Dynamic Changes in Nucleosome Occupancy Are Not Predictive of Gene Expression Dynamics but Are Linked to Transcription and Chromatin Regulators

Impulse Control: Temporal Dynamics in Gene Transcription

(2011) Nir Yosef et al.   CELL

Stable and dynamic nucleosome states during a meiotic developmental process

(2011) L. Zhang et al.   GENOME RESEARCH

A Comprehensive Genomic Binding Map of Gene and Chromatin Regulatory Proteins in Saccharomyces

(2011) Bryan J. Venters et al.   MOLECULAR CELL

A dynamic model of proteome changes reveals new roles for transcript alteration in yeast

(2011) M. V. Lee et al.   Molecular Systems Biology

Antisense expression increases gene expression variability and locus interdependency

(2011) Z. Xu et al.   Molecular Systems Biology

A RSC/Nucleosome Complex Determines Chromatin Architecture and Facilitates Activator Binding

(2010) Monique Floer et al.   CELL

Stb3 Plays a Role in the Glucose-Induced Transition from Quiescence to Growth in Saccharomyces cerevisiae

(2010) D. Liko et al.   GENETICS

In Vitro Reconstitution of PHO5 Promoter Chromatin Remodeling Points to a Role for Activator-Nucleosome Competition In Vivo

(2010) F. Ertel et al.   MOLECULAR AND CELLULAR BIOLOGY

Interaction of a DNA Zip Code with the Nuclear Pore Complex Promotes H2A.Z Incorporation and INO1 Transcriptional Memory

(2010) William H. Light et al.   MOLECULAR CELL

Noncanonical transcript forms in yeast and their regulation during environmental stress

(2010) O. K. Yoon et al.   RNA

Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species

(2010) Moran Yassour et al.   GENOME BIOLOGY

Dynamic and complex transcription factor binding during an inducible response in yeast

(2009) L. Ni et al.   GENES & DEVELOPMENT

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

(2009) C. Zhu et al.   GENOME RESEARCH

High-resolution nucleosome mapping reveals transcription-dependent promoter packaging

(2009) A. Weiner et al.   GENOME RESEARCH

FACT and the Proteasome Promote Promoter Chromatin Disassembly and Transcriptional Initiation

(2009) Monica Ransom et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Chromatin-dependent Transcription Factor Accessibility Rather than Nucleosome Remodeling Predominates during Global Transcriptional Restructuring in Saccharomyces cerevisiae

(2009) Karl A. Zawadzki et al.   MOLECULAR BIOLOGY OF THE CELL

Transcription Dynamics

(2009) Gordon L. Hager et al.   MOLECULAR CELL

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Protein kinase A and TORC1 activate genes for ribosomal biogenesis by inactivating repressors encoded by Dot6 and its homolog Tod6

(2009) S. I. Lippman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Non-Homogeneous Hidden-State Model on First Order Differences for Automatic Detection of Nucleosome Positions

(2009) Pei Fen Kuan et al.   Statistical Applications in Genetics and Molecular Biology

Epigenetic inheritance of an inducibly nucleosome-depleted promoter and its associated transcriptional state in the apparent absence of transcriptional activators

(2009) Ryosuke Ohsawa et al.   Epigenetics & Chromatin

The histone deacetylase Rpd3p is required for transient changes in genomic expression in response to stress

(2009) Adriana L Alejandro-Osorio et al.   GENOME BIOLOGY

A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome

(2009) Cizhong Jiang et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Comprehensive Transcriptional Analysis of the Oxidative Response in Yeast

(2008) María Micaela Molina-Navarro et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Stress-activated Genomic Expression Changes Serve a Preparative Role for Impending Stress in Yeast

(2008) David B. Berry et al.   MOLECULAR BIOLOGY OF THE CELL

Interaction of the Glucocorticoid Receptor with the Chromatin Landscape

(2008) Sam John et al.   MOLECULAR CELL

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

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

(2008) Sushma Shivaswamy et al.   PLOS BIOLOGY

Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals

(2008) Yair Field et al.   PLoS Computational Biology