Expanding the horizons of microRNA bioinformatics

MicroRNAs-mediated epithelial-mesenchymal transition in fibrotic diseases

(2017) Xiao-Zhou Zou et al.   EUROPEAN JOURNAL OF PHARMACOLOGY

Differential expression of microRNAs in plasma of patients with prediabetes and newly diagnosed type 2 diabetes

(2016) Shaoying Yan et al.   ACTA DIABETOLOGICA

Chronic miR‐29 antagonism promotes favorable plaque remodeling in atherosclerotic mice

(2016) Victoria Ulrich et al.   EMBO Molecular Medicine

Expression profile of micro-RNAs and functional annotation analysis of their targets in human chorionic villi from early recurrent miscarriage

(2016) Lisha Tang et al.   GENE

Database Resources of the National Center for Biotechnology Information

(2016)   NUCLEIC ACIDS RESEARCH

miEAA: microRNA enrichment analysis and annotation

(2016) Christina Backes et al.   NUCLEIC ACIDS RESEARCH

Expansion of the Gene Ontology knowledgebase and resources

(2016)   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

(2016) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

Guidelines for the functional annotation of microRNAs using the Gene Ontology

(2016) Rachael P. Huntley et al.   RNA

Differential Roles for DUSP Family Members in Epithelial-to-Mesenchymal Transition and Cancer Stem Cell Regulation in Breast Cancer

(2016) Tara Boulding et al.   PLoS One

Crosstalk between miRNAs and their regulated genes network in stroke

(2016) Ye Yuan et al.   Scientific Reports

Bias in microRNA functional enrichment analysis

(2015) Thomas Bleazard et al.   BIOINFORMATICS

The Role of miR-21 in Cancer

(2015) Susan R. Pfeffer et al.   DRUG DEVELOPMENT RESEARCH

Validated MicroRNA Target Databases: An Evaluation

(2015) Yun Ji Diana Lee et al.   DRUG DEVELOPMENT RESEARCH

Epithelial-mesenchymal transition: An emerging target in tissue fibrosis

(2015) Meirong Li et al.   EXPERIMENTAL BIOLOGY AND MEDICINE

Visual annotation display (VLAD): a tool for finding functional themes in lists of genes

(2015) Joel E. Richardson et al.   MAMMALIAN GENOME

miRWalk2.0: a comprehensive atlas of microRNA-target interactions

(2015) Harsh Dweep et al.   NATURE METHODS

Bioinformatic tools for microRNA dissection

(2015) Most Mauluda Akhtar et al.   NUCLEIC ACIDS RESEARCH

Pathway analysis from lists of microRNAs: common pitfalls and alternative strategy

(2015) Patrice Godard et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

DUSP10 regulates intestinal epithelial cell growth and colorectal tumorigenesis

(2015) C W Png et al.   ONCOGENE

Canto: an online tool for community literature curation

(2014) Kim M. Rutherford et al.   BIOINFORMATICS

A method for increasing expressivity of Gene Ontology annotations using a compositional approach

(2014) Rachael P Huntley et al.   BMC BIOINFORMATICS

MicroRNA mimicry blocks pulmonary fibrosis

(2014) R. L. Montgomery et al.   EMBO Molecular Medicine

IL-1β Promotes Malignant Transformation and Tumor Aggressiveness in Oral Cancer

(2014) Chia-Huei Lee et al.   JOURNAL OF CELLULAR PHYSIOLOGY

miR-21 overexpression enhances TGF-β1-induced epithelial-to-mesenchymal transition by target smad7 and aggravates renal damage in diabetic nephropathy

(2014) Jin-Yang Wang et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

The GOA database: Gene Ontology annotation updates for 2015

(2014) Rachael P. Huntley et al.   NUCLEIC ACIDS RESEARCH

RNAcentral: an international database of ncRNA sequences

(2014)   NUCLEIC ACIDS RESEARCH

Gene: a gene-centered information resource at NCBI

(2014) Garth R. Brown et al.   NUCLEIC ACIDS RESEARCH

Functional and Evolutionary Significance of Human MicroRNA Seed Region Mutations

(2014) Christopher G. Hill et al.   PLoS One

Large-scale gene function analysis with the PANTHER classification system

(2013) Huaiyu Mi et al.   Nature Protocols

A new reference implementation of the PSICQUIC web service

(2013) Noemi del-Toro et al.   NUCLEIC ACIDS RESEARCH

HMDD v2.0: a database for experimentally supported human microRNA and disease associations

(2013) Yang Li et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

miR-21 Promotes Fibrogenic Epithelial-to-Mesenchymal Transition of Epicardial Mesothelial Cells Involving Programmed Cell Death 4 and Sprouty-1

(2013) Hasse Brønnum et al.   PLoS One

Polycyclic aromatic hydrocarbon (PAH)-mediated upregulation of hepatic microRNA-181 family promotes cancer cell migration by targeting MAPK phosphatase-5, regulating the activation of p38 MAPK

(2013) Mi-Kyung Song et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

A guide to best practices for Gene Ontology (GO) manual annotation

(2013) R. Balakrishnan et al.   Database-The Journal of Biological Databases and Curation

Downregulation of Inflammatory MicroRNAs by Ig-like Transcript 3 Is Essential for the Differentiation of Human CD8+ T Suppressor Cells

(2012) C.-C. Chang et al.   JOURNAL OF IMMUNOLOGY

MicroRNA-21 targets the vitamin D–dependent antimicrobial pathway in leprosy

(2012) Philip T Liu et al.   NATURE MEDICINE

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

(2012) Sandra Orchard et al.   NATURE METHODS

Assessment of community-submitted ontology annotations from a novel database-journal partnership

(2012) T. Z. Berardini et al.   Database-The Journal of Biological Databases and Curation

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

Mutation Altering the miR-184 Seed Region Causes Familial Keratoconus with Cataract

(2011) Anne E. Hughes et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Therapeutic Inhibition of miR-208a Improves Cardiac Function and Survival During Heart Failure

(2011) Rusty L. Montgomery et al.   CIRCULATION

Inhibition of miR-15 Protects Against Cardiac Ischemic Injury

(2011) Thomas G. Hullinger et al.   CIRCULATION RESEARCH

A quick reality check for microRNA target prediction

(2011) Juergen Kast   Expert Review of Proteomics

The Impact of Focused Gene Ontology Curation of Specific Mammalian Systems

(2011) Yasmin Alam-Faruque et al.   PLoS One

Regulation and function of miRNA-21 in health and disease

(2011) Regalla Kumarswamy et al.   RNA Biology

A Distinct Interaction Mode Revealed by the Crystal Structure of the Kinase p38  with the MAPK Binding Domain of the Phosphatase MKP5

(2011) Y.-Y. Zhang et al.   Science Signaling

TAM: A method for enrichment and depletion analysis of a microRNA category in a list of microRNAs

(2010) Ming Lu et al.   BMC BIOINFORMATICS

Matrix Metalloproteinase-Induced Epithelial-Mesenchymal Transition in Breast Cancer

(2010) Evette S. Radisky et al.   JOURNAL OF MAMMARY GLAND BIOLOGY AND NEOPLASIA

A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans

(2010) Marko Jovanovic et al.   NATURE METHODS

Towards computational prediction of microRNA function and activity

(2010) Igor Ulitsky et al.   NUCLEIC ACIDS RESEARCH

QuickGO: a web-based tool for Gene Ontology searching

(2009) D. Binns et al.   BIOINFORMATICS

MicroRNA expression in response to murine myocardial infarction: miR-21 regulates fibroblast metalloprotease-2 via phosphatase and tensin homologue

(2009) Sashwati Roy et al.   CARDIOVASCULAR RESEARCH

The basics of epithelial-mesenchymal transition

(2009) Raghu Kalluri et al.   JOURNAL OF CLINICAL INVESTIGATION

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration

(2008) S. Bauer et al.   BIOINFORMATICS

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

SMAD proteins control DROSHA-mediated microRNA maturation

(2008) Brandi N. Davis et al.   NATURE

Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?

(2008) Witold Filipowicz et al.   NATURE REVIEWS GENETICS

miRecords: an integrated resource for microRNA-target interactions

(2008) F. Xiao et al.   NUCLEIC ACIDS RESEARCH