Small RNA profiling of low biomass samples: identification and removal of contaminants

Diet-derived microRNAs: unicorn or silver bullet?

(2017) Kenneth W. Witwer et al.   Genes and Nutrition

Survey of 800+ data sets from human tissue and body fluid reveals xenomiRs are likely artifacts

(2017) Wenjing Kang et al.   RNA

Total Extracellular Small RNA Profiles from Plasma, Saliva and Urine of Healthy Subjects

(2017) Ashish Yeri et al.   Scientific Reports

Diet-derived microRNAs: unicorn or silver bullet?

(2017) Kenneth W. Witwer et al.   Genes and Nutrition

Sources and Functions of Extracellular Small RNAs in Human Circulation

(2016) Joëlle V. Fritz et al.   Annual Review of Nutrition

The Host Shapes the Gut Microbiota via Fecal MicroRNA

(2016) Shirong Liu et al.   Cell Host & Microbe

How Our Other Genome Controls Our Epi-Genome

(2016) Antonella Celluzzi et al.   TRENDS IN MICROBIOLOGY

Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples

(2016) Angela Glassing et al.   Gut Pathogens

A Novel Mechanism of Host-Pathogen Interaction through sRNA in Bacterial Outer Membrane Vesicles

(2016) Katja Koeppen et al.   PLoS Pathogens

Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota

(2016) Abigail P. Lauder et al.   Microbiome

Uropathogenic Escherichia coli Releases Extracellular Vesicles That Are Associated with RNA

(2016) Cherie Blenkiron et al.   PLoS One

Uptake and Function Studies of Maternal Milk-derived MicroRNAs

(2015) Alexandra C. Title et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Dysregulation of microRNA-219 promotes neurodegeneration through post-transcriptional regulation of tau

(2015) Ismael Santa-Maria et al.   JOURNAL OF CLINICAL INVESTIGATION

Contamination or artifacts may explain reports of plant miRNAs in humans

(2015) Kenneth W. Witwer   JOURNAL OF NUTRITIONAL BIOCHEMISTRY

Database resources of the National Center for Biotechnology Information

(2015)   NUCLEIC ACIDS RESEARCH

The extracellular RNA complement ofEscherichia coli

(2015) Anubrata Ghosal et al.   MicrobiologyOpen

Transfer and functional consequences of dietary microRNAs in vertebrates: Concepts in search of corroboration

(2014) Kenneth W. Witwer et al.   BIOESSAYS

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Small RNAs from plants, bacteria and fungi within the order Hypocreales are ubiquitous in human plasma

(2014) Meabh Beatty et al.   BMC GENOMICS

Honeysuckle-encoded atypical microRNA2911 directly targets influenza A viruses

(2014) Zhen Zhou et al.   CELL RESEARCH

MicroRNAs Are Absorbed in Biologically Meaningful Amounts from Nutritionally Relevant Doses of Cow Milk and Affect Gene Expression in Peripheral Blood Mononuclear Cells, HEK-293 Kidney Cell Cultures, and Mouse Livers

(2014) Scott R. Baier et al.   JOURNAL OF NUTRITION

Optimization of Extraction of Circulating RNAs from Plasma – Enabling Small RNA Sequencing

(2014) Melanie Spornraft et al.   PLoS One

Diverse and Widespread Contamination Evident in the Unmapped Depths of High Throughput Sequencing Data

(2014) Richard W. Lusk   PLoS One

Mining of public sequencing databases supports a non-dietary origin for putative foreign miRNAs: underestimated effects of contamination in NGS

(2014) J. P. Tosar et al.   RNA

Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity

(2014) Amy H. Buck et al.   Nature Communications

Trans-kingdom Cross-Talk: Small RNAs on the Move

(2014) Marijn Knip et al.   PLoS Genetics

Assessing the survival of exogenous plant microRNA in mice

(2014) GaoFeng Liang et al.   Food Science & Nutrition

Characterization of human plasma-derived exosomal RNAs by deep sequencing

(2013) Xiaoyi Huang et al.   BMC GENOMICS

The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns

(2013) S. N. Naccache et al.   JOURNAL OF VIROLOGY

Lack of detectable oral bioavailability of plant microRNAs after feeding in mice

(2013) Brent Dickinson et al.   NATURE BIOTECHNOLOGY

Assessing an Improved Protocol for Plasma microRNA Extraction

(2013) Inés Moret et al.   PLoS One

Ineffective delivery of diet-derived microRNAs to recipient animal organisms

(2013) Jonathan W. Snow et al.   RNA Biology

Identification of extracellular miRNA in human cerebrospinal fluid by next-generation sequencing

(2013) K. L. Burgos et al.   RNA

Fungal Small RNAs Suppress Plant Immunity by Hijacking Host RNA Interference Pathways

(2013) Arne Weiberg et al.   SCIENCE

Method for microRNA isolation from clinical serum samples

(2012) Yu Li et al.   ANALYTICAL BIOCHEMISTRY

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

(2012) Limin Fu et al.   BIOINFORMATICS

Analysis of plant-derived miRNAs in animal small RNA datasets

(2012) Yuanji Zhang et al.   BMC GENOMICS

Translocation of Sickle Cell Erythrocyte MicroRNAs into Plasmodium falciparum Inhibits Parasite Translation and Contributes to Malaria Resistance

(2012) Gregory LaMonte et al.   Cell Host & Microbe

Combined Analysis of MicroRNome and 3′-UTRome Reveals a Species-specific Regulation of Progesterone Receptor Expression in the Endometrium of Rhesus Monkey

(2012) Ji-Long Liu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions

(2012) Esther N. M. Nolte-’t Hoen et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

A Systematic Analysis of miRNA Transcriptome in Marek’s Disease Virus-Induced Lymphoma Reveals Novel and Differentially Expressed miRNAs

(2012) Ling Lian et al.   PLoS One

The Complex Exogenous RNA Spectra in Human Plasma: An Interface with Human Gut Biota?

(2012) Kai Wang et al.   PLoS One

A global view of porcine transcriptome in three tissues from a full-sib pair with extreme phenotypes in growth and fat deposition by paired-end RNA sequencing

(2011) Congying Chen et al.   BMC GENOMICS

Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA

(2011) Lin Zhang et al.   CELL RESEARCH

Transcriptome-wide Analysis of Regulatory Interactions of the RNA-Binding Protein HuR

(2011) Svetlana Lebedeva et al.   MOLECULAR CELL

Characterization of extracellular circulating microRNA

(2011) Andrey Turchinovich et al.   NUCLEIC ACIDS RESEARCH

Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma

(2011) J. D. Arroyo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood

(2010) Candida Vaz et al.   BMC GENOMICS

Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum

(2010) Fabrice Legeai et al.   BMC GENOMICS

MicroRNAs of Bombyx mori identified by Solexa sequencing

(2010) Shiping Liu et al.   BMC GENOMICS

Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries

(2010) M. J.L. de Hoon et al.   GENOME RESEARCH

Regulation of MicroRNA Expression and Abundance during Lymphopoiesis

(2010) Stefan Kuchen et al.   IMMUNITY

Next-generation small RNA sequencing for microRNAs profiling in the honey beeApis mellifera

(2010) X. Chen et al.   INSECT MOLECULAR BIOLOGY

Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans

(2010) Ryan J Taft et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Integrative Analysis of microRNA and mRNA Expression in Mouse Uterus under Delayed Implantation and Activation

(2010) Ren-Wei Su et al.   PLoS One

Functional delivery of viral miRNAs via exosomes

(2010) D. M. Pegtel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small Silencing RNAs in Plants Are Mobile and Direct Epigenetic Modification in Recipient Cells

(2010) A. Molnar et al.   SCIENCE

Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

(2009) Christine Mayr et al.   CELL

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Delivery of MicroRNA-126 by Apoptotic Bodies Induces CXCL12-Dependent Vascular Protection

(2009) A. Zernecke et al.   Science Signaling

Characterization and comparative profiling of the small RNA transcriptomes in two phases of locust

(2009) Yuanyuan Wei et al.   GENOME BIOLOGY

Database indexing for production MegaBLAST searches

(2008) Aleksandr Morgulis et al.   BIOINFORMATICS

Detection and Characterization of Placental MicroRNAs in Maternal Plasma

(2008) S. S.C. Chim et al.   CLINICAL CHEMISTRY

Trans-specific gene silencing between host and parasitic plants

(2008) Alexey A. Tomilov et al.   PLANT JOURNAL

Circulating microRNAs as stable blood-based markers for cancer detection

(2008) P. S. Mitchell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA