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

Hybrid modeling of the crosstalk between signaling and transcriptional networks using ordinary differential equations and multi-valued logic

(2013) Faiz M. Khan et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions

(2012) Luiz A Bovolenta et al.   BMC GENOMICS

MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship

(2012) Amy E. Pasquinelli   NATURE REVIEWS GENETICS

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

(2012) Xin Lai et al.   NUCLEIC ACIDS RESEARCH

Computational Approaches for Analyzing Information Flow in Biological Networks

(2012) B. Kholodenko et al.   Science Signaling

NetDS: a Cytoscape plugin to analyze the robustness of dynamics and feedforward/feedback loop structures of biological networks

(2011) Duc-Hau Le et al.   BIOINFORMATICS

MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model

(2011) Antony Le Béchec et al.   BMC BIOINFORMATICS

miRWalk – Database: Prediction of possible miRNA binding sites by “walking” the genes of three genomes

(2011) Harsh Dweep et al.   JOURNAL OF BIOMEDICAL INFORMATICS

SABIO-RK--database for biochemical reaction kinetics

(2011) U. Wittig et al.   NUCLEIC ACIDS RESEARCH

PuTmiR: A database for extracting neighboring transcription factors of human microRNAs

(2010) Sanghamitra Bandyopadhyay et al.   BMC BIOINFORMATICS

Examination of the expanding pathways for the regulation of p21 expression and activity

(2010) Yong-Sam Jung et al.   CELLULAR SIGNALLING

miRTarBase: a database curates experimentally validated microRNA–target interactions

(2010) Sheng-Da Hsu et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Reactome: a database of reactions, pathways and biological processes

(2010) D. Croft et al.   NUCLEIC ACIDS RESEARCH

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

(2010) S Wu et al.   ONCOGENE

A model-based strategy to investigate the role of microRNA regulation in cancer signalling networks

(2010) Svetoslav Nikolov et al.   THEORY IN BIOSCIENCES

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Recent developments in parameter estimation and structure identification of biochemical and genomic systems

(2009) I-Chun Chou et al.   MATHEMATICAL BIOSCIENCES

The Systems Biology Graphical Notation

(2009) Nicolas Le Novère et al.   NATURE BIOTECHNOLOGY

miRGen 2.0: a database of microRNA genomic information and regulation

(2009) Panagiotis Alexiou et al.   NUCLEIC ACIDS RESEARCH

TransmiR: a transcription factor–microRNA regulation database

(2009) Juan Wang et al.   NUCLEIC ACIDS RESEARCH

BioNumbers—the database of key numbers in molecular and cell biology

(2009) Ron Milo et al.   NUCLEIC ACIDS RESEARCH

A methodology for performing global uncertainty and sensitivity analysis in systems biology

(2008) Simeone Marino et al.   JOURNAL OF THEORETICAL BIOLOGY

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

miRecords: an integrated resource for microRNA-target interactions

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

CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks

(2008) A. Funahashi et al.   PROCEEDINGS OF THE IEEE