Computational Biology in microRNA

Mirsynergy: detecting synergistic miRNA regulatory modules by overlapping neighbourhood expansion

(2014) Yue Li et al.   BIOINFORMATICS

Global Analyses of the Effect of Different Cellular Contexts on MicroRNA Targeting

(2014) Jin-Wu Nam et al.   MOLECULAR CELL

Unambiguous Identification of miRNA:Target Site Interactions by Different Types of Ligation Reactions

(2014) Stefanie Grosswendt et al.   MOLECULAR CELL

DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions

(2014) Ioannis S. Vlachos et al.   NUCLEIC ACIDS RESEARCH

Inferring probabilistic miRNA–mRNA interaction signatures in cancers: a role-switch approach

(2014) Yue Li et al.   NUCLEIC ACIDS RESEARCH

Potential microRNA-mediated oncogenic intercellular communication revealed by pan-cancer analysis

(2014) Yue Li et al.   Scientific Reports

Regression Analysis of Combined Gene Expression Regulation in Acute Myeloid Leukemia

(2014) Yue Li et al.   PLoS Computational Biology

Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation

(2013) Hai-Son Le et al.   BIOINFORMATICS

A probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information

(2013) Yue Li et al.   BIOINFORMATICS

Joint analysis of expression profiles from multiple cancers improves the identification of microRNA-gene interactions

(2013) X. Chen et al.   BIOINFORMATICS

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

Analysis of microRNA-target interactions across diverse cancer types

(2013) Anders Jacobsen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions

(2013) Sheng-Da Hsu et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Identifying Cancer Specific Functionally Relevant miRNAs from Gene Expression and miRNA-to-Gene Networks Using Regularized Regression

(2013) Aziz M. Mezlini et al.   PLoS One

miRNAs in ESC differentiation

(2012) Emanuele Berardi et al.   AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY

microRNAs in skeletal muscle differentiation and disease

(2012) Katarzyna Goljanek-Whysall et al.   CLINICAL SCIENCE

Inferring transcriptional and microRNA-mediated regulatory programs in glioblastoma

(2012) Manu Setty et al.   Molecular Systems Biology

Detecting overlapping protein complexes in protein-protein interaction networks

(2012) Tamás Nepusz et al.   NATURE METHODS

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

A Lasso regression model for the construction of microRNA-target regulatory networks

(2011) Yiming Lu et al.   BIOINFORMATICS

MicroRNAs regulatory networks in myeloid lineage development and differentiation: regulators of the regulators

(2011) Mohamed El Gazzar et al.   IMMUNOLOGY AND CELL BIOLOGY

MicroRNAs can generate thresholds in target gene expression

(2011) Shankar Mukherji et al.   NATURE GENETICS

Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs

(2011) David M Garcia et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Isoform-level microRNA-155 target prediction using RNA-seq

(2011) Nan Deng et al.   NUCLEIC ACIDS RESEARCH

MicroRNAs as Immune Regulators: Implications for Transplantation

(2010) A. Harris et al.   AMERICAN JOURNAL OF TRANSPLANTATION

A Bayesian approach for identifying miRNA targets by combining sequence prediction and gene expression profiling

(2010) Hui Liu et al.   BMC GENOMICS

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

Genome-wide Dissection of MicroRNA Functions and Cotargeting Networks Using Gene Set Signatures

(2010) John S. Tsang et al.   MOLECULAR CELL

Target mRNA abundance dilutes microRNA and siRNA activity

(2010) Aaron Arvey et al.   Molecular Systems Biology

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

MiRNA–miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features

(2010) Juan Xu et al.   NUCLEIC ACIDS RESEARCH

Human microRNAs co-silence in well-separated groups and have different predicted essentialities

(2009) Gábor Boross et al.   BIOINFORMATICS

DIANA-mirPath: Integrating human and mouse microRNAs in pathways

(2009) G. L. Papadopoulos et al.   BIOINFORMATICS

Computational identification of hepatitis C virus associated microRNA-mRNA regulatory modules in human livers

(2009) Xinxia Peng et al.   BMC GENOMICS

SnapShot: MicroRNAs in Cancer

(2009) Riccardo Spizzo et al.   CELL

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs

(2009) Aly A Khan et al.   NATURE BIOTECHNOLOGY

A PROBABILISTIC FRAMEWORK TO IMPROVE MICRORNA TARGET PREDICTION BY INCORPORATING PROTEOMICS DATA

(2009) JINGJING LI et al.   Journal of Bioinformatics and Computational Biology

Most mammalian mRNAs are conserved targets of microRNAs

(2008) R. C. Friedman et al.   GENOME RESEARCH

MicroRNAs: Novel Regulators During the Immune Response

(2008) Yujing Bi et al.   JOURNAL OF CELLULAR PHYSIOLOGY

The impact of microRNAs on protein output

(2008) Daehyun Baek et al.   NATURE

Widespread changes in protein synthesis induced by microRNAs

(2008) Matthias Selbach et al.   NATURE

MicroRNAs expressed by herpes simplex virus 1 during latent infection regulate viral mRNAs

(2008) Jennifer Lin Umbach et al.   NATURE

MicroRNAs: new regulators of immune cell development and function

(2008) David Baltimore et al.   NATURE IMMUNOLOGY

Detecting microRNA binding and siRNA off-target effects from expression data

(2008) Stijn van Dongen et al.   NATURE METHODS

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

(2008) Witold Filipowicz et al.   NATURE REVIEWS GENETICS