Understanding microRNA-mediated gene regulatory networks through mathematical modelling

Dicer and microRNA expression in multiple sclerosis and response to interferon therapy

(2016) William J. Magner et al.   JOURNAL OF NEUROIMMUNOLOGY

Endogenous microRNA sponges: evidence and controversy

(2016) Daniel W. Thomson et al.   NATURE REVIEWS GENETICS

RBM3 regulates temperature sensitive miR-142–5p and miR-143 (thermomiRs), which target immune genes and control fever

(2016) Justin J.-L. Wong et al.   NUCLEIC ACIDS RESEARCH

Probing the Limits to MicroRNA-Mediated Control of Gene Expression

(2016) Araks Martirosyan et al.   PLoS Computational Biology

Coupling transcriptional and post-transcriptional miRNA regulation in the control of cell fate

(2016) Reut Shalgi et al.   Aging-US

A microRNA molecular modeling extension for prediction of colorectal cancer treatment

(2015) Jian Li et al.   BMC CANCER

The RNA world in the 21st century—a systems approach to finding non-coding keys to clinical questions

(2015) Ulf Schmitz et al.   BRIEFINGS IN BIOINFORMATICS

A Biogenesis Step Upstream of Microprocessor Controls miR-17∼92 Expression

(2015) Peng Du et al.   CELL

Improving Cancer Treatment via Mathematical Modeling: Surmounting the Challenges Is Worth the Effort

(2015) Franziska Michor et al.   CELL

Hepatitis C Virus RNA Functionally Sequesters miR-122

(2015) Joseph M. Luna et al.   CELL

Computational oncology — mathematical modelling of drug regimens for precision medicine

(2015) Dominique Barbolosi et al.   Nature Reviews Clinical Oncology

Quantitative and logic modelling of molecular and gene networks

(2015) Nicolas Le Novère   NATURE REVIEWS GENETICS

MiRBooking simulates the stoichiometric mode of action of microRNAs

(2015) Nathanaël Weill et al.   NUCLEIC ACIDS RESEARCH

Model-guided quantitative analysis of microRNA-mediated regulation on competing endogenous RNAs using a synthetic gene circuit

(2015) Ye Yuan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-mediated degradation of microRNAs: A widespread viral strategy?

(2015) Jana McCaskill et al.   RNA Biology

Mathematical modeling of combinatorial regulation suggests that apparent positive regulation of targets by miRNA could be an artifact resulting from competition for mRNA

(2015) Dimpal Nyayanit et al.   RNA

MicroRNA control of protein expression noise

(2015) J. M. Schmiedel et al.   SCIENCE

The Whereabouts of microRNA Actions: Cytoplasm and Beyond

(2015) Anthony K.L. Leung   TRENDS IN CELL BIOLOGY

The miR-199a/Brm/EGR1 axis is a determinant of anchorage-independent growth in epithelial tumor cell lines

(2015) Kazuyoshi Kobayashi et al.   Scientific Reports

Modeling the Transitions between Collective and Solitary Migration Phenotypes in Cancer Metastasis

(2015) Bin Huang et al.   Scientific Reports

Computational Model of MicroRNA Control of HIF-VEGF Pathway: Insights into the Pathophysiology of Ischemic Vascular Disease and Cancer

(2015) Chen Zhao et al.   PLoS Computational Biology

MiR-192-Mediated Positive Feedback Loop Controls the Robustness of Stress-Induced p53 Oscillations in Breast Cancer Cells

(2015) Richard Moore et al.   PLoS Computational Biology

Computational Biology in microRNA

(2015) Yue Li et al.   Wiley Interdisciplinary Reviews-RNA

Implications of the Hybrid Epithelial/Mesenchymal Phenotype in Metastasis

(2015) Mohit Kumar Jolly   Frontiers in Oncology

Dynamics of miRNA driven feed-forward loop depends upon miRNA action mechanisms

(2015) Maria A Duk et al.   BMC GENOMICS

MicroRNA binding sites in the coding region of mRNAs: Extending the repertoire of post-transcriptional gene regulation

(2014) Anneke Brümmer et al.   BIOESSAYS

RNA-Based Regulation: Dynamics and Response to Perturbations of Competing RNAs

(2014) Matteo Figliuzzi et al.   BIOPHYSICAL JOURNAL

Interactions between Distant ceRNAs in Regulatory Networks

(2014) Mor Nitzan et al.   BIOPHYSICAL JOURNAL

Toward Decoding the Principles of Cancer Metastasis Circuits

(2014) Mingyang Lu et al.   CANCER RESEARCH

Exosomes as divine messengers: are they the Hermes of modern molecular oncology?

(2014) C Braicu et al.   CELL DEATH AND DIFFERENTIATION

Introduction to RNA-Seq and its Applications to Drug Discovery and Development

(2014) Zainab Khatoon et al.   DRUG DEVELOPMENT RESEARCH

A challenge for miRNA: multiple isomiRs in miRNAomics

(2014) Li Guo et al.   GENE

Feedback Control as a Framework for Understanding Tradeoffs in Biology

(2014) N. J. Cowan et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Assessing the ceRNA Hypothesis with Quantitative Measurements of miRNA and Target Abundance

(2014) Rémy Denzler et al.   MOLECULAR CELL

Endogenous miRNA and Target Concentrations Determine Susceptibility to Potential ceRNA Competition

(2014) Andrew D. Bosson et al.   MOLECULAR CELL

The multilayered complexity of ceRNA crosstalk and competition

(2014) Yvonne Tay et al.   NATURE

Competition between target sites of regulators shapes post-transcriptional gene regulation

(2014) Marvin Jens et al.   NATURE REVIEWS GENETICS

Regulation of microRNA-mediated gene silencing by microRNA precursors

(2014) Biswajoy Roy-Chaudhuri et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cooperative gene regulation by microRNA pairs and their identification using a computational workflow

(2014) Ulf Schmitz et al.   NUCLEIC ACIDS RESEARCH

A Mathematical Model of Bimodal Epigenetic Control of miR-193a in Ovarian Cancer Stem Cells

(2014) Frank H. C. Cheng et al.   PLoS One

Quantitative and stoichiometric analysis of the microRNA content of exosomes

(2014) J. R. Chevillet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional interactions among microRNAs and long noncoding RNAs

(2014) Je-Hyun Yoon et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

microRNA input into a neural ultradian oscillator controls emergence and timing of alternative cell states

(2014) Marc Goodfellow et al.   Nature Communications

A Combination of Transcriptional and MicroRNA Regulation Improves the Stability of the Relative Concentrations of Target Genes

(2014) Andrea Riba et al.   PLoS Computational Biology

Why model?

(2014) Olaf Wolkenhauer   Frontiers in Physiology

Trans-regulation of RNA-binding protein motifs by microRNA

(2014) Francis Doyle et al.   Frontiers in Genetics

Competing endogenous RNAs (ceRNAs): new entrants to the intricacies of gene regulation

(2014) Reena V. Kartha et al.   Frontiers in Genetics

Dynamic analysis of the combinatorial regulation involving transcription factors and microRNAs in cell fate decisions

(2013) Fang Yan et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Quantitative Analysis of Competition in Posttranscriptional Regulation Reveals a Novel Signature in Target Expression Variation

(2013) Filippos D. Klironomos et al.   BIOPHYSICAL JOURNAL

Coupled Reversible and Irreversible Bistable Switches Underlying TGFβ-induced Epithelial to Mesenchymal Transition

(2013) Xiao-Jun Tian et al.   BIOPHYSICAL JOURNAL

MicroRNAs as a Selective Channel of Communication between Competing RNAs: a Steady-State Theory

(2013) Matteo Figliuzzi et al.   BIOPHYSICAL JOURNAL

A modeled dynamic regulatory network of NF-κB and IL-6 mediated by miRNA

(2013) Xu Xue et al.   BIOSYSTEMS

Transcription factor and microRNA co-regulatory loops: important regulatory motifs in biological processes and diseases

(2013) H.-M. Zhang et al.   BRIEFINGS IN BIOINFORMATICS

Kinetic Modeling-Based Detection of Genetic Signatures That Provide Chemoresistance via the E2F1-p73/DNp73-miR-205 Network

(2013) J. Vera et al.   CANCER RESEARCH

Functional characteristics of a double negative feedback loop mediated by microRNAs

(2013) Shuiming Cai et al.   Cognitive Neurodynamics

Regulation of epithelial–mesenchymal and mesenchymal–epithelial transitions by microRNAs

(2013) Samy Lamouille et al.   CURRENT OPINION IN CELL BIOLOGY

MicroRNAs as therapeutic targets in chemoresistance

(2013) Michela Garofalo et al.   DRUG RESISTANCE UPDATES

Mathematical modelling of miRNA mediated BCR.ABL protein regulation in chronic myeloid leukaemia vis-a-vis therapeutic strategies

(2013) Malkhey Verma et al.   Integrative Biology

Modelling of glioblastoma growth by linking a molecular interaction network with an agent-based model

(2013) Tina A. Schuetz et al.   MATHEMATICAL AND COMPUTER MODELLING OF DYNAMICAL SYSTEMS

Timescales and bottlenecks in miRNA-dependent gene regulation

(2013) J. Hausser et al.   Molecular Systems Biology

From pseudo-ceRNAs to circ-ceRNAs: a tale of cross-talk and competition

(2013) Riccardo Taulli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

A Mathematical Model for MicroRNA in Lung Cancer

(2013) Hye-Won Kang et al.   PLoS One

Modelling Competing Endogenous RNA Networks

(2013) Carla Bosia et al.   PLoS One

Intrinsic Noise of microRNA-Regulated Genes and the ceRNA Hypothesis

(2013) Javad Noorbakhsh et al.   PLoS One

microRNA as a Potential Vector for the Propagation of Robustness in Protein Expression and Oscillatory Dynamics within a ceRNA Network

(2013) Claude Gérard et al.   PLoS One

MicroRNA-based regulation of epithelial-hybrid-mesenchymal fate determination

(2013) M. Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments

(2013) U. Ala et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

miRNAs confer phenotypic robustness to gene networks by suppressing biological noise

(2013) Velia Siciliano et al.   Nature Communications

RNAs with multiple personalities

(2013) Roy L. Maute et al.   Wiley Interdisciplinary Reviews-RNA

A Systems’ Biology Approach to Study MicroRNA-Mediated Gene Regulatory Networks

(2013) Xin Lai et al.   Biomed Research International

Trash or Treasure: extracellular microRNAs and cell-to-cell communication

(2013) Nobuyoshi Kosaka et al.   Frontiers in Genetics

Gene autoregulation via intronic microRNAs and its functions

(2012) Carla Bosia et al.   BMC Systems Biology

The MicroRNA-17-92 Family of MicroRNA Clusters in Development and Disease

(2012) Carla P. Concepcion et al.   CANCER JOURNAL

MicroRNAs in Stress Signaling and Human Disease

(2012) Joshua T. Mendell et al.   CELL

Roles for MicroRNAs in Conferring Robustness to Biological Processes

(2012) Margaret S. Ebert et al.   CELL

Molecular Pathways: MicroRNAs as Cancer Therapeutics

(2012) S. A. Melo et al.   CLINICAL CANCER RESEARCH

Clinical Applications for microRNAs in Cancer

(2012) S P Nana-Sinkam et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

MicroRNA biogenesis: regulating the regulators

(2012) Emily F. Finnegan et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Quantitative functions of Argonaute proteins in mammalian development

(2012) D. Wang et al.   GENES & DEVELOPMENT

Recent Insights and Novel Bioinformatics Tools to Understand the Role of MicroRNAs Binding to 5' Untranslated Region

(2012) Letizia Sacco et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Efficiency and specificity in microRNA biogenesis

(2012) Omer Barad et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Computational analysis of target hub gene repression regulated by multiple and cooperative miRNAs

(2012) Xin Lai et al.   NUCLEIC ACIDS RESEARCH

Mechanisms generating bistability and oscillations in microRNA-mediated motifs

(2012) Peipei Zhou et al.   PHYSICAL REVIEW E

Dynamical Behaviors of Rb-E2F Pathway Including Negative Feedback Loops Involving miR449

(2012) Fang Yan et al.   PLoS One

Noise Propagation in Gene Regulation Networks Involving Interlinked Positive and Negative Feedback Loops

(2012) Hui Zhang et al.   PLoS One

Kinetic signatures of microRNA modes of action

(2012) N. Morozova et al.   RNA

Computational Medicine: Translating Models to Clinical Care

(2012) R. L. Winslow et al.   Science Translational Medicine

MicroRNA turnover: when, how, and why

(2012) Stefan Rüegger et al.   TRENDS IN BIOCHEMICAL SCIENCES

IsomiRs – the overlooked repertoire in the dynamic microRNAome

(2012) Corine T. Neilsen et al.   TRENDS IN GENETICS

miR-34 – a microRNA replacement therapy is headed to the clinic

(2012) Andreas G. Bader   Frontiers in Genetics

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena et al.   CELL

Mouse miRNA-709 directly regulates miRNA-15a/16-1 biogenesis at the posttranscriptional level in the nucleus: evidence for a microRNA hierarchy system

(2011) Rui Tang et al.   CELL RESEARCH

Post-transcriptional control of circadian rhythms

(2011) S. Kojima et al.   JOURNAL OF CELL SCIENCE

Stochastic analysis of a miRNA–protein toggle switch

(2011) E. Giampieri et al.   Molecular BioSystems

Analysis of miRNA regulation suggests an explanation for ‘unexpected’ increase in target protein levels

(2011) Sucheta A. Gokhale et al.   Molecular BioSystems

MicroRNAs can generate thresholds in target gene expression

(2011) Shankar Mukherji et al.   NATURE GENETICS

Analysis of microRNA turnover in mammalian cells following Dicer1 ablation

(2011) Michael P. Gantier et al.   NUCLEIC ACIDS RESEARCH

Bistability and Oscillations in Gene Regulation Mediated by Small Noncoding RNAs

(2011) Dengyu Liu et al.   PLoS One

The Impact of miRNA Target Sites in Coding Sequences and in 3′UTRs

(2011) Zhuo Fang et al.   PLoS One

miR451 and AMPK Mutual Antagonism in Glioma Cell Migration and Proliferation: A Mathematical Model

(2011) Yangjin Kim et al.   PLoS One

MicroRNA-Mediated Positive Feedback Loop and Optimized Bistable Switch in a Cancer Network Involving miR-17-92

(2011) Yichen Li et al.   PLoS One

The Role of Incoherent MicroRNA-Mediated Feedforward Loops in Noise Buffering

(2011) Matteo Osella et al.   PLoS Computational Biology

Posttranscriptional Upregulation by MicroRNAs

(2011) Shobha Vasudevan   Wiley Interdisciplinary Reviews-RNA

Systems Biology Reveals MicroRNA-Mediated Gene Regulation

(2011) Yuka Watanabe et al.   Frontiers in Genetics

Regulation of mRNA Translation and Stability by microRNAs

(2010) Marc Robert Fabian et al.   Annual Review of Biochemistry

Functional Motifs in Biochemical Reaction Networks

(2010) John J. Tyson et al.   Annual Review of Physical Chemistry

Dynamical modeling of microRNA action on the protein translation process

(2010) Andrei Zinovyev et al.   BMC Systems Biology

Checks and balances: E2F—microRNA crosstalk in cancer control

(2010) Stephan Emmrich et al.   CELL CYCLE

MicroRNAs and gene regulatory networks: managing the impact of noise in biological systems

(2010) H. Herranz et al.   GENES & DEVELOPMENT

Slowly Produced MicroRNAs Control Protein Levels

(2010) Zakary L. Whichard et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Epithelial-Mesenchymal Transition in Cancer: Parallels Between Normal Development and Tumor Progression

(2010) Douglas S. Micalizzi et al.   JOURNAL OF MAMMARY GLAND BIOLOGY AND NEOPLASIA

MicroRNA Functions in Stress Responses

(2010) Anthony K.L. Leung et al.   MOLECULAR CELL

Target mRNA abundance dilutes microRNA and siRNA activity

(2010) Aaron Arvey et al.   Molecular Systems Biology

The widespread regulation of microRNA biogenesis, function and decay

(2010) Jacek Krol et al.   NATURE REVIEWS GENETICS

MicroRNA control of signal transduction

(2010) Masafumi Inui et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

MicroRNA assassins: factors that regulate the disappearance of miRNAs

(2010) Zoya S Kai et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data

(2010) Jian-Hua Yang et al.   NUCLEIC ACIDS RESEARCH

Multiple microRNAs modulate p21Cip1/Waf1 expression by directly targeting its 3′ untranslated region

(2010) S Wu et al.   ONCOGENE

Single cell analysis: the new frontier in ‘omics’

(2010) Daojing Wang et al.   TRENDS IN BIOTECHNOLOGY

MicroRNAs in Cancer

(2009) Ramiro Garzon et al.   Annual Review of Medicine

miRNA-regulated dynamics in circadian oscillator models

(2009) Amitabha Nandi et al.   BMC Systems Biology

New Tricks for Animal MicroRNAs: Targeting of Amino Acid Coding Regions at Conserved and Nonconserved Sites

(2009) I. Rigoutsos   CANCER RESEARCH

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Epithelial-Mesenchymal Transitions in Development and Disease

(2009) Jean Paul Thiery et al.   CELL

New class of microRNA targets containing simultaneous 5'-UTR and 3'-UTR interaction sites

(2009) I. Lee et al.   GENOME RESEARCH

Dynamics of microRNA-mediated motifs

(2009) F. Xu et al.   IET Systems Biology

Genome-wide survey of microRNA–transcription factor feed-forward regulatory circuits in human

(2009) Angela Re et al.   Molecular BioSystems

The Incoherent Feedforward Loop Can Provide Fold-Change Detection in Gene Regulation

(2009) Lea Goentoro et al.   MOLECULAR CELL

Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps

(2009) Sung Wook Chi et al.   NATURE

Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs

(2009) Aly A Khan et al.   NATURE BIOTECHNOLOGY

Causes and consequences of microRNA dysregulation in cancer

(2009) Carlo M. Croce   NATURE REVIEWS GENETICS

Revisiting the principles of microRNA target recognition and mode of action

(2009) Peter Brodersen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL

Most mammalian mRNAs are conserved targets of microRNAs

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

Computational Modeling of Post-Transcriptional Gene Regulation by MicroRNAs

(2008) Raya Khanin et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Design principles of biochemical oscillators

(2008) Béla Novák et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Analysis of regulatory network topology reveals functionally distinct classes of microRNAs

(2008) Xueping Yu et al.   NUCLEIC ACIDS RESEARCH

MicroRNA regulation of a cancer network: Consequences of the feedback loops involving miR-17-92, E2F, and Myc

(2008) B. D. Aguda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational analysis of miRNA-mediated repression of translation: Implications for models of translation initiation inhibition

(2008) T. Nissan et al.   RNA

Gene Regulation by Transcription Factors and MicroRNAs

(2008) O. Hobert   SCIENCE