High-throughput cellular RNA device engineering

Kinetic and Equilibrium Binding Characterization of Aptamers to Small Molecules using a Label-Free, Sensitive, and Scalable Platform

(2014) Andrew L. Chang et al.   ANALYTICAL CHEMISTRY

Hierarchy of RNA Functional Dynamics

(2014) Anthony M. Mustoe et al.   Annual Review of Biochemistry

Quantitative analysis of mammalian translation initiation sites by FACS-seq

(2014) W. L. Noderer et al.   Molecular Systems Biology

A general design strategy for protein-responsive riboswitches in mammalian cells

(2014) Simon Ausländer et al.   NATURE METHODS

Protein-responsive ribozyme switches in eukaryotic cells

(2014) Andrew B. Kennedy et al.   NUCLEIC ACIDS RESEARCH

Ribozyme-Based Aminoglycoside Switches of Gene Expression Engineered by Genetic Selection in S. cerevisiae

(2014) Benedikt Klauser et al.   ACS Synthetic Biology

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

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

Dynamically Reshaping Signaling Networks to Program Cell Fate via Genetic Controllers

(2013) K. E. Galloway et al.   SCIENCE

Causes and Effects of N-Terminal Codon Bias in Bacterial Genes

(2013) D. B. Goodman et al.   SCIENCE

Controlling Mammalian Gene Expression by Allosteric Hepatitis Delta Virus Ribozymes

(2013) Yoko Nomura et al.   ACS Synthetic Biology

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

A yeast-based rapid prototype platform for gene control elements in mammalian cells

(2012) Kathy Y. Wei et al.   BIOTECHNOLOGY AND BIOENGINEERING

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

A versatile cis-blocking and trans-activation strategy for ribozyme characterization

(2012) Andrew B. Kennedy et al.   NUCLEIC ACIDS RESEARCH

A high-throughput, quantitative cell-based screen for efficient tailoring of RNA device activity

(2012) Joe C. Liang et al.   NUCLEIC ACIDS RESEARCH

Selection of tetracycline inducible self-cleaving ribozymes as synthetic devices for gene regulation in yeast

(2011) Alexander Wittmann et al.   Molecular BioSystems

Large Scale Loss of Data in Low-Diversity Illumina Sequencing Libraries Can Be Recovered by Deferred Cluster Calling

(2011) Felix Krueger et al.   PLoS One

Identification of Hammerhead Ribozymes in All Domains of Life Reveals Novel Structural Variations

(2011) Jonathan Perreault et al.   PLoS Computational Biology

A ligand-dependent hammerhead ribozyme switch for controlling mammalian gene expression

(2010) Simon Ausländer et al.   Molecular BioSystems

Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems

(2010) Y. Y. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Design Principles for Riboswitch Function

(2009) Chase L. Beisel et al.   PLoS Computational Biology

Improved Aptazyme Design and In Vivo Screening Enable Riboswitching in Bacteria

(2008) Markus Wieland et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

A FACS-Based Approach to Engineering Artificial Riboswitches

(2008) Casey C. Fowler et al.   CHEMBIOCHEM

Analysis of combinatorial cis-regulation in synthetic and genomic promoters

(2008) Jason Gertz et al.   NATURE

A flow cytometry-based screen for synthetic riboswitches

(2008) Sean A. Lynch et al.   NUCLEIC ACIDS RESEARCH

Higher-Order Cellular Information Processing with Synthetic RNA Devices

(2008) M. N. Win et al.   SCIENCE

Capturing Hammerhead Ribozyme Structures in Action by Modulating General Base Catalysis

(2008) Young-In Chi et al.   PLOS BIOLOGY

Random Walks to Synthetic Riboswitches—A High-Throughput Selection Based on Cell Motility

(2007) Shana Topp et al.   CHEMBIOCHEM