De novo-designed translation-repressing riboregulators for multi-input cellular logic

Switching the activity of Cas12a using guide RNA strand displacement circuits

(2019) Lukas Oesinghaus et al.   Nature Communications

Conditional Guide RNAs: Programmable Conditional Regulation of CRISPR/Cas Function in Bacterial and Mammalian Cells via Dynamic RNA Nanotechnology

(2019) Mikhail H. Hanewich-Hollatz et al.   ACS Central Science

Programmable protein circuits in living cells

(2018) Xiaojing J. Gao et al.   SCIENCE

Cellular checkpoint control using programmable sequential logic

(2018) Lauren B. Andrews et al.   SCIENCE

A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers

(2018) Melissa K. Takahashi et al.   Nature Communications

Riboregulated toehold-gated gRNA for programmable CRISPR–Cas9 function

(2018) Ka-Hei Siu et al.   Nature Chemical Biology

Escherichia coli “Marionette” strains with 12 highly optimized small-molecule sensors

(2018) Adam J. Meyer et al.   Nature Chemical Biology

Complex cellular logic computation using ribocomputing devices

(2017) Alexander A. Green et al.   NATURE

Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells

(2017) Benjamin H Weinberg et al.   NATURE BIOTECHNOLOGY

Digital logic circuits in yeast with CRISPR-dCas9 NOR gates

(2017) Miles W. Gander et al.   Nature Communications

Computational design of small transcription activating RNAs for versatile and dynamic gene regulation

(2017) James Chappell et al.   Nature Communications

Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components

(2016) Keith Pardee et al.   CELL

Synthetic biology to access and expand nature's chemical diversity

(2016) Michael J. Smanski et al.   NATURE REVIEWS MICROBIOLOGY

Genetic circuit design automation

(2016) A. A. K. Nielsen et al.   SCIENCE

Synthetic recombinase-based state machines in living cells

(2016) N. Roquet et al.   SCIENCE

Improving fold activation of small transcription activating RNAs (STARs) with rational RNA engineering strategies

(2015) Sarai Meyer et al.   BIOTECHNOLOGY AND BIOENGINEERING

Creating small transcription activating RNAs

(2015) James Chappell et al.   Nature Chemical Biology

Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq

(2015) Kyle E. Watters et al.   NUCLEIC ACIDS RESEARCH

Toehold Switches: De-Novo-Designed Regulators of Gene Expression

(2014) Alexander A. Green et al.   CELL

Paper-Based Synthetic Gene Networks

(2014) Keith Pardee et al.   CELL

Permanent genetic memory with >1-byte capacity

(2014) Lei Yang et al.   NATURE METHODS

Genomically encoded analog memory with precise in vivo DNA writing in living cell populations

(2014) F. Farzadfard et al.   SCIENCE

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

Synthetic analog computation in living cells

(2013) Ramiz Daniel et al.   NATURE

Synthetic circuits integrating logic and memory in living cells

(2013) Piro Siuti et al.   NATURE BIOTECHNOLOGY

Genomic mining of prokaryotic repressors for orthogonal logic gates

(2013) Brynne C Stanton et al.   Nature Chemical Biology

A modular strategy for engineering orthogonal chimeric RNA transcription regulators

(2013) Melissa K. Takahashi et al.   NUCLEIC ACIDS RESEARCH

Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system

(2013) David Bikard et al.   NUCLEIC ACIDS RESEARCH

Combinatorial Displacement of DNA Strands: Application to Matrix Multiplication and Weighted Sums

(2012) Anthony J. Genot et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Programmable single-cell mammalian biocomputers

(2012) Simon Ausländer et al.   NATURE

Genetic programs constructed from layered logic gates in single cells

(2012) Tae Seok Moon et al.   NATURE

Ribozyme-based insulator parts buffer synthetic circuits from genetic context

(2012) Chunbo Lou et al.   NATURE BIOTECHNOLOGY

Rationally designed families of orthogonal RNA regulators of translation

(2012) Vivek K Mutalik et al.   Nature Chemical Biology

Rewritable digital data storage in live cells via engineered control of recombination directionality

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

Expanding the Rule Set of DNA Circuitry with Associative Toehold Activation

(2011) Xi Chen   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A sensing array of radically coupled genetic ‘biopixels’

(2011) Arthur Prindle et al.   NATURE

Versatile RNA-sensing transcriptional regulators for engineering genetic networks

(2011) J. B. Lucks et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NUPACK: Analysis and design of nucleic acid systems

(2010) Joseph N. Zadeh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A synchronized quorum of genetic clocks

(2010) Tal Danino et al.   NATURE

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

Higher-Order Cellular Information Processing with Synthetic RNA Devices

(2008) M. N. Win et al.   SCIENCE