Transcriptional Regulatory Circuits: Predicting Numbers from Alphabets

A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches

(2009) Irene Cantone et al.   CELL

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

Diversity-based, model-guided construction of synthetic gene networks with predicted functions

(2009) Tom Ellis et al.   NATURE BIOTECHNOLOGY

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

(2009) Harukazu Suzuki et al.   NATURE GENETICS

A Yeast Hybrid Provides Insight into the Evolution of Gene Expression Regulation

(2009) I. Tirosh et al.   SCIENCE

Using Network Component Analysis to Dissect Regulatory Networks Mediated by Transcription Factors in Yeast

(2009) Chun Ye et al.   PLoS Computational Biology

Learning a Prior on Regulatory Potential from eQTL Data

(2009) Su-In Lee et al.   PLoS Genetics

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

Frequency-modulated nuclear localization bursts coordinate gene regulation

(2008) Long Cai et al.   NATURE

Chromatin decouples promoter threshold from dynamic range

(2008) Felix H. Lam et al.   NATURE

Analysis of combinatorial cis-regulation in synthetic and genomic promoters

(2008) Jason Gertz et al.   NATURE

Variations in DNA elucidate molecular networks that cause disease

(2008) Yanqing Chen et al.   NATURE

Genetics of gene expression and its effect on disease

(2008) Valur Emilsson et al.   NATURE

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

Bead-based profiling of tyrosine kinase phosphorylation identifies SRC as a potential target for glioblastoma therapy

(2008) Jinyan Du et al.   NATURE BIOTECHNOLOGY

Direct multiplexed measurement of gene expression with color-coded probe pairs

(2008) Gary K Geiss et al.   NATURE BIOTECHNOLOGY

Regulatory changes underlying expression differences within and between Drosophila species

(2008) Patricia J Wittkopp et al.   NATURE GENETICS

Structure and function of a transcriptional network activated by the MAPK Hog1

(2008) Andrew P Capaldi et al.   NATURE GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

A quantitative model of transcription factor–activated gene expression

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

Global regulatory logic for specification of an embryonic cell lineage

(2008) P. Oliveri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Species-Specific Transcription in Mice Carrying Human Chromosome 21

(2008) M. D. Wilson et al.   SCIENCE

Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics

(2008) Stephen A. Ramsey et al.   PLoS Computational Biology