Unsupervised tensor decomposition-based method to extract candidate transcription factors as histone modification bookmarks in post-mitotic transcriptional reactivation

Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation

(2020) Hyeseon Kang et al.   GENES & DEVELOPMENT

Tensor-Decomposition-Based Unsupervised Feature Extraction Applied to Prostate Cancer Multiomics Data

(2020) Y-h. Taguchi et al.   Genes

NRF2-dependent gene expression promotes ciliogenesis and Hedgehog signaling

(2019) Ana Martin-Hurtado et al.   Scientific Reports

Mitotic Gene Bookmarking: An Epigenetic Program to Maintain Normal and Cancer Phenotypes

(2018) Sayyed K Zaidi et al.   MOLECULAR CANCER RESEARCH

Lineage Specification from Prostate Progenitor Cells Requires Gata3-Dependent Mitotic Spindle Orientation

(2017) Maxwell E.R. Shafer et al.   Stem Cell Reports

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

(2016) Nicola Festuccia et al.   NATURE CELL BIOLOGY

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

A dynamic mode of mitotic bookmarking by transcription factors

(2016) Sheila S Teves et al.   eLife

A novel statistical method for quantitative comparison of multiple ChIP-seq datasets

(2015) Li Chen et al.   BIOINFORMATICS

A role of WT1 in cell division and genomic stability

(2015) Jayasha Shandilya et al.   CELL CYCLE

PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data

(2014) Yanxiao Zhang et al.   BIOINFORMATICS

Detecting differential peaks in ChIP-seq signals with ODIN

(2014) Manuel Allhoff et al.   BIOINFORMATICS

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding

(2014) Shaun Mahony et al.   PLoS Computational Biology

MMDiff: quantitative testing for shape changes in ChIP-Seq data sets

(2013) Gabriele Schweikert et al.   BMC GENOMICS

QChIPat: a quantitative method to identify distinct binding patterns for two biological ChIP-seq samples in different experimental conditions

(2013) Bin Liu et al.   BMC GENOMICS

diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates

(2013) Li Shen et al.   PLoS One

Tissue-Specific Mitotic Bookmarking by Hematopoietic Transcription Factor GATA1

(2012) Stephan Kadauke et al.   CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Histone modifications and mitosis: countermarks, landmarks, and bookmarks

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

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

(2012) Zhen Shao et al.   GENOME BIOLOGY

Identifying dispersed epigenomic domains from ChIP-Seq data

(2011) Qiang Song et al.   BIOINFORMATICS

Detecting differential binding of transcription factors with ChIP-seq

(2011) Kun Liang et al.   BIOINFORMATICS

FoxO1 Is a Positive Regulator of Bone Formation by Favoring Protein Synthesis and Resistance to Oxidative Stress in Osteoblasts

(2010) Marie-Therese Rached et al.   Cell Metabolism

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

Gata2 is a tissue-specific post-mitotic selector gene for midbrain GABAergic neurons

(2008) K. Kala et al.   DEVELOPMENT

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY