Promoters maintain their relative activity levels under different growth conditions

Dissecting specific and global transcriptional regulation of bacterial gene expression

(2013) L. Gerosa et al.   Molecular Systems Biology

Coordination of bacterial proteome with metabolism by cyclic AMP signalling

(2013) Conghui You et al.   NATURE

Revisiting Global Gene Expression Analysis

(2012) Jakob Lovén et al.   CELL

Nutritional Control of Growth and Development in Yeast

(2012) J. R. Broach   GENETICS

PaxDb, a Database of Protein Abundance Averages Across All Three Domains of Life

(2012) M. Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

Cellular Noise Regulons Underlie Fluctuations in Saccharomyces cerevisiae

(2012) Jacob Stewart-Ornstein et al.   MOLECULAR CELL

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

(2012) Eilon Sharon 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

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

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

(2011) D. Zeevi et al.   GENOME RESEARCH

Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics

(2011) R. Costenoble et al.   Molecular Systems Biology

Extensive divergence of yeast stress responses through transitions between induced and constitutive activation

(2011) I. Tirosh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional regulation of respiration in yeast metabolizing differently repressive carbon substrates

(2010) Sarah-Maria Fendt et al.   BMC Systems Biology

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

Transcript length bias in RNA-seq data confounds systems biology

(2009) Alicia Oshlack et al.   Biology Direct

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Growth Rate-Dependent Global Effects on Gene Expression in Bacteria

(2009) Stefan Klumpp et al.   CELL

Coordination of gene expression with growth rate: A feedback or a feed-forward strategy?

(2009) Sagi Levy et al.   FEBS LETTERS

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

(2009) C. Zhu et al.   GENOME RESEARCH

Shifts in growth strategies reflect tradeoffs in cellular economics

(2009) Douwe Molenaar et al.   Molecular Systems Biology

Quantification of the yeast transcriptome by single-molecule sequencing

(2009) Doron Lipson et al.   NATURE BIOTECHNOLOGY

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing

(2009) M. Yassour et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Invariant Distribution of Promoter Activities in Escherichia coli

(2009) Alon Zaslaver et al.   PLoS Computational Biology

Two strategies for gene regulation by promoter nucleosomes

(2008) I. Tirosh et al.   GENOME RESEARCH

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

Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation

(2008) Ophir Shalem et al.   Molecular Systems Biology

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

(2008) Lyris M. F. de Godoy et al.   NATURE

Analysis of combinatorial cis-regulation in synthetic and genomic promoters

(2008) Jason Gertz et al.   NATURE

Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network

(2008) Gal Chechik et al.   NATURE BIOTECHNOLOGY

Growth-rate-dependent partitioning of RNA polymerases in bacteria

(2008) S. Klumpp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

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

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