An improved ChIP-seq peak detection system for simultaneously identifying post-translational modified transcription factors by combinatorial fusion, using SUMOylation as an example

BayesPeak—an R package for analysing ChIP-seq data

(2011) Jonathan Cairns et al.   BIOINFORMATICS

SUMO conjugation of STAT1 protects cells from hyperresponsiveness to IFN 

(2011) A. Begitt et al.   BLOOD

Shape-based peak identification for ChIP-Seq

(2011) Valerie Hower et al.   BMC BIOINFORMATICS

ncRNA- and Pc2 Methylation-Dependent Gene Relocation between Nuclear Structures Mediates Gene Activation Programs

(2011) Liuqing Yang et al.   CELL

Emerging roles of the SUMO pathway in development

(2011) Hilda Lomelí et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

DNA Repair and Global Sumoylation Are Regulated by Distinct Ubc9 Noncovalent Complexes

(2011) J. Prudden et al.   MOLECULAR AND CELLULAR BIOLOGY

SUMOylation promotes de novo targeting of HP1α to pericentric heterochromatin

(2011) Christèle Maison et al.   NATURE GENETICS

Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices

(2011) Young Min Oh et al.   NUCLEIC ACIDS RESEARCH

Inferring transcription factor complexes from ChIP-seq data

(2011) Tom Whitington et al.   NUCLEIC ACIDS RESEARCH

Microsomal prostaglandin E synthase-1 promotes hepatocarcinogenesis through activation of a novel EGR1/β-catenin signaling axis

(2011) D Lu et al.   ONCOGENE

Mechanisms, regulation and consequences of protein SUMOylation

(2010) Kevin A. Wilkinson et al.   BIOCHEMICAL JOURNAL

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

SUMO functions in constitutive transcription and during activation of inducible genes in yeast

(2010) E. Rosonina et al.   GENES & DEVELOPMENT

Evaluation of Algorithm Performance in ChIP-Seq Peak Detection

(2010) Elizabeth G. Wilbanks et al.   PLoS One

SUMOylation regulates the nuclear mobility of CREB binding protein and its association with nuclear bodies in live cells

(2009) Colm M. Ryan et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

The sumoylation pathway is dysregulated in multiple myeloma and is associated with adverse patient outcome

(2009) J. J. Driscoll et al.   BLOOD

Global Map of SUMO Function Revealed by Protein-Protein Interaction and Genetic Networks

(2009) Taras Makhnevych et al.   MOLECULAR CELL

Growth Factor-induced Phosphorylation of Sterol Regulatory Element-binding Proteins Inhibits Sumoylation, Thereby Stimulating the Expression of Their Target Genes, Low Density Lipoprotein Uptake, and Lipid Synthesis

(2008) Mitsumi Arito et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY