithelial cells through PI3K/AKT Signaling Pathway

(2017) Wei Yang et al.   PeerJ

Mining long noncoding RNA in livestock

(2016) R. Weikard et al.   ANIMAL GENETICS

Integrative Transcriptome Analyses of Metabolic Responses in Mice Define Pivotal LncRNA Metabolic Regulators

(2016) Ling Yang et al.   Cell Metabolism

Simulation-based comprehensive benchmarking of RNA-seq aligners

(2016) Giacomo Baruzzo et al.   NATURE METHODS

Unraveling the oral cancer lncRNAome: Identification of novel lncRNAs associated with malignant progression and HPV infection

(2016) Nijiro Nohata et al.   ORAL ONCOLOGY

Microarray analysis of long noncoding RNA and mRNA expression profiles in human macrophages infected with Mycobacterium tuberculosis

(2016) Xiaofan Yang et al.   Scientific Reports

Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells

(2015) Jennifer Y. Tan et al.   GENOME RESEARCH

Discovery, Annotation, and Functional Analysis of Long Noncoding RNAs Controlling Cell-Cycle Gene Expression and Proliferation in Breast Cancer Cells

(2015) Miao Sun et al.   MOLECULAR CELL

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Long Noncoding RNAs: A New Regulatory Code in Metabolic Control

(2015) Xu-Yun Zhao et al.   TRENDS IN BIOCHEMICAL SCIENCES

Analysis of long non-coding RNAs highlights tissue-specific expression patterns and epigenetic profiles in normal and psoriatic skin

(2015) Lam C Tsoi et al.   GENOME BIOLOGY

A catalogue of novel bovine long noncoding RNA across 18 tissues

(2015) Lambros T. Koufariotis 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

Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing

(2014) Coline Billerey et al.   BMC GENOMICS

Identification of novel transcripts and noncoding RNAs in bovine skin by deep next generation sequencing

(2013) Rosemarie Weikard et al.   BMC GENOMICS

The Tissue-Specific lncRNA Fendrr Is an Essential Regulator of Heart and Body Wall Development in the Mouse

(2013) Phillip Grote et al.   DEVELOPMENTAL CELL

Repression of the Long Noncoding RNA-LET by Histone Deacetylase 3 Contributes to Hypoxia-Mediated Metastasis

(2013) Fu Yang et al.   MOLECULAR CELL

CLP1 links tRNA metabolism to progressive motor-neuron loss

(2013) Toshikatsu Hanada et al.   NATURE

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

Posttranscriptional Gene Regulation by Long Noncoding RNA

(2012) Je-Hyun Yoon et al.   JOURNAL OF MOLECULAR BIOLOGY

SRSF1 regulates the assembly of pre-mRNA processing factors in nuclear speckles

(2012) Vidisha Tripathi et al.   MOLECULAR BIOLOGY OF THE CELL

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

(2012) Cole Trapnell et al.   Nature Protocols

Bovine ncRNAs Are Abundant, Primarily Intergenic, Conserved and Associated with Regulatory Genes

(2012) Zhipeng Qu et al.   PLoS One

In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli- mastitis

(2011) Bart Buitenhuis et al.   BMC GENOMICS

Mammary tissue damage during bovine mastitis: Causes and control1

(2011) X. Zhao et al.   JOURNAL OF ANIMAL SCIENCE

Molecular Epidemiology of Mastitis Pathogens of Dairy Cattle and Comparative Relevance to Humans

(2011) Ruth N. Zadoks et al.   JOURNAL OF MAMMARY GLAND BIOLOGY AND NEOPLASIA

Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression

(2011) John R Prensner et al.   NATURE BIOTECHNOLOGY

Economic aspects of mastitis: New developments

(2011) H Hogeveen et al.   NEW ZEALAND VETERINARY JOURNAL

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Exploring long non-coding RNAs through sequencing

(2011) Sophie R. Atkinson et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Comparative Kinetics ofEscherichia coli- andStaphylococcus aureus-Specific Activation of Key Immune Pathways in Mammary Epithelial Cells Demonstrates ThatS. aureusElicits a Delayed Response Dominated by Interleukin-6 (IL-6) but Not by IL-1A or Tumor Necrosis Factor Alpha

(2010) Juliane Günther et al.   INFECTION AND IMMUNITY

Proteomics, Genomics, and Pathway Analyses ofEscherichia coliandStaphylococcus aureusInfected Milk Whey Reveal Molecular Pathways and Networks Involved in Mastitis

(2010) Eveline M. Ibeagha-Awemu et al.   JOURNAL OF PROTEOME RESEARCH

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

(2010) Matthew D Young et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH