ChromID identifies the protein interactome at chromatin marks

Borealin–nucleosome interaction secures chromosome association of the chromosomal passenger complex

(2019) Maria A. Abad et al.   JOURNAL OF CELL BIOLOGY

Histone epiproteomic profiling distinguishes oligodendroglioma, IDH-mutant and 1p/19q co-deleted from IDH-mutant astrocytoma and reveals less tri-methylation of H3K27 in oligodendrogliomas

(2019) C. Feller et al.   ACTA NEUROPATHOLOGICA

RNA–protein interaction detection in living cells

(2018) Muthukumar Ramanathan et al.   NATURE METHODS

Tandem Histone-Binding Domains Enhance the Activity of a Synthetic Chromatin Effector

(2018) Stefan J. Tekel et al.   ACS Synthetic Biology

Super-Resolution Imaging of Higher-Order Chromatin Structures at Different Epigenomic States in Single Mammalian Cells

(2018) Jianquan Xu et al.   Cell Reports

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Chromatin-state discovery and genome annotation with ChromHMM

(2017) Jason Ernst et al.   Nature Protocols

Impact of cytosine methylation on DNA binding specificities of human transcription factors

(2017) Yimeng Yin et al.   SCIENCE

Application of dual reading domains as novel reagents in chromatin biology reveals a new H3K9me3 and H3K36me2/3 bivalent chromatin state

(2017) Rebekka Mauser et al.   Epigenetics & Chromatin

Genome-wide screen of cell-cycle regulators in normal and tumor cells identifies a differential response to nucleosome depletion

(2016) Maria Sokolova et al.   CELL CYCLE

Nucleoporin-mediated regulation of cell identity genes

(2016) Arkaitz Ibarra et al.   GENES & DEVELOPMENT

An improved smaller biotin ligase for BioID proximity labeling

(2016) Dae In Kim et al.   MOLECULAR BIOLOGY OF THE CELL

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

The molecular hallmarks of epigenetic control

(2016) C. David Allis et al.   NATURE REVIEWS GENETICS

Dynamic and flexible H3K9me3 bridging via HP1β dimerization establishes a plastic state of condensed chromatin

(2016) Kyoko Hiragami-Hamada et al.   Nature Communications

Determination of local chromatin composition by CasID

(2016) Elisabeth Schmidtmann et al.   Nucleus

Determination of local chromatin composition by CasID

(2016) Elisabeth Schmidtmann et al.   Nucleus

The molecular basis of variable phenotypic severity among common missense mutations causing Rett syndrome

(2015) Kyla Brown et al.   HUMAN MOLECULAR GENETICS

Global and Specific Responses of the Histone Acetylome to Systematic Perturbation

(2015) Christian Feller et al.   MOLECULAR CELL

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

(2015) Chih-Chiang Tsou et al.   NATURE METHODS

Epigenetic silencing by the HUSH complex mediates position-effect variegation in human cells

(2015) I. A. Tchasovnikarova et al.   SCIENCE

Tip60 complex binds to active Pol II promoters and a subset of enhancers and co-regulates the c-Myc network in mouse embryonic stem cells

(2015) Sarina Ravens et al.   Epigenetics & Chromatin

Single-Step Generation of Conditional Knockout Mouse Embryonic Stem Cells

(2015) Matyas Flemr et al.   Cell Reports

Regulation of gene transcription by Polycomb proteins

(2015) S. Aranda et al.   Science Advances

genomation: a toolkit to summarize, annotate and visualize genomic intervals

(2014) A. Akalin et al.   BIOINFORMATICS

QuasR: quantification and annotation of short reads in R

(2014) Dimos Gaidatzis et al.   BIOINFORMATICS

Redundant Mechanisms to Form Silent Chromatin at Pericentromeric Regions Rely on BEND3 and DNA Methylation

(2014) Nehmé Saksouk et al.   MOLECULAR CELL

Methylation-Dependent and -Independent Genomic Targeting Principles of the MBD Protein Family

(2013) Tuncay Baubec et al.   CELL

Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives

(2013) Cornelia G. Spruijt et al.   CELL

Distinct and Combinatorial Functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in Mouse Embryonic Stem Cell Identity

(2013) Partha Pratim Das et al.   MOLECULAR CELL

Asymmetrically Modified Nucleosomes

(2012) Philipp Voigt et al.   CELL

A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells

(2012) Kyle J. Roux et al.   JOURNAL OF CELL BIOLOGY

A Map of General and Specialized Chromatin Readers in Mouse Tissues Generated by Label-free Interaction Proteomics

(2012) H. Christian Eberl et al.   MOLECULAR CELL

Perceiving the epigenetic landscape through histone readers

(2012) Catherine A Musselman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

Recognition of modification status on a histone H3 tail by linked histone reader modules of the epigenetic regulator UHRF1

(2012) K. Arita et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RYBP and Cbx7 Define Specific Biological Functions of Polycomb Complexes in Mouse Embryonic Stem Cells

(2012) Lluis Morey et al.   Cell Reports

Control of Embryonic Stem Cell Lineage Commitment by Core Promoter Factor, TAF3

(2011) Zhe Liu et al.   CELL

Chromatin Affinity Purification and Quantitative Mass Spectrometry Defining the Interactome of Histone Modification Patterns

(2011) Miroslav Nikolov et al.   MOLECULAR & CELLULAR PROTEOMICS

DNA-binding factors shape the mouse methylome at distal regulatory regions

(2011) Michael B. Stadler et al.   NATURE

TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

(2011) Kristine Williams et al.   NATURE

Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions

(2010) Aaron D. Goldberg et al.   CELL

Nucleosome-Interacting Proteins Regulated by DNA and Histone Methylation

(2010) Till Bartke et al.   CELL

Quantitative Interaction Proteomics and Genome-wide Profiling of Epigenetic Histone Marks and Their Readers

(2010) Michiel Vermeulen et al.   CELL

Molecular Interplay of the Noncoding RNA ANRIL and Methylated Histone H3 Lysine 27 by Polycomb CBX7 in Transcriptional Silencing of INK4a

(2010) Kyoko L. Yap et al.   MOLECULAR CELL

Human POGZ modulates dissociation of HP1α from mitotic chromosome arms through Aurora B activation

(2010) Ryu-Suke Nozawa et al.   NATURE CELL BIOLOGY

Purification of Proteins Associated with Specific Genomic Loci

(2009) Jérôme Déjardin et al.   CELL

FLASH, a Proapoptotic Protein Involved in Activation of Caspase-8, Is Essential for 3′ End Processing of Histone Pre-mRNAs

(2009) Xiao-cui Yang et al.   MOLECULAR CELL

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases

(2009) John R Horton et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements

(2008) G. Mittler et al.   GENOME RESEARCH

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY