Systematic Dissection of the Sequence Determinants of Gene 3’ End Mediated Expression Control

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Gene Expression Is Circular: Factors for mRNA Degradation Also Foster mRNA Synthesis

(2013) Gal Haimovich et al.   CELL

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

(2013) P. Kheradpour et al.   GENOME RESEARCH

Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants

(2013) Ilaria Mogno et al.   GENOME RESEARCH

Promoters maintain their relative activity levels under different growth conditions

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

Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks

(2013) M. A. White et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Species-specific factors mediate extensive heterogeneity of mRNA 3' ends in yeasts

(2013) Z. Moqtaderi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Composability of regulatory sequences controlling transcription and translation inEscherichia coli

(2013) Sriram Kosuri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Measurements of the Impact of 3′ End Sequences on Gene Expression Reveal Wide Range and Sequence Dependent Effects

(2013) Ophir Shalem et al.   PLoS Computational Biology

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

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

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

Promoter Elements Regulate Cytoplasmic mRNA Decay

(2011) Almog Bregman et al.   CELL

Single-Molecule mRNA Decay Measurements Reveal Promoter- Regulated mRNA Stability in Yeast

(2011) Tatjana Trcek et al.   CELL

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

(2011) D. Zeevi et al.   GENOME RESEARCH

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

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

Unravelling the means to an end: RNA polymerase II transcription termination

(2011) Jason N. Kuehner et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Transcriptome Kinetics Is Governed by a Genome-Wide Coupling of mRNA Production and Degradation: A Role for RNA Pol II

(2011) Ophir Shalem et al.   PLoS Genetics

Signals for pre-mRNA cleavage and polyadenylation

(2011) Bin Tian et al.   Wiley Interdisciplinary Reviews-RNA

RNA Polymerase II Subunits Link Transcription and mRNA Decay to Translation

(2010) Liat Harel-Sharvit et al.   CELL

Comprehensive Polyadenylation Site Maps in Yeast and Human Reveal Pervasive Alternative Polyadenylation

(2010) Fatih Ozsolak et al.   CELL

Crosstalk between mRNA 3′ End Processing and Transcription Initiation

(2010) Christophe K. Mapendano et al.   MOLECULAR CELL

Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process

(2010) Emily M. LeProust et al.   NUCLEIC ACIDS RESEARCH

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

Transcriptional Termination Enhances Protein Expression in Human Cells

(2009) Steven West et al.   MOLECULAR CELL

Fail-Safe Transcriptional Termination for Protein-Coding Genes in S. cerevisiae

(2009) Ana G. Rondón et al.   MOLECULAR CELL

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

(2009) Rupali P Patwardhan 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

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

(2008) Ophir Shalem et al.   Molecular Systems Biology

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

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

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

Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System

(2008) Daniel J Hogan et al.   PLOS BIOLOGY

A Feature-Based Approach to Modeling Protein–DNA Interactions

(2008) Eilon Sharon et al.   PLoS Computational Biology