Cell cycle-resolved chromatin proteomics reveals the extent of mitotic preservation of the genomic regulatory landscape

Transcription factor retention on mitotic chromosomes: regulatory mechanisms and impact on cell fate decisions

(2017) Mahé Raccaud et al.   FEBS LETTERS

The control of DNA repair by the cell cycle

(2017) Nicole Hustedt et al.   NATURE CELL BIOLOGY

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells

(2017) Horng D. Ou et al.   SCIENCE

Widespread Mitotic Bookmarking by Histone Marks and Transcription Factors in Pluripotent Stem Cells

(2017) Yiyuan Liu et al.   Cell Reports

Coordinating cell proliferation and differentiation: Antagonism between cell cycle regulators and cell type-specific gene expression

(2016) Suzan Ruijtenberg et al.   CELL CYCLE

Chromosome condensation and decondensation during mitosis

(2016) Wolfram Antonin et al.   CURRENT OPINION IN CELL BIOLOGY

A role for mitotic bookmarking of SOX2 in pluripotency and differentiation

(2016) Cédric Deluz et al.   GENES & DEVELOPMENT

Proteomics to study DNA-bound and chromatin-associated gene regulatory complexes

(2016) Michael Wierer et al.   HUMAN MOLECULAR GENETICS

Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments

(2016) Erik Ahrné et al.   JOURNAL OF PROTEOME RESEARCH

Proteomics Analysis with a Nano Random Forest Approach Reveals Novel Functional Interactions Regulated by SMC Complexes on Mitotic Chromosomes

(2016) Shinya Ohta et al.   MOLECULAR & CELLULAR PROTEOMICS

Human Leukocyte Antigen (HLA) Peptides Derived from Tumor Antigens Induced by Inhibition of DNA Methylation for Development of Drug-facilitated Immunotherapy

(2016) Bracha Shraibman et al.   MOLECULAR & CELLULAR PROTEOMICS

3D-CLEM Reveals that a Major Portion of Mitotic Chromosomes Is Not Chromatin

(2016) Daniel G. Booth et al.   MOLECULAR CELL

Mitotic binding of Esrrb marks key regulatory regions of the pluripotency network

(2016) Nicola Festuccia et al.   NATURE CELL BIOLOGY

Human mutations affect the epigenetic/bookmarking function of HNF1B

(2016) Jonathan Lerner et al.   NUCLEIC ACIDS RESEARCH

Aurora kinase-induced phosphorylation excludes transcription factor RUNX from the chromatin to facilitate proper mitotic progression

(2016) Linda Shyue Huey Chuang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The contribution of mass spectrometry-based proteomics to understanding epigenetics

(2016) Roberta Noberini et al.   Epigenomics

Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesis

(2016) Shelby A Blythe et al.   eLife

A dynamic mode of mitotic bookmarking by transcription factors

(2016) Sheila S Teves et al.   eLife

Graded requirement for the spliceosome in cell cycle progression

(2015) Zemfira Karamysheva et al.   CELL CYCLE

Mitotic Transcriptional Activation: Clearance of Actively Engaged Pol II via Transcriptional Elongation Control in Mitosis

(2015) Kaiwei Liang et al.   MOLECULAR CELL

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links

(2015) M. Raschle et al.   SCIENCE

MultiNotch MS3 Enables Accurate, Sensitive, and Multiplexed Detection of Differential Expression across Cancer Cell Line Proteomes

(2014) Graeme C. McAlister et al.   ANALYTICAL CHEMISTRY

QuasR: quantification and annotation of short reads in R

(2014) Dimos Gaidatzis et al.   BIOINFORMATICS

Proteomics of a fuzzy organelle: interphase chromatin

(2014) G. Kustatscher et al.   EMBO JOURNAL

Pioneer transcription factors in cell reprogramming

(2014) Makiko Iwafuchi-Doi et al.   GENES & DEVELOPMENT

Genome accessibility is widely preserved and locally modulated during mitosis

(2014) Chris C.-S. Hsiung et al.   GENOME RESEARCH

Chromatin enrichment for proteomics

(2014) Georg Kustatscher et al.   Nature Protocols

RBPJ, the Major Transcriptional Effector of Notch Signaling, Remains Associated with Chromatin throughout Mitosis, Suggesting a Role in Mitotic Bookmarking

(2014) Robert J. Lake et al.   PLoS Genetics

Bookmarking by specific and nonspecific binding of FoxA1 pioneer factor to mitotic chromosomes

(2013) J. M. Caravaca et al.   GENES & DEVELOPMENT

Regulating DNA Replication in Eukarya

(2013) K. Siddiqui et al.   Cold Spring Harbor Perspectives in Biology

Mitotic bookmarking by transcription factors

(2013) Stephan Kadauke et al.   Epigenetics & Chromatin

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Tissue-Specific Mitotic Bookmarking by Hematopoietic Transcription Factor GATA1

(2012) Stephan Kadauke et al.   CELL

In vivo Polycomb kinetics and mitotic chromatin binding distinguish stem cells from differentiated cells

(2012) J. P. Fonseca et al.   GENES & DEVELOPMENT

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

Proteomic Cornerstones of Hematopoietic Stem Cell Differentiation: Distinct Signatures of Multipotent Progenitors and Myeloid Committed Cells

(2012) Daniel Klimmeck et al.   MOLECULAR & CELLULAR PROTEOMICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Camera: a competitive gene set test accounting for inter-gene correlation

(2012) Di Wu et al.   NUCLEIC ACIDS RESEARCH

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Histone modifications and mitosis: countermarks, landmarks, and bookmarks

(2012) Fangwei Wang et al.   TRENDS IN CELL BIOLOGY

A Polycomb Group Protein Is Retained at Specific Sites on Chromatin in Mitosis

(2012) Nicole E. Follmer et al.   PLoS Genetics

APCluster: an R package for affinity propagation clustering

(2011) U. Bodenhofer et al.   BIOINFORMATICS

Plk1 Phosphorylation of Orc2 Promotes DNA Replication under Conditions of Stress

(2011) B. Song et al.   MOLECULAR AND CELLULAR BIOLOGY

AnimalTFDB: a comprehensive animal transcription factor database

(2011) H.-M. Zhang et al.   NUCLEIC ACIDS RESEARCH

Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells

(2011) Yuexi Wang et al.   PROTEOMICS

ROAST: rotation gene set tests for complex microarray experiments

(2010) Di Wu et al.   BIOINFORMATICS

The Protein Composition of Mitotic Chromosomes Determined Using Multiclassifier Combinatorial Proteomics

(2010) Shinya Ohta et al.   CELL

A phospho/methyl switch at histone H3 regulates TFIID association with mitotic chromosomes

(2010) Radhika A Varier et al.   EMBO JOURNAL

Addressing Accuracy and Precision Issues in iTRAQ Quantitation

(2010) Natasha A. Karp et al.   MOLECULAR & CELLULAR PROTEOMICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Tackling the epigenome: challenges and opportunities for collaboration

(2010) John S Satterlee et al.   NATURE BIOTECHNOLOGY

Regulation of the Transcription Factor YY1 in Mitosis through Phosphorylation of Its DNA-binding Domain

(2009) Raed Rizkallah et al.   MOLECULAR BIOLOGY OF THE CELL

Polycomb Group Protein-associated Chromatin Is Reproduced in Post-mitotic G1Phase and Is Required for S Phase Progression

(2008) Takahiro Aoto et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

A quantitative atlas of mitotic phosphorylation

(2008) N. Dephoure et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA