PTHGRN: unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data

CMGRN: a web server for constructing multilevel gene regulatory networks using ChIP-seq and gene expression data

(2014) Daogang Guan et al.   BIOINFORMATICS

Inferring gene networks from discrete expression data

(2013) Lin Zhang et al.   BIOSTATISTICS

Gaussian graphical model for identifying significantly responsive regulatory networks from time course high-throughput data

(2013) Zhi-Ping Liu et al.   IET Systems Biology

Status of Large-scale Analysis of Post-translational Modifications by Mass Spectrometry

(2013) Jesper V. Olsen et al.   MOLECULAR & CELLULAR PROTEOMICS

Unraveling Regulatory Programs for NF-kappaB, p53 and MicroRNAs in Head and Neck Squamous Cell Carcinoma

(2013) Bin Yan et al.   PLoS One

APG: an Active Protein-Gene Network Model to Quantify Regulatory Signals in Complex Biological Systems

(2013) Jiguang Wang et al.   Scientific Reports

Identifying multi-layer gene regulatory modules from multi-dimensional genomic data

(2012) W. Li et al.   BIOINFORMATICS

Stemness-related Factor Sall4 Interacts with Transcription Factors Oct-3/4 and Sox2 and Occupies Oct-Sox Elements in Mouse Embryonic Stem Cells

(2012) Nobuyuki Tanimura et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Post-Translational Modification of Human Heat Shock Factors and Their Functions: A Recent Update by Proteomic Approach

(2012) Yan-Ming Xu et al.   JOURNAL OF PROTEOME RESEARCH

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

MAGNET: MicroArray Gene expression and Network Evaluation Toolkit

(2012) G. C. Linderman et al.   NUCLEIC ACIDS RESEARCH

Inferring the regulatory network behind a gene expression experiment

(2012) M. Bleda et al.   NUCLEIC ACIDS RESEARCH

Hierarchical Modularity in ERα Transcriptional Network Is Associated with Distinct Functions and Implicates Clinical Outcomes

(2012) Binhua Tang et al.   Scientific Reports

Identification of context-specific gene regulatory networks with GEMULA—gene expression modeling using LAsso

(2011) Geert Geeven et al.   BIOINFORMATICS

Modeling microRNA-mRNA Interactions Using PLS Regression in Human Colon Cancer

(2011) Xiaohong Li et al.   BMC Medical Genomics

Post-translational modification of the androgen receptor

(2011) Daniel Gioeli et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

The transcriptional and signalling networks of pluripotency

(2011) Huck-Hui Ng et al.   NATURE CELL BIOLOGY

ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor

(2011) Jing Qin et al.   NUCLEIC ACIDS RESEARCH

mirExplorer: Detecting microRNAs from genome and next generation sequencing data using the AdaBoost method with transition probability matrix and combined features

(2011) Dao-Gang Guan et al.   RNA Biology

FastPval: a fast and memory efficient program to calculate very low P-values from empirical distribution

(2010) Mulin Jun Li et al.   BIOINFORMATICS

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

(2010) Alexander Lachmann et al.   BIOINFORMATICS

An Oct4-Centered Protein Interaction Network in Embryonic Stem Cells

(2010) Debbie L.C. van den Berg et al.   Cell Stem Cell

Jarid2 and PRC2, partners in regulating gene expression

(2010) G. Li et al.   GENES & DEVELOPMENT

JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells

(2010) Diego Pasini et al.   NATURE

Genome-wide identification of post-translational modulators of transcription factor activity in human B cells

(2009) Kai Wang et al.   NATURE BIOTECHNOLOGY

Sox2 and Oct-3/4: a versatile pair of master regulators that orchestrate the self-renewal and pluripotency of embryonic stem cells

(2009) Angie Rizzino   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Unraveling Epigenetic Regulation in Embryonic Stem Cells

(2008) Marina Bibikova et al.   Cell Stem Cell

ERα and AP-1 interact in vivo with a specific sequence of the F promoter of the human ERα gene in osteoblasts

(2008) Elisabetta Lambertini et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Chromatin remodeling in Embryonic stem cells: Regulating the balance between pluripotency and differentiation

(2008) Bridget Keenen et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Discovering microRNAs from deep sequencing data using miRDeep

(2008) Marc R Friedländer et al.   NATURE BIOTECHNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY