Mapping the fine structure of a eukaryotic promoter input-output function

Differential binding of the related transcription factors Pho4 and Cbf1 can tune the sensitivity of promoters to different levels of an induction signal

(2013) Jonathan S. Z. Aow et al.   NUCLEIC ACIDS RESEARCH

A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions

(2012) Ahmad S. Khalil et al.   CELL

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast

(2012) Tali Raveh-Sadka et al.   NATURE GENETICS

Complex effects of nucleotide variants in a mammalian cis-regulatory element

(2012) J. C. Kwasnieski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid Synthesis of Defined Eukaryotic Promoter Libraries

(2012) Arun S. Rajkumar et al.   ACS Synthetic Biology

Experimental strategies for studying transcription factor-DNA binding specificities

(2011) M. Geertz et al.   Briefings in Functional Genomics

Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters

(2011) D. Zeevi et al.   GENOME RESEARCH

Integrated Approaches Reveal Determinants of Genome-wide Binding and Function of the Transcription Factor Pho4

(2011) Xu Zhou et al.   MOLECULAR CELL

Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast

(2011) C. Miller et al.   Molecular Systems Biology

ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species

(2011) Aaron T. Spivak et al.   NUCLEIC ACIDS RESEARCH

Organizational constraints on Ste12 cis-elements for a pheromone response in Saccharomyces cerevisiae

(2010) Ting-Cheng Su et al.   FEBS Journal

Functional Dissection of IME1 Transcription Using Quantitative Promoter-Reporter Screening

(2010) S. Kahana et al.   GENETICS

TATA is a modular component of synthetic promoters

(2010) I. Mogno et al.   GENOME RESEARCH

Quantitative analysis of the transcription control mechanism

(2010) Changhui Mao et al.   Molecular Systems Biology

Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence

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

Incorporating nucleosomes into thermodynamic models of transcription regulation

(2009) T. Raveh-Sadka et al.   GENOME RESEARCH

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

(2009) C. Zhu et al.   GENOME RESEARCH

Environment-specific combinatorial cis-regulation in synthetic promoters

(2009) Jason Gertz et al.   Molecular Systems Biology

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis

(2009) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

From DNA sequence to transcriptional behaviour: a quantitative approach

(2009) Eran Segal et al.   NATURE REVIEWS GENETICS

Experimental determination of the evolvability of a transcription factor

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

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

(2008) T. N. Mavrich et al.   GENOME RESEARCH

Analysis of combinatorial cis-regulation in synthetic and genomic promoters

(2008) Jason Gertz et al.   NATURE

A quantitative model of transcription factor–activated gene expression

(2008) Harold D Kim et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY