Altered non-coding RNA expression profile in F1 progeny 1 year after parental irradiation is linked to adverse effects in zebrafish

Gamma radiation induces locus specific changes to histone modification enrichment in zebrafish and Atlantic salmon

(2019) Leif Christopher Lindeman et al.   PLoS One

WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs

(2019) Yuxing Liao et al.   NUCLEIC ACIDS RESEARCH

Effects of ionizing radiation at Drosophila melanogaster with differently active hobo transposons

(2019) Elena Yushkova   INTERNATIONAL JOURNAL OF RADIATION BIOLOGY

Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish

(2018) Wen Chen et al.   BMC GENOMICS

Identification of differentially expressed genes and pathways in mice exposed to mixed field neutron/photon radiation

(2018) Constantinos G. Broustas et al.   BMC GENOMICS

Parental exposure to gamma radiation causes progressively altered transcriptomes linked to adverse effects in zebrafish offspring

(2018) Selma Hurem et al.   ENVIRONMENTAL POLLUTION

Alternative-splicing defects in cancer: Splicing regulators and their downstream targets, guiding the way to novel cancer therapeutics

(2018) Laura M. Urbanski et al.   Wiley Interdisciplinary Reviews-RNA

Ionizing radiation induces transgenerational effects of DNA methylation in zebrafish

(2018) Jorke H. Kamstra et al.   Scientific Reports

Expression and function of lncRNA MALAT-1 in the embryonic development of zebrafish

(2018) Mengli Wu et al.   GENE

Parental gamma irradiation induces reprotoxic effects accompanied by genomic instability in zebrafish ( Danio rerio ) embryos

(2017) Selma Hurem et al.   ENVIRONMENTAL RESEARCH

Dose-dependent effects of gamma radiation on the early zebrafish development and gene expression

(2017) Selma Hurem et al.   PLoS One

piRNA Biogenesis in Drosophila melanogaster

(2017) Xiawei Huang et al.   TRENDS IN GENETICS

Optimization of miRNA-seq data preprocessing

(2015) S. Tam et al.   BRIEFINGS IN BIOINFORMATICS

DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts

(2015) Maria D. Paraskevopoulou et al.   NUCLEIC ACIDS RESEARCH

Systematic characterization of small RNAome during zebrafish early developmental stages

(2014) Yuangen Yao et al.   BMC GENOMICS

piRNAs: from biogenesis to function

(2014) E.-M. Weick et al.   DEVELOPMENT

Expanding the annotation of zebrafish microRNAs based on small RNA sequencing

(2014) Thomas Desvignes et al.   GENE

UVA and UVB Irradiation Differentially Regulate microRNA Expression in Human Primary Keratinocytes

(2014) Anne Kraemer et al.   PLoS One

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Embryonic ionizing radiation exposure results in expression alterations of genes associated with cardiovascular and neurological development, function, and disease and modified cardiovascular function in zebrafish

(2014) Jennifer L. Freeman et al.   Frontiers in Genetics

Radiation-induced epigenetic DNA methylation modification of radiation-response pathways

(2013) Deborah A Antwih et al.   Epigenetics

Radiation-induced microRNA: Discovery, functional analysis, and cancer radiotherapy

(2013) M. Ahmad Chaudhry   JOURNAL OF CELLULAR BIOCHEMISTRY

Using machine learning and high-throughput RNA sequencing to classify the precursors of small non-coding RNAs

(2013) Paul Ryvkin et al.   METHODS

Distinctive microRNA expression signatures in proton-irradiated mice

(2013) Shahid Yar Khan et al.   MOLECULAR AND CELLULAR BIOCHEMISTRY

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Long-Term Effects of Ionizing Radiation on Gene Expression in a Zebrafish Model

(2013) Lahcen Jaafar et al.   PLoS One

proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis

(2012) David Rosenkranz et al.   BMC BIOINFORMATICS

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

Evaluation of normalization methods in mammalian microRNA-Seq data

(2012) L. X. Garmire et al.   RNA

Transcriptome-wide analysis of small RNA expression in early zebrafish development

(2012) C. Wei et al.   RNA

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

(2011) Igor Ulitsky et al.   CELL

Let-7 and miR-200 microRNAs: Guardians against pluripotency and cancer progression

(2011) Marcus E. Peter   CELL CYCLE

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

(2011) Marc R. Friedländer et al.   NUCLEIC ACIDS RESEARCH

An Investigation of a Role for U2 snRNP Spliceosomal Components in Regulating Transcription

(2011) Susannah L. McKay et al.   PLoS One

The emerging role of miR-200 family of MicroRNAs in epithelial-mesenchymal transition and cancer metastasis

(2011) Manav Korpal et al.   RNA Biology

Conserved Regulation of p53 Network Dosage by MicroRNA–125b Occurs through Evolving miRNA–Target Gene Pairs

(2011) Minh T. N. Le et al.   PLoS Genetics

Guarding the ‘translation apparatus’: defective ribosome biogenesis and the p53 signaling pathway

(2011) Anirban Chakraborty et al.   Wiley Interdisciplinary Reviews-RNA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

Novel roles of U1 snRNP in alternative splicing regulation

(2010) Emanuele Buratti et al.   RNA Biology

Down-Regulation of a Host MicroRNA by a Herpesvirus saimiri Noncoding RNA

(2010) D. Cazalla et al.   SCIENCE

MicroRNA-125b is a novel negative regulator of p53

(2009) M. T.N. Le et al.   GENES & DEVELOPMENT

How to map billions of short reads onto genomes

(2009) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Zili is required for germ cell differentiation and meiosis in zebrafish

(2008) Saskia Houwing et al.   EMBO JOURNAL

DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes

(2008) S. Kuramochi-Miyagawa et al.   GENES & DEVELOPMENT