Reprogramming of H3K9bhb at regulatory elements is a key feature of fasting in the small intestine

The regulatory enzymes and protein substrates for the lysine β-hydroxybutyrylation pathway

(2021) He Huang et al.   Science Advances

Fasting reduces intestinal radiotoxicity enabling dose-escalated radiotherapy for pancreatic cancer

(2019) Marimar de la Cruz Bonilla et al.   INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS

Molecular basis for hierarchical histone de-β-hydroxybutyrylation by SIRT3

(2019) Xingrun Zhang et al.   Cell Discovery

Ketone Body Signaling Mediates Intestinal Stem Cell Homeostasis and Adaptation to Diet

(2019) Chia-Wei Cheng et al.   CELL

Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

(2018) Yuanxin Xi et al.   BMC GENOMICS

Fasting Activates Fatty Acid Oxidation to Enhance Intestinal Stem Cell Function during Homeostasis and Aging

(2018) Maria M. Mihaylova et al.   Cell Stem Cell

Stem cell enriched-epithelial spheroid cultures for rapidly assaying small intestinal radioprotectors and radiosensitizers in vitro

(2018) Marimar de la Cruz Bonilla et al.   Scientific Reports

Caloric restriction delays age-related methylation drift

(2017) Shinji Maegawa et al.   Nature Communications

Metabolic Regulation of Gene Expression by Histone Lysine β-Hydroxybutyrylation

(2016) Zhongyu Xie et al.   MOLECULAR CELL

High-fat diet enhances stemness and tumorigenicity of intestinal progenitors

(2016) Semir Beyaz et al.   NATURE

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Fasting protects mice from lethal DNA damage by promoting small intestinal epithelial stem cell survival

(2015) Kelsey L. Tinkum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type

(2015) Angela Yen et al.   Nature Communications

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

SAMBLASTER: fast duplicate marking and structural variant read extraction

(2014) G. G. Faust et al.   BIOINFORMATICS

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

Intestinal crypt homeostasis revealed at single-stem-cell level by in vivo live imaging

(2014) Laila Ritsma et al.   NATURE

Dietary disinhibition modulates neural valuation of food in the fed and fasted states

(2013) Ying Lee et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Continuous Clonal Labeling Reveals Small Numbers of Functional Stem Cells in Intestinal Crypts and Adenomas

(2013) Sarah Kozar et al.   Cell Stem Cell

In vitro expansion and genetic modification of gastrointestinal stem cells in spheroid culture

(2013) Hiroyuki Miyoshi et al.   Nature Protocols

High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states

(2013) Ronnie Blecher-Gonen et al.   Nature Protocols

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Successful adaptation to ketosis by mice with tissue-specific deficiency of ketone body oxidation

(2012) David G. Cotter et al.   AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM

A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

(2012) Manuel Garber et al.   MOLECULAR CELL

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Suppression of Oxidative Stress by  -Hydroxybutyrate, an Endogenous Histone Deacetylase Inhibitor

(2012) T. Shimazu et al.   SCIENCE

Wnt5a Potentiates TGF-  Signaling to Promote Colonic Crypt Regeneration After Tissue Injury

(2012) H. Miyoshi et al.   SCIENCE

Stem cell self-renewal in intestinal crypt

(2011) Benjamin D. Simons et al.   EXPERIMENTAL CELL RESEARCH

Interorgan Coordination of the Murine Adaptive Response to Fasting

(2011) Theodorus B. M. Hakvoort et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Contributions Made by CDC25 Phosphatases to Proliferation of Intestinal Epithelial Stem and Progenitor Cells

(2011) Gwanghee Lee et al.   PLoS One

Cistrome: an integrative platform for transcriptional regulation studies

(2011) Tao Liu et al.   GENOME BIOLOGY

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Identification of retinoic acid-regulated nuclear matrix-associated protein as a novel regulator of gastric cancer

(2009) J Li et al.   BRITISH JOURNAL OF CANCER

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche

(2009) Toshiro Sato et al.   NATURE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Identification of Tumor-Initiating Cells in a p53-Null Mouse Model of Breast Cancer

(2008) M. Zhang et al.   CANCER RESEARCH

Retinoblastoma Protein (pRb), but Not p107 or p130, Is Required for Maintenance of Enterocyte Quiescence and Differentiation in Small Intestine

(2008) Jun Guo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY