The Yin and Yang of Yeast Transcription: Elements of a Global Feedback System between Metabolism and Chromatin

Analog regulation of metabolic demand

(2011) Nikolaus Sonnenschein et al.   BMC Systems Biology

SIRT1, metabolism and cancer

(2011) John R.P. Knight et al.   CURRENT OPINION IN ONCOLOGY

The RSC chromatin remodelling ATPase translocates DNA with high force and small step size

(2011) George Sirinakis et al.   EMBO JOURNAL

Coupling among growth rate response, metabolic cycle, and cell division cycle in yeast

(2011) Nikolai Slavov et al.   MOLECULAR BIOLOGY OF THE CELL

Acetyl-CoA Induces Cell Growth and Proliferation by Promoting the Acetylation of Histones at Growth Genes

(2011) Ling Cai et al.   MOLECULAR CELL

XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast

(2011) E. L. van Dijk et al.   NATURE

Cracking the chromatin code: Precise rule of nucleosome positioning

(2011) Edward N. Trifonov   Physics of Life Reviews

Metabolic cycling without cell division cycling in respiring yeast

(2011) N. Slavov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Packing Mechanism for Nucleosome Organization Reconstituted Across a Eukaryotic Genome

(2011) Z. Zhang et al.   SCIENCE

Mammalian circadian clock and metabolism - the epigenetic link

(2010) M. M. Bellet et al.   JOURNAL OF CELL SCIENCE

Chromatin Remodeling around Nucleosome-Free Regions Leads to Repression of Noncoding RNA Transcription

(2010) A. N. Yadon et al.   MOLECULAR AND CELLULAR BIOLOGY

Rapamycin increases rDNA stability by enhancing association of Sir2 with rDNA in Saccharomyces cerevisiae

(2010) Cheol Woong Ha et al.   NUCLEIC ACIDS RESEARCH

Functional Clustering of Periodic Transcriptional Profiles through ARMA(p,q)

(2010) Ning Li et al.   PLoS One

Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate

(2010) S. J. Silverman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Acetylation of Metabolic Enzymes Coordinates Carbon Source Utilization and Metabolic Flux

(2010) Q. Wang et al.   SCIENCE

Regulation of Cellular Metabolism by Protein Lysine Acetylation

(2010) S. Zhao et al.   SCIENCE

The Role of Nucleosome Positioning in the Evolution of Gene Regulation

(2010) Alexander M. Tsankov et al.   PLOS BIOLOGY

flowClust: a Bioconductor package for automated gating of flow cytometry data

(2009) Kenneth Lo et al.   BMC BIOINFORMATICS

G+C content dominates intrinsic nucleosome occupancy

(2009) Desiree Tillo et al.   BMC BIOINFORMATICS

Chromatin Places Metabolism Center Stage

(2009) Andreas G. Ladurner   CELL

Mechanisms that Specify Promoter Nucleosome Location and Identity

(2009) Paul D. Hartley et al.   CELL

High-resolution DNA-binding specificity analysis of yeast transcription factors

(2009) C. Zhu et al.   GENOME RESEARCH

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

(2009) Helen Neil et al.   NATURE

Multiple Aspects of ATP-Dependent Nucleosome Translocation by RSC and Mi-2 Are Directed by the Underlying DNA Sequence

(2009) Joke J. F. A. van Vugt et al.   PLoS One

Oscillations in supercoiling drive circadian gene expression in cyanobacteria

(2009) Vikram Vijayan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatio-Temporal Dynamics of Yeast Mitochondrial Biogenesis: Transcriptional and Post-Transcriptional mRNA Oscillatory Modules

(2009) Gaëlle Lelandais et al.   PLoS Computational Biology

Normalization of oligonucleotide arrays based on the least-variant set of genes

(2008) Stefano Calza et al.   BMC BIOINFORMATICS

Comparison of the transcriptomic "stress response" evoked by antimycin A and oxygen deprivation in saccharomyces cerevisiae

(2008) Liang-Chuan Lai et al.   BMC GENOMICS

Automated gating of flow cytometry data via robust model-based clustering

(2008) Kenneth Lo et al.   CYTOMETRY PART A

A Library of Yeast Transcription Factor Motifs Reveals a Widespread Function for Rsc3 in Targeting Nucleosome Exclusion at Promoters

(2008) Gwenael Badis et al.   MOLECULAR CELL

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY

Epigenetic regulation and the variability of gene expression

(2008) Jung Kyoon Choi et al.   NATURE GENETICS

Design principles of biochemical oscillators

(2008) Béla Novák et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Scale-Free Dynamics of Eukaryotic Cells

(2008) Miguel A. Aon et al.   PLoS One

Dynamic Remodeling of Individual Nucleosomes Across a Eukaryotic Genome in Response to Transcriptional Perturbation

(2008) Sushma Shivaswamy et al.   PLOS BIOLOGY

An Increase in Mitochondrial DNA Promotes Nuclear DNA Replication in Yeast

(2008) Heidi M. Blank et al.   PLoS Genetics

Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast

(2007) Matthew J. Brauer et al.   MOLECULAR BIOLOGY OF THE CELL